Science Meetings & Events

This year the Cell Science 2024 Meeting brought together more than 160+ researchers, community partners, and patient organizations across our Ancestry and Pediatric Networks for the Human Cell Atlas to share their progress and identify opportunities to continue this important work. Participants shared how their groups are working to increase the diversity and representation of single-cell reference atlases across many modalities and building new tools developed to identify key developmental or ancestral markers. This meeting included over 50 talks and welcomed researchers representing over 30 countries from across the globe.

CZI hosted the fourth annual Faculty Application Bootcamp, FAB@CZI, for 69 PhD students and postdocs from CZI-supported and associated labs. The week-long online course covered all written and verbal components of the faculty job search process, such as research, teaching & diversity statements, job & chalk talks, interviewing, negotiation, and more. All participants planned to apply for U.S. faculty positions in the 2023-2024 cycle and connected with small homegroups throughout the week to discuss their application materials and strategies with their peers.

This meeting brought together over 50 researchers specializing in reproductive biology to align on shared nomenclature, including cell ontology terms and frameworks for defining cell states for cell types in the ovary, fallopian tube, and uterus.

This workshop brought together academic and industry researchers to discuss the current and prospective states of synthetic biology. Participants discussed state-of-the-art methods to manipulate cellular functions which aim to better understand fundamental biology and potential biomedical applications. The group discussed challenges in the field and surfaced potential opportunities to address them. They also explored how artificial intelligence could help design and predict biological systems better. Researchers expressed interest in ensuring their work has real-world impact, such as developing new tools to study diseases or creating more efficient methods to produce medicines or biomaterials. The workshop highlighted how synthetic biology brings together ideas from many different scientific and engineering fields and its potential to yield important breakthroughs that could benefit society in numerous ways.

Attendees

• Omar Abudayyeh, Harvard Medical School
• Karen Adelman, Harvard Medical School
• Geoff Baldwin, Imperial College London
• Caleb Bashor, William Marshall Rice University
• Justin Crocker, European Molecular Biology Laboratory
• Carl de Boer, University of British Columbia
• Tara Deans, University of Utah
• Alistair Elfick, University of Edinburgh
• MIchael Elowitz, Caltech
• Emma Farley, University of California, San Diego
• Paul Freemont, Imperial College London
• John Glass, J. Craig Venter Institute
• Fokion Glykofrydis, University of Southern California
• Jonathan Gootenberg, Harvard Medical School
• Farren Isaacs, Yale University
• Craig Lowe, Duke University
• Leslie Mitchell Mitchell, Neochromosome
• Sarah Munro, University of Minnesota
• Alec Nielsen, Asimov
• Jean Peccoud, Colorado State University
• Sudarshan Pinglay, University of Washington
• Georg Seelig, University of Washington
• Elizabeth Strychalski, National Institute of Standards and Technology
• Claudia Vickers, BioBuilt Solutions
• Ron Weiss, Massachusetts Institute of Technology
• Michael White, Washington University in St. Louis
• Knut Woltjen, Center for iPS Cell Research and Application (CiRA), Kyoto University
• Julia Zeitlinger, Stowers Institute for Medical Research
• Siqi Zhao, Ginkgo Bioworks
• Ronghui (Ron) Zhu, Gladstone Institutes

The Neuroscience 2024 Meeting brought together CZI Neuroscience program investigators and collaborators, CZI program staff, and Chan Zuckerberg Biohub Network staff for several days of programming to foster new connections and collaborations. The meeting highlighted the diversity of projects and invited investigators to discuss fundamental neuroscience and neurodegenerative disease. Key sessions included discussions on neuron-glial interactions led by Dr. Michelle Monje and patient perspectives on the rare disease CADASIL. Other sessions focused on new technologies and methods developed by the network, AI applications in neuroscience, and bridging the gap in neurotherapeutics from basic research to industry.

The Open Science 2024 Meeting convened program grantees, community members, funders, and science policymakers to foster collaboration and advance open science. The program included plenary sessions, project demonstrations, breakout conversations, and unstructured collaborative time, enabling attendees to forge new connections across scientific domains. This year’s meeting focused on cultivating an equitable and accessible open science ecosystem through methods like preprints, international collaborations, community-engaged science, emerging technologies like AI, and organizations like open source program offices. Participants also received updates on open, reproducible research practices in Latin America and new developments in open source software tools and project sustainability practices. Presentations from the meeting are available on Zenodo.

The “Frontiers of Cellular Neuroscience” workshop, co-organized by CZI’s Neuroscience and Imaging programs, brought together cell biologists, neuroscientists, imaging scientists, and technology developers to explore questions at the frontiers of cellular neuroscience, with a focus on the synapse as the fundamental unit of neural network. Over two days, participants discussed the complexities of synaptic function, plasticity, and homeostasis, emphasizing the need for advanced imaging and biochemical tools to address the gaps in current understanding and opportunities for new approaches to progress the field. Key session themes included synaptic architecture, cellular metabolism and organelle biology of neurons, and the development of next-generation imaging technologies, all of which are pivotal for driving future research in this field. The workshop highlighted the importance of interdisciplinary collaboration and the development and dissemination of tools and technology to bridge cellular and systems neuroscience, aiming to advance our knowledge of synaptic dynamics and their implications for behavior and disease.

Attendees

• Daniel Choquet, CNRS-Bordeaux University
• Adam Cohen, Harvard University
• Daniel Colón-Ramos, Yale University
• Grae Davis, University of California, San Francisco
• Graham Dempsey, Quiver Bioscience
• Guoping Feng, Massachusetts Institute of Technology
• Seth Grant, University of Edinburgh
• Casper Hoogenraad, Genentech
• Na Ji, University of California, Berkeley
• Luke Lavis, Janelia Research Campus, Howard Hughes Medical Institute
• Michael Lin, Stanford University
• Rob Meijers, Institute for Protein Innovation
• Elly Nedivi, Massachusetts Institute of Technology
• Kira Poskanzer, Arcadia Science
• Tim Ryan, Weill Cornell Medicine
• Peter Scheiffele, Biozentrum of the University of Basel
• Kang Shen, Stanford University
• Karel Svoboda, Allen Institute for Neural Dynamics
• Gina Turrigiano, Brandeis University

The “Plasticity Across Scales” workshop, co-organized by CZI’s Neuroscience and Imaging programs, brought together experimentalists, technology developers, and theorists to explore questions related to circuit-level plasticity in the nervous system, intending to illuminate critical scientific questions, gaps, and opportunities and identifying potential strategies and technologies for progressing the field. Over two days, participants engaged in discussions emphasizing the necessity for next-generation circuit mapping tools and the role of data and computational models in enhancing our understanding of the brain’s adaptability across scales and in broad contexts. The workshop highlighted the importance of context in neural function, particularly how the brain’s environment influences plasticity. Discussions underscored the critical need for collaborative research efforts to develop innovative, non-invasive imaging technologies and the continued development of genetically encoded tools to capture real-time neurochemical dynamics, setting the stage for future advancements in the field.

Attendees

• Misha Ahrens, Janelia Research Campus, Howard Hughes Medical Institute
• Tobias Bonhoeffer, MPI for Biological Intelligence
• Ed Callaway, The Salk Institute for Biological Studies
• Peter Denes, Lawrence Berkeley National Laboratory
• Anita Disney, Duke University
• Gül Dölen, University of California, Berkeley
• Adrienne Fairhall, University of Washington
• André Fenton, New York University
• Loren Frank, Howard Hughes Medical Institute
• Sebastian Haesler, Neuro-Electronics Research Flanders
• Michael Hausser, University College London
• Udi Isacoff, University of California, Berkeley
• Viren Jain, Google Research
• Christina Kim, University of California, Davis
• Yevgenia Kozorovitskiy, Northwestern University
• Loren Looger, University of California, San Diego
• John Ngai, NIH Brain Initiative
• Mark Schnitzer, Stanford University
• Jason Shepherd, University of Utah
• Nelson Spruston, Janelia Research Campus, Howard Hughes Medical Institute
• Scott Sternson, University of California, San Diego
• Andreas Tolias, Stanford University
• Rafael Yuste, Columbia University

The Exploratory Cell Networks kick off meeting discussed recent advancements and challenges in RNA biology and tissue engineering, including the development of new technologies, and the need for more integrated approaches. Attendee discussions on tissue engineering emphasized connecting single-cell data to higher-level tissue models and addressing issues of heterogeneity and standardization. Key themes were improving accessibility and utilization of tools, as well as leveraging artificial intelligence and machine learning and integrating data across different scales. Attendees also explored emerging technologies and collaborative research initiatives.

The Science Diversity Leadership 2024 Community Meeting brought together Science Diversity Leadership (SDL) grantees, SDL mentors, and CZI Science staff. The meeting fostered community and built collaborative networks amongst the attendees. Attendees shared their research and joined sessions focused on outreach, mentorship, and leadership work within the SDL community.

In March 2024, the CZI Cell Science and Science Technology teams co-hosted a three-day workshop to bring together leading experts in artificial intelligence, machine learning, and single-cell biology. Attendees discussed evaluating and validating models, translating AI predictions into biological discoveries, and exploring new frontiers with multi-modal models through a series of invited talks, panel discussions, and small group sessions. At the workshop, researchers shared their expertise, fostered collaborations, and collectively envisioned a future where AI plays a crucial role in advancing our understanding of biology and human health at the single-cell level.

Attendees

• Marcus Alvarez, University of California, San Francisco
• Alma Andersson, Genentech
• Ethan Armand, University of California, San Diego
• Gary Bader, University of Toronto
• Rebecca Boiarsky, Massachusetts Institute of Technology
• Charlotte Bunne, Stanford University
• Daniel Burkhardt, Cellarity
• Robrecht Cannoodt, Data Intuitive
• Hu Chen, Baylor College of Medicine
• Joe Ecker, Salk Institute of Biological Science
• Can Ergen, University of California, Berkeley
• Scott Gigante, Open Problems for Single-Cell Analysis
• Craig Glastonbury, Human Technopole
• Martin Hemberg, Brigham and Women’s Hospital
• Kenji Kamimoto, Washington University in St.Louis
• Kasia Kedzierska, University of Oxford
• David Kelley, Calico Life Sciences
• Yang-Joon Kim, Chan Zuckerberg Biohub San Francisco
• Smita Krishnaswamy, Yale University
• Avantika Lal, Genentech
• Merlin Lange, Chan Zuckerberg Biohub San Francisco
• Nathan Levy, Weizmann Institute of Science
• Michelle Li, Harvard University
• Tianyu Liu, Yale University
• Reet Mishra, University of California, Berkeley
• Angela Oliveira Pisco, insitro
• Giovanni Palla, Helmholtz Munich
• Luca Pinello, Broad Institute of MIT and Harvard
• Pia Rautenstrauch, Max Delbrück Center
• Yanay Rosen, Stanford University
• Yusuf Roohani, Stanford University
• Loic Royer, Chan Zuckerberg Biohub San Francisco
• Alejandro Tejada Lapuerta, Helmholtz Munich
• Fabian Theis, Helmholtz Munich
• Christina Theodoris, Gladstone Institutes
• Wei Tian, Salk Institute of Biological Science
• Xinming Tu, University of Washington
• Chloe (Xueqi) Wang, University of Toronto
• Hanchen Wang, Stanford University
• Joshua Welch, University of Michigan
• Ronald Xie, University of Toronto
• Jimmie Ye, University of California, San Francisco
• Han Yuan, Calico Life Sciences
• Haoyang Zeng, insitro
• Andy Zhou, Chan Zuckerberg Biohub San Francisco
• James Zou, Stanford University

The Neuroscience Early Career Acceleration Retreat brought together grantees funded through the first and second cycles of the Ben Barres Early Career Acceleration award, CZI Neuroscience program staff, and invited guest speakers from the Chan Zuckerberg Biohub Network and other CZI Neuroscience grant programs to connect and share science and work experiences around career development, mentoring, and collaboration.

The Metabolism Network Kickoff Meeting marked the launch of a new initiative to enhance the study of metabolism across various biological scales. This effort seeks to spur innovative advancements in understanding metabolism and its implications for health and disease. Over two days, principal investigators from 18 different projects connected and shared research. Expert guest speakers delivered presentations that encouraged networking and laid the groundwork for future collaborations. The meeting promoted active engagement, fostered a commitment to pushing metabolic research forward, and stimulated discussions on using shared tools, resources, and strategies for collective achievements in cell science and metabolism research.

The Accelerate Precision Health (APH) partnership supports the genomics research programs at the four Historically Black Medical Colleges (HBMCs) – Charles Drew University College of Medicine, Howard University College of Medicine, Meharry Medical College, and Morehouse School of Medicine. This meeting encouraged collaboration and facilitated partnerships between the faculty at the HBMCs and CZI’s Science programs. The science-driven meeting showcased the range of science being conducted at the four HBMCs.

CZI’s Single-Cell Biology Annual Meeting brought together over 285 attendees in Carlsbad, California to share their work on topics spanning single-cell transcriptomics, rare disease, computational biology, spatial technologies, methods development, community engagement, and more. Attendees presented over 70 talks and 100 demos and posters, many sharing early and unpublished results.

CZI hosted a hackathon on Mapping the Impact of Research Software in Science on October 24-27, 2023. This hackathon convened 60 practitioners from 13 countries in different areas of computer science, data science, and machine learning, as well as organizations active in this space. Over the course of three days, attendees identified nine high-priority projects to tackle together using a broad range of resources and publicly available datasets. Check out the main repository of the hackathon and our blog post of the event.

Attendees

• Anita Bandrowski, SciCrunch Inc.
• Eva Brown, University of Washington Information School
• Serafeim Chatzopoulos, OpenAIRE AMKE
• Rodrigo Costas, Centre for Science and Technology Studies (CWTS)
• Stephan Druskat, German Aerospace Center (DLR)
• Scott Fisher, California Digital Library
• Josh Fisher, Elsevier
• Daniel Garijo, Universidad Politécnica de Madrid (UPM)
• Sean Goggins, University of Missouri
• Esteban González, Universidad Politécnica de Madrid (UPM)
• Josh Greenberg, Alfred P. Sloan Foundation
• Casey Greene, University of Colorado
• Kaitlyn Hair, University of Edinburgh
• Melissa Harrison, European Molecular Biology Laboratory-European Informatics (EMBL-EBI Europe PMC)
• Laurent Hébert-Dufresne, Vermont Complex Systems Center
• Tom Honeyman, Australian Research Data Commons
• James Howison, University of Texas at Austin
• Yingnan Ju, Indiana University
• Alexy Khrabrov, IBM
• Jinseok Kim, University of Michigan
• Martin Klein, Los Alamos National Laboratory
• Frank Krüger, Wismar University of Applied Sciences
• Anne L’Hôte, French Ministry of Higher Education and Research
• Kai Li, University of Tennessee, Knoxville
• Arcangelo Massari, University of Bologna
• Jennifer Melot, Center for Security and Emerging Technology
• Shahan Ali Memon, University of Washington
• Daniel Mietchen, Scholia
• Kara Moraw, Software Sustainability Institute
• Andrew Nesbitt, Ecosyste.ms
• Joao Felipe Pimentel, Universidade Federal Fluminense
• Joseph Rhoads, DataCite
• David Schindler, University of Rostock
• Arfon Smith, GitHub
• Peter Staar, IBM Research
• Nicola Tarocco, CERN
• Dominika Tkaczyk, Crossref
• Christoph Treude, The University of Melbourne
• Fuqi Xu, University of Manchester
• Huimin Xu, University of Texas at Austin
• Xinyu Yang, Cornell University
• Puyu Yang, University of Amsterdam

The Frontiers in Imaging Workshop explored opportunities for advances in imaging technology to accelerate our understanding of the structure and function of the basic building blocks of human biology. Topics of interest included techniques that can probe the dynamics of molecular and cellular interactions in biological development, homeostasis, and disease. The workshop also incorporated the application of AI and machine learning to imaging.

Session themes included:

• Biological structure and organization
• Dynamic imaging to understand function of molecules in cells
• Dynamic imaging to understand cell function in tissues
• Dynamic imaging in developmental biology and neuroscience
• AI and machine learning in imaging systems and biological insights

Common focus areas and key opportunities that emerged included: 

• Dynamic imaging and imaging across scales
• Integrated complementary technologies
• Imaging “life forces” in biology such as bioelectricity and mechanical forces
• The ability to perturb a biological system and measure the response
• Building biological image databases to accelerate AI and deep learning research

Attendees

• Muyinatu Bell, Johns Hopkins University
• Amy Bernard, The Kavli Foundation
• Joerg Bewersdorf, Yale University 
• Tobias Bonhoeffer, MPI for Biological Intelligence
• Axel Brunger, Stanford University
• Elaine Bui, The Kavli Foundation
• Adam Cohen, Harvard University
• Xavier Darzacq, University of California, Berkeley
• Scott Fraser, Chan Zuckerberg Initiative
• Viren Jain, Google Research
• Tom Kirchhausen, Harvard Medical School
• Anna Kreshuk, European Molecular Biology Laboratory (EMBL)
• Wesley Legant, University of North Carolina, Chapel Hill
• Emma Lundberg, Stanford University
• Aydogan Ozcan, University of California, Los Angeles
• Hemai Parthasarathy, X, The Moonshot Factory
• Robert Prevedel, European Molecular Biology Laboratory (EMBL)
• Jonas Ries, European Molecular Biology Laboratory (EMBL)
• Jason Swedlow, University of Dundee
• Robert Tjian, University of California, Berkeley
• Gokul Upadhyayula, University of California, Berkeley
• Laura Waller, University of California, Berkeley

In October 2023, the CZI Science in Society program and Every Cure co-hosted a two-day, in-person workshop to bring together over 60 people advancing data-driven approaches to drug repurposing. Participants represented a range of sectors and expertise across data sharing, biocuration, computational biology, AI/ML research, and rare disease therapeutic development. Through a series of panel discussions, the workshop identified shared challenges and highlighted opportunities to strengthen synergies. The workshop ended with a half-day hackathon aimed at encouraging collaboration and developing solutions.

Session themes included:

• Case Studies: Defining Success & Identifying Opportunities for Data-Driven Drug Repurposing
• Sourcing and Harnessing Data for Drug Repurposing
• Curating and Representing Biomedical Knowledge in Network-Based Approaches
• Developing and Applying Inference Methods to Identify Targets and Repurposable Candidates
• Interrogating Biology and Evaluating Therapeutic Effects

Following the workshop, we launched a virtual meeting series to stay connected and dive deeper into the challenges and opportunities that were raised. If you’re interested in joining the virtual meeting series, please contact info@everycure.org with the subject heading “Data-Driven Drug Repurposing Virtual Workshop Series”.

Attendees

• Chris Bizon, Renaissance Computing Institute, University of North Carolina
• Bruce Bloom, Kabuki Syndrome Foundation
• Alex Burgin, Broad Institute
• Christine Colvis, National Center for Advancing Translational Sciences (NCATS), NIH
• Devon Crittenden, Reboot Rx
• Lex Cowsert, DADA2 Foundation
• Jason Cross, Rymedi
• David Fajgenbaum, Every Cure
• Nasha Fitter, FOXG1 Research Foundation and Citizen
• Claudia Fuchs, EURORDIS, Rare Disease Europe
• Barbara Goodman, Cures Within Reach
• Scott Gorman, Advanced Research Projects Agency for Health (ARPA-H)
• Melissa Haendel, University of Colorado Anschutz Medical Campus
• Daniel Himmelstein, Related Sciences
• Michelle Holko, Airfinity
• Eric Horvitz, Microsoft
• Larry Hunter, University of Colorado School of Medicine
• Brigham Hyde, Atropos Health
• Adam Kolom, Related Sciences
• Daniel Korn, Every Cure
• David Koslicki, The Pennsylvania State University
• Rebecca Li, Vivli
• Zan Lowe-Skillern, Public Good Pharma
• Chris Lunt, NIH All of Us Research Program
• Finlay MacLean, Charm Therapeutics
• Malcolm Macleod, University of Edinburgh
• Ellie McDonagh, Open Targets
• Grant Mitchell, Every Cure
• Chris Moxham, Rarebase
• Bernard Munos, FasterCures (Milken Institute)
• Sally Nijim, Every Cure
• Tudor Oprea, Expert Systems Inc
• Mike Palovich, Recursion
• Ethan Perlstein, Perlara PBC
• Michael Raymond, The Snyder-Robinson Foundation
• Hitesh Sanganee, AstraZeneca
• Marco Schito, Critical Path Institute
• Jillian Shaw, Broad Institute of MIT and Harvard
• Brent Shaw, Every Cure
• Tracey Sikora, Every Cure
• G. Sitta Sittampalam, NewFoundMed
• Alex Tropsha, UNC-Chapel Hill
• Becky Upton, Pistoia Alliance
• Bryn Williams-Jones, Connected Discovery/Pistoia Alliance
• Garabet Yeretssian, Chan Zuckerberg Initiative
• Anton Yuryev, Elsevier
• Marinka Zitnik, Harvard Medical School

Representatives of 60 patient-led rare disease advocacy organizations comprising the Rare As One (RAO) Network, joined patient leader, clinician, and researcher grantees and partners from across the Science in Society program in Newport Beach, CA, on September 20-23, 2023, to highlight wins in patient-driven rare disease research, identify opportunities for collaborations, and build relationships. The agenda and activities touched on topics spanning from diagnosis to data collection models. Over the three days, over 200 attendees participated in person, and 100 remote participants joined via livestream. The meeting consisted of a combination of talks and panel discussions, breakouts, poster sessions, and time for networking.

CZI hosted the third edition of the week-long Faculty Application Bootcamp, FAB@CZI for 56 PhD students and postdocs who work at CZI-supported and -associated labs. The course covered all written and verbal components of the Faculty Job Search process, such as research, teaching & diversity statements, job & chalk talks, interviewing, negotiation, and more. All participants plan to apply for U.S. faculty positions in the 2023-2024 cycle, and connected with small homegroups throughout the week to discuss their application materials and strategies with their peers.

This meeting brought together 20+ researchers spanning expertise working in the breast and mammary biology fields with the goal of aligning on shared nomenclature, such as cell ontology terms.

The Imaging 2023 Annual Meeting brought together over 250 members of the CZI Imaging community, including grantees, program advisors, funders, publishers, and commercial partners. Attendees joined roundtable discussions to ideate solutions to accelerate imaging technology development and adoption, heard case studies on disseminating new technology, and connected with new and existing collaborators through networking events. Participants shared their live reactions on Twitter during the event via the #ImagingTheFuture hashtag.

The fifth annual meeting of the Neurodegeneration Challenge Network brought together (NDCN) 195 participants including NDCN investigators, collaborators, partners, alumni, project affiliates (students, postdocs, and staff scientists), and CZI program and Chan Zuckerberg Biohub staff. This 3.5-day event held in San Diego, California included a pre-meeting with two technology-focused tracks for investigators working on genetic engineering technologies, and advanced computational tools for neuroscience. The general meeting highlighted the strong collaborative spirit of the NDCN community through investigator talks and discussion, a panel highlighting the Network’s patient-partnered research, a keynote on global science, and lightning talks and poster sessions aimed at providing an opportunity for NDCN trainees to present and network.

Pioneer studies in cryo-electron tomography (cryo-ET) have demonstrated the potential to deepen our understanding of cellular architecture at the molecular scale. Nevertheless, there are significant computational challenges in making it practical to view any desired cellular complex, structure or organelle by cryotomography at the highest possible resolution and to understand these structures in a broader biological context. This workshop discussed the challenges and opportunities in computational methods for cryo-ET such as improvements in data collection, preprocessing, reconstruction algorithms, segmentation, annotation and visualization. The workshop was streamed live to the public, and the recordings of the sessions can be viewed here.

Attendees

• Jeremy Axelrod, University of California, Berkeley
• Wah Chiu, Stanford University
• Peter Dahlberg, SLAC National Accelerator Laboratory
• Radostin Danev, University of Tokyo
• Peter Denes, Lawrence Berkeley National Laboratory
• David DeRosier, Brandeis University
• Maud Dumoux, Rosalind Franklin Institute
• Leeya Engel, Technion, Israel Institute of Technology
• Armin Feist, Max Planck Institute for Multidisciplinary Sciences (MPI-NAT)
• Michael Grange, Rosalind Franklin Institute
• Grant Jensen, Brigham Young University
• Thomas Juffmann, University of Vienna
• Sagar Khavnekar, Max Planck Institute of Biochemistry
• Angus Kirkland, Rosalind Franklin Institute
• Sven Klumpe, Max Planck Institute of Biochemistry
• Jessica Matthias, Abberior Instruments America
• Holger Mueller, University of California, Berkeley
• Eric Mulhall, Scripps Research
• David Muller, Cornell University
• Katerina Naydenova, MRC Laboratory of Molecular Biology
• Olivia Pfeil-Gardiner, Max Planck Institute of Biophysics
• Juergen Plitzko, Max Planck Institute of Biochemistry
• Christopher Russo, MRC Laboratory of Molecular Biology
• Carsten Sachse, Forschungszentrum Jülich (Germany)
• Srigokul Upadhyayula, University of California, Berkeley
• Peiyi Wang, Southern University of Science & Technology
• Cangshan Xu, Yale School of Medicine
• Yue Yu, Cornell University
• Qingxiong Zheng, University of California, San Francisco

The Infectious Disease Grantee Community Meeting brought together grantees and their lab members from cohorts one and two of the Grand Challenges grant. The meeting aimed to build community among grantees as they worked to establish metagenomic sequencing capacity in their labs. The 2-day virtual meeting included attendees from around the world to discuss best practices for experimental design, using generated data to create actionable impact, training and capacity building, and strategies for building lab sustainability.

This kickoff meeting convened investigators and group members of the14 Advancing Imaging Through Collaborative Projects which focus on accelerating the pace of novel imaging technology dissemination. We also heard from five regional and global imaging scientist network organizations and a distinguished keynote speaker.

CZI’s Open Science program convened 50+ researchers, software engineers, and community leaders in Buenos Aires, Argentina on April 17-19, 2023 to discuss open science and computational capacity in Latin America. The two-day workshop brought together existing grantees and new partners from Latin America. Participants engaged in sustainable, collaborative projects. This was the first CZI meeting hosted in the southern hemisphere and granted the opportunity for us to learn more about Latin American participation and collaboration in computational biomedicine and open science.

The Science Diversity Leadership (SDL) Kickoff Meeting provided a space for participants to learn and share about the excellent scientific research and outreach that is being conducted by the grantees. Through presentations, breakout sessions, and other activities, attendees built community, shared challenges and opportunities, and discussed strategies for long-term impact.

This workshop brought together 21 leading practitioners of AI-based design, high throughput screening, and molecular probe design to highlight the current state of the field and to identify bottlenecks and critical gaps in technology that could accelerate progress.

The session themes included:

• Overview of Imaging Probes

• Generative Modeling

• Synthesis and Screening

• Inverse Molecular Design

• Opportunities for the Future

As one of the immediate outcomes of this workshop, CZI launched the Cryo-CLEM Labels RFA to drive development of complete, general-purpose, intracellular imaging probes for cryo-correlative light and electron microscopy (cryo-CLEM).

Attendees

• Regina Barzilay, MIT
• Camille Bilodeau, University of Virginia
• Robert E. Campbell, University of Tokyo
• Rafa Gomez-Bombarelli, MIT
• James Green, University College London
• Carol Hall, N.C. State University
• Chloe Hsu, University of California, Berkeley
• Possu Huang, Stanford University
• Viren Jain, Google Research
• Eric Jonas, University of Chicago
• Pete Kelly, Align Innovation
• Luke Lavis, Janelia Research Campus, HHMI
• Loren Looger, Howard Hughes Medical Institute; University of California, San Diego
• Adam Marblestone, Convergent Research
• Jenn Prescher, University of California, Irvine
• Alex Rives, Meta FAIR
• Martin Seifrid, University of Toronto
• Alison Tebo, Janelia Research Campus, HHMI
• Alice Ting, Stanford University; Chan Zuckerberg Biohub
• Joe Watson, Institute for Protein Design, University of Washington
• Zach Wu, DeepMind

The Dynamic Imaging Kickoff meeting brought together 84 attendees, including members of 20 project teams, partners, and CZI staff. Attendees met virtually for two days to learn about each other’s projects, seek areas of synergy and potential areas of collaboration, and discuss important topics related to dynamic imaging. Participants were also invited to continue conversations started at the kickoff meeting through the formation of working groups.

The Metabolism Across Scales Workshop explored the frontiers of metabolism, identifying challenges, and determined how CZI could support advancements in the field. Experts discussed topics ranging from the metabolic dynamism of cellular organelles to computational approaches to metabolism across scales. Major challenges and opportunities identified included: the need to define metabolism in biologically relevant systems, understand the regulatory mechanisms that control metabolic pathways, develop tools for metabolic tracing in cells and organelles, and investigate how factors such as diet and physical activity influence metabolism. Technological development was highlighted as a top priority, including developing high-resolution imaging techniques and overcoming the limitations of current single-cell and spatial metabolomics methods. Data integration, standardization, and reuse were discussed, emphasizing the need for a common repository for proteomic and metabolomic data and developing guidelines for data standards, interdisciplinary research, and democratization of tools to study metabolism. The insights gained from the workshop will guide the CZI Single-Cell Biology Program in developing strategies for funding and advancing research in the field of metabolism.

Attendees

• Allon Wagner, University of California, Berkeley
• Anu Suomalainen, University of Helsinki
• Carlos Ribeiro, Champalimaud Centre for the Unknown, Lisbon, Portugal
• Christian Wolfrum, ETH Zürich
• David Chan, California Institute of Technology
• David James, The University of Sydney
• Doug Wallace, Children’s Hospital of Philadelphia
• Emily Goldberg, University of California, San Francisco
• Emma Lundberg, Stanford University
• Erika Pearce, Johns Hopkisn University, School of Medicine
• Evanna Mills, Dana-Farber Cancer Institute
• Gerta Hoxhaj, UTSW Children’s Research Institute
• Heather Christofk, University of California, Los Angeles
• Hongbo Chi, St, Jude Children’s Research Hospital
• Jared Rutter, University of Utah
• Katja Lamia, Scripps Research
• Laith Samarah, Princeton University
• Rushika Perera, University of California, San Francisco
• Samantha Lewis, University of California, Berkeley
• Satchin Panda, Salk Institute
• Shingo Kajimura, Harvard Medical School, Beth Israel Deaconess Medical Center
• Theo Alexandrov, EMBL
• Tony Lam, Toronto General Hospital & University of Toronto

The Rare As One (RAO) Network Community Meeting brought together the 50 patient-led, rare disease advocacy organizations of the RAO Network for a virtual meeting to build community and share resources. The first day included a celebration of Cycle 1’s accomplishments during the three years of grant funding, including group presentations of shared learning and tools used to create collaborative research networks driven by patient foundations. The second day highlighted Cycle 2 grantees and their progress in year one toward the grant objectives.

The single cell community continues to deliver a large quantity of high-quality data and the necessary metadata to interpret it. The field has reached a point where attempts to integrate and compile the individual data into increasingly comprehensive and valuable datasets are ongoing. Consequently, it is important that the broader single cell community both understands the single cell data ecosystem and the many ways that it can support them to enable and accelerate research. This meeting brought together various members of the ecosystem, including tool developers, consortia leaders, and data generators to discuss current challenges in the ecosystem and establish a unified vision moving forward.

Attendees

• Evan Biederstedt, Harvard Medical School
• Rui Chen, Baylor College of Medicine
• David Fischer, Broad Institute
• Maximilian Haeussler, UC Santa Cruz
• Peng He, The European Bioinformatics Institute and Wellcome Sanger Institute
• Trevor Heathorn, UC Santa Cruz
• Graham Heimberg, Genentech
• Jason Hilton, Lattice, Stanford University
• Alejandro Jimenez Sanchez, Memorial Sloan Kettering Cancer Center
• Peter Kharchenko, Altos Labs
• Liz Kiernan, Broad Institute
• Lian Morales, Lattice
• Michaela Mueller, ICB Helmholtz Muenchen
• Parisa Nejad, UC Santa Cruz Genomics Institute
• David Osumi-Sutherland, EMBL/EBI
• Benedict Paten, UC Santa Cruz Genomics Institute
• Francesca Perrone, Wellcome-MRC Cambridge Stem Cell Institute
• John Randell, Human Cell Atlas
• David Rogers, Clever Canary
• Hannes Schmidt, UC Santa Cruz
• Rachel Schwartz, Human Cell Atlas Data Coordination Platform
• William Sullivan, UC Santa Cruz Genomics Institute
• Kathleen Tibbett, Broad Institute
• Tim Tickle, Broad Institute
• Ellen Todres, Human Cell Atlas Bionetworks
• Chloe Villani, MGH, Broad Institute, Harvard Medical School
• Brittney Wick, UC Santa Cruz Cell Browser
• Gabby Yordanova, European Bioinformatics Institute
• Ida Zucchi, European Bioinformatics Institute

The Single-Cell Biology 2022 Annual meeting brought together over 200 grantees from the five active funding programs: Data Insights, Ancestry Networks for the HCA, Pediatric Networks for the HCA, Inflammation, and Seed Networks to foster collaboration, celebrate progress, connect in person, and identify research synergies. A central theme of this meeting was the integration of draft atlases and bringing together community efforts to assemble and extend them. CZI also hosted a one-day pre-meeting focused on CZ CELLxGENE training, data sharing discussions, and other computational-focused breakouts.

Cryo-electron tomography (cryoET) has made enormous strides over the past few years, and pioneering studies have shown the promise of understanding cellular architecture at the molecular scale. Nevertheless, there are significant computational challenges in making it practical to view any desired cellular complex, structure, or organelle by cryotomography at the highest possible resolution and to understand these structures in a broader biological context. The goal of this workshop was to discuss the challenges and opportunities in computational methods for cryoET. Discussions included improvements in data collection, preprocessing, reconstruction algorithms, segmentation, annotation, and visualization.

Attendees

• Alberto Bartesaghi, Duke University
• Tristan Bepler, New York Structural Biology Center
• Alister Burt, MRC Laboratory of Molecular Biology
• Jose-Maria Carazo, Spanish National Biotechnology Center CNB-CSIC
• Anchi Cheng, New York Structural Biology Center
• Wah Chiu, Stanford University
• Utz Ermel, Goethe University Frankfurt
• Tom Goddard, University of California, San Francisco
• Tim Grant, Morgridge Institute/UW-Madison
• Viren Jain, Google Research
• Dari Kimanius, MRC Laboratory of Molecular Biology
• Abhay Kotecha, Thermo Fisher Scientific
• Thomas Laughlin, University of California, San Diego
• Bronwyn Lucas, UMass Chan Medical School
• Julia Mahamid, European Molecular Biology Laboratory
• Antonio Martinez-Sanchez, University of Oviedo
• John Rubinstein, The Hospital for Sick Children
• Sjors Scheres, MRC Laboratory of Molecular Biology
• Mike Schmid, Stanford-SLAC CryoET Specimen Preparation Center (SCSC)
• Dimitry Tegunov, Genentech
• Shawn Zheng, University of California, San Francisco
• Ellen Zhong, Princeton University
• James Zou, Stanford University

This meeting launched the Accelerate Precision Health partnership, a new set of grants to advance genomics research at the four Historically Black Medical Colleges (HBMCs). The partnership aims to address significant gaps in genomics research, create new tools and methods to prevent and treat disease, and accelerate precision health for everyone, particularly Black people and other people of color. During the meeting, we welcomed 14 representatives from the four HBMCs to share project goals and identify opportunities to collaborate with each other.

The Open Science 2022 Annual Meeting brought together the CZI Open Science community, including grantees, program advisors, funders, researchers, and CZI staff. With 169 in-person and 55 virtual attendees over three days, this event was an opportunity to foster collaboration among grantees and partners, identify shared needs, and help craft future funding and partnership opportunities to address these needs. The meeting was structured as a combination of presentations, project demos, breakout sessions, and unstructured time for collaboration. Presentations from the meeting are available on Zenodo and the participants shared their live reactions on Twitter during the event via the #CZIOpenSci hashtag. Recordings of the two Keynote presentations can be viewed here.

CZI hosted the second edition of the week-long Faculty Application Bootcamp, FAB@CZI, for 62 PhD students and postdocs who work at CZI-supported and -associated labs. The course covered all written and verbal components of the Faculty Job Search process, such as research, teaching & diversity statements, job & chalk talks, interviewing, negotiation, and more. All participants planned to apply for U.S. faculty positions in the 2022-2023 cycle, and connected with small homegroups throughout the week to discuss their application materials and strategies with their peers.

This meeting launched the first cycle of Single-Cell Biology Data Insights, a new grant opportunity from the Single-Cell Biology program that aims to advance tools and resources that make it possible to gain greater insights into health and disease from existing single-cell biology datasets. The goal of the meetings was to bring together the 20 new Data Insights teams to learn about the projects, and get to know one another. This meeting provided an opportunity to connect, share science, discuss plans for shared resources and tools, and start thinking about how this community can work collaboratively towards common goals.

The napari Plugin Accelerator Showcase provided an opportunity for napari Plugin Accelerator Grantees to showcase their work building and maintaining image analysis plugins for the napari community. Participants learned about new growth in the growing napari community while plugin developers reconnected, discussed challenges, and looked to the future together. A total of 30 different plugins were presented during the showcase. More information on these and other plugins can be found on the napari Hub.

The 50 patient-led, rare disease advocacy organizations of the Rare As One (RAO) Network, affiliated researchers and clinicians, CZI staff, and invited leaders in patient-driven research gathered near San Diego, California for the Network’s first in-person convening. Over three days, more than 200 in-person attendees plus 80 remote participants joining via livestream built on relationship foundations forged virtually throughout the COVID-19 pandemic, strengthening lasting connections, identifying scientific synergies, and learning and collaborating in the context of approaches to patient driven research and addressing diagnosis and diversity, equity and inclusion challenges in rare disease, key goals of the RAO Network Cycle 2 grants.

The Imaging 2022 Annual Meeting was a three day meeting focused on bringing together the grantees of the CZI Imaging community, as well as representatives of imaging network organizations, program advisors, and CZI staff. This was the first meeting to bring together members from across all of CZI’s Imaging Program areas, including investigators and affiliates from projects funded under six Imaging RFAs (Deep Tissue Imaging, Scialog: Advancing Bioimaging, Visual Proteomics, Expanding Global Access to Bioimaging, and Imaging Scientists (Cycles 1-2)) as well as napari developers, representatives from Global BioImaging (GBI), BioImaging North America (BINA), and UK Biobank, and industry representatives. In total, 180 people from 16 countries participated. The Imaging 2022 Annual Meeting was a success in creating a strong foundation for bridging disciplines and networks in order to accelerate the development and dissemination of imaging technologies.

This three day workshop stimulated rapid iteration toward integration of tissue references. The event convened leaders of the single-cell community with an interest in assembling a large number of datasets generated by many different labs into a harmonized reference. Six groups that have developed leading data integration methods were invited along with an array of labs that have generated high-quality reference data. Data generation groups provided over 10 million cells worth of data, both published and unpublished, in advance of the meeting that enabled computational groups to produce integrated references in advance of the workshop. The focus of the meeting was on data generated from blood and kidney samples. By exploring a variety of strategies to perform this task, the workshop successfully raised and initiated work on key questions in the field including quality control, scale of current tools, gene selection, consistent annotations, integration of healthy and disease data vs. healthy alone, and many more. The workshop was a mixture of group discussion and targeted working time that provided time for collaborative groups of computational experts.

The Neurodegeneration Challenge Network (NDCN) 2022 Annual Meeting was the first CZI Science in-person meeting in over two years, with 149 participants from the United States, Europe, and the United Kingdom coming together in Berkeley, California. The 3.5-day event included a pre-meeting for NDCN early career investigators where interactive sessions with senior and mid-career researchers focused on career development and topics pertinent to lab culture and health and wellness. The main meeting included focused presentations on key advances and current challenges in neurodegenerative research from NDCN investigators and invited guests, a technology showcase, patient-clinician talks, and panel discussions. The program highlighted the strong collaborative spirit NDCN investigators bring to their science.

The CZI Ancestry Networks for the Human Cell Atlas grantees consist of 16 teams of 120 researchers across 31 countries that have come together to generate data for 12 tissue/organ systems from donors of multiple underrepresented ancestries. This network will contribute to making the Human Cell Atlas (HCA) a globally representative healthy reference. This kickoff meeting provided a venue for teams to meet other members of the network for the first time and lay the groundwork for early collaborations. The format of the meeting was two half days with project talks from each of the 16 networks, keynote presentations from the HCA Equity Working group and Genetic Diversity Bionetwork, networking sessions on Zoom and Spatial Chat, and an open group discussion session focused on some of the major challenges for this network such as ancestry categorization, ontology, and metadata collection.

On February 23-24, 2022, CZI held a virtual kickoff meeting for the Imaging program’s Expanding Global Access to Bioimaging grantees. More than 80 participants from 20 countries included members of 17 project teams from Africa, Latin America, and former Soviet countries, CZI staff, and representatives of network organizations. Grantees of the new program introduced their projects, networked with each other and the invited guests, and discussed ways to work together to increase access to imaging expertise and technologies in their regions. You can watch recordings of the meeting sessions here.

At this virtual meeting, recipients of the napari Plugin Accelerator Grant came together to kick off their work on 41 plugins for the napari image analysis platform. Participants shared their projects with one another, ranging from machine learning algorithms for image analysis to high-performance visualization. Participants brainstormed ways to collaborate to improve image analysis for biologists and opportunities for CZI to continue to support this community.

All grantees of the Rare As One (RAO) Network, 30 Cycle 1 grantees and 20 Cycle 2 grantees, gathered virtually December 8-9, 2021, for a community event dedicated to highlighting progress made by Cycle 1 grantees in the first two years of their grants and welcoming Cycle 2 grantees, who recently joined the network. The meeting provided opportunities for networking and community-building across cohorts, discussion of capacity building opportunities during the grant period and a public narrative-development workshop. In this short timeframe, grantees were already identifying opportunities for collaboration across challenges and shared synergies in disease research.

In 2016 CZI co-founders and co-CEOs, Priscilla Chan and Mark Zuckerberg, announced the launch of the Chan Zuckerberg Science Initiative with a bold mission: to support the science and technology that will make it possible to cure, prevent, or manage all disease by the end of the century.

Fast forward 5 years later and together with our colleagues, grantees, partners, and collaborators, we have learned a tremendous amount about how to accelerate biomedical science to advance human health. Together with the scientific community, our science and technology teams have made progress in characterizing human cells and visualizing biological processes; in bringing together experts across disciplines and career stages to tackle disease; in identifying and democratizing valuable and emerging methods, tools, and datasets; and in supporting patient communities. And we’re just getting started!

Visit the anniversary website to watch the full video from the virtual symposium celebrating our work over the past five years and looking ahead to what’s next.

The 2021 Essential Open Source Software for Science Meeting brought together all grantees from the four EOSS funding cycles, along with program advisors, funders, researchers, and CZI staff. With 256 attendees over three days, this event was an opportunity to build connections among the maintainers of these projects, foster collaborations, and have open conversations about the challenges faced and potential solutions. Many of the presentations from the meeting (including invited talks) are available on Zenodo and the participants shared their live reactions on Twitter during the event via the #EOSSmtg hashtag.

The 2021 Single-Cell Biology Annual Meeting was a four-day event focused on bringing together researchers from the CZI Seed, Inflammation, and Pediatrics Networks, with the first day dedicated as a kickoff meeting for the new Pediatrics Network. The kickoff meeting allowed investigators to introduce themselves, their teams and projects, form connections, and identify research synergies. Following the Pediatrics Network kickoff meeting, Seed and Inflammation Network grantees actively participated over the remaining three days in a program that included keynotes, panels and project presentations. With 603 attendees, this marks the Single-Cell Biology program’s, and CZI Science at large, largest meeting to date and the first meeting with grantees across all currently active networks. Since the CZI Single-Cell Biology program supports scientists around the globe, we introduced split sessions each day between a morning and evening block that allowed broader engagement with grantees in Australia, India and throughout Asia.

On September 22-23, 2021, CZI held a kickoff meeting for the CZI Imaging Program’s Visual Proteomics grantees. Members of 14 teams, invited attendees and CZI staff met virtually for two days to learn about each other’s projects, look for areas of synergy and potential collaborations, and to discuss important topics related to visual proteomics. These researchers are developing technologies to improve the visualization and identification of proteins within cells. A total of 77 attendees participated in the meeting.

The CZI Open Science Program supports training and education for biomedical researchers. To enable collaboration and community building across the organizations in this space, we hosted a workshop with representatives from 13 groups to determine ways CZI can best support the open science and computational training ecosystem. The meeting goals were to: (1) bring together groups to discuss and identify areas of collaboration; and (2) identify potential areas of funding for CZI — both short and long term.

Attendees

• Laura Ación, Universidad de Buenos Aires – CONICET, Argentina
• Amanda Charbonneau, University of California, Davis
• April Clyburne-Sherin, Reproducibility for Everyone
• Selene L Fernandez-Valverde, Advanced Genomics Unit, Langebio, Cinvestav
• Toby Hodges, The Carpentries
• Kari Jordan, The Carpentries
• François Michonneau, The Carpentries
• Sarah Morgan, EMBL-European Bioinformatics Institute
• Micaela Parker, Academic Data Science Alliance
• Danielle Robinson, Code for Science & Society
• Erin Robinson, Metadata Game Changers LLC/Openscapes
• Malvika Sharan, The Alan Turing Institute
• Emmy Tsang, TU Delft & Open Life Science
• Kirstie Whitaker, The Alan Turing Institute
• Jason Williams, Cold Spring Harbor Laboratory
• Lou Woodley, CSCCE
• Yo Yehudi, Open Life Science

CZI hosted a week-long Faculty Application Bootcamp, FAB@CZI, for 52 PhD students and postdocs who work at CZI-supported and associated labs. The course covered all written and verbal components of the Faculty Job Search process, such as Research, Teaching & Diversity Statements, Job & Chalk Talks, Interviewing, Negotiation, and more. All participants planned to apply for U.S. faculty positions in the 2021-2022 cycle, and connected with small homegroups throughout the week to discuss their application materials and strategies with their peers.

This two-day workshop brought together a small group of experts in Medical Imaging and covered three section areas: Large Scale Human Imaging Studies (focusing on increasing representation from marginalized communities), AI & ML in Diagnostics (focusing in part on racial disparities in diagnostics), and the creation and dissemination of Low-Cost Portable Medical Devices. A common theme throughout the workshop was what can be done to increase Diversity, Equity and Inclusion in the Medical Imaging field. Each session consisted of short (15 minute) overview talks on one of the three topic areas, followed by break-out group discussions and report outs.Learn more about DEI approaches in medical imaging in this presentation by senior science advisor for CZI, Hannah Valantine.

Attendees

• Muyinatu Bell, Johns Hopkins University
• Mehdi Benchoufi, echOpen
• Tobias Bonhoeffer, Max Planck Institute of Neurobiology
• William Brody, Salk Institute
• Madeleine Cule, Calico
• Jérôme Dubois
• Lillian Ekem, Duke University
• Maryellen Giger, University of Chicago
• Viren Jain, Google
• Brian Litt, University of Pennsylvania
• Leonel Malacrida, Universidad de la República
• Paul Matthews, Imperial College London
• Ziad Obermeyer, UC Berkeley
• Nimmi Ramanujam, Duke Global Women’s Health Technologies
• Rebecca Richards-Kortum, Rice University
• David Rosenthal, 4Catalyzer
• Amber Simpson, Queen’s University
• Nick van Bruggen, Calico
• Lukas Winter, Physikalisch-Technische Bundesanstalt (PTB)
• Adam Yala, MIT

The Neurodegeneration Challenge Network (NDCN) 2021 Annual Meeting brought together 423 participants, representing NDCN the laboratories funded under three RFAs, to share their recent scientific discoveries, network with each other, and learn about tools and resources available to the network. 

This three-day virtual meeting included 15 NDCN investigator presentations, 79 lightning talks from students, postdoctoral fellows and staff scientists, scientific and professional mentoring opportunities for attendees, two clinician and patient presentations, and a keynote presentation. The meeting format also included two parallel sessions organized by NDCN IPSC and CRISPR working group members highlighting current opportunities and challenges in these research areas. 

Learn more about the goals of the CZI Neurodegeneration Challenge Network in this video. 

There are over 7,000 rare diseases affecting over 450 million people worldwide. All diseases have underlying cellular mechanisms, and single-cell biology provides a valuable perspective for characterizing these mechanisms. This in turn has the potential to help  increase the percentage of patients that receive an actionable and informative diagnosis and treatment. This meeting brought together patient leaders, researchers in their respective rare disease fields, and other single-cell biology researchers to discuss challenges and opportunities for advancing diagnosis in rare disease that would be accelerated by single-cell methods and to identify possible avenues for supporting multi-disciplinary collaboration in this space.

Attendees

• Erin Anderson, Autoimmune Hepatitis Association
• Sam Behjati, Wellcome Sanger Institute
• Chamutal Gur, Weizmann Institute of Science
• Tracy Hart, Osteogenesis Imperfecta Foundation
• Joanne Hatchett, PSC Partners Seeking a Cure
• Sarah Henrickson, Children’s Hospital of Philadelphia
• Amjad Horani, Washington University in St Louis
• Vera Krymskaya, University of Pennsylvania
• Craig Lammert, Indiana University; Autoimmune Hepatitis Association
• Sonya MacParland, University Health Network
• Michele Manion, PCD Foundation
• Pleasantine Mill, MRC Human Genetics Unit
• Alexander Misharin, Northwestern University
• Vicki Modell, Jeffrey Modell Foundation
• Fred Modell, Jeffrey Modell Foundation
• Ruth-Anne Pai, PSC Partners Seeking a Cure
• Catherine Paul-Fijten, ZC4H2 Deficiency Research Foundation
• Charlotte Phillips, University of Missouri; Osteogenesis Imperfecta Foundation
• Jessica Quinn, Jeffrey Modell Foundation
• Debbie Requesens, Children’s Hospital of Philadelphia; Penn Orphan Disease Center
• Amy Ryan, University of Southern California
• Susi Shanks, PCD Foundation Support Group UK & Scotland
• Sue Sherman, The LAM Foundation
• Marshall Summar, Children’s National Hospital; Rare Disease Institute
• Michele Tana, University of California, San Francisco
• Shuang-Yin Wang, Weizmann Institute of Science
• Kathryn Wikenheiser-Brokamp, Cincinnati Children’s Hospital Medical Center; University of Cincinnati College of Medicine
• Garabet Yeretssian, YSG LLC

The Neurodegeneration Challenge Network and Science In Society programs led a four-part series focused on treatment and single-patient (“n-of-1”) therapeutics to explore challenges and identify opportunities for encouraging multidisciplinary engagement. The first three topic-based sessions shared patient and patient family perspectives. The final session used breakout groups and large discussions to ideate potential solutions for a more efficient and equitable process in developing n-of-1 therapeutics. During the meeting series, nearly 50 experts from the scientific community, patient groups, government, academia, and industry shared their experiences and participated in the discussions.

Attendees

• Rebecca Ahrens-Nicklas, University of Pennsylvania
• Alison Bateman-House, NYU Grossman School of Medicine
• Frank Bennett, Ionis Pharmaceuticals, Inc.
• Elizabeth Bhoj, Children’s Hospital of Philadelphia
• Max Bronstein, MGB Consulting; Journal of Science Policy & Governance
• Philip J. “P.J.” Brooks, National Institutes of Health; National Center for Advancing Translational Sciences
• Robert Brown, University of Massachusetts Medical School
• Lynn Bush, Boston Children’s Hospital; Harvard Medical School
• Holly Carmichael, Maggie’s Cure; Maggie’s Pearl; GT Independence
• Erin Chown, APBD Research Foundation
• Stanley Crooke, n-Lorem Foundation
• Graham Dempsey, Q-State Biosciences
• Orrin Devinsky, NYU Langone; NYU Grossman School of Medicine
• Kevin Eggan, BioMarin Pharmaceutical
• Michael Ehlers, Apple Tree Partners; Limelight Bio
• Keith Flanagan, BCH; TRV Newco
• Sara Goldkind, Goldkind Consulting, L.L.C.
• Michele Goodwin, University of California, Irvine; Center for Biotechnology and Global Health Policy
• Katherine High, Asklepios (AskBio) Pharmaceutical Inc.
• Rich Horgan, Cure Rare Disease
• Jill Jarecki, Cure SMA
• Walter Kowtoniuk, Third Rock Ventures
• Art Krieg, Checkmate Pharmaceuticals
• Larissa Lapteva, FDA, Center for Biologics Evaluation and Research
• Andrew Lo, MIT Sloan School of Management
• Diane Maloney (invited), FDA, Center for Biologics Evaluation and Research
• Eric Marsh, Penn Orphan Disease Center; Children’s Hospital of Philadelphia
• Matt Might, Hugh Kaul Precision Medicine Institute; University of Alabama at Birmingham
• Tim Miller, Washington University School of Medicine in St. Louis
• Eric Minikel, Broad Institute
• Colleen Olson, DHPS Foundation
• Natacha Pires, APBD Research Foundation
• Terry Pirovolakis, CureSPG50
• Scott Pomeroy, Harvard Medical School; Boston Children’s Hospital
• Deanna Portero, National Institutes of Health, National Center for Advancing Translational Sciences
• Tejashri Purohit-Sheth, DCEPT, OTAT/CBER/FDA
• Sanath Ramesh, OpenTreatments
• Gopa Raychaudhuri, FDA, Center for Biologics Evaluation and Research
• Rachel Sher, National Organization for Rare Disorders
• Neil Shneider, Columbia University
• Maggie Spoth, Mila’s Miracle Foundation, Inc.
• Reed Tuckson, Tuckson Health Connections
• Sonia Vallabh, Broad Institute of MIT and Harvard
• Julia Vitarello, Mila’s Miracle Foundation, Inc.
• Yael Weiss, Ultragenyx Pharmaceutical, Inc.
• Patricia Williams, Northeastern University
• Rick White, National Organization for Rare Disorders
• Tim Yu, Harvard Medical School

A two-day meeting, co-hosted by CZI and the Research Corporation for Science Advancement (RCSA), brought together a diverse group of over 70 early career investigators, facilitators, organizers, and guests. The early career Scialog attendees, who represent a wide range of expertise—engineering, physics, chemistry, mathematics, and biology—held discussions about the state of deep tissue and medical imaging, heard invited presentations, and identified challenges to advancing bioimaging. The meeting culminated in the formation of collaborative teams to submit proposals for pilot projects to be considered for funding by CZI and RCSA. As a direct outcome, CZI supported six of the pilot projects proposals and RCSA has funded three. Learn more about the CZI-funded projects.

During this two-day workshop, the Open Science and Imaging program teams joined efforts to convene major stakeholders in open hardware—developers, custom fabrication facilities managers in universities, and representatives of support organizations—to discuss major challenges and opportunities for the open source paradigm in biomedical instrumentation.

Open hardware provides a unique opportunity to accelerate biomedical science by democratizing access to key hardware and improving data quality, efficiency, and reproducibility through more transparency and quicker community development cycles. Open hardware development is growing quickly in the imaging field, where instrumentation can be inaccessible due to high costs and expensive maintenance.

Attendees

• Julieta Arancio, Fundación CENIT; UNSAM
• Tom Baden, University of Sussex
• Mehdi Benchoufi, echOpen
• Richard Bowman, University of Bath
• Anne Bowser, The Wilson Center
• Jeff Brooker, Thorlabs, Inc.
• Denise Cai, Icahn School of Medicine at Mount Sinai
• Chris Charlton, Chan Zuckerberg Biohub
• Janet Coffey, Gordon & Betty Moore Foundation
• Alicia Gibb, Open Source Hardware Association
• Josh Greenberg, Alfred P. Sloan Foundation
• Tarek Loubani, Glia
• Andre Maia Chagas, University of Sussex; Prometheus Science
• Meghan McCarthy, NIH, National Institute of Allergy and Infectious Diseases
• Shalin Mehta, Chan Zuckerberg Biohub
• Jenny Molloy, University of Cambridge
• Joshua Pearce, Michigan Technological University
• Nicolas Pegard, University of North Carolina at Chapel Hill
• Manu Prakash, Stanford University
• Lucia Prieto-Godino, Francis Crick Institute; TReND in Africa
• Javier Serrano, European Organization for Nuclear Research (CERN)
• Josh Siegle, Allen Institute
• Nico Stuurman, University of California, San Francisco; HHMI
• Fabian Voigt, University of Zurich
• Glenn Walters, University of North Carolina at Chapel Hill
• Bill Warger, Thorlabs, Inc.
• Michael Weinberg, Engelberg Center on Innovation Law & Policy at New York University Law // Open Source Hardware Association
• Lukas Winter, Physikalisch-Technische Bundesanstalt (PTB)

The napari Alfa Cohort is a collaboration between eight leading Python-based image analysis tool developers and the CZI Imaging team in support of the open source napari project. This one-day meeting was a celebration and demonstration of the napari plugins created over a three-month period by developers of Python-based segmentation tools. All teams presented demos of their plugins, shared their development trajectory, and connected with each other during the showcase meeting. 

The work presented at the napari Alfa Cohort Showcase is also highlighted in this Medium post.

Attendees

• Tania Allard, Quansight
• Matthias Bussonnier, Quansight
• Jianxu Chen, Allen Institute for Cell Science
• Na Hyung Choi, Allen Institute for Cell Science
• Pranjal Dhole, German Center for Neurodegenerative Diseases
• Thao Do, Allen Institute for Cell Science
• Miguel Fernandes,
• Eugenio Fava, German Center for Neurodegenerative Diseases (DZNE)
• Ru Gunawardane,
• Robert Haase, DFG Cluster of Excellence Physics of Life, TU Dresden
• Peter Horvath, Synthetic and Systems Biology Unit
• Brian Kim, Allen Institute for Cell Science
• Anna Kreshuk, European Molecular Biology Laboratory (EMBL)
• Dominik Kutra, European Molecular Biology Laboratory (EMBL)
• Talley Lambert, Harvard Medical School
• Andrew Leonard, Allen Institute for Cell Science
• Duway Nicolas Lesmes Leon, German Center for Neurodegenerative Diseases (DZNE)
• Molly Maleckar, Simula Research Laboratory
• Soham Mandal, European Bioinformatics Institute (EMBL-EBI), University of Cambridge
• Matt McCormick, Kitware
• Emil Melnikov, European Molecular Biology Laboratory (EMBL)
• Kimberly Metzler, Allen Institute for Cell Science
• Christoph Möhl, YAPIC
• Michael Morehead, syGlass
• Benjamin Morris, Allen Institute for Cell Science
• Juan Nunez-Iglesias, Monash University
• Gonzalo Pena-Castellanos, Quansight
• Susanne Rafelski, Allen Institute for Cell Science
• Megan Riel-Mehan,
• Uwe Schmidt,
• Sylvain Slaton, Allen Institute for Cell Science
• Ahmet Can Solak, Chan Zuckerberg Biohub
• Carsen Stringer, HHMI Janelia Research Campus
• Ervin Tasnadi, Biological Research Centre, Szeged
• Dan Toloudis, Allen Institute for Cell Science
• Adam Tyson, Sainsbury Wellcome Centre
• Virginie Uhlmann, European Bioinformatics Institute (EMBL-EBI)
• Matheus Viana, Allen Institute for Cell Science
• Pamela Wadhwa, Quansight
• Martin Weigert, École polytechnique fédérale de Lausanne (EPFL)
• Kevin Yamauchi, Swiss Federal Institute of Technology in Zürich (ETH Zurich)

This symposium, a partnership between CZI and the NIH Center for Alzheimer’s and Related Dementias (CARD), brought together experts in the fields of genetics, single-cell biology, computational biology, and neurodegenerative disease. Attendees discussed how single-cell and computational biology approaches can contribute to the discovery and validation of mechanisms and pathways associated with genetic discoveries in Alzheimer’s disease and related dementias. The symposium featured 22 speaker talks and moderated discussion with each speaker addressing two questions:

• What future work or technology are you most excited about?
• What are the key barriers to moving this area forward?

Nearly 600 people registered for this symposium. Recordings of the presentations can be found here.

Attendees

• Omer Bayraktar, Wellcome Sanger Institute
• Veronique Belzil, Mayo Clinic
• Carles Boix, Massachusetts Institute of Technology
• Inma Cobos, Stanford University
• Mark Cookson, NIH National Institute on Aging
• Ryan Corces, Gladstone Institutes
• Philip De Jager, Columbia University Irving Medical Center
• Ernest Fraenkel, Massachusetts Institute of Technology
• Alison Goate, Icahn School of Medicine at Mount Sinai
• Mina Gouti, Max Delbrück Center for Molecular Medicine
• Yuhan Hao, New York Genome Center
• Rebecca Hodge, Allen Institute for Brain Science
• Henne Holstege, Amsterdam UMC
• Johanna Jackson, Imperial College London
• Manolis Kellis, MIT / Broad Institute
• Rachel Liao, Broad Institute of MIT and Harvard
• Sten Linnarsson, Karolinska Institute
• Matthias Mann, Max Planck Institute of Biochemistry
• Huw Morris, University College London
• Eran Mukamel, University of California, San Diego
• Mats Nilsson, SciLifeLab, Stockholm University
• Hemali Phatnani, New York Genome Center and Columbia University
• Danielle Posthuma, VU University Amsterdam
• Towfique Raj, Icahn School of Medicine at Mount Sinai
• Abbas Rizvi, Columbia University, Zuckerman Mind Brain Behavior Institute
• Sam Rodriques, The Francis Crick Institute
• Andy Singleton, NIH Center for Alzheimer’s and Related Dementias (CARD)
• Leslie Thompson, University of California Irvine
• Michael Ward, NIH National Institute of Neurological Disorders and Stroke (NINDS)

This three-day event brought together over 200 attendees to share progress, explore collaborations, and surface computational challenges and opportunities through presentations and demos across the computational biology community within the Seed Networks for the Human Cell Atlas (HCA). Computational biology is a central focus of the CZI Single-Cell Biology program, and this meeting provided a space for meaningful discourse around several themes. The first day focused on training and learning with 10 invited presentations, demos, and workshops. Days two and three focused on 44 project presentations by various meeting attendees, and multiple sessions to dive deeper into various computational themes.

This annual meeting brought together grantees from two cycles of Imaging Scientists RFAs to build community, and identify the most transformative immediate steps and long-term strategy to advance the field of imaging. The three-day event had over 100 attendees and was organized with themes covering new approaches in core management, community development, imaging education, technology development, and image analysis pipelines. The event was hosted on MURAL whiteboard, a virtual environment designed to engage participants. The five invited keynote presentations of this meeting are available to watch here.

Over 30 participants representing 13 new projects joined CZI staff for the Deep Tissue Imaging program kickoff meeting. These new grantees will work to advance the field of deep tissue imaging by developing technologies that will allow researchers to view information at cellular resolution, in complex tissue and through skin and bone, in living organisms. Over the two-day meeting, participants introduced their projects. This meeting sought to foster collaboration among the grantees and to explore how to build capacity to accelerate the development and dissemination of deep tissue imaging technologies.

On February 3, 2021, the Patient-Driven Research Program virtually hosted the Patient-Led Registry Data Interoperability Strategy Session. A small group of experts across the rare disease community, along with informaticists, bioethicists, and ontologists, met to frame the challenges in rare disease registry data interoperability, identify key priorities, envision solutions, chart a path forward, and center patient-driven research. The focus on interoperability provides an opportunity to enable usability and analyses across rare disease data sources and systems, in turn, making it easier for patients to share data with researchers, and for those researchers to fully leverage patient voices in rare disease research.

Attendees

• Matthew Bellgard, Queensland University of Technology (QUT)
• Mildred Cho, Stanford University
• Melissa Haendel, Oregon Health & Science University; Oregon State University
• Daria Julkowska, European Joint Programme on Rare Diseases (EJP RD); National Institute of Health and Medical Research (INSERM)
• Sandra Lee, Columbia University
• Ken Mandl, Boston Children’s Hospital; Harvard Medical School
• Lucia Monaco, International Rare Diseases Research Consortium (IRDiRC); Fondazione Telethon
• Ana Rath, Orphanet; National Institute of Health and Medical Research (INSERM)
• Rachel Richesson, University of Michigan Medical School
• Marco Roos, Leiden University Medical Center; Rare Diseases GO FAIR
• Holly Tabor, Stanford University
• Ramona Walls, Critical Path Institute; University of Arizona
• John Wilbanks, Sage Bionetworks
• Yanji Xu, National Institutes of Health

The Open Science Program in collaboration with ASAPbio led a workshop to identify shared technology needs for preprints, bringing together several community members to discuss and prioritize needs surfaced in user stories through earlier consultations. Lessons learned from this workshop were distilled into a public report, summarizing nine emerging areas with unmet technology opportunities, and the associated user stories from interviews.

Attendees

• Anita Bandrowski, SciScore / Automated Screening Working Group
• Nokome Bentley, Stencila
• Rachel Besen, MIT Press
• Matt Bettonville, Emerson Collective
• Denis Bourguet, Peer Community In
• Rachel Burley, Research Square Company
• Humberto Debat, Instituto Nacional de Tecnología Agropecuaria
• Tom Demeranville, ORCID
• Hannah Drury, Sciety / eLife
• Gunther Eysenbach, Journal of Medical Internet Research
• Ashley Farley, Bill and Melinda Gates Foundation
• Kathryn Funk, NIH/National Library of Medicine
• Kate Grabowski
• Thomas Guillemaud, Peer Community In
• Chelsea Haupt, AI2 – Semantic Scholar
• Jo Havemann, AfricArXiv
• Daniel Himmelstein, Related Sciences
• Sam Hindle, PREreview
• John Inglis, Cold Spring Harbor Laboratory
• Alexander Ketchakmadze, Stencila
• Veronique Kiermer, PLOS
• Martin Klein, Los Alamos National Laboratory
• Sebastian Kohlmeier, Semantic Scholar
• Mike Lacy, American Society for Cell Biology
• Thomas Lemberger, European Molecular Biology Organization (EMBO) / Review Commons
• Nick Lindsay, MIT Press
• Giuliano Maciocci, eLife
• Jo McEntyre, European Bioinformatics Institute (EMBL-EBI)
• Heather McKay, Johns Hopkins University
• Alex Mendonça, SciELO
• Ross Mounce, Arcadia Fund
• Josh Nicholson, scite
• Michèle Nuijten, Statcheck / Tilburg University
• Louise Page, Bill and Melinda Gates Foundation
• Mate Palfy, preLights
• Michael Parkin, European Bioinformatics Institute (EMBL-EBI)
• Nici Pfeiffer, Center for Open Science
• Eleonora Presani, arXiv
• Kristen Ratan, Stratos
• Nico Riedel, QUEST
• Martyn Rittman, Crossref
• Andy Robinson, CABI
• John Sack, HighWire
• Daniela Saderi, PREreview
• Richard Sever, Cold Spring Harbor Laboratory / bioRxiv
• Paul Shannon, Sciety / eLife
• Kathleen Shearer, Confederation of Open Access Repositories
• Adrian Stanley, Journal of Medical Internet Research (JMIR) Publications
• Katherine Szarama, Emerson Collective
• Raphaël Tournoy, Center for Direct Scientific Communication (CCSD)
• EJ van Lanen, Helmholtz
• Tim Vines, DataSeer
• Tracey Weissgerber, QUEST
• Dan Whaley, Hypothesis

The 2020 Essential Open Source Software for Science Meeting brought together the grantees from the three EOSS funding cycles, with over 200 attendees. This three-day event was an opportunity to build connections among the maintainers of these projects, foster collaborations, and have open conversations about the challenges faced and potential solutions. Using a virtual meeting format created an opportunity to reach a wider audience with greater attendance, including program advisors, funders from philanthropic and governmental sectors, industry partners, and open science advocates, along with grantees, researchers and CZI staff. 

Recordings of the meeting presentations and demos can be found here, and many of the presentation slide decks are also available on Zenodo. The conversation on social media from the participants of this and subsequent EOSS meetings can be followed via the #EOSSmtg hashtag.

In CZI’s largest meeting in 2020, over 450 attendees met via Zoom over three days. The goal of the annual meeting of the Seed Networks for the Human Cell Atlas was to bring the research community of PIs, students, postdocs, and staff scientists together and celebrate the progress they have made. The meeting was a space to share findings to foster new ideas, collaborations, and discussions. During the three meeting days, participants listened to and participated in two plenary talks, 12 demo sessions, 44 project talks, 28 lightning talks, and 47 poster presentations. Both Keolu Fox and Katy Börner gave keynote presentations on ancestral genomics and knowledge representations, respectively.

Over 100 participants attended four webinar sessions to kick off a new grant program for the Neurodegeneration Challenge Network: 30 new Collaborative Pairs of investigators who will focus on neurodegenerative disease research. The goal of the webinar series was to introduce the 60 new investigators and their teams, connect them with one another and the rest of the Challenge Network, and connect them with CZI. Each of the Collaborative Pairs teams gave a short talk, with follow-up Q&A. The talks were followed by Zoom networking sessions, organized around key themes and topics. The kickoff series provided a strong foundation for establishing this new grant program structure with a collaborative focus.

Over 100 grantees of the Rare As One Network participated in a two-day virtual event to build community together. All 30 rare disease organizations of the Rare As One Network presented short overviews of their staff and mission and highlighted the progress they have made during the first six months of the program. In addition to the presentations, attendees got to know each other better via 1:1 and small group networking sessions using Icebreaker and Zoom breakout rooms. The event identified synergies within the network, set up potential future collaborations, and highlighted opportunities for additional learnings for Rare As One Network members. Most of all, it brought the network closer together.

Attendees

• Maria Isabel Achatz, Li-Fraumeni Syndrome Association
• Rachel Alvarez, Cure CMD
• Donna Appell, Hermansky-Pudlak Syndrome Network
• Kathryn Atchley, KIF1A.ORG
• Joe Barclay, CLOVES Syndrome Community
• Gabe Bassin, The Yaya Foundation for 4H Leukodystrophy
• Andrea Becerra, Association for Creatine Deficiencies
• Liz Berger, DDX3X Foundation
• Lindsey Bergstrom, CRMO Foundation
• Jonathan Boutelle, Systemic JIA Foundation
• Kristen Brantner, Hermansky-Pudlak Syndrome Network
• Beth Buccini, DDX3X Foundation
• Emily Burgess, CLOVES Syndrome Community
• Carmen Camacho, Hermansky-Pudlak Syndrome Network
• Jennifer Canvasser, HEC Society
• Hilda Cardona, Hermansky-Pudlak Syndrome Network
• Meegan Carey, PSC Partners Seeking a Cure
• Melissa Chaikof, Usher 1F Collaborative
• Chip Chambers, DADA2
• June Cheng, The Yaya Foundation for 4H Leukodystrophy
• Marianne Clancy, Cure HHT
• Meagan Collins, CureGRIN
• Marna Davis, Fibrolamellar Cancer Foundation
• Kristen Davis, CLOVES Syndrome Community
• Vincent Del Gaizo, CRMO Foundation
• Medha Deoras-Sutliff, The EHE Foundation
• Yssa DeWoody, Project 8p // Dup15q Alliance
• Jo-Tina DiGennaro, Hermansky-Pudlak Syndrome Network
• Gustavo Dziewczapolski, Cure CMD
• David Epstein, APBD Research Foundation
• Tiffany Ferry, Lymphangiomatosis & Gorham’s Disease Alliance
• Tal Friedman, Fibrolamellar Cancer Foundation
• Valerie Friedman, Hermansky-Pudlak Syndrome Network
• Mark Furth, Fibrolamellar Cancer Foundation
• Paula Gani, TESS Research Foundation
• Ron Garber, The Yaya Foundation for 4H Leukodystrophy
• Cat Gasol, TESS Research Foundation
• Ann Geffen, TANGO2 Research Foundation
• Natalie Gilmore, Lennox-Gastaut Syndrome Foundation
• Deberah Goldman, APBD Research Foundation
• Rachel Gomel, PSC Partners Seeking a Cure
• Linseigh Green, NEC Society
• Jennifer Griffin, Lennox-Gastaut Syndrome Foundation
• Karen Groff, Lennox-Gastaut Syndrome Foundation
• Cameron Hancock, The Snyder-Robinson Foundation
• Joanne Hatchett, PSC Partners Seeking a Cure
• Kristen Hayner, DADA2
• Davelyn Hood, Congenital Hyperinsulinism International
• Amanda Hope, INADcure Foundation
• John Hopper, Fibrolamellar Cancer Foundation
• Emily Hsu, TESS Research Foundation
• Sangeetha Iyer, Association for Creatine Deficiencies
• Kayleigh Keen, Lennox-Gastaut Syndrome Foundation
• Jack Kelly, Lymphangiomatosis & Gorham’s Disease Alliance
• Lisa Klepper, Lymphangiomatosis & Gorham’s Disease Alliance
• Teri Koerner, The Snyder-Robinson Foundation
• Amy Kotnik, Project 8p // Dup15q Alliance
• Nolie Krock, Cure HHT
• Kathy Leavens, Lennox-Gastaut Syndrome Foundation
• Nancy Lee, Hermansky-Pudlak Syndrome Network
• Dominique Lessard, KIF1A.ORG
• Jeff Levenson, APBD Research Foundation
• Kurt Losert, Fibrolamellar Cancer Foundation
• Katia Luedtke, The Snyder-Robinson Foundation
• Keith McArthur, CureGRIN
• Renee McEvoy, Hermansky-Pudlak Syndrome Network
• Megen Mckinney, Fibrolamellar Cancer Foundation
• James Meier, APBD Research Foundation
• Erica N. Miller, Usher 1F Collaborative
• Kasha Morris, TANGO2 Research Foundation
• Mike Morris, TANGO2 Research Foundation
• Emile Najm, KAT6A Foundation
• Becky Nieves, Hermansky-Pudlak Syndrome Network
• Kim Nye, TESS Research Foundation
• Meghan O’Keefe, Li-Fraumeni Syndrome Association
• Lynn O’Malley, Fibrolamellar Cancer Foundation
• Ruth-Anne Pai, CLOVES Syndrome Community
• Leena Panwala, INADcure Foundation
• Tai Pasquini, Congenital Hyperinsulinism International
• Jenn Perry, Li-Fraumeni Syndrome Association
• Natacha Pires, APBD Research Foundation
• Rob Rapaport, Glut1 Deficiency Foundation
• Julie Raskin, Congenital Hyperinsulinism International
• Michael Raymond, The Snyder-Robinson Foundation
• Denise Rehner, CureGRIN
• Elizabeth Reynolds, The Champ Foundation
• Jeff Reynolds, The Champ Foundation
• Sara Robertson, CLOVES Syndrome Community
• Luke Rosen, KIF1A.ORG
• Ricky Safer, PSC Partners Seeking a Cure
• Harriet Saxe, APBD Research Foundation
• Nicole Schaefer, Cure HHT
• Jennifer Schmitt, Congenital Hyperinsulinism International
• Shannon Scott, KIF1A.ORG
• Terry Selucky, Cure CMD
• Bina Shah, Project 8p // Dup15q Alliance
• Rashmi Sinha, Systemic JIA Foundation
• Justine Sinnaeve, DADA2
• Debbie Soprano, Li-Fraumeni Syndrome Association
• Glenna Steele, Glut1 Deficiency Foundation
• Kimberley Steele, Lymphangiomatosis & Gorham’s Disease Alliance
• Rob Sunris, Cure CMD
• Alex Theos, CRMO Foundation
• Sarah Theos, CRMO Foundation
• Laura Trutoiu, Association for Creatine Deficiencies
• Kimberly Tuminello, Association for Creatine Deficiencies
• Vanessa Vogel-Farley, Project 8p // Dup15q Alliance
• Mary Vyas, PSC Partners Seeking a Cure
• Heidi Wallis, Association for Creatine Deficiencies

Over 300 people gathered on Zoom for the three-day Neurodegeneration Challenge Network (NDCN) 2020 Annual Meeting to celebrate the progress made in the first funding year of the NDCN Ben Barres Early Career Awards and NDCN Collaborative Science Awards. During the meeting, investigators shared their latest research, PhD students and postdocs gave lightning talks, and attendees connected via 1:1 chats. Keynote presentations covered a range topics such as patient perspectives on multiple sclerosis, development of antisense oligonucleotide (ASO) therapies for neurological disorders, and diversity, equity and inclusion in neuroscience. We also hosted virtual poster, demo, and breakout sessions for the Challenge Network to share accomplishments and set up new collaborations.

Watch one of the keynote presentations and learn about the powerful story of how Julia Vitarello and Timothy Yu collaborated to develop an ASO therapy for the rare disease Batten Disease.

Attendees

• Sanya Aggarwal, University of Cambridge
• Nicola Allen, Salk Institute for Biological Studies
• Carolina Alquezar, University of California, San Francisco
• Steven Altschuler, University of California, San Francisco
• Defne Amado, University of Pennsylvania
• Neal Amin, Stanford University
• Juan Arboleda, University of Florida
• Ernest Arenas, Karolinska Institute
• Andrea Argouarch, University of California, San Francisco
• Frederick Arnold, Duke University
• Shruti Arya, University of California, San Francisco
• Adekunle Bademosi, VIB KU Leuven
• Sofia Bali, University of Texas Southwestern Medical Center
• Kylie Balotin, Vanderbilt University
• Luke Bartelt, Duke University
• Himanish Basu, Harvard Medical School
• Bruno A. Benitez, Washington University in St. Louis
• Frank Bennett, Ionis Pharmaceuticals
• Anastasya Birger, Duke University
• Elena Blanco-Suarez, Salk Institute for Biological Studies
• Isobel Bolger, Cold Spring Harbor Laboratory
• Allison Bosworth, Vanderbilt University
• Elizabeth Bradshaw, Columbia University
• Dries Braeken, imec
• Mary Rose Branch, Duke University
• Ashley Brandebura, Salk Institute for Biological Studies
• Kristopher Brannan, University of California, San Diego
• Kelly Brock, Harvard Medical School
• Anita Bröllochs, protocols.io
• Jillybeth Burgado, Salk Institute for Biological Studies
• Elena Caceres, University of California, San Francisco
• Nicole Calakos, Duke University
• Carles Calatayud Aristoy, VIB KU Leuven
• Laura Campisi, Icahn School of Medicine at Mount Sinai
• Cortina Chen, University of Cambridge
• Dailu Chen, University of Texas Southwestern Medical Center
• Xinhong Chen, California Institute of Technology
• Alice Chen-Plotkin, University of Pennsylvania
• Isaac Chiu, Harvard Medical School
• Rati Chkheidze, University of Texas Southwestern Medical Center
• So Yoen Choi, Harvard Medical School
• Amit Chouhan, VIB KU Leuven
• George Church, Harvard Medical School
• Don W. Cleveland, Ludwig Institute for Cancer Research // University of California, San Diego
• Inma Cobos, Stanford University
• Will Connell, University of California, San Francisco
• Alyssa Coyne, Johns Hopkins University School of Medicine
• Carlos Cruchaga, Washington University
• Beverly Davidson, Children’s Hospital of Philadelphia
• Gregg Day, Mayo Clinic
• Philip De Jager, Columbia University
• Marianna Decet, VIB KU Leuven
• Jorge del Aguila, Washington University in St. Louis
• Elizabeth Delgado, University of Florida
• Lance Denes, University of Florida
• Aksinya Derevyanko, Salk Institute for Biological Studies
• Eliza Dhungel, Washington University in St. Louis
• Marc Diamond, University of Texas Southwestern Medical Center
• Mafalda Dias, Harvard Medical School
• David Ding, Harvard University
• Xiaozhe Ding, California Institute of Technology
• Yue Dong, Stanford University
• Gustavo Dziewczapolski, Cure CMD
• Jenifer Einstein, University of Utah
• Cagla Eroglu, Duke University Medical Center
• Isabella Farhy, Salk Institute for Biological Studies
• Fabiana Farias, Washington University in St. Louis
• Victoria Fernandez, Washington University
• Fabia Filipello, Washington University in St. Louis
• Talitha Forcier, Cold Spring Harbor Laboratory
• Jonathan Frazer, Harvard Medical School
• Marc Freeman, Vollum Institute, OHSU
• Molly Gale Hammell, Cold Spring Harbor Laboratory
• Li Gan, Weill Cornell Medicine
• Ron Garber, The Yaya Foundation for 4H Leukodystrophy
• Stephanie Gaus, University of California, San Francisco
• Ann Geens, VIB KU Leuven
• Lorenzo Ghezzi, VIB KU Leuven
• Kristina Gibbs, OnPoint Scientific
• Natalie Gilmore, Lennox-Gastaut Syndrome Foundation
• Yunzi Gou, Duke University
• Viviana Gradinaru, California Institute of Technology
• Tessa Green, Harvard Medical School
• Anastasia Gromova, Duke University
• Ravinder Gulia, Duke University
• Laura Gunsalus, University of California, San Francisco
• Yuwan Guo, University of Texas at Austin
• Mitchell Guttman, California Institute of Technology
• Daniel Gyllborg, Stockholm University
• Michael Hantak, University of Utah
• Oscar Harari, Washington University in St. Louis
• Ed Harding, University of Cambridge
• Meik Henningsen, VIB KU Leuven
• Ryan Hildebrandt, University of Florida
• Acacia Hori, California Institute of Technology
• Elaine Hsiao, University of California, Los Angeles
• Ji-Hye Hwang, University of California, San Francisco
• Bradley Hyman, Massachusetts General Hospital
• Laura Ibanez, Washington University in St. Louis
• Abhirami Iyer, Washington University in St. Louis
• Jana Jenquin, University of Florida
• Jenny Jiang, University of Texas at Austin
• Lukasz Joachimiak, University of Texas Southwestern Medical Center
• Natalie Kaempf, VIB KU Leuven
• Martin Kampmann, University of California, San Francisco
• Celeste Karch, Washington University in St. Louis
• Ketaki Katdare, Vanderbilt University
• Megan Keiser, Children’s Hospital of Philadelphia
• Michael Keiser, University of California, San Francisco
• Ayse Kilic, VIB KU Leuven
• Hyosung Kim, Vanderbilt University
• Teri Koerner, The Snyder-Robinson Foundation
• Robin Komisar
• Alexandra Kroshilina, Columbia University Medical Center
• Karl Kumbier, University of California, San Francisco
• Al La Spada, Duke University
• Pablo Largo-Barrientos, VIB KU Leuven
• Roey Lazarovits, Harvard University
• Julia Lazzari-Dean, University of California, San Francisco
• Chelsey LeBlang, Stanford University
• Alex Lee, University of California, San Francisco
• Ka Wai Lee, Karolinska Institute
• David Leib, Children’s Hospital of Philadelphia
• Kun Leng, University of California, San Francisco
• Dominique Lessard, KIF1A.ORG
• Jeff Levenson, APBD Research Foundation
• Lili Li, University of Cambridge
• David Lieb, Children’s Hospital of Philadelphia
• Sten Linnarsson, Karolinska Institute
• Ethan Lippmann, Vanderbilt University
• Olga Sula Litvin, University of California, San Francisco
• Jonathan Lynch, University of California, Los Angeles
• Viviana Macarelli, University of Cambridge
• Iman Mali, University of Cambridge
• Mrunali Manjrekar, Harvard Medical School
• Shilpa Mantri, University of California, San Francisco
• Ivan Marazzi, Icahn School of Medicine at Mount Sinai
• Sergio Marco Salas, Stockholm University
• Ryan Marina, University of California, San Diego
• Debora Marks, Harvard University
• Jacob Marsh, Washington University in St. Louis
• Craig Marshall, Cold Spring Harbor Laboratory
• Rita Martinez, Washington University in St. Louis
• Jessica McKinley, University of California, San Francisco
• Spencer McKinstry, Duke University
• Xiangling Meng, Stanford University
• Vilas Menon, Columbia University
• Florian Merkle, University of Cambridge
• Nick Mew, University of California, San Francisco
• Beatrice Miccoli, imec
• Tim Miles, California Institute of Technology
• Lise Minaud, University of California, San Francisco
• Miguel Minaya, Washington University
• Yuki Miura, Stanford University
• Gregory Mohl, University of California, San Francisco
• Alejandro Monteys, Children’s Hospital of Philadelphia
• Alejandro Mossi Albiach, Karolinska Institute
• Emile Najm, KAT6A Foundation
• Vasavi Nallur Srinivasaraghavan, Stanford University
• Alissa Nana Li, University of California, San Francisco
• Dylan Neel, Harvard Medical School
• Achal Neupane, Washington University in St. Louis
• Maia Norman, Harvard University // Wyss Institute
• Kim Nye, TESS Research Foundation
• Niko-Petteri Nykaenen, Washington University in St. Louis
• Alana O’Brien, University of Florida
• Brian O’Grady, Vanderbilt University
• Kathryn O’Neill, Cold Spring Harbor Laboratory
• Marta Olah, Columbia University Medical Center
• Christine Olson, University of California, Los Angeles
• Rose Orenbuch, Harvard University
• Brittney Otero, University of Florida
• Leena Panwala, INADcure Foundation
• Sergiu Pasca, Stanford University
• Lorenzo Pasquini, University of California, San Francisco
• Gentry Patrick, University of California, San Diego
• Ethan Perlstein
• Vladislav Petyuk, Pacific Northwest National Laboratory
• Julien Philippe, Duke University
• Belinda Pinto, University of Florida
• Luca Ponzoni, University of California, San Francisco
• Kiril Poukalov, University of Florida
• Devin Powell, Sight In Sight Studios
• Roman Praschberger, VIB KU Leuven
• Jack Prazich, University of Texas at Austin
• Juan Ramirez, Duke University
• Paul Ranum, Children’s Hospital of Philadelphia
• Sripriya Ravindra Kumar, California Institute of Technology
• Urmimala Raychaudhuri, Duke University
• Aleksandra Recupero, Columbia University
• Capria Rinaldi, University of California, San Francisco
• Pia Rodriguez, Duke University
• Joshua Rollins, Harvard Medical School
• Nathan Rollins, Harvard Medical School
• Brendan Rooney, University of California, San Francisco
• Jonah Rosch, Vanderbilt University
• Luke Rosen, KIF1A.ORG
• Matthew Rosene, Washington University in St. Louis School of Medicine
• Maike Roth, University of California, San Francisco
• Jeffrey Rothstein, Johns Hopkins University
• Isabel Salas, Salk Institute for Biological Studies
• Carmen Saltó, Karolinska Institute
• Zoe Scherzer, University of Florida
• Birgitt Schuele, Stanford University
• Nina Schultz, University of California, San Francisco
• William Serkin, VIB KU Leuven
• Francesco Severino, Duke University
• Aashna Shah, Harvard University
• Bina Shah, Project 8p // Dup15q Alliance
• Ada Shaw, Harvard University
• Regina Shaw, Cold Spring Harbor Laboratory
• Wen-Chuan Shen, Duke University
• Jason Shepherd, University of Utah
• Yajuan Shi, Vanderbilt University
• June Shin, Harvard University
• Minjung Song, University of Cambridge
• Alexander Sorets, Vanderbilt University
• Carolina Soriano, Washington University in St. Louis
• Salvatore Spina, University of California, San Francisco
• Glenna Steele, Glut1 Deficiency Foundation
• Eric Sun, University of Texas at Austin
• Mariko Taga, Columbia University Irving Medical Center
• Andrew Taibi, University of Utah
• Amy Tam, Harvard Medical School
• Oliver Tam, Cold Spring Harbor Laboratory
• Luis Tecedor, Children’s Hospital of Philadelphia
• Dima Ter-Ovanesyan, Harvard University // Wyss Institute
• Olivia Teter, University of California, San Francisco
• Lenny Teytelman, protocols.io
• Nicole Thadani, Harvard Medical School
• Emily Thompson, Johns Hopkins University
• Sam Thompson, Vanderbilt University
• Terri Thompson, OnPoint Scientific
• Cedric Thues, VIB KU Leuven
• Ruilin Tian, University of California, San Francisco
• Carmen Alejandra Torres, Stanford University
• Wendy Trieu, Wyss Institute
• Laura Trutoiu, Association for Creatine Deficiencies
• John Tuddenham, Columbia University Medical Center
• Mitali Tyagi, University of Utah
• Sameehan Uday Mahajani, Stanford University
• Valerie Uytterhoeven, VIB KU Leuven
• Carmen Valero, University of Florida
• Jaime Vaquer-Alicea, University of Texas Southwestern Medical Center
• Sarat Vatsavayai, University of California, San Francisco
• Patrik Verstreken, VIB KU Leuven
• Vinoy Vijayan, VIB KU Leuven
• Julia Vitarello, Mila’s Miracle Foundation
• Ariel Vitenzon, Duke University
• Vanessa Vogel-Farley, Project 8p // Dup15q Alliance
• Helen Vuong, University of California, Los Angeles
• David Walt, Harvard Medical School // Wyss Institute // Brigham and Women’s Hospital
• Eric Wang, University of Florida
• Fengxian Wang, Washington University in St. Louis
• Shiyi Wang, Duke University
• Christopher Waters, University of California, San Francisco
• Charles White, University of Texas Southwestern Medical Center
• John Williams, University of California, San Diego
• Daniel Wong, University of California, San Francisco
• Elizabeth Wood, Broad Institute
• Cole Wunderlich, Cold Spring Harbor Laboratory
• Amanda Xia, University of Texas at Austin
• Junjie Xu, University of Utah
• Andrian Yang, European Bioinformatics Institute
• Chengran Yang, Washington University in St. Louis
• Shanzheng Yang, Karolinska Institute
• Alexis Yates, Vanderbilt University
• Gene Yeo, University of California, San Diego
• Shih-Feng You, Washington University in St. Louis
• Carolyn Yrigollen, Children’s Hospital of Philadelphia
• Lewis Yu, University of California, Los Angeles
• Timothy Yu, Boston Children’s Hospital
• Christina Yung, Columbia University Medical Center
• Faria Zafar, Stanford University
• Yu Zhou, University of Florida

With this virtual meeting of over 200 attendees, we launched the Single-Cell Analysis of Inflammation program. This new program supports 29 projects that will utilize a spectrum of technologies with single-cell resolution to explore commonalities among inflammatory states and disease. The goal of this initial kickoff meeting was to convene the community, provide a forum for sharing projects, and begin to identify mutual interests and challenges that can be addressed by the community. 

CZI is excited to support this community around a new wave of inflammation research that adopts a systems biology approach for questions that have historically been constrained by a focus on single tissues, disease area, or cell types that provide a narrow window into an exquisitely complex process.

Attendees

• Britt Adamson, Princeton University
• Cristhiane Aguiar, University of Campinas (UNICAMP)
• Abdul Alabi, Harvard Medical School
• Palloma Almeida, National Institute of Cancer
• Letizia Amadori, Icahn School of Medicine at Mount Sinai
• Julien Ayroles, Princeton University
• Lakshmi Batachari, UC San Diego
• Nicole Baumgarth, UC Davis
• Doron Betel, Weill Cornell Medicine
• Ami Bhatt, Stanford University
• Danny Bin, Harvard Medical School
• Mariana Boroni, Brazilian National Cancer Institute
• Deisi Braga Shimo, University of Campinas
• Anne Brunet, Stanford University
• Rachael Brust, Harvard Medical School
• Simon Bucher, UCSF Department of Medicine
• Matthew Buckley, Stanford
• Deviana Burhan, UCSF
• Minji Byun, Icahn School of Medicine at Mount Sinai
• Jingli Cao, Weill Cornell Medical College
• Marvic Carrillo, UC San Diego
• Michadel Carroll, Boston Children’s Hospital
• Javier Castro, Zuckerberg San Francisco General Hospital (UCSF)
• Gisele Castro, University of São Paulo
• Antonio Cembellin-Prieto, UC Davis
• Paulina Chamely, Weill Cornell Medicine
• Wenqiang Chen, Harvard Medical School

This meeting assembled CZI’s Imaging Scientist grantees and Imaging Software fellows after their first year of funding. The main focus was group working sessions to address possible solutions to some of the biggest challenges that imaging core facilities face. Working groups covered these topic areas:

• Image analysis and data management
• Teaching and training
• Imaging core management and career development
• Quality control

Throughout these working sessions, we heard presentations from Global BioImaging and BioImaging North America (BINA) on how to train imaging trainers. Watch recordings of these three imaging presentations.

Attendees

• Claire Brown, McGill University
• Teng-Leong Chew, HHMI Janelia
• Martin Fischer, Duke University
• Holly Gibbs, Texas A&M University
• Allen Goodman, Broad Institute of MIT and Harvard
• Cvic Innocent, BCH & HMS
• Michelle Itano, University of North Carolina
• Abhishek Kumar, Marine Biological Laboratory
• Scot Kuo, John Hopkins University
• Caroline Magnain, Martinos Center, MGH/HMS
• Sara McArdle, La Jolla Institute
• Alison North, Rockefeller University
• Federica Paina, European Molecular Biology Laboratory
• Thierry Pecot, Medical University of South Carolina
• Douglas Rowland, University of California, Davis
• Curtis Rueden, University of Wisconsin
• Anthony Santella, Sloan Kettering Cancer Center, Molecular Cytology Core
• Brandon Scott, South Dakota School of Mines and Technology
• Caterina Strambio de Castillia, University of Massachusetts Medical School
• Aaron Taylor, University of Michigan
• Gokul Upadhyayula, UC Berkeley
• Jennifer Waters, Harvard Medical School
• Michael Weber, Morgridge Institute for Research

CZI launched the Rare As One Network with a virtual kickoff meeting in March of 2020. To welcome the Rare As One cohort of 30 grantee organizations, we hosted 106 attendees, including Rare As One grantee staff and board members, CZI staff, and patient speakers at this two-day event. During this time we provided an overview of CZI and the Rare As One program, highlighted inspirational stories of patient-led research initiatives, provided a storytelling workshop by The Story Collider, and built community and opportunities for collaboration among grantees.

Attendees

• Ghassan Abou-Alfa, Memorial Sloan Kettering Cancer Center
• Anne Adler, Fibrolamellar Cancer Foundation
• Rachel Alvarez, Cure CMD
• Ashley Appell, Hermansky-Pudlak Syndrome Network
• Donna Appell, Hermansky-Pudlak Syndrome Network
• Kathryn Atchley, KIF1A.ORG
• Christopher Austin, National Center for Advancing Translational Sciences
• Joe Barclay, CLOVES Syndrome Community
• Erin Barker, The Story Collider
• Andrea Becerra, Association for Creatine Deficiencies
• Elizabeth Berger, DDX3X Foundation
• Lindsey Bergstrom, CRMO Foundation
• Scott Berns, Progeria Research Foundation
• Terry Jo Bichell, COMBINEDBrain
• Kristen Brantner, Hermansky Pudlak Syndrome Network
• Carmen Camacho, Hermansky Pudlak Syndrome Network
• Jennifer Canvasser, Necrotizing Enterocolitis Society
• Hilda Cardona, Hermansky-Pudlak Syndrome Network
• Meegan Carey, Partners Seeking a Cure
• Elliot Chaikof, Usher 1F Collaborative
• Melissa Chaikof, Usher 1F Collaborative
• Chip Chambers, DADA2 Foundation
• June Cheng, The Yaya Foundation for 4H Leukodystrophy
• Marianne Clancy, Cure HHT
• Meagan Collins, CureGRIN Foundation
• Kristen Davis, CLOVES Syndrome Community
• Vincent Del Gaizo, CRMO Foundation
• Medha Deoras-Sutliff, The EHE Foundation
• Yssa DeWoody, Project 8p / Ring 15 USA
• Jo-Tina DiGennaro, Hermansky-Pudlak Syndrome Network
• David Fajgenbaum, Castleman Disease Collaborative Network
• Tal Friedman, Fibrolamellar Cancer Foundation
• Patricia Furlong, Parent Project Muscular Dystrophy
• Mark Furth, Fibrolamellar Cancer Foundation
• Paula Gani, TESS Research Foundation
• Ron Garber, The Yaya Foundation for 4H Leukodystrophy
• Natalie Gilmore, Lennox-Gastaut Syndrome Foundation
• Deberah Goldman, Adult Polyglucosan Body Disease Research Foundation
• Rachel Gomel, Partners Seeking a Cure
• Leslie Gordon, Progeria Research Foundation
• Jennifer Griffin, Lennox-Gastaut Syndrome Foundation
• Cameron Hancock, The Snyder-Robinson Foundation
• Joanne Hatchett, Partners Seeking a Cure
• Kristen Hayner, DADA2 Foundation
• Melissa Hieger, DDX3X Foundation
• Davelyn Hood, Congenital Hyperinsulinism International
• Amanda Hope, INADCure Foundation
• John Hopper, Fibrolamellar Cancer Foundation
• Heather Kirkwood, Hermansky-Pudlak Syndrome Network
• Lisa Klepper, Lymphangiomatosis & Gorham’s Disease Alliance
• Teri Koerner, The Snyder-Robinson Foundation
• Seema Lalani, TANGO2 Research Foundation
• Kathy Leavens, Lennox-Gastaut Syndrome Foundation
• Nancy Lee, Hermansky-Pudlak Syndrome Network
• Dominique Lessard, KIF1A.ORG
• Jeff Levenson, Adult Polyglucosan Body Disease Research Foundation
• Ali Mattu, The Story Collider
• Keith McArthur, CureGRIN Foundation
• Renee McEvoy, Hermansky-Pudlak Syndrome Network
• Megen McKinney, Fibrolamellar Cancer Foundation
• Ashley McNamara, CLOVES Syndrome Community
• James Meier, Adult Polyglucosan Body Disease Research Foundation
• Greg Millett, amfAR
• Kasha Morris, TANGO2 Research Foundation
• Mike Morris, TANGO2 Research Foundation
• Emile Najm, KAT6A Foundation
• Becky Nieves, Hermansky-Pudlak Syndrome Network
• Kim Nye, TESS Research Foundation
• Leena Panwala, INADCure Foundation
• Tai Pasquini, Congenital Hyperinsulinism International
• Rob Rapaport, Glut1 Deficiency Foundation
• Julie Raskin, Congenital Hyperinsulinism International
• Michael Raymond, The Snyder-Robinson Foundation
• Denise Rehner, CureGRIN Foundation
• Elizabeth Reynolds, The Champ Foundation
• Luke Rosen, KIF1A.ORG
• Harriet Saxe, Adult Polyglucosan Body Disease Research Foundation
• Nicole Schaefer, Cure HHT
• Jennifer Schmitt, Congenital Hyperinsulinism International
• Shannon Scott, KIF1A.ORG
• Terry Selucky, Cure CMD
• Bina Shah, Project 8P / Dup15q Alliance
• Dorie Shapiro, Usher 1F Collaborative
• Rashmi Sinha, Systemic JIA Foundation
• Glenna Steele, Glut1 Deficiency Foundation
• Robert Sunris, Cure CMD
• Alex Theos, CRMO Foundation
• Sarah Theos, CRMO Foundation
• Laura Trutoiu, Association for Creatine Deficiencies
• Kim Tuminello, Association for Creatine Deficiencies
• Erin Umberger, Necrotizing Enterocolitis Society
• Vanessa Vogel-Farley, Project 8P / Dup15q Alliance
• Mary Vyas, Partners Seeking a Cure
• Heidi Wallis, Association for Creatine Deficiencies
• Ehsan Yazdi, Nomocan Pharmaceuticals

In February 2020, over 100 people gathered in Berkeley, California to launch CZI’s Essential Open Source Software for Science (EOSS) program. Members of the first cohort of 32 EOSS grantees came together for three days to meet with each other and external partners from a variety of philanthropic and governmental funding organizations, fiscal sponsors, advocates and researchers of open source for science, along with CZI staff. Open source software is crucial to modern scientific research, and this program aims to support software maintenance, growth, development, and community engagement for these critical tools.

Learn more about this meeting in this Medium post. The presentations from this meeting are available at our EOSS repository.

Attendees

• Hannah Aizenman, City College of New York (CUNY)
• Cat Allman, Google
• Will Ayd, innobi
• Peter Bankhead, University of Edinburgh
• Marcel Bargull, University Hospital Essen // University of Duisburg-Essen
• Carl Boettiger, UC Berkeley
• Robert Buels, UC Berkeley
• Minh Bui, Australian National University
• Georgia Bullen, Simply Secure
• Andrew Butler, New York Genome Center
• Abigail Cabunoc Mayes, Mozilla Foundation
• Greg Caporaso, Northern Arizona University
• Vincent Carey, Harvard Medical School
• Thomas Caswell, Brookhaven National Lab
• Yunshun Chen, Walter and Eliza Hall Institute of Medical Research
• Meena Choi, Northeastern University
• Neil Chue Hong, University of Edinburgh
• Antonin Delpeuch, University of Oxford
• Matthew Dillon, Northern Arizona University
• Daniela Duca, SAGE Publishing
• Nathan Dunn, UC Berkeley
• Kevin Eliceiri, University of Wisconsin at Madison
• Jeremy Freeman, carbonplan.org
• Bhanu Gandham, Broad Institute of MIT and Harvard
• Pradyun Gedam, Python Software Foundation
• Matt Germonprez, University of Nebraska at Omaha
• Amel Ghouila, H3ABioNet
• Sean Goggins, University of Missouri
• Ralf Gommers, Quansight
• Emmanuelle Gouillart, Plotly
• Josh Greenberg, Alfred P. Sloan Foundation
• Dan Guo, Northeastern University
• Matt Haberland, Cal Poly San Luis Obispo
• Josef Hardi, Stanford University
• Sumana Harihareswara, Changeset Consulting // Python Software Foundation
• Alison Hill, RStudio
• Paul Hoffman, New York Genome Center
• Christopher Holdgraf, UC Berkeley
• James Howison, University of Texas at Austin
• Nicolas Hug, Columbia University
• Kari Jordan, The Carpentries
• Daniel Katz, University of Illinois at Urbana-Champaign
• John Kirkham, NVIDIA
• Nicolas Kruchten, Plotly
• Charity Law, Walter and Eliza Hall Institute of Medical Research
• Heng Li, Dana-Farber Cancer Institute // Harvard Medical School
• Sophie Liu, UC San Diego School of Medicine
• Alexander Mathis, Harvard University
• Mackenzie Mathis, Harvard University
• Danil Mikhailov, Wellcome Trust
• Andrew Milich, Schmidt Futures
• Josh Moore, University of Dundee
• Andreas Mueller, Columbia University
• Mark Musen, Stanford University
• Suha Naser-Khdour, Australian National University
• Juan Nunez-Iglesias, Monash University
• Tim O’Reilly, O’Reilly Media
• Joanne Ong, NUS
• Manish Parashar, National Science Foundation
• Jonathan Peirce, University of Nottingham
• Fernando Perez, UC Berkeley
• Alex Pico, Gladstone Institutes // UCSF
• Alain Pitiot, Ilixa Ltd.
• Dexter Pratt, UC San Diego
• Aaron Quinlan, University of Utah
• Karthik Ram, UC Berkeley
• Matthew Roeschke, HouseCanary
• Noam Ross, EcoHealth Alliance
• Leah Silen, NumFOCUS
• Heidi Sofia, National Institutes of Health
• Owen Stephens, Owen Stephens Consulting Ltd
• BJ Stubbs, CDNM/Bioconductor
• Jason Swedlow, University of Dundee
• Andy Terrel, NumFOCUS
• Mark Tsuchida, University of Wisconsin at Madison
• Lucas van Dijk, Broad Institute of MIT and Harvard
• Olga Vitek, Northeastern University
• Leah Wasser, University of Colorado Boulder
• Warren Weckesser, UC Berkeley
• Kirstie Whitaker, Alan Turing Institute
• Ryan Williams, Mount Sinai School of Medicine
• Alyssa Wright, Open Source Collective
• Devon Zuegel, GitHub

SpaceJam 2 (Spatial Transcriptomics Jamboree 2) was the second data analysis jamboree hosted by CZI and the Allen Institute for Brain Science. The goal of this jamboree was to convene members of the SpaceTx consortium, a CZI-funded Human Cell Atlas (HCA) pilot project, to analyze, compare, and contrast each individually generated image-based transcriptomics dataset and assess their ability to differentiate cell types in the brain. This comparison relied on analysis of processed data from each consortium member’s assay. Providing data was therefore a prerequisite for attending the meeting, and the end goal was to position the consortium for compilation and a path toward publication.

The three-and-a-half-day-meeting was formatted to have large blocks of working time. We started the meeting with lightning talks to get up to speed on current efforts, spent the majority of the meeting in groups working through analysis with regular report outs, and ended the meeting with presentations on progress. Throughout the event there were evening social events for the attendees, largely students and postdocs, to get to know each other and foster collaborations.

You can find more information on this event, including the final presentations at the end of the meeting, on the SpaceJam 2 website.

We appreciate the partnership with the Allen Institute for Brain Science to make this event possible.

Attendees

• Brian Aevermann, J Craig Venter
• Alma Andersson, Karolinska Institutet
• Mehrtash Babadi, Broad Institute
• Tommaso Biancalani, Broad Institute
• Dylan Cable, Broad Institute
• Simone Codeluppi, Karolinska Institutet
• Oleh Dzyubachyk, Leiden University
• Aleksandrina Goeva, Broad Institute
• Daniel Goodwin, MIT
• Markus Hilscher, Stockholm University
• Naveed Ishaque, Berlin Institute of Health and Charité
• Ed Lein, Allen Institute
• Boudewijn Lelieveldt, Leiden University
• Brian Long, Allen Institute
• Jonas Maaskola, Karolinska Institutet
• Christoffer Mattsson Langseth, Stockholm University
• Jeremy Miller, Allen Institute
• Dimitris Nicoloutsopoulos, University College London
• Jeongbin Park, Berlin Institute of Health and Charité
• Viktor Petukhov, University of Copenhagen
• Richard Que, UC San Diego
• Richard Scheuermann, J Craig Venter
• Eeshit Vaishnav, Broad Institute
• Chenglong Xia, Harvard University
• Renee Zhang, J Craig Venter
• Yilin Zhao, Allen Institute

At this workshop, 22 imaging experts from around the world explored the frontiers of imaging. The meeting consisted of short talks and panel discussions focused on: 

• Whole organisms imaging 
• Molecular imaging
• Deep tissue imaging
• Fast dynamic imaging
• Distribution and dissemination of complex imaging systems 

The participants then identified four major facets of imaging technology that must be supported today in order to enable breakthroughs in our understanding of complex biological systems:

• Visualizing Cells in Deep Tissue: Methods to enable cellular or even sub-cellular resolution for imaging deep in tissues. 
• Visualizing Proteins in Cells: The ability to observe proteins in cells and monitor changes in their structure, quantity, distribution, and interactions. 
• Creating Universal Standards for Quantitative Imaging: Well-defined computational standards and infrastructure and commonly shared open source workflows to process tremendous amounts of imaging data.
• Democratizing Technology: Ensuring that new technologies and analysis workflows are available, accessible, and affordable to broad groups of biomedical researchers.

Read more about the outcomes of this meeting in our Medium post.

We appreciate the partnership with Bob Tjian and Tobias Bonhoeffer, who co-organized this meeting with CZI.

Attendees

• Sara Abrahamsson, UC Santa Cruz
• Wolfgang Baumeister, Max Planck Institute of Biochemistry
• Joerg Bewersdorf, Yale University
• Tobias Bonhoeffer, Max Planck Institute of Neurobiology
• Winfried Denk, Max Planck Institute of Neurobiology
• Katrin Heinze, University of Würzburg
• Harald Hess, Janelia Research Campus // HHMI
• Jan Huisken, Morgridge Institute for Research
• Markita Landry, UC Berkeley
• Luke Lavis, Janelia Research Campus // HHMI
• Loren Looger, Janelia Research Campus // HHMI
• Jim Marshel, Stanford University
• Gail McConnell, University of Strathclyde
• Shalin Mehta, Chan Zuckerberg Biohub
• Eugene Myers, Max Planck Institute of Molecular Cell Biology and Genetics
• Daniel Razansky, University and ETH Zurich
• Rebecca Richards-Kortum, Rice University
• Loic Royer, Chan Zuckerberg Biohub
• Mikhail Shapiro, California Institute of Technology
• Robert Tjian, UC Berkeley
• Srigokul Upadhyayula, UC Berkeley
• Laura Waller, UC Berkeley
• Yi Zuo, UC Santa Cruz

The Preprints I/O workshop brought together open science advocates, preprint service providers, researchers in biomedicine invested in rapid dissemination, scholarly publishers, and tool developers. Designed as a two-day event featuring lightning talks and breakout group discussions, the workshop focused on exploring open practices that can be built on top of preprints, in order to accelerate the pace of scientific discovery and collaboration. Participants discussed these prompts:

• What are researchers’ unmet needs that preprints can help support? What would the world look like if these needs were addressed?
• What are the blockers? What stands in the way of meeting these needs?
• What opportunities should the community consider in the short term? What should be built?

Throughout the workshop, the group identified several emerging themes and opportunities in response to these prompts. Read more about the outcomes of the workshop in this Medium post. 

We appreciate the partnership with Jessica Polka of ASAPbio to make this event possible.

Attendees

• Richard Abdill, University of Minnesota
• Jeffrey Beck, NCBI // NLM // NIH
• Bill Burkholder, Chan Zuckerberg Biohub
• Clarissa Carneiro, Federal University of Rio de Janeiro
• Humberto Debat, Instituto Nacional de Tecnología Agropecuarian
• Ricardo Henriques, University College London
• Katie Hickling, PLOS
• Daniel Himmelstein, University of Pennsylvania
• Anthony Holtmaat, University of Geneva
• Michele Ide-Smith, EMBL-EBI
• Erin McKiernan, Universidad Nacional Autónoma de México
• Jennifer Molloy, ContentMine // University of Cambridge
• Nici Pfeiffer, Center for Open Science
• Jessica Polka, ASAPbio
• Jason Priem, Our Research
• Kristen Ratan, Stratos
• Daniela Saderi, PREreview
• Shyam Saladi, California Institute of Technology
• Richard Sever, bioRxiv
• Arfon Smith, Space Telescope Science Institute
• Bodo Stern, Howard Hughes Medical Institute
• Sowmya Swaminathan, Nature Research, Springer Nature
• Vincent Tunru, Plaudit
• Dan Whaley, Hypothesis
• Andrew York, Calico Labs

Single cell RNA sequencing data represent the majority data type in the Human Cell Atlas (HCA). Normalization is a critical and fundamental initial processing step in the analysis of these data. A wide variety of algorithms exist for normalization — these range from simple scaling methods to the analysis of generative models of the data. However, it’s difficult to know which approach to use when, and what the consequences may be for downstream biological analysis. Normjam convened a group of experts to discuss and collaborate on several topics related to these problems.

You can find more information on this event, including the meeting presentations, at the Normjam website.

We appreciate the partnership with Rahul Satija and the New York Genome Center to make this event possible.

Attendees

• Rhonda Bacher, University of Florida
• Joshua Batson, Chan Zuckerberg Biohub
• Jared Brown, University of Florida
• Adam Gayoso, University of California, Berkeley
• Christoph Hafemeister, New York Genome Center
• Yuhan Hao, New York Genome Center
• Stephanie Hicks, Johns Hopkins Bloomberg School of Public Health
• Rafael Irizarry, Dana-Farber Cancer Institute
• Peter Kharchenko, Harvard Medical School
• Romain Lopez, University of California, Berkeley
• Malte Luecken, Helmholtz Center Munich
• Marmar Moussa, University of Connecticut
• Alan O’Callaghan, MRC Human Genetics Unit
• Angela Oliveira Pisco, Chan Zuckerberg Biohub
• Sandhya Prabhakaran, Moffitt Cancer Centre
• Dana Pe’er, Sloan Kettering Institute
• Rahul Satija, New York Genome Center
• Manu Setty, Memorial Sloan Kettering Cancer Center
• Valentine Svensson, California Institute of Technology
• Will Townes, Princeton Computer Science
• Sophie Tritschler, Helmholtz Zentrum Munich
• Catalina Vallejos, MRC Human Genetics Unit / The Alan Turing Institute
• Lukas Weber, Johns Hopkins University

At this workshop, we brought together a range of experts in the electron microscopy field with the goal of understanding the current state of the field and hearing about opportunities to move it forward. Experts in cryo-EM, cryo-ET, and in software and hardware development discussed current projects, key bottlenecks, and possible opportunities that can have an impact on the field.

Read about the learnings of this meeting in this Medium post.

Attendees

• David Agard, University of California, San Francisco
• Daniela Boassa, University of California, San Diego
• Jamie Cate, University of California, Berkeley
• Yifan Cheng, University of California, San Francisco // HHMI
• Wah Chiu, Stanford University
• Karen Davies, Lawrence Berkeley National Laboratory
• David Dynerman, Chan Zuckerberg Biohub
• Adam Frost, University of California, San Francisco
• Robert Glaeser, Lawrence Berkeley National Laboratory
• Garrett Greenan, University of California, San Francisco
• Grant Jensen, California Institute of Technology
• Danielle Jorgens, University of California, Berkeley
• Vignesh Kasinath, University of California, Berkeley
• Andrey Malyutin, California Institute of Technology
• Paul Mooney, Gatan, Inc.
• Holger Müller, University of California, Berkeley
• Brent Nannenga, Arizona State University
• John Ngo, Boston University
• Talita Perciano, Lawrence Berkeley National Laboratory
• Juergen Plitzko, Max Planck Institute of Biochemistry
• J. Peter Rickgauer, Janelia // HHMI
• Alexis Rohou, Genentech
• James Sethian, University of California, Berkeley
• Elizabeth Villa, University of California, San Diego
• Carolina Soriano-Tárraga, Washington University St. Louis
• Amy Tam, Harvard Medical School
• Ruilin Tian, University of California, San Francisco
• Alejandra Torres, Stanford University
• Francesco Paolo Ulloa Severino, Duke University
• Paige Vega (Spencer), Vanderbilt University
• Austin Wang, University of California, San Francisco
• David Welch, US Crop Sciences
• Ben Zaepfel, Johns Hopkins University

We brought together PhD students and postdocs that are part of our Neurodegeneration Challenge Network program for a two-day computational training workshop in Chicago. The first day focused on plotting and programming in Python and was led by trainers from The Carpentries. The second day covered both single- cell analysis and image analysis techniques and was led by instructors from CZI.

Read more about our support for computational biology training in this Medium post</a.   Attendees

The need for clear and compelling science communication is greater than ever. Improving science communication and elevating diverse voices and perspectives in the scientific community breaks down barriers between science and society, creating a more responsive field and increasing public trust in science. The more science communication trainers connect, communicate, and collaborate with one another, the greater their individual and collective impact will be. This belief inspired a community of science communication trainers, researchers, and funders to come together to officially launch the new SciComm Trainers Network at this meeting in Redwood City, California.

We appreciate the partnership with the Kavli Foundation, COMPASS, the Alan Alda Center for Science Communication, and Converge.net to make this workshop happen.
Attendees

• Elyse Aurbach, University of Michigan
• Chantal Barriault, Laurentian University
• Diana Brazzell, Footnote
• Alison Caldwell, ComSciCon // UC San Diego
• Allison Coffin, Science Talk
• Meredith Drosback, SciLine
• Anthony Dudo, University of Texas at Austin
• Jesse Dunietz, MIT Communication Lab
• David Ehrlichman, Converge
• Mónica Feliú-Mójer, Ciencia Puerto Rico // iBiology
• Suzanne Ffolkes, The Optical Society
• Radha Ganesan, Alan Alda Center for Communicating Science
• Darcy Gentleman, DJG Communications LLC
• Rose Hendricks, ComSciCon // American Society for Cell Biology
• Raquell Holmes, improvscience
• Faith Kearns, University of California, Ag & Natural Resources
• Erica Kimmerling, Association of Science and Technology Centers
• Eve Klein, Institute for Learning Innovation
• Kristi Kremers, University of Minnesota
• Laura Lindenfeld, Alan Alda Center for Communicating Science
• Mary Catherine Longshore, American Association for the Advancement of Science
• Reyhaneh Maktoufi, Northwestern University // Adler Planetarium // The Story Collider
• John Meyer, University of Washington College of the Environment
• Mary Anne Moser, Spark, the Calgary Science Centre
• Barbara Natalizio, Rita Allen Foundation
• Liz Neeley, The Story Collider
• Todd Newman, University of Wisconsin-Madison
• Amelia Pape, Converge
• Jai Ranganathan, SciFund Challenge
• Alberto Roca, DiverseScholar
• Jessica Rohde, Interagency Arctic Research Policy Committee
• Brooke Smith, Kavli Foundation
• Amanda Stanley, COMPASS
• Sarah Sunu, COMPASS
• Rackeb Tesfaye, Broad Science
• Evelyn Valdez-Ward, Reclaiming STEM
• Nick Viele, Converge
• Kyle Marian Viterbo, The Symposium: Academic StandUp
• Caitlin Weber, University of Utah STEM Ambassador Program
• Elizabeth Weinberg, NOAA Office of National Marine Sanctuaries // National Marine Sanctuary Foundation

CZI staff attended the Reaching Diverse and Underrepresented Groups in Multimodal Studies meeting held in Aurora, Colorado. This meeting gave us the opportunity to connect with speakers and attendees at a satellite workshop after the main meeting. At this workshop, participants highlighted barriers to achieving heterogeneity in cohort research and discussed possible solutions.

We appreciate the partnership with the University of Colorado to make this workshop happen.

Attendees

• Adam Auton, 23andMe
• Gillian Belbin, Icahn School of Medicine at Mount Sinai
• Vence Bonham, National Human Genome Research Institute
• Joan Casey, Columbia University
• Katrina Claw, University of Colorado
• Burcu Darst, University of Southern California
• Joshua Galanter, Genentech
• Chris Gignoux, University of Colorado
• Arbel Harpak, Columbia University
• Lucia Hindorff, National Human Genome Research Institute
• Latifa Jackson, Howard University
• Chirag Lakhani, Harvard University
• Martin Maiers, Be The Match
• Jennifer Manly, Columbia University
• William Patterson, University of Colorado
• Genevieve Wojcik, Johns Hopkins University
• Noah Zaitlen, University of California, Los Angeles

At the end of July 2019, over 200 people traveled to Toronto, Canada to launch CZI’s Seed Networks for the Human Cell Atlas (HCA) program during a three-day meeting. This program funds 38 collaborative teams to support the continued development of the Human Cell Atlas. The meeting group consisted of more than 150 of the Seed Networks investigators, external partners from a variety of funders and institutions, and representatives from the HCA Data Coordination Platform, along with CZI program staff, computational biologists, and engineers. Building the HCA is a complex challenge that demands diverse contributions, and the goal of this first meeting was to help individual labs and projects understand the many activities across the HCA community.

Read more about what we learned at this meeting in our Medium post.

Attendees

• Kamran Ahmad, Fred Hutchinson Cancer Research Center
• Robert Amezquita, Fred Hutchinson Cancer Research Center
• Kristin Ardlie, Broad Institute of MIT and Harvard
• Bruce Aronow, Cincinnati Children’s Hospital Medical Center
• Gary Bader, University of Toronto
• Keren Bahar Halpern, Weizmann Institute of Science
• Mathew Baldwin, University of Oxford
• Pascal Barbry, Université Côte d’Azur // CNRS
• Anindita Basu, University of Chicago
• Tommaso Biancalani, Broad Institute of MIT and Harvard
• Markus Bitzer, University of Michigan
• Brian Black, University of California, San Francisco
• Olga Botvinnik, Chan Zuckerberg Biohub
• Anita Bröllochs, protocols.io
• Daniel Burkhardt, Yale University
• Robrecht Cannoodt, Ghent University
• Fei Chen, Broad Institute of MIT and Harvard
• Ken Chen, The University of Texas MD Anderson Cancer Center
• Mengjie Chen, University of Chicago
• Rui Chen, Baylor College of Medicine
• Zhen Chen, City of Hope
• Dawn Chong, National Cancer Centre Singapore
• Jürgen Cox, Max Planck Institute of Biochemistry
• Adam Cribbs, University of Oxford
• Aedin Culhane, Dana-Farber Cancer Institute
• Ramanuj DasGupta, Genome Institute of Singapore
• Margaret DeAngelis, University of Utah School of Medicine
• Thu Duong, University of California, San Diego
• Joseph Ecker, Howard Hughes Medical Institute // The Salk Institute for Biological Studies
• Mark Eckert, University of Chicago
• Oliver Eickelberg, University of Colorado Anschutz Medical Campus
• Wolfgang Enard, Ludwig Maximilians University Munich
• Samouil Farhi, Broad Institute of MIT and Harvard
• Greg Finak, Fred Hutchinson Cancer Research Center
• Clay Fischer, University of California, Santa Cruz
• David Fischer, Helmholtz Zentrum Munich
• Edward Fon, Montreal Neurological Institute
• Zorina Galis, National Institutes of Health
• Nicholas Gauthier, Harvard Medical School
• Ronald Germain, National Institute of Allergy and Infectious Diseases, National Institutes of Health
• Katrina Gold, Wellcome Trust
• Dominic Grün, Max Planck Institute of Immunobiology and Epigenetics
• Roderic Guigó, Centre for Genomic Regulation
• Rajat Gupta, Brigham and Women’s Hospital // Broad Institute of MIT and Harvard
• Gavin Ha, Fred Hutchinson Cancer Research Center
• Naomi Habib, Hebrew University of Jerusalem
• Marc Halushka, Johns Hopkins University
• Muzlifah Haniffa, Newcastle University
• Matthias Heinig, Helmholtz Zentrum Munich
• Neil Henderson, University of Edinburgh
• Steven Henikoff, Fred Hutchinson Cancer Research Center // Howard Hughes Medical Institute
• Chung-Chau Hon, RIKEN Center for Integrative Medical Sciences
• Sahand Hormoz, Harvard Medical School // Dana-Farber Cancer Institute
• Peter Horvath, Biological Research Centre of the Hungarian Academy of Sciences
• Norbert Huebner, Max Delbrück Center for Molecular Medicine in the Helmholtz
• Joanna Jones, University of Cambridge
• Dejan Juric, Massachusetts General Hospital
• Hadas Keren-Shaul, Weizmann Institute of Science
• Kai Kessenbrock, University of California, Irvine
• Allon Klein, Harvard Medical School
• Antje Körner, University Hospital Leipzig
• Anshul Kundaje, Stanford University
• Gioele La Manno, École Polytechnique Fédérale de Lausanne
• Jessica Langer, Helmsley Charitable Trust
• Ken Lau, Vanderbilt University
• Georg Lauer, Massachusetts General Hospital // Harvard Medical School
• Devon Lawson, University of California, Irvine
• Je Lee, Cold Spring Harbor Laboratory
• Ed Lein, Allen Institute for Brain Science
• Joshua Levin, Broad Institute of MIT and Harvard
• Jun Li, University of Michigan
• Bora Lim, The University of Texas MD Anderson Cancer Center
• Shin Lin, University of Washington
• Yiing Lin, Washington University in St. Louis
• Yunlong Liu, Indiana University School of Medicine
• Malte Lücken, Helmholtz Zentrum Munich
• Emma Lundberg, KTH Royal Institute of Technology
• Eline Luning Prak, University of Pennsylvania
• Sonya MacParland, University Health Network // University of Toronto
• Michael Mancini, Baylor College of Medicine
• Tom Maniatis, Columbia University // New York Genome Center
• Debora Marks, Harvard Medical School
• Jamie Marshall, Broad Institute of MIT and Harvard
• Ian McGilvray, University of Toronto
• Andrew McMahon, University of Southern California
• Elisabetta Mereu, Centro Nacional de Análisis Genómico – Centre for Genomic Regulation
• Alexander Misharin, Northwestern University
• Jeffrey Moffitt, Boston Children’s Hospital
• Jonathan Moody, RIKEN Center for Integrative Medical Sciences
• Martin Morgan, Roswell Park Comprehensive Cancer Center
• Samantha Morris, Washington University in St. Louis
• Norman Morrison, European Bioinformatics Institute
• Eran Mukamel, University of California, San Diego
• Ann Mullally, Harvard Medical School
• Alan Mullen, Massachusetts General Hospital
• Rinki Murphy, University of Auckland
• Harikrishna Nakshatri, Indiana University School of Medicine
• Nicholas Navin, The University of Texas MD Anderson Cancer Center
• Michela Noseda, Imperial College London
• Angela Oliveira Pisco, Chan Zuckerberg Biohub
• Woong-Yang Park, Samsung Genome Institute
• Mary-Elizabeth Patti, Joslin Diabetes Center, Harvard Medical School
• Dana Pe’er, Sloan Kettering Institute
• Mark Phillips, McGill University
• Luca Pinello, Massachusetts General Hospital
• Sebastian Pott, University of Chicago
• Steve Potter, Cincinnati Children’s Hospital Medical Center
• Joseph Powell, Garvan Institute of Medical Research
• Shyam Prabhakar, Genome Institute of Singapore
• Thomas Quertermous, Stanford University
• Gerald Quon, University of California, Davis
• Adeeb Rahman, Icahn School of Medicine at Mount Sinai
• Matthew Ritchie, The Walter and Eliza Hall Institute of Medical Research
• Abbas Rizvi, Columbia University
• Sara Rouhanifard, Northeastern University
• Orit Rozenblatt-Rosen, Broad Institute of MIT and Harvard
• Chris Sander, Harvard Medical School
• Stephan Sanders, University of California, San Francisco
• Joshua Sanes, Harvard University
• Minnie Sarwal, University of California, San Francisco
• Rahul Satija, New York Genome Center
• Herbert Schiller, Helmholtz Zentrum Munich
• Rachel Sealfron, Princeton University
• Ayellet Segre, Harvard Medical School
• Jonathan Seidman, Harvard Medical School
• Xiling Shen, Duke University
• Douglas Shepherd, University of Colorado Anschutz Medical Campus
• Ariella Shikanov, University of Michigan
• Tara Sigdel, University of California San Francisco
• Peter Sims, Columbia University
• Nikolai Slavov, Northeastern University
• Peter Smibert, New York Genome Center
• Sarah Snelling, University of Oxford
• Becky Steck, University of Michigan
• Lars Steinmetz, European Molecular Biology Laboratory
• Anna Maria Storniolo, Indiana University School of Medicine
• J Seth Strattan, Stanford University
• Aaron Streets, University of California, Berkeley
• Tom Taghon, Ghent University
• Purushothama Rao Tata, Duke University
• Sarah Teichmann, Wellcome Sanger Institute
• Lenny Teytelman, protocols.io
• Timothy Tickle, Broad Institute of MIT and Harvard
• Sarah Tishkoff, University of Pennsylvania
• Hanane Touil, Columbia University
• Cole Trapnell, University of Washington
• Kyle Travaglini, Stanford University
• Alexander Tsankov, Icahn School of Medicine at Mount Sinai
• Yu-Hua Tseng, Joslin Diabetes Center, Harvard Medical School
• Stefan Tullius, Brigham and Women’s Hospital
• David van Bruggen, Karolinska Institute
• Tavé van Zyl, Harvard Medical School
• Roser Vento-Tormo, Wellcome Sanger Institute
• Thierry Voet, Katholieke Universiteit Leuven
• Sushrut Waikar, Brigham and Women’s Hospital // Boston Medical Center
• Wenyi Wang, The University of Texas MD Anderson Cancer Center
• James Webber, Chan Zuckerberg Biohub
• Parker Wilson, Washington University in St. Louis
• Chun Jimmie Ye, University of California, San Francisco
• Esti Yeger-Lotem, Ben-Gurion University of the Negev
• Garabet Yeretssian, Helmsley Charitable Trust
• Peng Yin, Harvard Medical School
• Nir Yosef, University of California, Berkeley
• Benjamin Zaitlen, NVIDIA
• Bo Zhang, Washington University in St. Louis
• Xuegong Zhang, Tsinghua University
• Mei Zhen, Lunenfeld-Tanenbaum Research Institute
• Sheng Zhong, University of California, San Diego
• James Zou, Stanford University

In June, we brought together three partners working together to increase diversity of STEM students on their college campuses. This program is a partnership between UMBC, UC San Diego and UC Berkeley to increase recruitment and retention of underrepresented students pursuing studies in science, technology, engineering, and mathematics. During this one-day meeting, participants shared learnings and set practical goals to expand the UMBC Meyerhoff Scholars Program to both UC San Diego and UC Berkeley.

Attendees

• Diana Bautista, University of California, Berkeley
• Jamie Cate, University of California, Berkeley
• Glynda Davis, University of California, San Diego
• Oscar Dubon, University of California, Berkeley
• Leigh Eck, University of California, San Diego
• Keith Harmon, University of Maryland, Baltimore County
• Gentry Patrick, University of California, San Diego
• Becky Petitt, University of California, San Diego
• Mike Summers, University of Maryland, Baltimore County
• Ira Young, University of California, Berkeley

This workshop brought together experts from academia, medicine, and industry to discuss diverse areas of inflammation. We learned about shared bottlenecks, discussed where the field wants to go, and heard ideas of how to possibly get there.

Read more about what we learned at this meeting in our Medium post.
Attendees

• Yasmine Belkaid, National Institute of Allergy and Infectious Diseases, NIH
• Bérénice Benayoun, University of Southern California
• Semir Beyaz, Cold Spring Harbor Laboratory
• Diego Bohórquez, Duke University
• Bryan Bryson, MIT
• Nicolas Chevrier, University of Chicago
• Jason Cyster, UC San Francisco
• Adrian Erlebacher, UC San Francisco
• Don Ganem, Chan Zuckerberg Biohub
• Sarah Henrickson, The Children’s Hospital of Philadelphia
• Henri Jasper, Genentech
• Cynthia Kenyon, Calico Labs
• Kathryn Miller-Jensen, Yale University
• Anna Molofsky, UC San Francisco
• Kari Nadeau, Stanford University
• Shruti Naik, New York University School of Medicine
• Mary Nakamura, UC San Francisco
• Jose Ordovas-Montanes, MIT, Broad, Ragon Institute
• John Tsang, National Institute of Allergy and Infectious Diseases, NIH
• Henrique Veiga-Fernandes, Fundação Champalimaud
• Roser Vento, Wellcome Sanger Institute
• Alexandra-Chloé Villani, Massachusetts General Hospital, Harvard Medical School
• Allon Wagner, UC Berkeley
• Wanxin Wang, Stanford University
• Gerlinde Wernig, Stanford University
• Garabet Yeretssian, Helmsley Charitable Trust
• Matt Zinter, UC San Francisco

In March, grantees from CZI’s two imaging programs came together in San Francisco to meet with each other and with other imaging experts from the CZ Biohub and Bay Area universities.

The Imaging Scientists will work at imaging centers across the United States and interface between biology, microscopy hardware, and imaging software to accelerate progress in the imaging field, enabling biologists to leverage modern technology for microscopy data.

The Imaging Software Fellows work on three critical and widely-used tools — scikit-image, FIJI / ImageJ, and CellProfiler — that play a critical role in the imaging ecosystem.

Read more about what we learned at the imaging event.
Attendees

• Sara Abrahamsson, University of California, Santa Cruz
• Teng-Leong Chew, HHMI Janelia Research Campus
• Bryant Chhun, Chan Zuckerberg Biohub
• Beth Cimini, Broad Institute
• Rory Donovan-Maiye, Allen Institute for Cell Science
• Kevin Eliceiri, University of Wisconsin at Madison
• Martin Fischer, Duke University
• Jenny Folkesson, Chan Zuckerberg Biohub
• Marina Garrett, Allen Institute for Brain Science
• Holly Gibbs, Texas A&M University
• Allen Goodman, Broad Institute
• Syuan-Ming Guo, Chan Zuckerberg Biohub
• Greg Huber, Chan Zuckerberg Biohub
• Cassandravictoria Innocent, Boston Children’s Hospital // Harvard Medical School
• Michelle Itano, University of North Carolina
• Ivan Ivanov, Chan Zuckerberg Biohub
• Viren Jain, Google AI
• Gregory Johnson, Allen Institute for Cell Science
• Antje Keppler, Euro-BioImaging // EMBL
• John Kirkham, NVIDIA
• AnithaPriya Krishnan, Chan Zuckerberg Biohub
• Abhishek Kumar, University of Maryland, College Park // NIST
• Scot Kuo, Johns Hopkins University
• Merlin Lange, Chan Zuckerberg Biohub
• Manuel Leonetti, Chan Zuckerberg Biohub
• Emma Lundberg, KTH Royal Institute of Technology // Stanford University
• Caroline Magnain, Martinos Center for Biomedical Imaging, MGH/HMS
• Sara McArdle, La Jolla Institute for Immunology
• Shalin Mehta, Chan Zuckerberg Biohub
• Juan Nunez-Iglesias, Monash University
• Wei Ouyang, KTH Royal Institute of Technology // SciLifeLab
• Thierry Pécot, Medical University of South Carolina
• Matthew Rocklin, NVIDIA
• Douglas Rowland, University of California, Davis
• Loic Royer, Chan Zuckerberg Biohub
• Curtis Rueden, University of Wisconsin, Madison
• Anthony Santella, Sloan Kettering Institute for Cancer Research
• Johannes Schöneberg, University of California, Berkeley
• Brandon Scott, South Dakota School of Mines and Technology
• Jan Skotheim, Stanford University
• Ahmet Can Solak, Chan Zuckerberg Biohub
• Caterina Strambio De Castillia, University of Massachusetts Medical School
• Aaron Taylor, University of Michigan
• Srigokul Upadhyayula, University of California, Berkeley
• Stéfan van der Walt, Berkeley Institute for Data Science
• Laura Waller, University of California, Berkeley
• Jennifer Waters, Harvard Medical School
• Michael Weber, Morgridge Institute for Research
• Kevin Yamauchi, Chan Zuckerberg Biohub

The Neurodegeneration Challenge Network is a collaborative network that brings new ideas and people into the field of neurodegeneration, supports them with well validated tools and resources, and asks them to look at this problem from a cross-disease perspective. The kickoff event for the Challenge Network included over 100 staff scientists, physician scientists, postdocs, and students, representing 17 early career investigators and nine collaborative science teams from 26 institutions.

 
Read more about what we learned at this meeting.

Attendees

• Nicola Allen, Salk Institute for Biological Studies
• Steven Altschuler, University of California, San Francisco
• Ernest Arenas, Karolinska Institutet
• Kylie Balotin, Vanderbilt University
• Bruno Benitez, Washington University in St. Louis
• Mario Blanco, California Institute of Technology
• Elena Blanco-Suarez, Salk Institute for Biological Studies
• Elizabeth Bradshaw, Columbia University
• Dries Braeken, imec Leuven
• Kristopher Brannan, University of California, San Diego
• Patrick Brannelly, Rainwater Charitable Foundation
• Patricia Brennan, Chan Zuckerberg Initiative
• Anita Bröllochs, protocols.io
• Nicole Calakos, Duke University
• Xiaoyu Chen, Stanford University
• Alice Chen-Plotkin, University of Pennsylvania
• Isaac Chiu, Harvard Medical School
• Rati Chkheidze, University of Texas Southwestern Medical Center
• Kangway Chuang, University of California, San Francisco
• Inma Cobos, University of California, Los Angeles
• Lori Cox, AFTD Volunteer and Awareness Advocate
• Thomas Cox, UCSF Memory & Aging Center Clinical and Research Patient
• Carlos Cruchaga, Washington University in St. Louis
• Gregory Day, Washington University in St. Louis
• Philip De Jager, Columbia University
• Yongning Deng, University of California, Los Angeles
• Marc Diamond, University of Texas Southwestern Medical Center
• Mafalda Dias, Harvard Medical School
• Maria Diaz Ortiz, University of Pennsylvania
• Jenifer Einstein, University of Utah
• Cagla Eroglu, Duke University
• Ping Fang, University of California, Los Angeles
• Fabia Filipello, Washington University in St. Louis
• Nicholas Flytzanis, California Institute of Technology
• Molly Gale Hammell, Cold Spring Harbor Laboratory
• Garrett Gaskins, University of California, San Francisco
• Viviana Gradinar, California Institute of Technology
• Anastasia Gromova, Duke University / University of California, San Diego
• Mitchell Guttman, California Institute of Technology
• Michael Hantak, University of Utah
• David Haussler, University of California, Santa Cruz
• Ryan Hildebrandt, University of Florida
• Sook Yuin Jessica Ho, Icahn School of Medicine at Mount Sinai
• Elaine Hsiao, University of California, Los Angeles
• Ning Jenny Jiang, University of Texas, Austin
• Lukasz Joachimiak, University of Texas Southwestern Medical Center
• Martin Kampmann, University of California, San Francisco
• Aimee Kao, University of California, San Francisco
• Celeste Karch, Washington University School of Medicine
• Michael Keiser, University of California, San Francisco
• Maia Kipman, Brigham and Women’s Hospital
• Albert La Spada, Duke University
• Alex Lee, University of California, San Francisco
• Ka Wai Lee, Karolinska Institutet
• Kun Leng, University of California, San Francisco
• Ethan Lippmann, Vanderbilt University
• Yixuan Ma, Icahn School of Medicine at Mount Sinai
• Jennifer Manly, Columbia University
• Ivan Marazzi, Icahn School of Medicine at Mount Sinai
• Debora Marks, Harvard University
• Rebecca Marton, Stanford University
• Vilas Menon, Columbia University
• Florian Merkle, University of Cambridge
• Beatrice Miccoli, imec Leuven
• Alejandro Mossi Albiach, Karolinska Institutet
• Emma Neal, Vanderbilt University
• Dylan Neel, Harvard Medical School
• Marta Olah, Columbia University
• Christine Olson, University of California, Los Angeles
• Lyle Ostrow, Johns Hopkins University School of Medicine
• Marcos Otero, University of California, Los Angeles
• Sergiu Pasca, Stanford University
• Vladislav Petyuk, Pacific Northwest National Laboratory
• Keril Poukalov, University of Florida
• Brook Pyhtila, Addgene
• Sofia Quinodoz, California Institute of Technology
• Sripriya Ravindra Kumar, California Institute of Technology
• Ekemini Riley, Milken Institute Center for Strategic Philanthropy
• Capria Rinaldi, University of California, San Francisco
• Nathan Rollins, Harvard Medical School
• Jeffrey Rothstein, Johns Hopkins University
• Nikolay Rozhkov, Cold Spring Harbor Laboratory
• Isabel Salas, Salk Institute for Biological Studies
• Randy Schekman, Aligning Science Across Parkinson’s Disease
• Birgitt Schuele, Stanford University School of Medicine
• William Seeley, University of California, San Francisco
• Jason Shepherd, University of Utah
• Heather Smith, University of Cambridge
• Benjamin Stecher, Tomorrow Edition
• Mariko Taga, Columbia University
• Oliver Tam, Cold Spring Harbor Laboratory
• Dima Ter-Ovanesyan, Harvard University
• Lenny Teytelman, protocols.io
• Ruilin Tian, University of California, San Francisco
• Valerie Uytterhoeven, VIB / KU Leuven
• Wim Vandenberghe, KU Leuven
• Jaime Vaquer-Alicea, University of Texas Southwestern Medical Center
• Patrik Verstreken, VIB / KU Leuven
• Brian Wallach, I AM ALS
• Eric Wang, University of Florida
• Shiyi Wang, Duke University
• Charles White, University of Texas Southwestern Medical Center
• Lani Wu, University of California, San Francisco
• Andrian Yang, EMBL-EBI
• Gene Yeo, University of California, San Diego

In the past few years, demand for scientist communication training programs has increased from scientific institutions. Even though there is significant demand for these programs, there has been little development of best practices, shared metrics, and an overall sense of professionalism of the field. At a December 2017 workshop convened by the Kavli Foundation, the community of trainers expressed a strong appetite to forge a community of practice as the field continues to grow to meet demand.

To meet this need, CZI and the Kavli Foundation partnered with COMPASS, the Alan Alda Center for Communicating Science, and facilitators from Converge to convene a Science Communication Training Summit, with the objective of building an inclusive science communication training community of practice and advancing the field. The organizations and programs represented at this meeting train an estimated 20,000 to 30,000 scientists each year.

Read more about the outcomes of this meeting.
Attendees

• Olivia Ambrogio, American Geophysical Union
• Elyse Aurbach-Pruitt, University of Michigan
• Arne Bakker, Chan Zuckerberg Initiative
• Nancy Baron, COMPASS
• John Besley, Michigan State University
• Bronwyn Bevan, University of Washington
• Anna Lisa Briseño, Research!America
• Judi Brown Clarke, Michigan State University
• Alison Caldwell, ComSciCon
• Anne Claiborne, Chan Zuckerberg Initiative
• Emily Therese Cloyd, American Association for the Advancement of Science
• Matt Crommett, Lyda Hill Philanthropies
• Jayatri Das, The Franklin Institute
• Steve Depoe, University of Cincinnati
• Anthony Dudo, The University of Texas at Austin
• David Ehrlichman, Converge
• Chad English, David and Lucile Packard Foundation
• Marta Entradas, LSE
• Mónica Feliú-Mójer, Ciencia Puerto Rico / iBiology
• Suzanne Ffolkes, The Optical Society
• Danielle Fox, Union of Concerned Scientists
• Radha Ganesan, Alan Alda Center for Communicating Science
• Sarah Garlick, Hubbard Brook Research Foundation
• Kishore Hari, Chan Zuckerberg Initiative
• Anna Johnson, Institute for Learning Innovation
• Marina Joubert, Stellenbosch University
• Sawsan Khuri, Sawsan Khuri consulting
• Erica Kimmerling, ComSciCon
• Margaret Krebs, Leopold Leadership Program, Stanford Woods Institute for the Environment
• Kristi Kremers, University of Minnesota
• Laura Lindenfeld, Alan Alda Center for Communicating Science
• Jeff MacGregor, Chan Zuckerberg Initiative
• Eric Marshall, The Kavli Foundation
• Shayle Matsuda, Hawaii Institute of Marine Biology
• Sunshine Menezes, Metcalf Institute, University of Rhode Island
• John Meyer, University of Washington College of the Environment
• Mary Anne Moser, Beakerhead
• Barbara Natalizio, The Rita Allen Foundation
• Liz Neeley, The Story Collider
• Jai Ranganathan, SciFund Challenge
• Mark Rosin, Guerilla Science / Pratt Institute
• David Sawyer, Converge
• Ann Searight Christiano, Center for Public Interest Communications, University of Florida
• Tania Simoncelli, Chan Zuckerberg Initiative
• Brooke Smith, The Kavli Foundation
• Madeline Sofia, National Public Radio
• Amanda Stanley, COMPASS
• Bruno Takahashi, Michigan State University
• Greg Tananbaum, Chan Zuckerberg Initiative
• Rackeb Tesfaye, Broad Science
• Caitlin Weber, STEM Ambassador Program, University of Utah
• Jory Weintraub, Duke Initiative for Science & Society Duke University

In October, we held the third and last of our 2018 student and postdoc meetings at the Marine Biological Laboratory in Woods Hole, Mass. We met with graduate students, postdocs, and staff scientists who have contributed to Pilot Projects for a Human Cell Atlas and learned about their great work through talks and poster sessions. The group shared knowledge, talked through challenges they’ve encountered, and started new collaborations while building a community around single-cell technologies and data analysis techniques.

Attendees

• Abdulraouf Abdulraouf, Broad Institute of MIT and Harvard
• Fatma Ayhan, UT Southwestern Medical Center
• Shanshan Bai, MD Anderson Cancer Center
• Brent Biddy, Washington University in St. Louis
• Francesco G. Brundu, Columbia University
• Daniel DeLaughter, Harvard Medical School
• Ryan Dohn, University of Chicago
• Heather Eckart, University of Chicago
• Simon Gritsch, Massachusetts General Hospital
• Harvard Medical School
• Paul Hoffman, New York Genome Center
• Min Hu, MD Anderson Cancer Center
• Tushar Kamath, Broad Institute of MIT and Harvard
• Kenji Kamimoto, Washington University in St. Louis
• Elena Kandror, Columbia University
• Jeffrey Koenitzer, Washington University in St. Louis
• Ashwinikumar Kulkarni, UT Southwestern Medical Center
• Tapsi Kumar, MD Anderson Cancer Center
• Hanna Levitin, Columbia University
• Weizhe Li, National Institute of Health
• Carly Martin, Broad Institute of MIT and Harvard
• Linus Mazutis, Memorial Sloan Kettering Cancer Centre
• Jeffrey Moffitt, Harvard Medical School
• Andrew Potter, Cincinnati Children’s Hospital Medical Center
• Sandhya Prabhakaran, Memorial Sloan Kettering Cancer Centre
• Brian Rabe, Harvard Medical School
• Daniel Reichart, Harvard Medical School
• Abbas Rizvi, Columbia University
• Sara Rouhanifard, University of Pennsylvania
• Dana Silverbush, Broad Institute of MIT and Harvard
• Michal Slyper, Broad Institute of MIT and Harvard
• Marlon Stoeckius, New York Genome Center
• Emma West, Harvard Medical School
• Haojia Wu, Washington University in St. Louis
• Jinzhou Yuan, Columbia University
• Shiwei Zheng, New York Genome Center

Recent technological advances have resulted in an increasing amount of health data in multiple modalities, including genomic, imaging, and medical record data. Multi-domain data is incredibly powerful and can be used to identify trends within a population cohort or gain insights into a complex multi-factored disease, far beyond what is possible when looking at only a single modality. We brought together experts working at the intersections of these different modalities to discuss the challenges and possibilities in aggregating, exploring, and analyzing these complex data.

Attendees

• Toby Bloom, New York Genome Center
• Patrick Bradley, University of California, San Francisco & Gladstone Institutes
• Carlos Bustamante, Stanford University
• Annamarie Bustion University of California, San Francisco & Gladstone Institutes
• Alison Callahan, Stanford University
• Andrew Carroll, Google
• Lindsey Criswell, University of California, San Francisco
• Pier Federico Gherardini, Parker Institute for Cancer Immunotherapy
• Milena Gianfrancesco, University of California, San Francisco
• Chris Gignoux, University of Colorado Anschutz Medical Campus
• Julie Granka, AncestryDNA
• Ragan Hart, Stanford University
• Thomas Hoffmann, University of California, San Francisco
• Sarah Kaewert, Colorado Center for Personalized Medicine
• Kathleen Keough, University of California, San Francisco & Gladstone Institutes
• Idit Kosti, University of California, San Francisco
• Cyrus Maher, Grail Bio
• Hemali Phatnani, New York Genome Center
• Sylvia Plevritis, Stanford University
• Neil Risch, University of California, San Francisco
• Nigam Shah, Stanford University
• Marina Sirota, University of California, San Francisco
• Christian Stolte, New York Genome Center
• Iakovos Toumazis, Stanford University
• Michela Traglia, University of California, San Francisco
• Lauren Weiss, University of California, San Francisco
• Daniel Wells, Parker Institute for Cancer Immunotherapy
• Genevieve Wojcik, Stanford University School of Medicine

In August, we held the second of our 2018 student and postdoc meetings, this time in Stockholm, Sweden. At these events, we invite the graduate students, postdocs, and staff scientists who have contributed to Pilot Projects for a Human Cell Atlas to share their work. We specifically don’t invite the principal investigators leading each of these projects, focusing instead on the researchers in the labs. Our aim is to create a unique opportunity for these ambitious researchers, who are still early on in their careers, to showcase their work, share knowledge, and discuss challenges they’ve encountered.

Attendees

• Jonathan Alles, Max Delbrück Center for Molecular Medicine
• Muhammad Arif, SciLifeLab / KTH Royal Institute of Technology
• Michaela Asp, SciLifeLab / KTH Royal Institute of Technology
• Burcu Ayoglu, SciLifeLab / KTH Royal Institute of Technology
• Victor Badillo Lisakowski, Max Delbrück Center for Molecular Medicine
• Daria Belokhvostova, King’s College London
• Lars Borm, Karolinska Institutet
• Emmanuel Bouilhol, CNRS
• Emelie Braun, Karolinska Institutet
• Sijie Chen, Tsinghua University
• Simone Codeluppi, Karolinska Institutet
• Marie Deprez, Institut de Pharmacologie Moléculaire et Cellulaire
• John Ferdinand, University of Cambridge
• Daniel Gyllborg, SciLifeLab / Stockholm University
• Christoph Hafemeister, New York Genome Center
• Zhisong He, Max Planck Institute for Evolutionary Anthropology
• Markus Hilscher, SciLifeLab / Stockholm University
• Karoline Holler, Max Delbrück Center for Molecular Medicine
• Bo Hu, Max Delbrück Center for Molecular Medicine
• Kui Hua, Tsinghua University
• Caron Jacobs, University of Cape Town
• Sabina Kanton, Max Planck Institute for Evolutionary Anthropology
• Nikolaos Karaiskos, Max Delbrück Center for Molecular Medicine
• Xiangyu Li, Tsinghua University
• Monika Litvinukova, Max Delbrück Center for Molecular Medicine
• Henrike Maatz, Max Delbrück Center for Molecular Medicine
• Anna Martinez Casals, SciLifeLab / KTH Royal Institute of Technology
• Zhun Miao, Tsinghua University
• Ricardo Miragaia, Wellcome Sanger Institute
• Nina Mitic, Max Delbrück Center for Molecular Medicine
• Nick Mitsios, Karolinska Institutet
• Sandra Ruiz Garcia, Institut de Pharmacologie Moléculaire et Cellulaire
• Ines Sequeira, King’s College London
• Benjamin Stewart, University of Cambridge
• Devin Sullivan, SciLifeLab / KTH Royal Institute of Technology
• Christin Sünkel, Max Delbrück Center for Molecular Medicine
• Luca Tosti, Charité – BIH Digital Health
• Timo Trefzer, Charité – BIH Digital Health
• Chenglin Wu, SciLifeLab / Stockholm University
• Hao Xu, SciLifeLab / KTH Royal Institute of Technology
• Chika Yokota, SciLifeLab / Stockholm University
• Laure-Emmanuelle Zaragosi, Institut de Pharmacologie Moléculaire et Cellulaire
• Cheng Zhang, SciLifeLab / KTH Royal Institute of Technology
• Vera Zywitza, Max Delbrück Center for Molecular Medicine

This was our second knowledge environments workshop. We brought together a broad group of people: experts from academia, tech, publishing, representatives of online knowledge platforms, funders with interests in scholarly communication and digital information technologies, and others with expertise in this space. At this workshop we focused on how knowledge is extracted, curated, and integrated from data and literature sources, and on ways in which computational approaches can help make sense of today’s explosion of scientific data and information to ultimately drive scientific progress.

Attendees

• Cecilia Arighi, CBCB, University of Delaware
• Amy Bernard, Allen Institute for Brain Science
• Peter Brantley, UC Davis
• Patricia Brennan, NIH National Library of Medicine
• Ying Ding, Indiana University
• Oren Etzioni, Allen Institute for Artificial Intelligence
• Casey Greene, University of Pennsylvania
• Daniel Himmelstein, University of Pennsylvania
• Victoria Lin, Salesforce Research
• Andrew McCallum, University of Massachusetts, Amherst
• Johanna McEntyre, EMBL-EBI
• Ian Mulvany, SAGE Publishing
• Mark Musen, Stanford University
• Alexander Ratner, Stanford University
• Paul Sternberg, CalTech
• Andrew Su, The Scripps Research Institute
• Daniel Whaley, Hypothesis
• Elizabeth Wu, AlzForum

In June 2018, we held the first of three student and postdoc meetings convening graduate students, postdoctoral researchers, and staff scientists who have contributed to Pilot Projects for a Human Cell Atlas. At CZI we want to accelerate science by strengthening collaboration and scientific networks. We believe a key part of that is connecting the scientists who actually do the work— the graduate students, postdocs, and staff scientists. For this event, we asked the principal investigators leading each of these projects not to come along or participate. Focusing on investigators in the labs creates a unique opportunity for these researchers to showcase their work, learn from one another, and start new collaborations.

Attendees

• Abubakar Abid, Zou Lab, Stanford University
• Graham Barlow, Nolan Lab & Bollyky Lab, Stanford University
• Kerrigan Blake, Lawson Lab, UC Irvine
• Joan Camunas-Soler, Quake Lab, Stanford University
• Oana Carja, Lundberg Lab, Stanford University & CZ Biohub
• Michelle Chan, Weissman Lab, UCSF
• Jennie Close, Allen Institute for Brain Science
• Xiaoqing Dai, MacDonald Lab, University of Alberta
• Ryan Davis, Lawson Lab, UC Irvine
• Susanna Elledge, Wells Lab, UCSF
• Rachel Gate, Ye Lab, UCSF
• Yan Hang, Kim Lab, Stanford University
• Derek Janssens, Henikoff Lab, Fred Hutchinson Cancer Research Center
• Sizun Jiang, Nolan Lab, Stanford University
• Noushin Koulena, Cai Lab, California Institute of Technology
• Ulrike Litzenburger, Chang Lab, Stanford University
• Jeremy Lombardo, Haun Lab, UC Irvine
• Brian Long, Lein Lab & Nicovich Lab, Allen Institute for Brain Science
• Jocelyn Manning Fox, MacDonald Lab, University of Alberta
• Jeremy Miller, Lein Lab, Allen Institute for Brain Science
• Kevin Nee, Kessenbrock Lab, UC Irvine
• Kenneth Ng, Kueh Lab, University of Washington
• Quy Nguyen, Kessenbrock Lab, UC Irvine
• Thomas Norman, Weissman Lab, UCSF
• Nicholas Pervolarakis, Kessenbrock Lab, UC Irvine
• Nikolay Samusik, Nolan Lab, Stanford University
• Jay Sarthy, Henikoff Lab, Fred Hutchinson Cancer Research Center
• Sasha Targ, Ye Lab, UCSF
• Valerie Thomas, Fraser Lab, USC
• Marcus Woodworth, Vaughan Lab, University of Washington
• Jingyan Wu, Steinmetz Lab, Stanford University

Biobanks and repositories are some of the greatest resources for researchers and physicians to study, understand, and treat diseases. Patients are at the center of biobanking, which necessitates carefully thought out solutions around ethical and practical challenges. This workshop brought experts from academia, medicine, biobanks, and organ donation organizations together to discuss what the key issues and challenges are that biobanking faces today, as well as where the field wants to go and how to get there.

Attendees

• Kristin Ardlie, Broad Institute
• John Bradley, University of Cambridge
• Tatiana Foroud, Indiana University School of Medicine
• Michelle Freund, National Institute of Mental Health
• Lea Tenenholz Grinberg, University of California, San Francisco
• Jason Karamchandani, Montréal Neurological Institute, McGill University
• Jane Kaye, University of Oxford
• Barbara Koenig, University of California, San Francisco
• Sandra Soo-Jin Lee, Stanford University
• Patrick MacDonald, University of Alberta
• Eric Meslin, Council of Canadian Academies
• Michelle Monje, Stanford University
• Nikole Neidlinger, Donor Network West
• Sergiu Pasca, Stanford University
• Ajay Pillai, National Institutes of Health
• Fredrik Ponten, Uppsala University
• Jenny Reardon, University of California, Santa Cruz
• Ahmad Salehi, Donor Network West / Stanford School of Medicine
• David Sandak, Pattern.org
• Adrian Thorogood, McGill University / Global Alliance for Genomics and Health
• John Wilbanks, Sage Bionetworks
• Magdalena Zernicka-Goetz, University of Cambridge
• Wenyu Zhu, Stanford University

CZI hosted a hackathon in San Francisco with software developers from several groups working on or using open source image visualization tools: Allen Institute for Cell Science, CellProfiler (Broad Institute), ImageJ / FIJI (University of Wisconsin), Neuroglancer (Google), ChimeraX (UCSF), and the CZ Biohub. We tried to frame needs for, and begin prototyping, web-based visualization components for image and volume rendering. The small size and overlapping interests provided an exciting learning opportunity for all involved — and we built some nice prototypes and started some collaborations in the process.

Attendees

• Basu Chaudhuri, Allen Institute for Cell Science
• Tom Ferrin, University of California, San Francisco
• Tom Goddard, University of California, San Francisco / Chimera
• Allen Goodman, Broad Institute
• Syuan-Ming Guo, Chan Zuckerberg Biohub
• Lisa Harrylock, Allen Institute for Cell Science
• Graham Johnson, Allen Institute for Cell Science
• Benny Lin, University of Texas, Austin
• Samuel Lord, University of California, San Francisco / Howard Hughes Medical Institute
• Jeremy Maitin-Shephard, Google
• Molly Maleckar, Allen Institute for Cell Science
• Shalin Mehta, Chan Zuckerberg Biohub
• Dyche Mullins, University of California, San Francisco
• Eric Perlman, Johns Hopkins University
• Megan Riel-Mehan, Allen Institute for Cell Science
• Curtis Rueden, University of Wisconsin, Madison
• Dan Toloudis, Allen Institute for Cell Science
• Dave Williams, Allen Institute for Cell Science

We organized a four-day, interdisciplinary event in Aptos, Calif. of over 200 scientists, computational biologists and software engineers who will contribute to Collaborative Computational Tools for the Human Cell Atlas. The conference kicked off a new collection of grants to researchers working collaboratively to solve computational challenges presented by the Human Cell Atlas, including developing a new cloud-based data infrastructure and analytical methods for processing and interpreting large, complex datasets. Participating researchers were grouped into 12 loose research areas and asked to present collectively about their projects. Much of the meeting also consisted of structured and unstructured working time, encouraging researchers to share ideas, recontextualize their work, and think about how they may be able to work together. 

Read more about this event in our Medium post.

Attendees

• Miri Adler, Weizmann Institute of Science
• Brian Aevermann, J. Craig Venter Institute
• Benedict Anchang, Stanford University
• Tallulah Andrews, Wellcome Sanger Institute
• Mark Arends, University of Edinburgh
• Mehrtash Babadi, Broad Institute
• Gary Bader, University of Toronto
• Richard Baldock, University of Edinburgh
• Eric Banks, Broad Institute
• Joshua Batson, Chan Zuckerberg Biohub
• Alexis Battle, Johns Hopkins University
• Lauren Beck, University of Pennsylvania
• Sidney Bell, Fred Hutchinson Cancer Research Center
• Matthew Bernstein, University of Wisconsin, Madison
• Olga Botvinnik, Chan Zuckerberg Biohub
• Albert Burger, Heriot-Watt University
• Andrew Butler, New York Genome Center
• Juan Caicedo, Broad Institute
• Andrea Califano, Columbia University Medical Center
• Vincent Carey, Harvard Medical School
• Anne Carpenter, Broad Institute
• Huidong Chen, Mass General Hospital / Harvard Medical School
• Ken Chen, University of Texas MD Anderson Cancer Center
• Rebecca Chen, University of Illinois, Urbana Champaign
• Isidro Cortés-Ciriano, Harvard Medical School
• Brian Craft, University of California, Santa Cruz
• Bart Deplancke, École Polytechnique Fédérale de Lausanne
• David DeTomaso, University of California, Berkeley
• Colin Dewey, University of Wisconsin, Madison
• Rory Donovan-Maiye, Allen Institute for Cell Science
• David Dynerman, Chan Zuckerberg Biohub
• Axel Ekman, University of California, San Francisco
• Rebecca Elyanow, Brown University
• Barbara Engelhardt, Princeton University
• Carlos Espinosa, University of California, Santa Cruz
• Elana Fertig, Johns Hopkins University
• Clay Fischer, University of California, Santa Cruz
• Vincent Gardeux, École Polytechnique Fédérale de Lausanne
• Nicholas Gauthier, Dana-Farber Cancer Institute
• Ariel Gewirtz, Princeton University
• Anna Gilbert, University of Michigan
• Loyal Goff, Johns Hopkins University
• Raphael Gottardo, Fred Hutchinson Cancer Research Center
• William Greenleaf, Stanford University
• Danna Gurari, University of Texas, Austin
• Maximilian Haeussler, University of California, Santa Cruz
• Joe Hand, Code for Science
• Kasper Hansen, Johns Hopkins University
• Nicholas Haradhvala, The Broad Institute / Mass General Hospital
• Kenneth Harris, University College London
• Ville Hautamäki, University of Eastern Finland
• Merja Heinäniemi, University of Eastern Finland
• Martin Hemberg, Wellcome Sanger Institute
• Mikel Hernaez, University of Illinois, Urbana Champaign
• Michael Heuer, University of California, Berkeley
• Holger Heyn, Centre for Genomic Regulation
• Peter Hickey, Johns Hopkins University
• Sahand Hormoz, Harvard Medical School / Dana-Farber Cancer Institute
• Chiaowen Hsiao, University of Chicago
• Qiwen Hu, University of Pennsylvania
• Wolfgang Huber, European Molecular Biology Laboratory
• Jukka Intosalmi, Aalto University
• Mike Jiang, Fred Hutchinson Cancer Research Center
• Gregory Johnson, Allen Institute for Cell Science
• Anthony Joseph, University of California, Berkeley
• Hyun Min Kang, University of Michigan
• Sarah Kefayati, Chan Zuckerberg Biohub
• Jim Kent, University of California, Santa Cruz
• Peter Kharchenko, Harvard Medical School
• Jaegil Kim, Broad Institute
• Wenjun Kong, Washington University in St. Louis
• Yael Korem Kohanim, Weizmann Institute of Science
• Keegan Korthauer, Dana-Farber Cancer Institute
• Smita Krishnaswamy, Yale University
• Harri Lähdesmäki, Aalto University
• Carolyn Larabell, University of California, San Francisco
• Uri, Laserson, Icahn School of Medicine at Mount Sinai
• Kim-Anh Lê Cao, University of Melbourne
• Ruoxin Li, University of California, Davis
• Simon Li, University of Dundee
• Chi Lin, University of Texas, Austin
• Ruishan Liu, Stanford University
• Santiago Lombeyda, California Institute of Technology
• Brian Long, Allen Institute for Cell Science
• Jackson Loper, Columbia University
• Aaron Lun, CRUK Cambridge Institute
• Molly Maleckar, Allen Institute for Cell Science
• Jonathan Manning, European Bioinformatics Institute
• John Marioni, European Bioinformatics Institute
• Michael Martin, Lawrence Berkeley National Laboratory
• Davis McCarthy, European Bioinformatics Institute
• Duncan McColl, University of California, Santa Cruz
• Cynthia McMurray, Lawrence Berkeley National Laboratory
• Elisabetta Mereu, Centre for Genomic Regulation
• Jill Mesirov, University of California, San Diego
• Kerstin Meyer, Wellcome Sanger Institute
• Olgica Milenkovic, University of Illinois, Urbana Champaign
• Josh Moore, University of Dundee
• Martin Morgan, Roswell Park Comprehensive Cancer Center
• John Morris, University of California, San Francisco
• Samantha Morris, Washington University in St. Louis
• Eran Mukamel, University of California, San Diego
• Fabian Müller, Stanford University
• Benjamin Neale, Mass General Hospital / Broad Institute
• Parisa Nejad, University of California, Santa Cruz
• Dmitris Nicoloutsopoulos, University College London
• Brian O’Connor, University of California, Santa Cruz
• Idoia Ochoa, University of Illinois, Urbana Champaign
• Kevin Osborn, University of California, Santa Cruz
• Liam Paninski, Columbia University
• Irene Papatheodorou, European Bioinformatics Institute
• Peter Park, Harvard Medical School
• Robert Patro, Stony Brook University
• Dana Pe’er, Memorial Sloan Kettering Cancer Center
• Jianhao Peng, University of Illinois, Urbana Champaign
• Luca Pinello, Mass General Hospital / Harvard Medical School
• Angela Pisco, Chan Zuckerberg Biohub
• Peng Qiu, Georgia Institute of Technology / Emory University
• Gerald Quon, University of California, Davis
• Arjun Raj, University of Pennsylvania
• Ben Raphael, Princeton University
• Michael Reich, University of California, San Diego
• Philippe Rigollet, Massachusetts Institute of Technology
• Davide Risso, Weill Cornell Medicine
• Matthew Ritchie, The Walter and Eliza Hall Institute of Medical Research
• Danielle Robinson, Code for Science
• Mark Robinson, University of Zurich
• Chris Sander, cBio Center
• Hirak Sarkar, Stony Brook University
• Rahul Satija, New York Genome Center
• Richard Scheuermann, J. Craig Venter Institute
• Geoffrey Schiebinger, Broad Institute
• Hannes Schmidt, University of California, Santa Cruz
• Clayton Scott, University of Michigan
• Cotton Seed, Broad Institute
• Lucas Seninge, University of California, Santa Cruz
• Manu Setty, Memorial Sloan Kettering Cancer Center
• Richard Sever, bioRxiv / Cold Spring Harbor Laboratory
• Thomas Sherman, Johns Hopkins University
• Meromit Singer, Broad Institute
• Mike Smith, European Molecular Biology Laboratory
• Trent Smith, University of California, Santa Cruz
• Charlotte Soneson, University of Zurich
• Matthew Speir, University of California, Santa Cruz
• Duluxan Sritharan, Harvard University
• Genevieve Stein-O’Brien, Johns Hopkins University
• Matthew Stephens, University of Chicago
• Joshua Stuart, University of California, Santa Cruz
• BJ Stubbs, Harvard Medical School
• Meena Subramaniam, University of California, San Francisco
• William Sullivan, University of California, Santa Cruz
• Shiquan Sun, University of Michigan
• Fabian Theis, Helmholtz Center Munich, Institute of Computational Biology
• Matt Thomson, California Institute of Technology
• Luyi Tian, Walter and Eliza Hall Institute of Medical Research
• Timothy Tickle, Broad Institute
• Pascal Timshel, Chan Zuckerberg Biohub
• Duygu Ucar, Jackson Laboratory
• David van Dijk, Yale university
• Daniel van Twisk, Roswell Park Comprehensive Cancer Center
• Umang Varma, University of Michigan
• Lav Varshney, University of Illinois, Urbana Champaign
• Archit Verma, Princeton University
• Chris Villarreal, University of California, Santa Cruz
• Isaac Virshup, University of Melbourne
• Jan Voges, Leibniz Universität Hannover
• Fangming Wang, University of Texas MD Anderson Cancer Center
• Yutong Wang, University of Michigan
• Gregory Way, University of Pennsylvania
• James Webber, Chan Zuckerberg Biohub
• Caleb Weinreb, Harvard Medical School
• Eric Weitz, Broad Institute
• Joshua Welch, University of Michigan
• Michael Wicks, University of Edinburgh
• Adam Williams, Jackson Laboratory
• Ryan Williams, Mount Sinai School of Medicine
• Alex Wolf, Helmholtz Center Munich, Institute of Computational Biology
• Sam Wolock, Harvard Medical School
• Jeremy Worley, Columbia University
• Fangming Xie, University of California, San Diego
• Xiujia Yang, University of Illinois, Urbana Champaign
• Jimmie Ye, University of California, San Francisco
• Alice Yu, Stanford University
• Guo-Cheng Yuan, Dana-Farber Cancer Institute
• Fan Zhang, University of Michigan
• Xiang Zhou, University of Michigan
• Jingchun Zhu, University of California, Santa Cruz
• Qian Zhu, Dana-Farber Cancer Institute
• James Zou, Stanford University

This workshop brought experts from academia, medicine, the pharmacological industry, and leading advocacy and cohort groups to discuss the field’s approaches to intervention, different ways of utilizing genetic information, and how the health systems, cohorts, and industry are moving the field forward.

Attendees

• Alan Aderem, Center for Infectious Disease Research
• Euan Ashley, Stanford University
• Aris Baras, Regeneron Pharmaceuticals
• Carlos Bustamante, Stanford University
• Wendy Chung, Columbia University
• Rob Collin Radboud, University Medical Center
• Rory Collins, University of Oxford
• Bruce Conklin, UC San Francisco/Gladstone Institutes
• Joe DeRisi, Chan Zuckerberg Biohub
• Jennifer Doudna, UC Berkeley
• Michael Dunn, The Wellcome Trust
• Mark Effingham, UK Biobank
• Charles Gersbach, Duke University
• Geoffrey Ginsburg, Duke University
• Maria Giovanni, NIAID/NIH
• Viviana Gradinaru Caltech
• David Haussler, UC Santa Cruz
• Katherine High, Spark Therapeutics
• Monica Justice, Hospital for Sick Children/UToronto
• David Ledbetter, Geisinger Health System
• Rhiannon Macrae, Broad Institute of MIT and Harvard
• Alex Marson, UC San Francisco
• Andrew May, Chan Zuckerberg Biohub
• Elizabeth McGlynn, Kaiser Permanente
• Maynard Olson, University of Washington
• Clodagh O’Shea, Salk Institute for Biological Studies
• Niki Paulk, UC San Francisco
• Deenan Pillay, Africa Health Research Institute/UCL
• Steve Quake, Chan Zuckerberg Biohub
• Nazneen Rahman, Institute of Cancer Research
• Heidi Rehm, Partners Healthcare/Broad/MGH
• Oren Rosenberg, UC San Francisco
• David Rowitch University of Cambridge/UCSF
• Nancy Spinner, Children’s Hospital of Philadelphia/UPenn
• Lubert Stryer, Stanford University
• Sharon Terry, Genetic Alliance
• Adrian Thrasher, University College London
• Sarah Tishkoff University of Pennsylvania
• Robert Tjian, UC Berkeley
• Fyodor Urnov, Altius Institute for Biomedical Sciences
• Jonathan Weissman, UC San Francisco
• George Yancopoulos, Regeneron Pharmaceuticals
• James Zou, Stanford University

As many as 7,000 rare diseases affect 400 million people globally. The vast majority are not well understood, and less than 5% have approved treatments. Yet worldwide, patients are meeting these challenges by partnering with scientists and clinicians and actively driving research. While this patient-driven research approach shows promise in many disease areas, it has proven especially powerful in accelerating rare disease research. In March, we engaged a small group of patient advocates — individuals who have significantly advanced research in their own disease area — to explore the challenges and opportunities for facilitating patient-driven research.

Attendees

• Heidi Bjornson Pennell, PCD Foundation
• David Fajgenbaum, Castleman Disease Collaborative Network / University of Pennsylvania’s
• Orphan Disease Center
• Erin Hoffmann, Patient Advocate and Philanthropist
• Daniel MacArthur, Rare Genomes Project / Broad Institute / Massachusetts General Hospital
• Matt Might, Hugh Kaul Personalized Medicine Institute, University of Alabama at Birmingham
• Megan O’Boyle, Phelan-McDermid Syndrome Data Network
• Josh Sommer, Chordoma Foundation

This workshop explored topics including model interpretability and visualization, tools, and infrastructure to accelerate the use of these techniques in the lab and the clinic, and the curation and accessibility of benchmark datasets. Scientists discussed applications across many modalities, including structures (chemistry, proteins), images (microscopy), sequences (genomics), and text and time series (health data).

Attendees

• Mohammed AlQuraishi, Harvard University
• Regina Barzilay, MIT
• Matt Conlen, University of Washington
• Alex Ford, University of Washington
• Anna Goldenberg, University of Toronto
• Casey Greene, University of Pennsylvania
• David Haussler, UCSC
• Daphne Koller, Stanford University
• Molly Maleckar, Allen Institute for Cell Science
• Narges Razavian, NYU
• Andrey Rzhetsky, University of Chicago
• Franziska Seeger, University of Washington
• Jascha Sohl-Dickstein, Google
• Ronald Summers, NIH
• Jenna Wiens, University of Michigan

We held a two-day meeting to discuss and frame collaborations around cell imaging and Human Cell Atlas projects, including both experimental technology (imaging, labeling, cell lines, high-throughput screens, genetic perturbations) and analytical challenges (image processing, visualization, platforms for sharing, organizing, and disseminating data), bringing together collaborators from the Human Protein Atlas team, the Allen Institute for Cell Science, the CZ Biohub, CZI, and the open source imaging tools community.

Attendees

• Josh Batson, CZ Biohub
• Olga Botvinnik, CZ Biohub
• Oana Carja, HPA
• Anne Carpenter, Broad Institute (Cell Profiler)
• Basudev Chaudhuri, Allen Cell
• Richard Conroy, NIH
• Spyros Darmanis, CZ Biohub
• Rafael Gomez-Sjoberg, CZ Biohub
• Ru Gunawardane, Allen Cell
• Jean-Karim Heriche, EMBL
• Martin Hjelmare, HPA
• Rick Horwitz, Allen Cell
• Greg Huber, Biohub
• Shannon Hughes, NIH
• Graham Johnson, Allen Cell
• Gregory Johnson, Allen Cell
• Jim Karkanias, CZ Biohub
• Sarah Kefayati, CZ Biohub
• Manuel Leonetti, CZ Biohub
• Cecilia Lindskog-Bergström, HPA
• Emma Lundberg, HPA
• Molly Maleckar, Allen Cell
• Andrew May, CZ Biohub
• Shalin Mehta, CZ Biohub
• Norma Neff, CZ Biohub
• Steve Quake, CZ Biohub
• Susanne Rafelski, Allen Cell
• Loic Royer, CZ Biohub
• Curtis Rueden, U Wisconsin (ImageJ)
• Devin Sullivan, HPA
• Jason Swedlow, U Dundee (OME)
• Julie Theriot, Allen Cell
• Christian Tischer, EMBL
• Stéfan van der Walt, UC Berkeley (scikit-image)
• Kalle von Feilitzen, HPA
• James Webber, CZ Biohub
• Jonathan Weissman, CZ Biohub
• Winfried Wiegraebe, Allen Cell
• Hao Xu, HPA
• Kevin Yamauchi, CZ Biohub

In 2017 we invited applications for one-year pilot projects to help develop technologies and establish best practices for the Human Cell Atlas. In early 2018, the researchers leading the awarded projects met in San Francisco to connect, share their project plans, and initiate further collaborations.

These investigators span eight countries and four continents, so it was a special treat to have everyone together in person to discuss their projects and learn about each other’s work. The energy in the room was great. We heard from scientists studying specific cell types, like those who are working to optimize the analysis of cells in healthy human skin. We also heard from technologists, including a collaboration of 16 groups who are benchmarking methods together.

We learned so much over those two days. This event was a fantastic way to start the new year.

Attendees

• Ido Amit, Weizmann Institute of Science
• Nick Banovich, TGen
• Pascal Barbry, University Côte d’Azur, CNRS
• Oni Basu, University of Chicago; Argonne National Laboratory
• Olga Botvinnik, Chan Zuckerberg Biohub
• Ed Boyden, Massachusetts Institute of Technology
• Long Cai, Caltech
• Gray Camp, Max Planck Institute for Evolutionary Anthropology
• Connie Cepko, Harvard Medical School, HHMI
• Fei Chen, Broad Institute of MIT and Harvard
• George Church, Harvard Medical School
• Menna Clatworthy, University of Cambridge
• Christian Conrad, German Cancer Research Center
• Scott Fraser, University of Southern California
• Michael Gotthardt, Max Delbrück Center for Molecular Medicine
• Will Greenleaf, Stanford University
• Jin Gu, Tsinghua University
• Jered Haun, University of California, Irvine
• Steve Henikoff, Fred Hutchinson Cancer Research Center
• Norbert Hübner, Max Delbrück Center for Molecular Medicine
• Ben Humphreys, Washington University in St. Louis
• Sam Inverso, ReadCoor
• Jonathan Keats, TGen
• Sarah Kefayati, Chan Zuckerberg Biohub
• Kai Kessenbrock, University of California, Irvine
• Seung Kim, Stanford University School of Medicine
• Genevieve Konopka, UT Southwestern Medical Center
• Hao Yuan Kueh, University of Washington
• Devon Lawson, University of California, Irvine
• Ed Lein, Allen Institute for Brain Science
• Sten Linnarsson, Karolinska Institutet
• Emma Lundberg, KTH Royal Institute of Technology, Stanford University
• Joakim Lundeberg, KTH Royal Institute of Technology, SciLifeLab
• Patrick MacDonald, University of Alberta
• Evan Macosko, Broad Institute of MIT and Harvard
• Tom Maniatis, Columbia University
• Adil Mardinoglu, KTH Royal Institute of Technology
• Musa Mhlanga, University of Cape Town
• Michelle Monje, Stanford University
• Samantha Morris, Washington University in St. Louis
• Jan Mulder, Karolinska Institutet
• Nick Navin, MD Anderson Cancer Center
• Macha Nikolski, Bordeaux Bioinformatics Center / CNRS
• Garry Nolan, Stanford University
• Sebastian Pott, University of Chicago
• Steve Potter, Cincinnati Children’s Medical Center
• Raul Rabadan, Columbia University
• Arjun Raj, University of Pennsylvania
• Abbas Rizvi, Columbia University
• Orit Rosen, Broad Institute of MIT and Harvard
• Rahul Satija, New York Genome Center, NYU
• Christine Seidman, Harvard Medical School
• Jonathan Seidman, Harvard Medical School
• Peter Sims, Columbia University Medical Center
• Peter Smibert, New York Genome Center
• Lars Steinmetz, Stanford University, EMBL Heidelberg
• Mike Stubbington, Wellcome Trust Sanger Institute
• Mario Suva, Massachusetts General Hospital, Broad Institute of MIT and Harvard
• Joshua Vaughan, University of Washington
• Fiona Watt, King’s College London
• James Webber, Chan Zuckerberg Biohub
• Jonathan Weissman, University of California, San Francisco, HHMI
• Jim Wells, University of California, San Francisco
• Jimmie Ye, University of California, San Francisco
• Hongkui Zeng, Allen Institute for Brain Science
• Xuegong Zhang, Tsinghua University
• Kun Zhang, University of California, San Diego
• Xiaowei Zhuang, Harvard University, HHMI
• James Zou, Stanford University

Our third workshop on neurodegeneration was jointly organized with the New York Stem Cell Foundation and focused on iPSCs, 3D models, and their applications for neurodegenerative disorders. The event was attended by 28 researchers in New York, with discussions addressing the state of the science and infrastructure needs.

Attendees

• Kristin Baldwin, Scripps Research Institute
• Kristen Brennand, Icahn School of Medicine – Mount Sinai
• Gray Camp, Max Planck Institute for Evolutionary Anthropology
• Kevin Eggan, Harvard Stem Cell Institute
• Steven Finkbeiner, Gladstone Institutes
• Kelly Frazer, UC San Diego
• Daniel Gaffney, Wellcome Sanger
• Ming Guo, UCLA
• Ritchie Ho, Cedars-Sinai, Los Angeles
• Justin Ichida, University of Southern California
• Martin Kampmann, UCSF / CZ Biohub
• Jennifer Lewis, Harvard University
• Scott Noggle, New York Stem Cell Foundation
• Daniel Paull, New York Stem Cell Foundation
• Serge Prezdborski, Columbia University
• Botond Roska, Friedrich Miescher Institute, Basel
• Jason Spence, University of Michigan
• Sally Temple, Neural Stem Cell Institute
• Leslie Thompson, UC Irvine
• Richard Wade-Martins, Oxford University
• Hynek Wichterle, Columbia University
• Clifford Woolf, Harvard Medical School
• Gene Yeo, UC San Diego
• Tracy Young-Pearse, Harvard Medical School

Our second workshop on neurodegeneration addressed the role of non-neuronal influences such as inflammation, the immune system, glia, vasculature, the blood brain barrier, the gut, and microbiome. The event was attended by 20 researchers.

Attendees

• Katerina Akassoglou, Gladstone Institutes
• Jonathan Kipnis, University of Virginia
• Marco Colonna, Washington University in St. Louis
• Chengua Gu, Harvard Medical School
• Robert Moir, Harvard Medical School / MGH
• Michael Wilson, UCSF
• Frauke Zipp, Johannes Gutenberg University Mainz
• Samuel David, McGill University
• Asya Rolls, Technion, Israel Institute of Technology
• Paul Sawchenko, Salk Institute
• Dorian McGavern, NINDS/NIH
• Tony Wyss-Coray, Stanford University
• Philip de Jager, Columbia University
• Elizabeth Bradshaw, Columbia University
• Mimi Shirasu-Hiza, Columbia University
• Tim Sampson, California Institute of Technology
• Chris Bennett, Stanford University
• Gilbert Gallardo, Washington University in St. Louis
• Burcin Ikiz, Science writer
• Robert Thorne, University of Wisconsin, Madison

This workshop focused on methods for examining larger tissues,​ ranging from groups of cells all the way to whole human beings inside a PET scanner. The 15 invited external experts included researchers who are developing new microscopes and other ways of seeing what’s going on inside a living being, those thinking about new ways to monitor biological processes with chemical and biological probes, and users of these tools to make discoveries.

Attendees

• Elizabeth Hillman, Columbia University
• Hari Shroff, NIH
• Laura Waller, UC Berkeley
• Nicholas Sofroniew, Janelia
• Rebecca Richards-Kortu, Rice University
• Simon Cherry, UC Davis
• Jeff Bulte, Johns Hopkins University
• Lihong Wang, Caltech
• Ellen Robey, UC Berkeley
• Gabriel Victora, Rockefeller University
• Jan Huisken, Morgridge Institute of Research
• Scott Fraser, USC
• Daniela Boassa, UCSD
• Nicole Davis, Science Writer
• Bianca Migliori, Columbia University
• Marina Garrett, Allen Institute

In our talks about biological imaging, we explored the idea of developing teams of software engineers to work on problems in microscopy and imaging. We considered the benefit from specialized centers that would provide expertise, resources, and tools for more scientists to learn and apply advanced imaging techniques. And as in most scientific work, we saw a need for collaboration, in this case between chemists, engineers, physicists, and biologists, to broadly stimulate the sharing of knowledge, ideas, and tools between research microscopy and medical imaging.

Attendees

• Christophe Leterrier, NICN Institute
• David Hoffman, Janelia
• Luke Lavis, Janelia
• Stephen Adams, UC San Diego
• Aubrey Weigel, Janelia
• Robert Tjian, UC Berkeley
• Tobias Bonhoeffer, Max Planck Institute of Neurobiology
• Amy Palmer, University of Colorado, Boulder
• Xavier Darzacq, UC Berkeley
• Jeffrey Moffitt, Harvard University
• Xiaoyu Shi, UCSF
• Ulrike Boehm, National Cancer Institute at NIH
• Karen Davies, Lawrence Berkeley National Lab
• Carolyn Larabell, UCSF / Lawrence Berkeley National Lab
• Audrey Bowden, Stanford University
• Nicole Davis, Science writer
• Manuel Leonetti, Chan Zuckerberg Biohub

In our discussions about neurodegeneration, we talked about the need to understand the genes that have been linked to conditions such as Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis (ALS). We talked about the value of well-characterized antibodies, more scalable methods for subcellular proteomics, and new stem-cell-based tools. In order to make progress in this area, we discussed the potential of enriching the culture of science by bringing researchers together in new ways and providing better support for young scientists who study neurodegeneration.

Attendees

• Alison Goate, Icahn School of Medicine at Mount Sinai
• Bart De Strooper, VIB-KU Leuven Center for Brain and Disease Research
• Ben Barres, Stanford University
• Cristina Alberin, New York University
• Elizabeth Buffalo, University of Washington
• Huda Zoghbi, Baylor College of Medicine
• Paul Taylor, St. Jude Children’s Research Hospital
• Jeehye Park, The Hospital for Sick Children/University of Toronto
• Katie Bittner, Janelia and Avalere Health
• Kim Green, UC Irvine
• Lorenz Studer, Memorial Sloan Kettering Cancer Center
• Martin Hetzer, Salk Institute
• Maulik Patel, Vanderbilt University
• Maxime Rousseaux, Baylor College of Medicine
• Patrik Verstreken, VIB-KU Leuven Center for Brain & Disease Research
• Patrik Brundin, Van Andel Institute
• Philipp Niethammer, Memorial Sloan Kettering Cancer Center
• Richard Axel, Columbia University
• Richard Daneman, UC San Diego
• Roy Parker, University of Colorado Boulder
• Rui Costa, Columbia University
• Sandy Maday, University of Pennsylvania
• Shannon Macauley-Rambach, Washington University in St. Louis
• Shawn Ferguson, Yale University
• Vanessa Morais, Institute for Molecular Medicine/University of Lisbon

To address some of the key challenges around computational imaging, we convened a workshop in February 2017 to discuss the past, present, and future of computational microscopy tools. The workshop invitees included researchers, developers, and engineers who have created, enhanced, and/or utilized these tools. The group gathered over two days to discuss the opportunities and roadblocks to progress that, with strategic support, could catapult scientific research to new heights.

Attendees

• Anne Carpenter, Broad
• Jason Swedlow, U Dundee
• Kevin Eliceiri, U Wisconsin
• Nico Stuurman, UCSF
• Mark Tsuchida, Open Imaging
• Wesley Legant, Janelia
• Hernan Garcia, UC Berkeley
• Randal Burns, Johns Hopkins University
• Viren Jain, Google
• Eftychios Pnevmatikakis, Simons Foundation
• Fernando Amat, Netflix
• Nathan Clack, Vidrio
• Emma Ganley, PLOS
• Francois Aguet, Broad
• Carsten Haubold, Heidelberg
• Graham Johnson, Allen Institute
• Stefan van der Walt, UC Berkeley
• Amy Christensen, Stanford
• Nicole Davis, Science Writer

We convened a workshop on sharing scientific knowledge in January 2017. The invitees were drawn from a variety of key groups, including experts in academic publishing, both traditional scientific journals and newer, more open platforms; developers of digital technologies that promote scientific collaboration and data-sharing; funding agencies that seek to advance the use of digital information technology in science; and scientists and other professionals who have pioneered various open access and open science efforts. These individuals came together over two days to discuss key challenges and opportunities in scientific knowledge environments, with a special emphasis on innovation through technology.

Attendees

• Michael Aufreiter, Substance
• Katja Brose, Neuron
• Michael Eisen, UC Berkeley
• Lila Gierasch, Journal of Biological Chemistry
• Josh Greenberg, Sloan Foundation
• Kyle Kelley, Netflix
• Guiliano Maciocci, eLife
• Erin McKiernan, National Autonomous University of Mexico
• Andrew Odewahn, O’Reilly Media
• Max Ogden, Dat
• Louise Page, PLOS
• Fernando Pérez, UC Berkeley, LBNL
• Jessica Polka, ASAP Bio
• Kristen Ratan, Collaborative Knowledge Foundation
• Richard Sever, bioRxiv
• Carly Strasser, Moore Foundation
• Greg Tananbaum, CZI
• Ron Vale, UC San Francisco