Seed Networks for the Human Cell Atlas
The projects below bring together experimental scientists, computational biologists, software engineers, and physicians to support the continued development of the Human Cell Atlas (HCA), an international effort to map all cells in the human body as a resource for better understanding health and disease.
Showing 38 results
This network will develop a comprehensive, validated atlas of the human kidney at single cell resolution open to the entire scientific and clinical community.
Fei Chen Menna Clatworthy Anna Greka Matthias Kretzler Minnie Sarwal Olga Troyanskaya
Aviv Regev Sarah Teichmann Jimmie Ye
This project will characterize all cell types in the healthy female human reproductive tract using single cell RNA and ATAC sequencing and integrate transcriptomic and epigenetic information.
Anindita Basu Mengjie Chen Mark Eckert Ernst Lengyel
This network seeks to continue their development and implementation of a multimodal single cell sequencing strategy to determine cellular diversity within the human spinal cord.
Tom Maniatis Liam Paninski Raul Rabadan Abbas Rizvi
This team will analyze single cells and develop computational tools to build a single cell map of the human liver, combining transcriptomics, spatial organization, and cell-cell interactions across diverse individuals and developmental stages.
Gary Bader Ramanuj DasGupta Dominic Grün Martin Guilliams Neil Henderson Georg Lauer Sonya MacParland Ian McGilvray Alan Mullen Gerald Quon Charlotte Scott Ludovic Vallier Mei Zhen Ramnik Xavier
Muzlifah Haniffa Shalev Itzkovitz Aviv Regev
This project helps build the hematopoietic human cell atlas with single cell transcriptomics, multiplexed spatial imaging data, and a pilot lineage-tracing map in vitro, presented via a portal for exploration and data analysis in the context of the Human Cell Atlas.
Sahand Hormoz Allon Klein Debora Marks Ann Mullally Chris Sander Peng Yin
The goal of this project is to build a spatially resolved single-cell reference map of the adult human heart.
Alexandre Pereira Christine Seidman Gavin Oudit Jonathan Seidman Lars Steinmetz Matthias Heinig Michela Noseda Nikolaus Rajewsky Norbert Hübner Sebastian Pott Stuart Cook
Anindita Basu Dominic Grün Fabian Theis Sarah Teichmann
The goal of this project is to generate an integrated map of cellular diversity in the human immune system across multiple tissues and the human lifespan. It will provide a resource to study mechanisms of tissue residency and the effects of aging.
Donna Farber Joanne Jones Peter Sims Roser Vento-Tormo Nir Yosef Muzlifah Haniffa
Menna Clatworthy Sarah Teichmann
This network aims to build an atlas of Asian immune cell types and states and characterize differences between six major Asian population groups (Chinese, Japanese, Korean, Indian, Malay, Thai).
Ankita Chatterjee Arindam Maitra Chong Qingqing Dawn Chung-Chau Hon Eiryo Kawakami Iain Tan Jay Shin John Chambers Partha Majumder Ponpan Matangkasombut Shyam Prabhakar Woong-Yang Park Varodom Charoensawan
This network will define the normal developing and adult human kidney transcriptome and epigenome at cellular resolution, across ages and sex, and benchmark human kidney organoid cell types against this dataset.
Steven Chang Benjamin Humphreys Andrew McMahon Stefan Tullius Sushrut Waikar Bo Zhang
Nils Lindstrom Tracy Battaglia
This network’s collaborative effort enables the large community of users for the open source software R / Bioconductor to effectively access the Human Cell Atlas for statistical analysis, visualization, and novel scientific discovery.
Aedin Culhane Greg Finak Kasper Hansen Stephanie Hicks Wolfgang Huber Martin Morgan Davide Risso Matthew Ritchie
This team will use single cell and single nucleus RNA-sequencing, computational inference, and histological analysis to generate a comprehensive reference atlas of cell types in the human eye, incorporating data across the natural lifespan.
Tommaso Biancalani Gregory Hageman Dejan Juric Joshua Sanes Ayellet Segre Tavé van Zyl Karthik Shekhar
This project will establish a cell reference atlas of the human neural retina, build a high-resolution spatial map for all cell types in the retina, and develop single cell classification and integrative analysis software tools.
Rui Chen Margaret DeAngelis Kirsten Frieda Michael Mancini Wenyi Wang
With a goal of understanding how non-coding genetic variation in humans functionally impacts disease traits, this network proposes a framework to map and interpret intra- and inter-individual variation in complex tissues using single cell approaches.
Kristin Ardlie Roderic Guigó Rajat Gupta Orit Rozenblatt-Rosen
Alexis Battle Jason Buenrostro Aviv Regev Jimmie Ye
This network will develop an integrated technology to study human cells through a combination of highly multiplexed imaging, classification by deep learning, and ultra-sensitive mass spectrometry-based proteomics.
Peter Horvath Emma Lundberg Matthias Mann
This network proposes a benchmarking framework to generate guidelines, technologies, quality metrics, and new computational tools that will serve as a compass for the Human Cell Atlas’s generation of reproducible and high-quality tissue atlases.
Piero Carninci Wolfgang Enard Samouil Farhi Ernest Fraenkel Holger Heyn Matthias Kretzler Joshua Levin Thierry Voet
Menna Clatworthy Anna Greka Aviv Regev Orit Rozenblatt-Rosen Sarah Teichmann
This project will identify genetic variants that alter the frequency of cell types within human tissues or modulate gene expression or chromatin accessibility within those cell types.
Shin Lin Yiing Lin Cole Trapnell
This network’s goal is to generate an African Immune Cell Atlas using single-cell RNA sequencing techniques to profile the transcriptomic and epigenetic profile of peripheral blood mononuclear cells (PBMCs) from ethnically diverse Africans before and after immune stimulation.
Eline Luning Prak Yun Song Sarah Tishkoff Noah Zaitlen James Zou
This project will establish a comprehensive reference of cell types and cell states in human breast tissue with single cell and spatial resolution.
Ken Chen Kai Kessenbrock Devon Lawson Je Lee Bora Lim Nicholas Navin
This network will build a human cell atlas along the gut-brain axis by isolating and profiling vagal nodose ganglion and enteroendocrine cells using single cell RNA-seq and ATAC-seq.
Ken Lau Xiling Shen
This project will establish a human cell atlas of the female reproductive system, focusing on the ovaries, fallopian tube, and uterus.
Sue Hammoud Jun Z. Li Erica Marsh Ariella Shikanov
This project seeks to establish the normal range of immune phenotypic variability — both within and across individuals — and assess contributions from genetics and environment, such as diurnal, seasonal, and reproductive cycles and life experience.
Orr Ashenberg Alexis Battle Philip L. De Jager Stephan Sanders Jimmie Ye
This network will develop the first version of the Human Lung Cell Atlas by integrating single cell and spatial genomics, microscopy, anatomic, and computational methods.
Alexander Misharin Alexander Tsankov Douglas Shepherd Fabian Theis Herbert B. Schiller Jayaraj Rajagopal Jeffrey Whitsett Joseph Powell Kerstin Meyer Mark Krasnow Marko Nikolic Martijn Nawijn Naftali Kaminski Oliver Eickelberg Pascal Barbry Purushothama Rao Tata Thu Elizabeth Duong Tushar Desai
This network is contributing to an endothelial cell atlas in space and time by mapping the transcriptomes of endothelial cells from several tissues from donors of different ages and ancestry and developing cutting-edge computational tools.
Zhen Chen Guo-Cheng Yuan Xuegong Zhang Zemin Zhang Sheng Zhong
Mingxia Gu Zhenglong Gu
This project will identify inter-individual differences in molecular signatures of human brain cell types, including single cell transcriptomes and DNA methylomes.
Margarita Behrens Joseph Ecker Eran Mukamel
This project aims to combine spatially resolved and single cell transcriptional profiling to develop a systematic method for inferring cell-cell interactions, and to apply that method to create a high-resolution spatial atlas of healthy human lymph nodes.
Donna Farber Peter Kharchenko Jeffrey Moffit Peter Sims Catherine Wu
This project brings together scientists with broad and complementary expertise to generate a comprehensive cell atlas of the human thymus across development and aging.
Jakub Abramson Ronald Germain Yvan Saeys Tom Taghon Sarah Teichmann
This project’s goal is to map adipose tissue heterogeneity in healthy humans by integrating chemical imaging, single cell, and single nucleus RNA sequencing from adipocytes and adipocyte precursors with distinct anatomical origins and metabolic function.
Mary-Elizabeth Patti Aaron Streets Yu-Hua Tseng
This network will characterize the single nucleus transcriptomes and intercellular communication networks of human adipose tissue cells (adipocytes and stroma-vascular cells) across fat depots, sex, and ethnicity.
Matthias Blüher Naomi Habib Antje Körner Rinki Murphy Assaf Rudich Esti Yeger-Lotem
This network will map the human testis in 3D using paired single cell analysis by mass-spectrometry, clampFISH, and RNA-sequencing.
Jürgen Cox Alexander Franks Sara Rouhanifard Nikolai Slavov
This project will develop a set of generalizable tools, resources, and best practices for multi-modal cell and tissue phenotyping, integrating high-throughput and spatially resolved methods applied to tissues of the human immune system.
Adeeb Rahman Rahul Satija Peter Smibert
This project will investigate the transcriptional and chromatin accessibility landscapes of the human oligodendrocyte lineage during development and in adulthood in both males and females.
Gonçalo Castelo-Branco Gioele La Manno Anna Williams
This network introduces a novel chromatin profiling technology, CUT&Tag, and will demonstrate its single cell application, thus motivating the development of new experimental and computational tools to transfer their innovation to the global Human Cell Atlas effort and the broader scientific community.
Kami Ahmad Raphael Gottardo Gavin Ha Steven Henikoff Anoop Patel Scott Furlan
This network will perform single-cell mapping of the normal breast of ethnically diverse populations, including women of African, Latinx, Asian, Ashkenazi Jewish, and Native American descent.
Yunlong Liu Harikrishna Nakshatri Anna Maria Storniolo
This project will provide the Human Cell Atlas community with datasets, technological advancement, and computational methods for a high-resolution reconstruction of cell lineages and states combining chromatin accessibility and barcoding techniques.
Jason Buenrostro Samantha Morris Luca Pinello
The purpose of this project is to create an atlas of single cell transcriptomic and epigenomic features of the human vasculature to define the cellular composition and key regulatory features of these vessels.
Brian Black Anshul Kundaje Thomas Quertermous
This project will build a spatiotemporal atlas of a single individual’s multi-organ developmental program by applying integrated single-cell RNA-seq and 4i spatial maps to primary tissue and matched iPSC-derived organoids from the same individual.
Gray Camp Smita Krishnaswamy Prisca Liberali Lucas Pelkmans Jason Spence Barbara Treutlein
This project will develop the technology and analytics to sequence pairs of attached tissue cells to determine their interactions and spatial localization. The network will apply these approaches to reconstruct 3D maps and interaction models in the human intestine and bone marrow, studying how cell interactions impact differentiation, proliferation, metabolism, and more.
Ido Amit Shalev Itzkovitz Amos Tanay
The Tendon Seed Network will spatially define the transcriptome of extracellular matrix-rich tissues such as tendon across multiple anatomic and micro-anatomic sites. To enable this, the project will develop clinical, laboratory, bioinformatics, and mathematical modelling tools and platforms.
Adam Cribbs Andrew Carr Jess Snedeker Mathew Baldwin Michael Kjær Neal Millar Philippa Hulley Sarah Snelling Sarah Waters Stephanie Dakin Steven Gwilym
Chris Buckley Xavier Griffin
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