Our Science Research
The Chan Zuckerberg Initiative produces scientific research to advance our mission to support the science and technology that will make it possible to cure, prevent or manage all diseases by the end of the century. Explore a selection of publications and preprints from across our institutes and grant partners.
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Exploring the ‘Digital Age of Biology’
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Unlocking Human Health With AI-powered Virtual Cells
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February 20, 2025
Global organelle profiling reveals subcellular localization and remodeling at proteome scale
Marco Hein, Duo Peng, et al. | Cell
February 14, 2025
KLF2 maintains lineage fidelity and suppresses CD8 T cell exhaustion during acute LCMV infection
Fagerberg E, Attanasio J, Dien C, et al. | Science
January 25, 2025
Exon inclusion signatures enable accurate estimation of splicing factor activity.
Anglada-Girotto M, Moakley DF, Zhang C, Miravet-Verde S, et al. | bioRxiv
December 12, 2024
How to build the virtual cell with artificial intelligence: Priorities and opportunities
Charlotte Bunne, Yusuf Roohani, Yanay Rosen et al. (2024) | Cell
December 8, 2024
SubCell: Vision foundation models for microscopy capture single-cell biology
Ankit Gupta, Zoe Wefers, Konstantin Kahnert et al. (2024) | bioRxiv
December 5, 2024
Active-reset protein sensors enable continuous in vivo monitoring of inflammation
H. Zargartalebi, S. Mirzaie, A. Ghavaminejad et al. (2024) | Science
December 4, 2024
Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues
Stephen R. Quake, The Tabula Sapiens Consortium (2024) | bioRxiv
December 2, 2024
AI: A transformative opportunity in cell biology
Ambrose Carr, Jonah Cool, Theofanis Karaletsos et al. (2024) | Molecular Biology of the Cell
November 28, 2024
CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data
CZI Cell Science Program, Shibla Abdulla, Brian Aevermann et al. (2024) | Nucleic Acids Research
November 14, 2024
A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors
Merlin Lange, Alejandro Granados, Shruthi VijayKumar, et al. | Cell
November 13, 2024
Remoscope: a label-free imaging cytometer for malaria diagnostics
Paul M. Lebel, Ilakkiyan Jeyakumar, Michelle W.L. Khoo, et al. | medRxiv
October 28, 2024
scGenePT: Is language all you need for modeling single-cell perturbations?
Ana-Maria Istrate, Donghui Li, Theofanis Karaletsos (2024) | bioRxiv
October 21, 2024
A data portal for providing standardized annotations for cryo-electron tomography
Utz Ermel, Anchi Cheng, Jun Xi Ni et al. (2024) | Nature Methods
October 12, 2024
Targeted delivery of napabucasin with radiotherapy improves outcomes in diffuse midline glioma
Gallitto M, Zhang X, De Los Santos G, et al. | Society for Neuro-Oncology
October 11, 2024
Genome-wide studies define new genetic mechanisms of IgA vasculitis.
Liu L, Zhu L, Monteiro-Martins S, et al. | medRxiv
October 2, 2024
Mechanism of DNA Entrapment by the MukBEF SMC Complex and Its Inhibition by a Viral DNA Mimic
Frank Bürmann, Bryony Clifton, Sophie Koekemoer et al. (2024) | bioRxiv
September 19, 2024
Real-Space Heterogeneous Reconstruction, Refinement, and Disentanglement of CryoEM Conformational States with HetSIREN
D. Herreros, C.P. Mata, C. Noddings et al. (2024) | bioRxiv
September 11, 2024
Neoadjuvant androgen deprivation therapy with or without Fc-enhanced non-fucosylated anti-CTLA-4 (BMS-986218) in high risk localized prostate cancer: a randomized phase 1 trial
Ager CR, Obradovic A, McCann P, et al. | medRxiv
September 9, 2024
The Structure of Cilium Inner Junctions Revealed by Electron Cryo-Tomography
Sam Li, Jose-Jesus Fernandez, Marisa D. Ruehle et al. (2024) | bioRxiv
September 6, 2024
Entinostat in patients with relapsed or refractory abdominal neuroendocrine tumors
Jamison JK, Zhou M, Gelmann EP, Luk L, et al. | The Oncologist
August 28, 2024
Isotype-aware inference of B cell clonal lineage trees from single-cell sequencing data
Leah L. Weber, Derek Reiman, Mrinmoy S. Roddur et al. (2024) | Cell Genomics
August 14, 2024
Dose-Efficient Cryo-Electron Microscopy for Thick Samples Using Tilt-Corrected Scanning Transmission Electron Microscopy, Demonstrated on Cells and Single Particles
Yue Yu, Katherine A. Spoth, Michael Colletta et al. (2024) | bioRxiv
August 9, 2024
DynaMight: estimating molecular motions with improved reconstruction from cryo-EM images
Johannes Schwab, Dari Kimanius, Alister Burt et al. (2024) | Nature Methods
August 1, 2024
Ghostbuster: A Phase Retrieval Diffraction Tomography Algorithm for Cryo-EM
Joel Yeo, Benedikt J. Daurer, Dari Kimanius et al. (2024) | Ultramicroscopy
July 17, 2024
Symbolic recording of signalling and cis-regulatory element activity to DNA
Chen, W., Choi, J., Li, X. et al. (2024) | Nature
July 16, 2024
Multidimensional Analysis of the Adult Human Heart in Health and Disease Using Hierarchical Phase-Contrast Tomography
Joseph Brunet, Andrew Cook, Claire Walsh et al. (2024) | Radiology
July 16, 2024
Insights and Impact From Five Cycles of Essential Open Source Software for Science
Kate Hertweck, Carly Strasser, Dario Taraborelli (2024)
July 10, 2024
Phage anti-CRISPR control by an RNA- and DNA-binding helix–turn–helix protein
Nils Birkholz, Kotaro Kamata, Maximilian Feussner et al. (2024) | Nature
July 10, 2024
Interferon subverts an AHR–JUN axis to promote CXCL13+ T cells in lupus
Law, C., Wacleche, V.S., Cao, Y. et al. (2024) | Nature
July 3, 2024
The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases uncovers cholesterol as a regulator of astrocyte reactivity impaired by ApoE4
Femke M. Feringa, Sascha J. Koppes-den Hertog, Lian Wang et al. (2024) | bioRxiv
July 1, 2024
More Than a Phase: Uncovering the Structure of Materials with Electron Phase Retrieval Techniques
Stephanie Ribet, Georgios Varnavides, Yue Yu et al. (2024) | Microscopy and Microanalysis
July 1, 2024
Towards More Efficient Use of Electrons: Demonstrating Cryo-4D-STEM Phase Imaging Techniques on Thick and Thin Biological Specimens, from Organelles to Proteins
Yue Yu, Stephanie M Ribet, Georgios Varnavides et al. (2024) | Microscopy and Microanalysis
July 1, 2024
Single-cell analysis of human diversity in circulating immune cells
Kian Hong Kock, Le Min Tan, Kyung Yeon Han et al. (2024) | bioRxiv
June 27, 2024
T cell-mediated microglial activation triggers myelin pathology in a mouse model of amyloidosis
Kedia, S., Ji, H., Feng, R. et al. (2024) | Nature Neuroscience
June 26, 2024
protoSpaceJAM: an open-source, customizable and web-accessible design platform for CRISPR/Cas insertional knock-in
Duo Peng, Madhuri Vangipuram, Joan Wong, Manuel D Leonetti (2024) | Nucleic Acids Research
June 22, 2024
Mantis: high-throughput 4D imaging and analysis of the molecular and physical architecture of cells
Ivan E. Ivanov, Eduardo Hirata-Miyasaki, Talon Chandler et al. (2023) | bioRxiv
June 11, 2024
Data-driven regularization lowers the size barrier of cryo-EM structure determination
Kimanius, D., Jamali, K., Wilkinson, M.E. et al. (2024) | Nature Methods
June 10, 2024
Omega - harnessing the power of large language models for bioimage analysis
Royer, L.A. (2024) | Nature Methods
June 6, 2024
Isthmus progenitor cells contribute to homeostatic cellular turnover and support regeneration following intestinal injury
Isthmus progenitor cells contribute to homeostatic cellular turnover and support regeneration following intestinal injury | Cell
June 5, 2024
Genome Sequencing for Diagnosing Rare Diseases
Monica Wojcik, Gabrielle Lemire, Eva Berger et al. (2024) | New England Journal of Medicine
June 2, 2024
Surforama: interactive exploration of volumetric data by leveraging 3D surfaces
Kevin A. Yamauchi, Lorenz Lamm, Lorenzo Gaifas et al. (2024) | bioRxiv
June 1, 2024
Recent Advances in Data Collection for Cryo-EM Methods
Anchi Cheng and Yue Yu (2024) | Current Opinion in Structural Biology
May 30, 2024
Active biointegrated living electronics for managing inflammation
Jiuyun Shi, Saehyun Kim, Pengju Li et al. (2024) | Science
May 20, 2024
DeepLabCut: the motion-tracking tool that went viral
Jyoti Madhusoodanan (2024) | Nature
May 14, 2024
The Wnt-dependent master regulator NKX1-2 controls mouse pre-implantation development
Nakagawa S, Carnevali D, Tan X et al. (2024) | Stem Cell Reports
May 10, 2024
Patient-focused drug development in primary sclerosing cholangitis: Insights on patient priorities and involvement in clinical trials
Michael Li, Ruth-Anne Pai, Rachel Gomel et al. (2024) | Hepatology Communications
May 9, 2024
Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis
Rosenberger G, Li W, Turunen M, et al. | Nature Communications
May 6, 2024
Transthoracic ultrasound localization microscopy of myocardial vasculature in patients
Yan, J., Huang, B., Tonko, J. et al. (2024) | Nature Biomedical Engineering
May 1, 2024
Recognising the importance and impact of Imaging Scientists: Global guidelines for establishing career paths within core facilities
Graham Wright, Kerry Thompson, Yara Reis et al. (2024) | Journal of Microscopy
May 1, 2024
Beam-Induced Motion Mechanism and Correction for Improved Cryo-Electron Microscopy and Cryo-Electron Tomography
Shawn Zheng, Axel Brilot, Yifan Cheng and David Agard (2024) | Cryo-Electron Tomography: Structural Biology in Situ
April 27, 2024
An Image Processing Pipeline for Electron Cryo-Tomography in RELION-5
Alister Burt, Bodgan Toader, Rangana Warshamanage et al. (2024) | bioRxiv
April 27, 2024
Polarity-JaM: An Image Analysis Toolbox for Cell Polarity, Junction and Morphology Quantification
Wolfgang Giese, Jan Philipp Albrecht, Olya Oppenheim et al. (2024) | bioRxiv
April 25, 2024
AI-MARRVEL — A Knowledge-Driven AI System for Diagnosing Mendelian Disorders
Dongxue Mao, Chaozhong Liu, Linhua Wang et al. (2024) | New England Journal of Medicine
April 24, 2024
Antisense oligonucleotide therapeutic approach for Timothy syndrome
Chen, X., Birey, F., Li, MY. et al. (2024) | Nature
April 23, 2024
Confronting heterogeneity in cryogenic electron microscopy data: Innovative strategies and future perspectives with data-driven methods
Dari Kimanius and Johannes Schwab (2024) |
April 18, 2024
Molecular determinants and signaling effects of PKA RIα phase separation
Hardy JC, Pool EH, Bruystens JGH et al. (2024) | Molecular Cell
April 17, 2024
Nicheformer: a foundation model for single-cell and spatial omics
Anna C. Shaar, Alejandro Tejada-Lapuerta, Giovanni Palla et al. (2024) | bioRxiv
April 8, 2024
Tumour-selective activity of RAS-GTP inhibition in pancreatic cancer
Wasko, U.N., Jiang, J., Dalton, T.C. et al. (2024) | Nature
February 8, 2024
Advances in 4D-STEM Phase-Contrast Imaging of Frozen-Hydrated Biological Specimens
Yue Yu, Michael Colletta, Katherine Spoth et al. (2024) | Biophysical Journal
January 26, 2024
Mis-spliced transcripts generate de novo proteins in TDP-43–related ALS/FTD
Sahba Seddighi, Yue A. Qi, Anna-Leigh Brown et al. (2024) | Science Translational Medicine
January 4, 2024
Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age
Steven Wells, Daniel Rainbow, Michael Mark et al. (2024) | bioRxiv
November 28, 2023
Poc1 Is a Basal Body Inner Junction Protein That Promotes Triplet Microtubule Integrity and Interconnections
Marisa Ruehle, Sam Li, David Agard et al. (2023) | bioRxiv
November 2, 2023
The next Decade in Structural Biology
Martin A. Walsh, Brent L. Nannenga, Tamir Gonen et al. (2023) | Structure
October 23, 2023
Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues
Adam Glaser, Jayaram Chandrashekar, Joshua Vasquez et al. (2024) | eLife
August 1, 2023
Better, Faster, Cheaper, Smarter: Advancing Cryo-EM
Bridget Carragher and Clinton Potter (2023) | Microscopy and Microanalysis
June 28, 2023
A spatially resolved single-cell genomic atlas of the adult human breast
Kumar, T., Nee, K., Wei, R. et al. (2023) | Nature