Publications

A human commons cell atlas reveals cell type specificity for OAS1 isoforms
Ángel Galvez-Merchán, A. Sina Booeshaghi, Lior Pachter
bioRxiv, 2024

Algorithms for a Commons Cell Atlas
A. Sina Booeshaghi, Ángel Galvez-Merchán, Lior Pachter
bioRxiv, 2024

kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq
Delaney K. Sullivan, Kyung Hoi (Joseph) Min, Kristján Eldjárn Hjörleifsson, Laura Luebbert, Guillaume Holley, Lambda Moses, Johan Gustafsson, Nicolas L. Bray, Harold Pimentel, A. Sina Booeshaghi, Páll Melsted, Lior Pachter
bioRxiv, 2024

Accurate quantification of single-cell and single-nucleus RNA-seq transcripts using distinguishing flanking k-mers
Kristján Eldjárn Hjörleifsson, Delaney K. Sullivan, Nikhila P. Swarna, Guillaume Holley, Páll Melsted, Lior Pachter
bioRxiv, 2024

Trajectory inference from single-cell genomics data with a process time model
M Fang, G Gorin, L Pachter
bioRxiv, 2024

Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease
Michal Polonsky, Louisa M. S. Gerhardt, Jina Yun, Kari Koppitch, Katsuya Lex Colón, Henry Amrhein, Shiwei Zheng, Guo-Cheng Yuan, Matt Thomson, Long Cai, Andrew P. McMahon
bioRxiv, 2023

Generating counterfactual explanations of tumor spatial proteomes to discover therapeutic strategies for enhancing immune infiltration
Zitong Jerry Wang, Alexander M. Xu, Aman Bhargava and Matt W. Thomson
bioRxiv, 2023

Studying stochastic systems biology of the cell with single-cell genomics data
Gennady Gorin, John J. Vastola, Lior Pachter
Cell Systems, 2023

Voyager: exploratory single-cell genomics data analysis with geospatial statistics
Lambda Moses, Pétur Helgi Einarsson, Kayla Jackson, Laura Luebbert, A. Sina Booeshaghi, Sindri Antonsson, Nicolas Bray, Páll Melsted, Lior Pachter
bioRxiv, 2023

High-resolution spatial multi-omics reveals cell-type specific nuclear compartments
Yodai Takei, Yujing Yang, Jonathan White, Jina Yun, Meera Prasad, Lincoln J Ombelets, Simone Schindler, Long Cai
bioRxiv, 2023

TRILL: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and Engineering
Zachary A Martinez, Richard M. Murray, Matt W. Thomson
bioRxiv, 2023

Unexplored regions of the protein sequence-structure map revealed at scale by a library of foldtuned language models
Arjuna M. Subramanian, Matt Thomson
bioRxiv, 2023

D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response
Jialong Jiang, Sisi Chen, Tiffany Tsou, Christopher S McGinnis, Tahmineh Khazaei, Qin Zhu, Jong H Park, Inna-Marie Strazhnik, John Hanna, Eric D Chow, David A Sivak, Zev J Gartner, Matt Thomson
bioRxiv, 2023

A standard for sharing spatial transcriptomics data
Kayla C. Jackson, and Lior Pachter
Cell Genomics, 2023

Unraveling cell differentiation mechanisms through topological exploration of single-cell developmental trajectories
Emanuel Flores-Bautista, Matt Thomson
bioRxiv, 2023

Museum of spatial transcriptomics
Lambda Moses and Lior Pachter
Nature Methods, 2022

RNA velocity unraveled
Gennady Gorin, Meichen Fang, Tara Chari, Lior Pachter
PLoS Computational Biology, 2022

A human embryonic limb cell atlas resolved in space and time
Zhang, Bao; He, Peng et al.
bioRxiv, 2022

A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice
Reem Abdel-Haq, Johannes CM Schlachetzki, Joseph C Boktor, Thaisa M Cantu-Jungles, Taren Thron, Mengying Zhang, John W Bostick, Tahmineh Khazaei, Sujatha Chilakala, Livia H Morais, Greg Humphrey, Ali Keshavarzian, Jonathan E Katz, Matthew Thomson, Rob Knight, Viviana Gradinaru, Bruce R Haymaker, Christopher K Glass, Sarkis K Mazmanian
Microbiology and Infectious Disease Neuroscience, 2022

Enhanced recovery of single-cell RNA-sequencing reads for missing gene expression data
Allan-Hermann Pool, Helen Poldsam, Sisi Chen, Matt Thomson, Yuki Oka
BioRxiv, 2022

Stem cell-derived synthetic embryos self-assemble by exploiting cadherin codes and cortical tension
Min Bao, Jake Cornwall-Scoones, Estefania Sanchez-Vasquez, Andy L. Cox, Dong-Yuan Chen, Joachim De Jonghe, Shahriar Shadkhoo, Florian Hollfelder, Matt Thomson, David M. Glover & Magdalena Zernicka-Goetz
Nature Cell Biology, 2022

CloudPred: Predicting Patient Phenotypes From Single-cell RNA-seq
Bryan He, Matthew Thomson, Meena Subramaniam, Richard Perez, Chun Jimmie Ye, James Zou
Pacific Symposium on Biocomputing, 2022

Minimal gene set discovery in single-cell mRNA-seq datasets with ActiveSVM
Xiaoqiao Chen, Sisi Chen & Matt Thomson
Nature Computational Science, 2022

Single-cell nuclear architecture across cell types in the mouse brain
Yodai Takei, Shiwei Zheng, Jina Yun, Sheel Shah, Nico Pierson, Jonathan White, Simone Schindler, Carsten Tischbirek, Guo-Cheng Yuan, Long Cai
Science, 2021

Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq
Rebboah, Elisabeth;Reese, Fairlie et al.
Genome Biology, 2021

Multi-tissue integrative analysis of personal epigenomes
Rozowsky, Joel;Drenkow, Jorg et al.
bioRxiv, 2021

The changing mouse embryo transcriptome at whole tissue and single-cell resolution
He, Peng;Williams, Brian A. et al.
Nature, 2020