Chen Lab Single-Cell Multi-Omics and Leukemia Research

Publications

2026

Scalable data harmonization for single-cell image-based profiling with CytoTable
Scalable data harmonization for single-cell image-based profiling with CytoTable
Dave Bunten, Jenna Tomkinson, Erik Serrano, Michael J. Lippincott, Kenneth I. Brewer, Vince Rubinetti, Faisal Alquaddoomi, Gregory P. Way
Patterns  ·  01 May 2026  ·  doi:10.1016/j.patter.2026.101514

2025

Scalable data harmonization for single-cell image-based profiling with CytoTable
Scalable data harmonization for single-cell image-based profiling with CytoTable
Dave Bunten, Jenna Tomkinson, Erik Serrano, Michael J. Lippincott, Kenneth I. Brewer, Vince Rubinetti, Faisal Alquaddoomi, Gregory P. Way
openRxiv  ·  25 Jun 2025  ·  doi:10.1101/2025.06.19.660613
Single-cell panleukemia signatures of HSPC-like blasts predict drug response and clinical outcome
Single-cell panleukemia signatures of HSPC-like blasts predict drug response and clinical outcome
Changya Chen, Jason Xu, Jonathan H. Sussman, Tiffaney Vincent, Joseph S. Tumulty, …, David Frank, Jun J. Yang, Kathrin M. Bernt, David T. Teachey, Kai Tan
Blood  ·  05 Jun 2025  ·  doi:10.1182/blood.2024027270

2024

A multiomic atlas identifies a treatment-resistant, bone marrow progenitor-like cell population in T cell acute lymphoblastic leukemia
A multiomic atlas identifies a treatment-resistant, bone marrow progenitor-like cell population in T cell acute lymphoblastic leukemia
Jason Xu, Changya Chen, Jonathan H. Sussman, Satoshi Yoshimura, Tiffaney Vincent, …, Kathrin Bernt, Jun J. Yang, Charles G. Mullighan, Kai Tan, David T. Teachey
Nature Cancer  ·  25 Nov 2024  ·  doi:10.1038/s43018-024-00863-5

2023

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species
The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species
Tim E Putman, Kevin Schaper, Nicolas Matentzoglu, Vincent P Rubinetti, Faisal S Alquaddoomi, …, Damian Smedley, Peter N Robinson, Christopher J Mungall, Melissa A Haendel, Monica C Munoz-Torres
Nucleic Acids Research  ·  24 Nov 2023  ·  doi:10.1093/nar/gkad1082
Integration of 168,000 samples reveals global patterns of the human gut microbiome
Integration of 168,000 samples reveals global patterns of the human gut microbiome
Richard J. Abdill, Samantha P. Graham, Vincent Rubinetti, Frank W. Albert, Casey S. Greene, Sean Davis, Ran Blekhman
openRxiv  ·  11 Oct 2023  ·  doi:10.1101/2023.10.11.560955
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes
Ricardo Avila, Vincent Rubinetti, Xinghua Zhou, Dongbo Hu, Zhongchao Qian, Marco Alvarado Cano, Everaldo Rodolpho, Ginger Tsueng, Casey Greene, Chunlei Wu
Nucleic Acids Research  ·  18 Apr 2023  ·  doi:10.1093/nar/gkad289
Hetnet connectivity search provides rapid insights into how two biomedical entities are related
Hetnet connectivity search provides rapid insights into how two biomedical entities are related
Daniel S. Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J. Heil, …, David N. Nicholson, Yun Hao, Blair D. Sullivan, Michael W. Nagle, Casey S. Greene
openRxiv  ·  07 Jan 2023  ·  doi:10.1101/2023.01.05.522941

2022

Hetnet connectivity search provides rapid insights into how biomedical entities are related
Hetnet connectivity search provides rapid insights into how biomedical entities are related
Daniel S Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J Heil, …, David N Nicholson, Yun Hao, Blair D Sullivan, Michael W Nagle, Casey S Greene
GigaScience  ·  28 Dec 2022  ·  doi:10.1093/gigascience/giad047
Single-cell multiomics reveals increased plasticity, resistant populations, and stem-cell like blasts in i KMT2A i -rearranged leukemia
Single-cell multiomics reveals increased plasticity, resistant populations, and stem-cell–like blasts in KMT2A -rearranged leukemia
Changya Chen, Wenbao Yu, Fatemeh Alikarami, Qi Qiu, Chia-hui Chen, …, Patrick A. Brown, Erin M. Guest, David M. Barrett, Kathrin M. Bernt, Kai Tan
Blood  ·  07 Apr 2022  ·  doi:10.1182/blood.2021013442
MolEvolvR: A web-app for characterizing proteins using molecular evolution and phylogeny
MolEvolvR: A web-app for characterizing proteins using molecular evolution and phylogeny
Faisal S Alquaddoomi, Joseph T Burke, Lo Sosinski, David A Mayer, Evan P Brenner, …, Vincent P Rubinetti, Shaddai Amolitos, Kellen M Reason, John B Johnston, Janani Ravi
openRxiv  ·  22 Feb 2022  ·  doi:10.1101/2022.02.18.461833

2021

Integrative Bulk and Single-Cell Profiling of Premanufacture T-cell Populations Reveals Factors Mediating Long-Term Persistence of CAR T-cell Therapy
Integrative Bulk and Single-Cell Profiling of Premanufacture T-cell Populations Reveals Factors Mediating Long-Term Persistence of CAR T-cell Therapy
Gregory M. Chen, Changya Chen, Rajat K. Das, Peng Gao, Chia-Hui Chen, …, Qin Zhu, Regina M. Myers, Stephan A. Grupp, David M. Barrett, Kai Tan
Cancer Discovery  ·  05 Apr 2021  ·  doi:10.1158/2159-8290.CD-20-1677

2020

Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
Genome Biology  ·  11 May 2020  ·  doi:10.1186/s13059-020-02021-3

2019

Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells
Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells
Changya Chen, Wenbao Yu, Joanna Tober, Peng Gao, Bing He, Kiwon Lee, Tuan Trieu, Gerd A. Blobel, Nancy A. Speck, Kai Tan
Cell Reports  ·  01 Dec 2019  ·  doi:10.1016/j.celrep.2019.11.065
Open collaborative writing with Manubot
Open collaborative writing with Manubot
Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
PLOS Computational Biology  ·  24 Jun 2019  ·  doi:10.1371/journal.pcbi.1007128
Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality
Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality
Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
openRxiv  ·  11 Mar 2019  ·  doi:10.1101/573782

2015

A microfluidic device for epigenomic profiling using 100 cells
A microfluidic device for epigenomic profiling using 100 cells
Zhenning Cao, Changya Chen, Bing He, Kai Tan, Chang Lu
Nature Methods  ·  27 Jul 2015  ·  doi:10.1038/nmeth.3488