The Jha Lab at Yale Genetics

Research

3D Genome Architecture

Highlighted

Prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC
Prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC
Anupama Jha, Borislav Hristov, Xiao Wang, Sheng Wang, William J. Greenleaf, Anshul Kundaje, Erez Lieberman Aiden, Alessandro Bertero, William Stafford Noble
openRxiv  ·  21 Sep 2024  ·  doi:10.1101/2024.09.16.613355

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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
Generative modeling for RNA splicing prediction and design
Generative modeling for RNA splicing prediction and design
Di Wu, Natalie Maus, Anupama Jha, Kevin Yang, Benjamin D. Wales-McGrath, San Jewell, Anna Tangiyan, Peter Choi, Jacob R. Gardner, Yoseph Barash
openRxiv  ·  24 Jan 2025  ·  doi:10.1101/2025.01.20.633986

2024

Machine learning-optimized targeted detection of alternative splicing
Machine learning-optimized targeted detection of alternative splicing
Kevin Yang, Nathaniel Islas, San Jewell, Di Wu, Anupama Jha, Caleb M Radens, Jeffrey A Pleiss, Kristen W Lynch, Yoseph Barash, Peter S Choi
Nucleic Acids Research  ·  27 Dec 2024  ·  doi:10.1093/nar/gkae1260
A generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species
A generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species
Xiao Wang, Yuanyuan Zhang, Suhita Ray, Anupama Jha, Tangqi Fang, Shengqi Hang, Sergei Doulatov, William Stafford Noble, Sheng Wang
openRxiv  ·  20 Dec 2024  ·  doi:10.1101/2024.12.16.628821
Prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC
Prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC
Anupama Jha, Borislav Hristov, Xiao Wang, Sheng Wang, William J. Greenleaf, Anshul Kundaje, Erez Lieberman Aiden, Alessandro Bertero, William Stafford Noble
openRxiv  ·  21 Sep 2024  ·  doi:10.1101/2024.09.16.613355
Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model
Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model
Tangqi Fang, Yifeng Liu, Addie Woicik, Minsi Lu, Anupama Jha, …, Borislav Hristov, Zixuan Liu, Hanwen Xu, William S Noble, Sheng Wang
Bioinformatics  ·  28 Jun 2024  ·  doi:10.1093/bioinformatics/btae211
DNA-m6A calling and integrated long-read epigenetic and genetic analysis with i fibertools i
DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools
Anupama Jha, Stephanie C. Bohaczuk, Yizi Mao, Jane Ranchalis, Benjamin J. Mallory, …, Tony Li, Dale Whittington, William Stafford Noble, Andrew B. Stergachis, Mitchell R. Vollger
Genome Research  ·  07 Jun 2024  ·  doi:10.1101/gr.279095.124

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
Identifying common transcriptome signatures of cancer by interpreting deep learning models
Identifying common transcriptome signatures of cancer by interpreting deep learning models
Anupama Jha, Mathieu Quesnel-Vallières, David Wang, Andrei Thomas-Tikhonenko, Kristen W Lynch, Yoseph Barash
Genome Biology  ·  17 May 2022  ·  doi:10.1186/s13059-022-02681-3
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

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

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

2017

Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes
Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes
Matthew R. Gazzara, Michael J. Mallory, Renat Roytenberg, John P. Lindberg, Anupama Jha, Kristen W. Lynch, Yoseph Barash
Genome Research  ·  16 May 2017  ·  doi:10.1101/gr.220517.117