Selected publications

• Tangqi Fang, Xiao Wang, Zixuan Xiao, Shengqi Hang, Ghulam Murtaza, Jinrui Yang, Hanwen Xu, Anupama Jha, William Stafford Noble, Sheng Wang. Evo2HiC: a multimodal foundation model for integrative analysis of genome sequence and architecture. bioRxiv, 2025.
  [BibTeX]
  
  

      @article{fang2025evo2hic,
      title={Evo2HiC: a multimodal foundation model for integrative analysis of genome sequence and architecture},
      author={Fang, Tangqi and Wang, Xiao and Xiao, Zixuan and Hang, Shengqi and Murtaza, Ghulam and Yang, Jinrui and Xu, Hanwen and Jha, Anupama and Noble, William S and Wang, Sheng},
      journal={bioRxiv},
      year={2025},
      publisher={Cold Spring Harbor Laboratory}}
      



• Shengqi Hang, Xiao Wang, Ghulam Murtaza, Anupama Jha, Bingfei Wen, Tangqi Fang, Jacob Sanders, Sheng Wang, William Stafford Noble. Puget predicts gene expression across cell types using sequence and 3D chromatin organization data. bioRxiv, 2025.
  [BibTeX]
  
  

      @article{hang2025puget,
      title={Puget predicts gene expression across cell types using sequence and 3D chromatin organization data},
      author={Hang, Shengqi and Wang, Xiao and Murtaza, Ghulam and Jha, Anupama and Wen, Bingfei and Fang, Tangqi and Sanders, Jacob and Wang, Sheng and Noble, William S},
      journal={bioRxiv},
      year={2025},
      publisher={Cold Spring Harbor Laboratory}}
      

• Anupama Jha, Borislav Hristov, Xiao Wang, Sheng Wang, William J. Greenleaf, Anshul Kundaje, Erez L. Aiden, Alessandro Bertero, William Stafford Noble. Prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC. Nature Communications, in press, 2026.
  [BibTeX]
  
  

      @article{jha2026twinc,
      title={Prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC},
      author={Jha, Anupama and Hristov, Borislav and Wang, Xiao and Wang, Sheng and Greenleaf, William J and Kundaje, Anshul and Aiden, Erez L and Bertero, Alessandro and Noble, William S},
      journal={Nature Communications},
      year={2026},
      note={In press}}
      



• Xiao Wang, Yaqi Zhang, Shubham Ray, Anupama Jha, Tangqi Fang, Shengqi Hang, Slava Doulatov, William Stafford Noble, Sheng Wang. A generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species. Nature Methods, in press, 2026.
  [BibTeX]
  
  

      @article{wang2026hicfoundation,
      title={A generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species},
      author={Wang, Xiao and Zhang, Yaqi and Ray, Shubham and Jha, Anupama and Fang, Tangqi and Hang, Shengqi and Doulatov, Slava and Noble, William S and Wang, Sheng},
      journal={Nature Methods},
      year={2026},
      note={In press}}
      



• Di Wu, Natalie Maus, Anupama Jha, Kai Yang, Bailey D. Wales-McGrath, San Jewell, Aditya Tangiyan, Peter Choi, Jacob R Gardner, Yoseph Barash. Generative modeling for RNA splicing code predictions and design. eLife, 2025.
  [BibTeX]
  
  

      @article{wu2025generative,
      title={Generative modeling for RNA splicing code predictions and design},
      author={Wu, Di and Maus, Natalie and Jha, Anupama and Yang, Kai and Wales-McGrath, Bailey D and Jewell, San and Tangiyan, Aditya and Choi, Peter and Gardner, Jacob R and Barash, Yoseph},
      journal={eLife},
      year={2025}}
      



• Kai Yang, Nathanial Islas, San Jewell, Anupama Jha, Caleb M. Radens, John A. Pleiss, Kristen W. Lynch, Yoseph Barash, Peter S. Choi. Machine learning-optimized targeted detection of alternative splicing. Nucleic Acids Research, 2025.
  [BibTeX]
  
  

      @article{yang2025targeted,
      title={Machine learning-optimized targeted detection of alternative splicing},
      author={Yang, Kai and Islas, Nathanial and Jewell, San and Jha, Anupama and Radens, Caleb M and Pleiss, John A and Lynch, Kristen W and Barash, Yoseph and Choi, Peter S},
      journal={Nucleic Acids Research},
      year={2025}}
      



• Anupama Jha*, Stephanie C Bohaczuk*, Yizi Mao, Jane Ranchalis, Benjamin J Mallory, Alan T Min, Morgan O Hamm, Elliott Swanson, David Dubocanin, Connor Finkbeiner, Tony Li, Dale Whittington, William Stafford Noble, Andrew B Stergachis, Mitchell R Vollger*. DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools. Genome Research, 2024.
  [BibTeX]
  
  

      @article{jha2024fibertools,
      title={DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools},
      author={Jha, Anupama and Bohaczuk, Stephanie C and Mao, Yizi and Ranchalis, Jane and Mallory, Benjamin J and Min, Alan T and Hamm, Morgan O and Swanson, Elliott and Dubocanin, David and Finkbeiner, Connor and Li, Tony and Whittington, Dale and Noble, William S and Stergachis, Andrew B and Vollger, Mitchell R},
      journal={Genome Research},
      year={2024}}
      



• Tangqi Fang, Yifeng Liu, Addie Woicik, Minsi Lu, Anupama Jha, Xiao Wang, Gang Li, Borislav Hristov, Zixuan Liu, Hanwen Xu, William Stafford Noble, Sheng Wang. Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model. Bioinformatics, 2024.
  [BibTeX]
  
  

      @article{fang2024capricorn,
      title={Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model},
      author={Fang, Tangqi and Liu, Yifeng and Woicik, Addie and Lu, Minsi and Jha, Anupama and Wang, Xiao and Li, Gang and Hristov, Borislav and Liu, Zixuan and Xu, Hanwen and Noble, William S and Wang, Sheng},
      journal={Bioinformatics},
      volume={40},
      pages={i471--i480},
      year={2024}}
      



• Jorge Vaquero-Garcia, Joseph K Aicher, San Jewell, Matthew R Gazzara, Caleb M Radens*, Anupama Jha*, Scott S Norton, Nicholas F Lahens, Gregory R Grant, Yoseph Barash. RNA splicing analysis using heterogeneous and large RNA-seq datasets. Nature Communications, 2023.
  [BibTeX]
  
  

      @article{vaquero2023rna,
      title={RNA splicing analysis using heterogeneous and large RNA-seq datasets},
      author={Vaquero-Garcia, Jorge and Aicher, Joseph K and Jewell, San and Gazzara, Matthew R and Radens, Caleb M
      and Jha, Anupama and Norton, Scott S and Lahens, Nicholas F and Grant, Gregory R and Barash, Yoseph},
      journal={Nature Communications},
      volume={14},
      number={1},
      pages={1230},
      year={2023},
      publisher={Nature Publishing Group UK London}}
      



• Anupama Jha*, Mathieu Quesnel-Vallières*, David Wang, Andrei Thomas-Tikhonenko, Kristen W Lynch, Yoseph Barash. Identifying common transcriptome signatures of cancer by interpreting deep learning models. Genome Biology, 2022.
  [BibTeX]
  
  

      @article{jha2022identifying,
      title={Identifying common transcriptome signatures of cancer by interpreting deep learning models},
      author={Jha, Anupama and Quesnel-Valli{\`e}res, Mathieu and Wang, David and Thomas-Tikhonenko, Andrei and Lynch,
      Kristen W and Barash, Yoseph},
      journal={Genome Biology},
      volume={23},
      number={1},
      pages={1--23},
      year={2022},
      publisher={BioMed Central}}
      



• William P. Bone, Katherine M. Siewert, Anupama Jha, Derek Klarin, Scott M. Damrauer, the VA Million Veteran Project, Kyong-Mi Chang, Philip S. Tsao, Themistocles L. Assimes, Marylyn D. Ritchie, Benjamin F. Voight. Multi-trait association studies discover pleiotropic loci between Alzheimer’s disease and cardiometabolic traits. Alzheimer's research & therapy, 2021.
  [BibTeX]
  
  

      @article{bone2021multi,
      title={Multi-trait association studies discover pleiotropic loci between Alzheimer’s disease and cardiometabolic traits},
      author={Bone, William P and Siewert, Katherine M and Jha, Anupama and Klarin, Derek and Damrauer, Scott M and Chang,
      Kyong-Mi and Tsao, Philip S and Assimes, Themistocles L and Ritchie, Marylyn D and others},
      journal={Alzheimer's research \& therapy},
      volume={13},
      pages={1--14},
      year={2021},
      publisher={Springer}}
      



• Xinjun Ji, Anupama Jha, Jesse Humenik, Louis R Ghanem, Andrew Kromer, Christopher Duncan-Lewis, Elizabeth Traxler, Mitchell J Weiss, Yoseph Barash, Stephen A Liebhaber. RNA-binding proteins PCBP1 and PCBP2 are critical determinants of murine erythropoiesis. Molecular and Cellular Biology, 2021.
  [BibTeX]
  
  

      @article{ji2021rna,
      title={RNA-binding proteins PCBP1 and PCBP2 are critical determinants of murine erythropoiesis},
      author={Ji, Xinjun and Jha, Anupama and Humenik, Jesse and Ghanem, Louis R and Kromer, Andrew and Duncan-Lewis, Christopher and Traxler, Elizabeth and Weiss, Mitchell J and Barash, Yoseph and Liebhaber, Stephen A},
      journal={Molecular and Cellular Biology},
      volume={41},
      number={9},
      pages={e00668--20},
      year={2021},
      publisher={Taylor \& Francis}}
      



• Barry Slaff, Caleb Matthew Radens, Paul Jewell, Anupama Jha, Nicholas Lahens, Gregory R Grant, Andrei Thomas-Tikhonenko, Kristen W Lynch, Yoseph Barash. MOCCASIN: A method for correcting for known and unknown confounders in RNA splicing analysis. Nature Communications, 2021.
  [BibTeX]
  
  

      @article{slaff2021moccasin,
      title={MOCCASIN: a method for correcting for known and unknown confounders in RNA splicing analysis},
      author={Slaff, Barry and Radens, Caleb M and Jewell, Paul and Jha, Anupama and Lahens, Nicholas F and Grant, Gregory R and Thomas-Tikhonenko, Andrei and Lynch, Kristen W and Barash, Yoseph},
      journal={Nature communications},
      volume={12},
      number={1},
      pages={3353},
      year={2021},
      publisher={Nature Publishing Group UK London}}
      



• Anupama Jha, Joseph K Aicher, Matthew R Gazzara, Deependra Singh, Yoseph Barash. Enhanced integrated gradients: improving interpretability of deep learning models using splicing codes as a case study. Genome Biology, 2020.
  [BibTeX]
  
  

      @article{jha2020enhanced,
      title={Enhanced integrated gradients: improving interpretability of deep learning models using splicing codes as a case study},
      author={Jha, Anupama and K. Aicher, Joseph and R. Gazzara, Matthew and Singh, Deependra and Barash, Yoseph},
      journal={Genome biology},
      volume={21},
      pages={1--22},
      year={2020},
      publisher={Springer}}
      



• Anupama Jha, Matthew R Gazzara, Yoseph Barash. Integrative deep models for alternative splicing. Bioinformatics, 2017.
  [BibTeX]
  
  

      @article{jha2017integrative,
      title={Integrative deep models for alternative splicing},
      author={Jha, Anupama and Gazzara, Matthew R and Barash, Yoseph},
      journal={Bioinformatics},
      volume={33},
      number={14},
      pages={i274--i282},
      year={2017},
      publisher={Oxford University Press}}
      



• Matthew R Gazzara, Michael J Mallory, Renat Roytenberg, John P Lindberg, Anupama Jha, Kristen W Lynch, Yoseph Barash. Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes. Genome Research, 2017.
  [BibTeX]
  
  

      @article{gazzara2017ancient,
      title={Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes},
      author={Gazzara, Matthew R and Mallory, Michael J and Roytenberg, Renat and Lindberg, John P and
      Jha, Anupama and Lynch, Kristen W and Barash, Yoseph},
      journal={Genome research},
      volume={27},
      number={8},
      pages={1360--1370},
      year={2017},
      publisher={Cold Spring Harbor Lab}}
      

• Anupama Jha. Assembling the Building Blocks for a Unified Splicing Code. Doctoral Dissertation, University of Pennsylvania, 2020.
  [BibTeX]
  
  

      @phdthesis{jha2020assembling,
        title={Assembling the Building Blocks for a Unified Splicing Code},
        author={Jha, Anupama},
        year={2020},
        school={University of Pennsylvania}}