Selected publications
Submitted
* represents equal contribution
- Anupama Jha*, Stephanie C Bohaczuk*, Yizi Mao, Jane Ranchalis, Benjamin J Mallory, Alan T Min, Morgan O Hamm, Elliott Swanson, 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. bioRxiv, 2023.
[BibTeX]
@article{jha2023fibertools,
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 Finkbeiner, Connor and Li, Tony and others},
journal={bioRxiv},
pages={2023--04},
year={2023},
publisher={Cold Spring Harbor Laboratory}}
- Di Wu, Anupama Jha, San Jewell, Natalie Maus, Jacob R Gardner, Yoseph Barash. Generative modeling for RNA splicing code predictions and design. OpenReview, 2023.
[BibTeX]
@article{wu2023generative,
title={Generative modeling for RNA splicing code predictions and design},
author={Wu, Di and Jha, Anupama and Jewell, San and Maus, Natalie and Gardner, Jacob R and Barash, Yoseph},
year={2023}
}
- 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 multi-view diffusion model. bioRxiv, 2023.
[BibTeX]
@article{fang2023enhancing,
title={Enhancing Hi-C contact matrices for loop detection with Capricorn, a multi-view 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 others},
journal={bioRxiv},
pages={2023--10},
year={2023},
publisher={Cold Spring Harbor Laboratory}}
Published
- 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}}
- 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}}
- 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}}
- 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}}
PhD Thesis
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