Anshul Kundaje

41 papers A* 6B 2Misc 1Journal 26Unranked 6
YearRankTypeTitle / Venue / Authors
2025 B conf
Sequence-Based TCR-Peptide Representations Using Cross-Epitope Contrastive Fine-Tuning of Protein Language Models.
RECOMB
Chiho Im, Ryan Zhao, Scott D. Boyd, Anshul Kundaje
2025 — conf
Somatic Hypermutation Informed Vocabulary Encoder Representations.
MLCB
Chiho Im, Artem Mikelov, Ryan Zhao, Anshul Kundaje, Scott D. Boyd
2024 A* conf
DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA.
NeurIPS
Aman Patel, Arpita Singhal, Austin Wang, Anusri Pampari, Maya Kasowski, Anshul Kundaje
2024 J jnl
DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA.
CoRR
Aman Patel, Arpita Singhal, Austin Wang, Anusri Pampari, Maya Kasowski, Anshul Kundaje
2023 J jnl
GENCODE: reference annotation for the human and mouse genomes in 2023.
Nucleic Acids Res.
Adam Frankish, Silvia Carbonell Sala, Mark Diekhans, Irwin Jungreis, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Carme Arnan, If Barnes, Abhimanyu Banerjee, Ruth Bennett, Andrew E. Berry, Alexandra Bignell, Carles Boix, Ferriol Calvet Riera, Daniel Cerdán-Vélez, Fiona Cunningham, Claire Davidson, Sarah M. Donaldson, Cagatay Dursun, Reham Fatima, Stefano Giorgetti, Carlos García-Girón, Jose M. Gonzalez, Matthew Hardy, Peter W. Harrison, Thibaut Hourlier, Zoe Hollis, Toby Hunt, Benjamin James, Yunzhe Jiang, Rory Johnson, Mike P. Kay, Julien Lagarde, Fergal J. Martin, Laura Martínez Gómez, Surag Nair, Pengyu Ni, Fernando Pozo, Vivek Ramalingam, Magali Ruffier, Bianca M. Schmitt, Jacob M. Schreiber, Emily Steed, Marie-Marthe Suner, Dulika Sumathipala, Irina Sycheva, Barbara Uszczynska-Ratajczak, Elizabeth Wass, Yucheng T. Yang, Andrew D. Yates, Zahoor Zafrulla, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Anshul Kundaje, Benedict Paten, Michael L. Tress, Paul Flicek
2023 A* conf
Tartarus: A Benchmarking Platform for Realistic And Practical Inverse Molecular Design.
NeurIPS
AkshatKumar Nigam, Robert Pollice, Gary Tom, Kjell Jorner, John Willes, Luca A. Thiede, Anshul Kundaje, Alán Aspuru-Guzik
2022 J jnl
Accelerating
Bioinform.
Jacob M. Schreiber, Surag Nair, Akshay Balsubramani, Anshul Kundaje
2022 J jnl
Tartarus: A Benchmarking Platform for Realistic And Practical Inverse Molecular Design.
CoRR
AkshatKumar Nigam, Robert Pollice, Gary Tom, Kjell Jorner, Luca A. Thiede, Anshul Kundaje, Alán Aspuru-Guzik
2022 J jnl
fastISM: performant
Bioinform.
Surag Nair, Avanti Shrikumar, Jacob M. Schreiber, Anshul Kundaje
2021 — conf
Towards More Realistic Simulated Datasets for Benchmarking Deep Learning Models in Regulatory Genomics.
MLBC
Eva Prakash, Avanti Shrikumar, Anshul Kundaje
2021 — conf
Towards a Better Understanding of Reverse-Complement Equivariance for Deep Learning Models in Genomics.
MLBC
Hannah Zhou, Avanti Shrikumar, Anshul Kundaje
2021 A* conf
WILDS: A Benchmark of in-the-Wild Distribution Shifts.
ICML
Pang Wei Koh, Shiori Sagawa, Henrik Marklund, Sang Michael Xie, Marvin Zhang, Akshay Balsubramani, Weihua Hu, Michihiro Yasunaga, Richard Lanas Phillips, Irena Gao, Tony Lee, Etienne David, Ian Stavness, Wei Guo, Berton Earnshaw, Imran S. Haque, Sara M. Beery, Jure Leskovec, Anshul Kundaje, Emma Pierson, Sergey Levine, Chelsea Finn, Percy Liang
2020 A* conf
Fourier-transform-based attribution priors improve the interpretability and stability of deep learning models for genomics.
NeurIPS
Alex Tseng, Avanti Shrikumar, Anshul Kundaje
2020 A* conf
Maximum Likelihood with Bias-Corrected Calibration is Hard-To-Beat at Label Shift Adaptation.
ICML
Amr Alexandari, Anshul Kundaje, Avanti Shrikumar
2020 J jnl
WILDS: A Benchmark of in-the-Wild Distribution Shifts.
CoRR
Pang Wei Koh, Shiori Sagawa, Henrik Marklund, Sang Michael Xie, Marvin Zhang, Akshay Balsubramani, Weihua Hu, Michihiro Yasunaga, Richard Lanas Phillips, Sara Beery, Jure Leskovec, Anshul Kundaje, Emma Pierson, Sergey Levine, Chelsea Finn, Percy Liang
2019 J jnl
Calibration with Bias-Corrected Temperature Scaling Improves Domain Adaptation Under Label Shift in Modern Neural Networks.
CoRR
Avanti Shrikumar, Anshul Kundaje
2019 J jnl
GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs.
Bioinform.
Avanti Shrikumar, Eva Prakash, Anshul Kundaje
2019 J jnl
Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts.
Bioinform.
Surag Nair, Daniel S. Kim, Jacob Perricone, Anshul Kundaje
2018 J jnl
Computationally Efficient Measures of Internal Neuron Importance.
CoRR
Avanti Shrikumar, Jocelin Su, Anshul Kundaje
2018 J jnl
Discovering epistatic feature interactions from neural network models of regulatory DNA sequences.
Bioinform.
Peyton Greenside, Tyler Shimko, Polly Fordyce, Anshul Kundaje
2018 J jnl
GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs.
Bioinform.
Oana Ursu, Nathan Boley, Maryna Taranova, Y. X. Rachel Wang, Galip Gürkan Yardimci, William Stafford Noble, Anshul Kundaje
2018 J jnl
Learning to Abstain via Curve Optimization.
CoRR
Amr Alexandari, Avanti Shrikumar, Anshul Kundaje
2018 Misc conf
Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructures.
PSB
Peyton Greenside, Maureen Hillenmeyer, Anshul Kundaje
2018 J jnl
TF-MoDISco v0.4.4.2-alpha: Technical Note.
CoRR
Avanti Shrikumar, Katherine Tian, Anna Shcherbina, Ziga Avsec, Abhimanyu Banerjee, Mahfuza Sharmin, Surag Nair, Anshul Kundaje
2017 J jnl
Denoising genome-wide histone ChIP-seq with convolutional neural networks.
Bioinform.
Pang Wei Koh, Emma Pierson, Anshul Kundaje
2017 A* conf
Learning Important Features Through Propagating Activation Differences.
ICML
Avanti Shrikumar, Peyton Greenside, Anshul Kundaje
2017 J jnl
Learning Important Features Through Propagating Activation Differences.
CoRR
Avanti Shrikumar, Peyton Greenside, Anshul Kundaje
2017 J jnl
Vicus: Exploiting local structures to improve network-based analysis of biological data.
PLoS Comput. Biol.
Bo Wang, Lin Huang, Yuke Zhu, Anshul Kundaje, Serafim Batzoglou, Anna Goldenberg
2016 J jnl
Not Just a Black Box: Learning Important Features Through Propagating Activation Differences.
CoRR
Avanti Shrikumar, Peyton Greenside, Anna Shcherbina, Anshul Kundaje
2016 — conf
Unsupervised Learning from Noisy Networks with Applications to Hi-C Data.
NIPS
Bo Wang, Junjie Zhu, Armin Pourshafeie, Oana Ursu, Serafim Batzoglou, Anshul Kundaje
2015 J jnl
Integrative analysis of 111 reference human epigenomes Open.
Nat.
Roadmap Epigenomics Consortium, Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi Moussavi, Pouya Kheradpour, ZhiZhuo Zhang, Jianrong Wang, Michael J. Ziller, Viren Amin, John W. Whitaker, Matthew D. Schultz, Lucas D. Ward, Abhishek Sarkar, Gerald T. Quon, Richard S. Sandstrom, Matthew L. Eaton, Yi-Chieh Wu, Andreas R. Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R. Alan Harris, Noam Shoresh, Charles B. Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R. David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J. Mungall, Richard A. Moore, Eric Chuah, Angela Tam, Theresa K. Canfield, R. Scott Hansen, Rajinder Kaul, Peter J. Sabo, Mukul S. Bansal, Annaick Carles, Jesse R. Dixon, Kyle Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca F. Lowdon, GiNell Elliott, Tim R. Mercer, Shane J. Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C. Sallari, Kyle T. Siebenthall, Nicholas A. Sinnott-Armstrong, Michael Stevens, Robert E. Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E. Beaudet, Laurie A. Boyer, Philip L. De Jager, Peggy J. Farnham, Susan J. Fisher, David Haussler, Steven J. M. Jones, Wei Li, Marco A. Marra, Michael T. McManus, Shamil R. Sunyaev, James A. Thomson, Thea D. Tlsty, Li-Huei Tsai, Wei Wang, Robert A. Waterland, Michael Q. Zhang, Lisa H. Chadwick, Bradley E. Bernstein, Joseph F. Costello, Joseph R. Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A. Stamatoyannopoulos, Ting Wang, Manolis Kellis
2014 J jnl
Comparative analysis of metazoan chromatin organization Open.
Nat.
Joshua Wing Kei Ho, Youngsook L. Jung, Tao Liu, Burak Han Alver, Soohyun Lee, Kohta Ikegami, Kyung-Ah Sohn, Aki Minoda, Michael Y. Tolstorukov, Alex Appert, Stephen C. J. Parker, Tingting Gu, Anshul Kundaje, Nicole C. Riddle, Eric Bishop, Thea A. Egelhofer, Sheng'en Shawn Hu, Artyom A. Alekseyenko, Andreas Rechtsteiner, Dalal Asker, Jason A. Belsky, Sarah K. Bowman, Q. Brent Chen, Ron A.-J. Chen, Daniel S. Day, Yan Dong, Andrea C. Dose, Xikun Duan, Charles B. Epstein, Sevinc Ercan, Elise A. Feingold, Francesco Ferrari, Jacob M. Garrigues, Nils Gehlenborg, Peter J. Good, Psalm Haseley, Daniel He, Moritz Herrmann, Michael M. Hoffman, Tess E. Jeffers, Peter V. Kharchenko, Paulina Kolasinska-Zwierz, Chitra V. Kotwaliwale, Nischay Kumar, Sasha A. Langley, Erica Larschan, Isabel Latorre, Maxwell W. Libbrecht, Xueqiu Lin, Richard Park, Michael J. Pazin, Hoang N. Pham, Annette Plachetka, Bo Qin, Yuri B. Schwartz, Noam Shoresh, Przemyslaw Stempor, Anne Vielle, Chengyang Wang, Christina M. Whittle, Huiling Xue, Robert E. Kingston, Ju Han Kim, Bradley E. Bernstein, Abby F. Dernburg, Vincenzo Pirrotta, Mitzi I. Kuroda, William S. Noble, Thomas D. Tullius, Manolis Kellis, David M. MacAlpine, Susan Strome, Sarah C. R. Elgin, Xiaole Shirley Liu, Jason D. Lieb, Julie Ahringer, Gary H. Karpen, Peter J. Park
2014 J jnl
Comparative analysis of regulatory information and circuits across distant species Open.
Nat.
Alan P. Boyle, Carlos L. Araya, Cathleen Brdlik, Philip Cayting, Chao Cheng, Yong Cheng, Kathryn Gardner, LaDeana W. Hillier, Judith Janette, Lixia Jiang, Dionna Kasper, Trupti Kawli, Pouya Kheradpour, Anshul Kundaje, Jingyi Jessica Li, Lijia Ma, Wei Niu, E. Jay Rehm, Joel S. Rozowsky, Matthew Slattery, Rebecca Spokony, Robert Terrell, Dionne Vafeados, Daifeng Wang, Peter Weisdepp, Yi-Chieh Wu, Dan Xie, Koon-Kiu Yan, Elise A. Feingold, Peter J. Good, Michael J. Pazin, Haiyan Huang, Peter J. Bickel, Steven E. Brenner, Valerie Reinke, Robert H. Waterston, Mark Gerstein, Kevin P. White, Manolis Kellis, Michael Snyder
2013 J jnl
Clustering reveals ubiquitous heterogeneity and asymmetry of genomic signals at functional elements.
Tiny Trans. Comput. Sci.
Anshul Kundaje, Sofia Kyriazopoulou-Panagiotopoulou, Max W. Libbrecht, Cheryl L. Smith, Debasish Raha, Elliott E. Winters, Steven M. Johnson, Michael P. Snyder, Serafim Batzoglou, Arend Sidow
2008 J jnl
A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast.
PLoS Comput. Biol.
Anshul Kundaje, Xiantong Xin, Changgui Lan, Steve Lianoglou, Mei Zhou, Li Zhang, Christina S. Leslie
2006 J jnl
A classification-based framework for predicting and analyzing gene regulatory response.
BMC Bioinform.
Anshul Kundaje, Manuel Middendorf, Mihir Shah, Chris Wiggins, Yoav Freund, Christina S. Leslie
2005 J jnl
Combining Sequence and Time Series Expression Data to Learn Transcriptional Modules.
IEEE ACM Trans. Comput. Biol. Bioinform.
Anshul Kundaje, Manuel Middendorf, Feng Gao, Chris Wiggins, Christina S. Leslie
2005 B conf
Motif Discovery Through Predictive Modeling of Gene Regulation.
RECOMB
Manuel Middendorf, Anshul Kundaje, Mihir Shah, Yoav Freund, Chris Wiggins, Christina S. Leslie
2004 — conf
Predicting Genetic Regulatory Response Using Classification: Yeast Stress Response.
Regulatory Genomics
Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund, Christina S. Leslie
2004 — conf
Predicting genetic regulatory response using classification.
ISMB/ECCB (Supplement of Bioinformatics)
Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund, Christina S. Leslie
2004 J jnl
Spectrogram Analysis of Genomes.
EURASIP J. Adv. Signal Process.
David Sussillo, Anshul Kundaje, Dimitris Anastassiou