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2020 – today
- 2023
[j15]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:
GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. 51(D1): 942-949 (2023)- [c12]AkshatKumar Nigam, Robert Pollice, Gary Tom, Kjell Jorner, John Willes, Luca A. Thiede, Anshul Kundaje, Alán Aspuru-Guzik:
Tartarus: A Benchmarking Platform for Realistic And Practical Inverse Molecular Design. NeurIPS 2023 - 2022
- [j14]Jacob M. Schreiber, Surag Nair, Akshay Balsubramani, Anshul Kundaje:
Accelerating in silico saturation mutagenesis using compressed sensing. Bioinform. 38(14): 3557-3564 (2022) - [i9]AkshatKumar Nigam, Robert Pollice, Gary Tom, Kjell Jorner, Luca A. Thiede, Anshul Kundaje, Alán Aspuru-Guzik:
Tartarus: A Benchmarking Platform for Realistic And Practical Inverse Molecular Design. CoRR abs/2209.12487 (2022) - 2021
- [c11]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:
WILDS: A Benchmark of in-the-Wild Distribution Shifts. ICML 2021: 5637-5664 - [c10]Hannah Zhou, Avanti Shrikumar, Anshul Kundaje:
Towards a Better Understanding of Reverse-Complement Equivariance for Deep Learning Models in Genomics. MLBC 2021: 1-33 - [c9]Eva Prakash, Avanti Shrikumar, Anshul Kundaje:
Towards More Realistic Simulated Datasets for Benchmarking Deep Learning Models in Regulatory Genomics. MLBC 2021: 58-77 - 2020
- [c8]Amr Alexandari, Anshul Kundaje, Avanti Shrikumar:
Maximum Likelihood with Bias-Corrected Calibration is Hard-To-Beat at Label Shift Adaptation. ICML 2020: 222-232 - [c7]Alex Tseng, Avanti Shrikumar, Anshul Kundaje:
Fourier-transform-based attribution priors improve the interpretability and stability of deep learning models for genomics. NeurIPS 2020 - [i8]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:
WILDS: A Benchmark of in-the-Wild Distribution Shifts. CoRR abs/2012.07421 (2020)
2010 – 2019
- 2019
- [j13]Surag Nair, Daniel S. Kim, Jacob Perricone, Anshul Kundaje:
Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts. Bioinform. 35(14): i108-i116 (2019) - [j12]Avanti Shrikumar, Eva Prakash, Anshul Kundaje:
GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs. Bioinform. 35(14): i173-i182 (2019) - [i7]Avanti Shrikumar, Anshul Kundaje:
Calibration with Bias-Corrected Temperature Scaling Improves Domain Adaptation Under Label Shift in Modern Neural Networks. CoRR abs/1901.06852 (2019) - 2018
- [j11]Oana Ursu, Nathan Boley, Maryna Taranova, Y. X. Rachel Wang, Galip Gürkan Yardimci, William Stafford Noble, Anshul Kundaje:
GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs. Bioinform. 34(16): 2701-2707 (2018) - [j10]Peyton Greenside, Tyler Shimko, Polly Fordyce, Anshul Kundaje:
Discovering epistatic feature interactions from neural network models of regulatory DNA sequences. Bioinform. 34(17): i629-i637 (2018) - [c6]Peyton Greenside, Maureen Hillenmeyer, Anshul Kundaje:
Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructures. PSB 2018: 20-31 - [i6]Amr Alexandari, Avanti Shrikumar, Anshul Kundaje:
Learning to Abstain via Curve Optimization. CoRR abs/1802.07024 (2018) - [i5]Avanti Shrikumar, Jocelin Su, Anshul Kundaje:
Computationally Efficient Measures of Internal Neuron Importance. CoRR abs/1807.09946 (2018) - [i4]Avanti Shrikumar, Katherine Tian, Anna Shcherbina, Ziga Avsec, Abhimanyu Banerjee, Mahfuza Sharmin, Surag Nair, Anshul Kundaje:
TF-MoDISco v0.4.4.2-alpha: Technical Note. CoRR abs/1811.00416 (2018) - 2017
- [j9]Pang Wei Koh, Emma Pierson, Anshul Kundaje:
Denoising genome-wide histone ChIP-seq with convolutional neural networks. Bioinform. 33(14): i225-i233 (2017) - [j8]Bo Wang, Lin Huang, Yuke Zhu, Anshul Kundaje, Serafim Batzoglou, Anna Goldenberg:
Vicus: Exploiting local structures to improve network-based analysis of biological data. PLoS Comput. Biol. 13(10) (2017) - [c5]Avanti Shrikumar, Peyton Greenside, Anshul Kundaje:
Learning Important Features Through Propagating Activation Differences. ICML 2017: 3145-3153 - [i3]Avanti Shrikumar, Peyton Greenside, Anshul Kundaje:
Learning Important Features Through Propagating Activation Differences. CoRR abs/1704.02685 (2017) - 2016
- [c4]Bo Wang, Junjie Zhu, Armin Pourshafeie, Oana Ursu, Serafim Batzoglou, Anshul Kundaje:
Unsupervised Learning from Noisy Networks with Applications to Hi-C Data. NIPS 2016: 3297-3305 - [i2]Avanti Shrikumar, Peyton Greenside, Anna Shcherbina, Anshul Kundaje:
Not Just a Black Box: Learning Important Features Through Propagating Activation Differences. CoRR abs/1605.01713 (2016) - 2015
- [j7]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:
Integrative analysis of 111 reference human epigenomes Open. Nat. 518(7539): 317-330 (2015) - 2014
- [j6]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:
Comparative analysis of metazoan chromatin organization Open. Nat. 512(7515): 449-452 (2014) - [j5]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:
Comparative analysis of regulatory information and circuits across distant species Open. Nat. 512(7515): 453-456 (2014) - 2013
- [i1]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:
Clustering reveals ubiquitous heterogeneity and asymmetry of genomic signals at functional elements. Tiny Trans. Comput. Sci. 2 (2013)
2000 – 2009
- 2008
- [j4]Anshul Kundaje, Xiantong Xin, Changgui Lan, Steve Lianoglou, Mei Zhou, Li Zhang, Christina S. Leslie:
A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast. PLoS Comput. Biol. 4(11) (2008) - 2006
- [j3]Anshul Kundaje, Manuel Middendorf, Mihir Shah, Chris Wiggins, Yoav Freund, Christina S. Leslie:
A classification-based framework for predicting and analyzing gene regulatory response. BMC Bioinform. 7(S-1) (2006) - 2005
- [j2]Anshul Kundaje, Manuel Middendorf, Feng Gao, Chris Wiggins, Christina S. Leslie:
Combining Sequence and Time Series Expression Data to Learn Transcriptional Modules. IEEE ACM Trans. Comput. Biol. Bioinform. 2(3): 194-202 (2005) - [c3]Manuel Middendorf, Anshul Kundaje, Mihir Shah, Yoav Freund, Chris Wiggins, Christina S. Leslie:
Motif Discovery Through Predictive Modeling of Gene Regulation. RECOMB 2005: 538-552 - 2004
- [j1]David Sussillo, Anshul Kundaje, Dimitris Anastassiou:
Spectrogram Analysis of Genomes. EURASIP J. Adv. Signal Process. 2004(1): 29-42 (2004) - [c2]Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund, Christina S. Leslie:
Predicting genetic regulatory response using classification. ISMB/ECCB (Supplement of Bioinformatics) 2004: 232-240 - [c1]Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund, Christina S. Leslie:
Predicting Genetic Regulatory Response Using Classification: Yeast Stress Response. Regulatory Genomics 2004: 1-13
Coauthor Index
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