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[akundaje]

@Article{middendorf2004predicting,
title={Predicting genetic regulatory response using classification},
author={Middendorf, Manuel and Kundaje, Anshul and Wiggins, Chris and Freund, Yoav and Leslie, Christina},
journal={arXiv preprint q-bio/0411028},
year={2004}
}

@Article{sussillo2004spectrogram,
title={Spectrogram analysis of genomes},
author={Sussillo, David and Kundaje, Anshul and Anastassiou, Dimitris},
journal={EURASIP Journal on Advances in Signal Processing},
volume={2004},
pages={1--14},
year={2004},
publisher={Springer International Publishing}
}

@inproceedings{middendorf2005motif,
title={Motif discovery through predictive modeling of gene regulation},
author={Middendorf, Manuel and Kundaje, Anshul and Shah, Mihir and Freund, Yoav and Wiggins, Chris H and Leslie, Christina},
booktitle={Research in Computational Molecular Biology: 9th Annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005. Proceedings 9},
pages={538--552},
year={2005},
organization={Springer Berlin Heidelberg}
}

@Article{kundaje2005combining,
title={Combining sequence and time series expression data to learn transcriptional modules},
author={Kundaje, Anshul and Middendorf, Manuel and Gao, Feng and Wiggins, Chris and Leslie, Christina},
journal={IEEE/ACM transactions on computational biology and bioinformatics},
volume={2},
number={3},
pages={194--202},
year={2005},
publisher={IEEE}
}

@Article{kundaje2008predictive,
title={A predictive model of the oxygen and heme regulatory network in yeast},
author={Kundaje, Anshul and Xin, Xiantong and Lan, Changgui and Lianoglou, Steve and Zhou, Mei and Zhang, Li and Leslie, Christina},
journal={PLoS computational biology},
volume={4},
number={11},
pages={e1000224},
year={2008},
publisher={Public Library of Science San Francisco, USA}
}

@inproceedings{kundaje2006classification,
title={A classification-based framework for predicting and analyzing gene regulatory response},
author={Kundaje, Anshul and Middendorf, Manuel and Shah, Mihir and Wiggins, Chris H and Freund, Yoav and Leslie, Christina},
booktitle={BMC bioinformatics},
volume={7},
pages={1--14},
year={2006},
organization={BioMed Central}
}

@Article{kundaje2002learning,
title={Learning regulatory networks from sparsely sampled time series expression data},
author={Kundaje, Anshul and Antar, Omar and Jebara, Tony and Leslie, Christina},
journal={Columbia University, New York, NY, USA},
year={2002}
}

@Article{kundaje2007learning,
title={Learning regulatory programs that accurately predict differential expression with MEDUSA},
author={Kundaje, Anshul and Lianoglou, Steve and Li, Xuejing and Quigley, David and Arias, Marta and Wiggins, Chris H and Zhang, Li and Leslie, Christina},
journal={Annals of the New York Academy of Sciences},
volume={1115},
number={1},
pages={178--202},
year={2007},
publisher={Blackwell Publishing Inc Malden, USA}
}

@inproceedings{middendorf2005predicting,
title={Predicting genetic regulatory response using classification: Yeast stress response},
author={Middendorf, Manuel and Kundaje, Anshul and Wiggins, Chris and Freund, Yoav and Leslie, Christina},
booktitle={Regulatory Genomics: RECOMB 2004 International Workshop, RRG 2004, San Diego, Ca, USA, March 26-27, 2004, Revised Selected Papers 1},
pages={1--13},
year={2005},
organization={Springer Berlin Heidelberg}
}

@PhDThesis{kundaje2008predictive,
title={Predictive models of gene regulation},
author={Kundaje, Anshul Bharat},
year={2008},
school={Columbia University}
}

@Article{zhang2007cp,
title={CP motifs, Hap1 and Heme Signaling},
author={Zhang, L and Leslie, C and Lee, HC and Kundaje, A and Ie, E and Xin, X and Freund, Y},
journal={Biochemistry, Biophysics and Functional Genomics},
pages={45--51},
year={2007}
}

@inproceedings{kundaje2003inferring,
title={Inferring network connections from time series data},
author={Kundaje, Anshul and Wiggins, Chris},
booktitle={APS March Meeting Abstracts},
volume={2003},
pages={N15--009},
year={2003}
}

@Article{baroumand2004support,
title={Support vector machine (SVM) classification of multifocal visual evoked potential responses (mfVEP) from Glaucoma patients.},
author={Baroumand, F and Kundaje, AB and Zhang, X and Leslie, C and Hood, DC},
journal={Investigative Ophthalmology & Visual Science},
volume={45},
number={13},
pages={3302--3302},
year={2004},
publisher={The Association for Research in Vision and Ophthalmology}
}

@Article{hoffman2013integrative,
title={Integrative annotation of chromatin elements from ENCODE data},
author={Hoffman, Michael M and Ernst, Jason and Wilder, Steven P and Kundaje, Anshul and Harris, Robert S and Libbrecht, Max and Giardine, Belinda and Ellenbogen, Paul M and Bilmes, Jeffrey A and Birney, Ewan and others},
journal={Nucleic acids research},
volume={41},
number={2},
pages={827--841},
year={2013},
publisher={Oxford University Press}
}

@Article{banfai2012long,
title={Long noncoding RNAs are rarely translated in two human cell lines},
author={B{'a}nfai, Bal{'a}zs and Jia, Hui and Khatun, Jainab and Wood, Emily and Risk, Brian and Gundling, William E and Kundaje, Anshul and Gunawardena, Harsha P and Yu, Yanbao and Xie, Ling and others},
journal={Genome research},
volume={22},
number={9},
pages={1646--1657},
year={2012},
publisher={Cold Spring Harbor Lab}
}

@Article{gerstein2012architecture,
title={Architecture of the human regulatory network derived from ENCODE data},
author={Gerstein, Mark B and Kundaje, Anshul and Hariharan, Manoj and Landt, Stephen G and Yan, Koon-Kiu and Cheng, Chao and Mu, Xinmeng Jasmine and Khurana, Ekta and Rozowsky, Joel and Alexander, Roger and others},
journal={Nature},
volume={489},
number={7414},
pages={91--100},
year={2012},
publisher={Nature Publishing Group UK London}
}

@Article{schaub2012linking,
title={Linking disease associations with regulatory information in the human genome},
author={Schaub, Marc A and Boyle, Alan P and Kundaje, Anshul and Batzoglou, Serafim and Snyder, Michael},
journal={Genome research},
volume={22},
number={9},
pages={1748--1759},
year={2012},
publisher={Cold Spring Harbor Lab}
}

@Article{yip2012classification,
title={Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors},
author={Yip, Kevin Y and Cheng, Chao and Bhardwaj, Nitin and Brown, James B and Leng, Jing and Kundaje, Anshul and Rozowsky, Joel and Birney, Ewan and Bickel, Peter and Snyder, Michael and others},
journal={Genome biology},
volume={13},
pages={1--22},
year={2012},
publisher={BioMed Central}
}

@Article{kundaje2012ubiquitous,
title={Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements},
author={Kundaje, Anshul and Kyriazopoulou-Panagiotopoulou, Sofia and Libbrecht, Max and Smith, Cheryl L and Raha, Debasish and Winters, Elliott E and Johnson, Steven M and Snyder, Michael and Batzoglou, Serafim and Sidow, Arend},
journal={Genome research},
volume={22},
number={9},
pages={1735--1747},
year={2012},
publisher={Cold Spring Harbor Lab}
}

@Article{dong2012modeling,
title={Modeling gene expression using chromatin features in various cellular contexts},
author={Dong, Xianjun and Greven, Melissa C and Kundaje, Anshul and Djebali, Sarah and Brown, James B and Cheng, Chao and Gingeras, Thomas R and Gerstein, Mark and Guig{'o}, Roderic and Birney, Ewan and others},
journal={Genome biology},
volume={13},
pages={1--17},
year={2012},
publisher={BioMed Central}
}

@Article{wang2012sequence,
title={Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors},
author={Wang, Jie and Zhuang, Jiali and Iyer, Sowmya and Lin, XinYing and Whitfield, Troy W and Greven, Melissa C and Pierce, Brian G and Dong, Xianjun and Kundaje, Anshul and Cheng, Yong and others},
journal={Genome research},
volume={22},
number={9},
pages={1798--1812},
year={2012},
publisher={Cold Spring Harbor Lab}
}

@Article{landt2012chip,
title={ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia},
author={Landt, Stephen G and Marinov, Georgi K and Kundaje, Anshul and Kheradpour, Pouya and Pauli, Florencia and Batzoglou, Serafim and Bernstein, Bradley E and Bickel, Peter and Brown, James B and Cayting, Philip and others},
journal={Genome research},
volume={22},
number={9},
pages={1813--1831},
year={2012},
publisher={Cold Spring Harbor Lab}
}

@Article{encode2011user,
title={A user's guide to the encyclopedia of DNA elements (ENCODE)},
author={ENCODE Project Consortium and others},
journal={PLoS Biol},
volume={9},
number={4},
pages={e1001046},
year={2011}
}

@Article{consortium2012integrated,
title={An integrated encyclopedia of DNA elements in the human genome},
author={Consortium, ENCODE Project},
journal={Nature},
volume={489},
number={7414},
pages={57--74},
year={2012}
}

@Article{kundaje2013clustering,
title={Clustering reveals ubiquitous heterogeneity and asymmetry of genomic signals at functional elements.},
author={Kundaje, Anshul and Kyriazopoulou-Panagiotopoulou, Sofia and Libbrecht, Max W and Smith, Cheryl L and Raha, Debasish and Winters, Elliott E and Johnson, Steven M and Snyder, Michael and Batzoglou, Serafim and Sidow, Arend},
journal={Tiny Trans. Comput. Sci.},
volume={2},
year={2013}
}

@Article{yip2012genome,
title={Genome-wide analysis of the binding sites of more than 100 transcription-related factors defines different types of genomic regions with distinct biological properties},
author={Yip, Kevin Y and Cheng, Chao and Bhardwaj, Nitin and Brown, James B and Leng, Jing and Kundaje, Anshul and Rozowsky, Joel and Birney, Ewan and Bickel, Peter J and Snyder, Michael and others},
journal={Genome Res},
year={2012}
}

@Article{kasowski2013extensive,
title={Extensive variation in chromatin states across humans},
author={Kasowski, Maya and Kyriazopoulou-Panagiotopoulou, Sofia and Grubert, Fabian and Zaugg, Judith B and Kundaje, Anshul and Liu, Yuling and Boyle, Alan P and Zhang, Qiangfeng Cliff and Zakharia, Fouad and Spacek, Damek V and others},
journal={Science},
volume={342},
number={6159},
pages={750--752},
year={2013},
publisher={American Association for the Advancement of Science}
}

@Article{hardee2013stat3,
title={STAT3 targets suggest mechanisms of aggressive tumorigenesis in diffuse large B-cell lymphoma},
author={Hardee, Jennifer and Ouyang, Zhengqing and Zhang, Yuping and Kundaje, Anshul and Lacroute, Philippe and Snyder, Michael},
journal={G3: Genes, Genomes, Genetics},
volume={3},
number={12},
pages={2173--2185},
year={2013},
publisher={Oxford University Press}
}

@Article{marinov2014large,
title={Large-scale quality analysis of published ChIP-seq data},
author={Marinov, Georgi K and Kundaje, Anshul and Park, Peter J and Wold, Barbara J},
journal={G3: Genes, Genomes, Genetics},
volume={4},
number={2},
pages={209--223},
year={2014},
publisher={Oxford University Press}
}

@Article{kellis2014defining,
title={Defining functional DNA elements in the human genome},
author={Kellis, Manolis and Wold, Barbara and Snyder, Michael P and Bernstein, Bradley E and Kundaje, Anshul and Marinov, Georgi K and Ward, Lucas D and Birney, Ewan and Crawford, Gregory E and Dekker, Job and others},
journal={Proceedings of the National Academy of Sciences},
volume={111},
number={17},
pages={6131--6138},
year={2014},
publisher={National Academy of Sciences}
}

@Article{slattery2014diverse,
title={Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster},
author={Slattery, Matthew and Ma, Lijia and Spokony, Rebecca F and Arthur, Robert K and Kheradpour, Pouya and Kundaje, Anshul and Negre, Nicolas and Crofts, Alex and Ptashkin, Ryan and Zieba, Jennifer and others},
journal={Genome research},
volume={24},
number={7},
pages={1224--1235},
year={2014},
publisher={Cold Spring Harbor Lab}
}

@Article{benayoun2014h3k4me3,
title={H3K4me3 breadth is linked to cell identity and transcriptional consistency},
author={Benayoun, B{'e}r{'e}nice A and Pollina, Elizabeth A and Ucar, Duygu and Mahmoudi, Salah and Karra, Kalpana and Wong, Edith D and Devarajan, Keerthana and Daugherty, Aaron C and Kundaje, Anshul B and Mancini, Elena and others},
journal={Cell},
volume={158},
number={3},
pages={673--688},
year={2014},
publisher={Elsevier}
}

@Article{kellis2014reply,
title={Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease},
author={Kellis, Manolis and Wold, Barbara and Snyder, Michael P and Bernstein, Bradley E and Kundaje, Anshul and Marinov, Georgi K and Ward, Lucas D and Birney, Ewan and Crawford, Gregory E and Dekker, Job and others},
journal={Proceedings of the National Academy of Sciences},
volume={111},
number={33},
pages={E3366--E3366},
year={2014},
publisher={National Academy of Sciences}
}

@Article{ho2014comparative,
title={Comparative analysis of metazoan chromatin organization},
author={Ho, Joshua WK and Jung, Youngsook L and Liu, Tao and Alver, Burak H and Lee, Soohyun and Ikegami, Kohta and Sohn, Kyung-Ah and Minoda, Aki and Tolstorukov, Michael Y and Appert, Alex and others},
journal={Nature},
volume={512},
number={7515},
pages={449--452},
year={2014},
publisher={Nature Publishing Group UK London}
}

@Article{boyle2014comparative,
title={Comparative analysis of regulatory information and circuits across distant species},
author={Boyle, Alan P and Araya, Carlos L and Brdlik, Cathleen and Cayting, Philip and Cheng, Chao and Cheng, Yong and Gardner, Kathryn and Hillier, LaDeana W and Janette, Judith and Jiang, Lixia and others},
journal={Nature},
volume={512},
number={7515},
pages={453--456},
year={2014},
publisher={Nature Publishing Group UK London}
}

@Article{araya2014regulatory,
title={Regulatory analysis of the C. elegans genome with spatiotemporal resolution},
author={Araya, Carlos L and Kawli, Trupti and Kundaje, Anshul and Jiang, Lixia and Wu, Beijing and Vafeados, Dionne and Terrell, Robert and Weissdepp, Peter and Gevirtzman, Louis and Mace, Daniel and others},
journal={Nature},
volume={512},
number={7515},
pages={400--405},
year={2014},
publisher={Nature Publishing Group UK London}
}

@Article{blumberg2014transcription,
title={Transcription factors bind negatively selected sites within human mtDNA genes},
author={Blumberg, Amit and Sri Sailaja, Badi and Kundaje, Anshul and Levin, Liron and Dadon, Sara and Shmorak, Shimrit and Shaulian, Eitan and Meshorer, Eran and Mishmar, Dan},
journal={Genome biology and evolution},
volume={6},
number={10},
pages={2634--2646},
year={2014},
publisher={Oxford University Press}
}

@Article{cheng2014principles,
title={Principles of regulatory information conservation between mouse and human},
author={Cheng, Yong and Ma, Zhihai and Kim, Bong-Hyun and Wu, Weisheng and Cayting, Philip and Boyle, Alan P and Sundaram, Vasavi and Xing, Xiaoyun and Dogan, Nergiz and Li, Jingjing and others},
journal={Nature},
volume={515},
number={7527},
pages={371--375},
year={2014},
publisher={Nature Publishing Group UK London}
}

@Article{yue2014comparative,
title={A comparative encyclopedia of DNA elements in the mouse genome},
author={Yue, Feng and Cheng, Yong and Breschi, Alessandra and Vierstra, Jeff and Wu, Weisheng and Ryba, Tyrone and Sandstrom, Richard and Ma, Zhihai and Davis, Carrie and Pope, Benjamin D and others},
journal={Nature},
volume={515},
number={7527},
pages={355--364},
year={2014},
publisher={Nature Publishing Group UK London}
}

@Article{kundaje2015integrative,
title={Integrative analysis of 111 reference human epigenomes},
author={Kundaje, Anshul and Meuleman, Wouter and Ernst, Jason and Bilenky, Misha and Yen, Angela and Heravi-Moussavi, Alireza and Kheradpour, Pouya and Zhang, Zhizhuo and Wang, Jianrong and Ziller, Michael J and others},
journal={Nature},
volume={518},
number={7539},
pages={317--330},
year={2015},
publisher={Nature Publishing Group}
}

@Article{gjoneska2015conserved,
title={Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease},
author={Gjoneska, Elizabeta and Pfenning, Andreas R and Mathys, Hansruedi and Quon, Gerald and Kundaje, Anshul and Tsai, Li-Huei and Kellis, Manolis},
journal={Nature},
volume={518},
number={7539},
pages={365--369},
year={2015},
publisher={Nature Publishing Group UK London}
}

@Article{onengut2015fine,
title={Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers},
author={Onengut-Gumuscu, Suna and Chen, Wei-Min and Burren, Oliver and Cooper, Nick J and Quinlan, Aaron R and Mychaleckyj, Josyf C and Farber, Emily and Bonnie, Jessica K and Szpak, Michal and Schofield, Ellen and others},
journal={Nature genetics},
volume={47},
number={4},
pages={381--386},
year={2015},
publisher={Nature Publishing Group US New York}
}

@Article{stolovitzky2005statistical,
title={Statistical analysis of MPSS measurements: application to the study of LPS-activated macrophage gene expression},
author={Stolovitzky, GA and Kundaje, A and Held, GA and Duggar, KH and Haudenschild, CD and Zhou, D and Vasicek, TJ and Smith, KD and Aderem, A and Roach, JC},
journal={Proceedings of the National Academy of Sciences},
volume={102},
number={5},
pages={1402--1407},
year={2005},
publisher={National Academy of Sciences}
}

@Article{sazonova2015characterization,
title={Characterization of TCF21 downstream target regions identifies a transcriptional network linking multiple independent coronary artery disease loci},
author={Sazonova, Olga and Zhao, Yuqi and N{"u}rnberg, Sylvia and Miller, Clint and Pjanic, Milos and Castano, Victor G and Kim, Juyong B and Salfati, Elias L and Kundaje, Anshul B and Bejerano, Gill and others},
journal={PLoS genetics},
volume={11},
number={5},
pages={e1005202},
year={2015},
publisher={Public Library of Science San Francisco, CA USA}
}

@Article{kukurba2016impact,
title={Impact of the X chromosome and sex on regulatory variation},
author={Kukurba, Kimberly R and Parsana, Princy and Balliu, Brunilda and Smith, Kevin S and Zappala, Zachary and Knowles, David A and Fav{'e}, Marie-Julie and Davis, Joe R and Li, Xin and Zhu, Xiaowei and others},
journal={Genome research},
volume={26},
number={6},
pages={768--777},
year={2016},
publisher={Cold Spring Harbor Lab}
}

@Article{grubert2015genetic,
title={Genetic control of chromatin states in humans involves local and distal chromosomal interactions},
author={Grubert, Fabian and Zaugg, Judith B and Kasowski, Maya and Ursu, Oana and Spacek, Damek V and Martin, Alicia R and Greenside, Peyton and Srivas, Rohith and Phanstiel, Doug H and Pekowska, Aleksandra and others},
journal={Cell},
volume={162},
number={5},
pages={1051--1065},
year={2015},
publisher={Elsevier}
}

@Article{araya2015correction,
title={Correction: Corrigendum: Regulatory analysis of the C. elegans genome with spatiotemporal resolution},
author={Araya, Carlos L and Kawli, Trupti and Kundaje, Anshul and Jiang, Lixia and Wu, Beijing and Vafeados, Dionne and Terrell, Robert and Weissdepp, Peter and Gevirtzman, Louis and Mace, Daniel and others},
journal={Nature},
volume={528},
number={7580},
pages={152--152},
year={2015},
publisher={Nature Publishing Group UK London}
}

@Article{webb2016characterization,
title={Characterization of the direct targets of FOXO transcription factors throughout evolution},
author={Webb, Ashley E and Kundaje, Anshul and Brunet, Anne},
journal={Aging cell},
volume={15},
number={4},
pages={673--685},
year={2016}
}

@Article{brady2016arntl2,
title={An Arntl2-driven secretome enables lung adenocarcinoma metastatic self-sufficiency},
author={Brady, Jennifer J and Chuang, Chen-Hua and Greenside, Peyton G and Rogers, Zo{"e} N and Murray, Christopher W and Caswell, Deborah R and Hartmann, Ursula and Connolly, Andrew J and Sweet-Cordero, E Alejandro and Kundaje, Anshul and others},
journal={Cancer cell},
volume={29},
number={5},
pages={697--710},
year={2016},
publisher={Elsevier}
}

@inproceedings{shrikumar2017learning,
title={Learning important features through propagating activation differences},
author={Shrikumar, Avanti and Greenside, Peyton and Kundaje, Anshul},
booktitle={International conference on machine learning},
pages={3145--3153},
year={2017},
organization={PMlR}
}

@Article{koh2017denoising,
title={Denoising genome-wide histone ChIP-seq with convolutional neural networks},
author={Koh, Pang Wei and Pierson, Emma and Kundaje, Anshul},
journal={Bioinformatics},
volume={33},
number={14},
pages={i225--i233},
year={2017},
publisher={Oxford University Press}
}

@Article{blumberg2017initiation,
title={Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution},
author={Blumberg, Amit and Rice, Edward J and Kundaje, Anshul and Danko, Charles G and Mishmar, Dan},
journal={Genome research},
volume={27},
number={3},
pages={362--373},
year={2017},
publisher={Cold Spring Harbor Lab}
}

@Article{loh2016mapping,
title={Mapping the pairwise choices leading from pluripotency to human bone, heart, and other mesoderm cell types},
author={Loh, Kyle M and Chen, Angela and Koh, Pang Wei and Deng, Tianda Z and Sinha, Rahul and Tsai, Jonathan M and Barkal, Amira A and Shen, Kimberle Y and Jain, Rajan and Morganti, Rachel M and others},
journal={Cell},
volume={166},
number={2},
pages={451--467},
year={2016},
publisher={Elsevier}
}

@Article{corces2016lineage,
title={Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution},
author={Corces, M Ryan and Buenrostro, Jason D and Wu, Beijing and Greenside, Peyton G and Chan, Steven M and Koenig, Julie L and Snyder, Michael P and Pritchard, Jonathan K and Kundaje, Anshul and Greenleaf, William J and others},
journal={Nature genetics},
volume={48},
number={10},
pages={1193--1203},
year={2016},
publisher={Nature Publishing Group US New York}
}

@Article{bien2016using,
title={Using functional data from Roadmap Epigenomics to inform analysis of rare variants linked to gene expression in a large colorectal cancer study},
author={Bien, Stephanie A and Harrison, Tabitha A and Auer, Paul L and Qu, Flora and Huyghe, Jeroen and Banbury, Barbara and Greenside, Peyton and Abecasis, Goncalo R and Berndt, Sonja I and B{'e}zieau, Stephane and others},
journal={Cancer Research},
volume={76},
number={14_Supplement},
pages={4489--4489},
year={2016},
publisher={The American Association for Cancer Research}
}

@Article{onengut2015type,
title={Type 1 Diabetes Genetics C, Todd JA, Wallace C, Concannon P, Rich SS. Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers},
author={Onengut-Gumuscu, S and Chen, WM and Burren, O and Cooper, NJ and Quinlan, AR and Mychaleckyj, JC and Farber, E and Bonnie, JK and Szpak, M and Schofield, E and others},
journal={Nat Genet},
volume={47},
pages={381--386},
year={2015}
}

@Article{roberts2016semi,
title={Semi-automated genome annotation using epigenomic data and Segway},
author={Roberts, Eric G and Mendez, Micka{"e}l and Viner, Coby and Karimzadeh, Mehran and Chan, Rachel and Ancar, Rachel and Chicco, Davide and Hesselberth, Jay R and Kundaje, Anshul and Hoffman, Michael M},
journal={bioRxiv},
pages={080382},
year={2016},
publisher={Cold Spring Harbor Laboratory}
}

@Article{daugherty2017chromatin,
title={Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans},
author={Daugherty, Aaron C and Yeo, Robin W and Buenrostro, Jason D and Greenleaf, William J and Kundaje, Anshul and Brunet, Anne},
journal={Genome research},
volume={27},
number={12},
pages={2096--2107},
year={2017},
publisher={Cold Spring Harbor Lab}
}

@Article{banovich2018impact,
title={Impact of regulatory variation across human iPSCs and differentiated cells},
author={Banovich, Nicholas E and Li, Yang I and Raj, Anil and Ward, Michelle C and Greenside, Peyton and Calderon, Diego and Tung, Po Yuan and Burnett, Jonathan E and Myrthil, Marsha and Thomas, Samantha M and others},
journal={Genome research},
volume={28},
number={1},
pages={122--131},
year={2018},
publisher={Cold Spring Harbor Lab}
}

@Article{koh2016atlas,
title={An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development},
author={Koh, Pang Wei and Sinha, Rahul and Barkal, Amira A and Morganti, Rachel M and Chen, Angela and Weissman, Irving L and Ang, Lay Teng and Kundaje, Anshul and Loh, Kyle M},
journal={Scientific data},
volume={3},
number={1},
pages={1--15},
year={2016},
publisher={Nature Publishing Group}
}

@Article{karimzadeh2018umap,
title={Umap and Bismap: quantifying genome and methylome mappability},
author={Karimzadeh, Mehran and Ernst, Carl and Kundaje, Anshul and Hoffman, Michael M},
journal={Nucleic acids research},
volume={46},
number={20},
pages={e120--e120},
year={2018},
publisher={Oxford University Press}
}

@Article{shrikumar2017reverse,
title={Reverse-complement parameter sharing improves deep learning models for genomics},
author={Shrikumar, Avanti and Greenside, Peyton and Kundaje, Anshul},
journal={BioRxiv},
pages={103663},
year={2017},
publisher={Cold Spring Harbor Laboratory}
}

@Article{chuang2017molecular,
title={Molecular definition of a metastatic lung cancer state reveals a targetable CD109--Janus kinase--Stat axis},
author={Chuang, Chen-Hua and Greenside, Peyton G and Rogers, Zo{"e} N and Brady, Jennifer J and Yang, Dian and Ma, Rosanna K and Caswell, Deborah R and Chiou, Shin-Heng and Winters, Aidan F and Gr{"u}ner, Barbara M and others},
journal={Nature medicine},
volume={23},
number={3},
pages={291--300},
year={2017},
publisher={Nature Publishing Group US New York}
}

@Article{kreimer2017predicting,
title={Predicting gene expression in massively parallel reporter assays: A comparative study},
author={Kreimer, Anat and Zeng, Haoyang and Edwards, Matthew D and Guo, Yuchun and Tian, Kevin and Shin, Sunyoung and Welch, Rene and Wainberg, Michael and Mohan, Rahul and Sinnott-Armstrong, Nicholas A and others},
journal={Human mutation},
volume={38},
number={9},
pages={1240--1250},
year={2017}
}

@Article{morgens2017genome,
title={Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens},
author={Morgens, David W and Wainberg, Michael and Boyle, Evan A and Ursu, Oana and Araya, Carlos L and Tsui, C Kimberly and Haney, Michael S and Hess, Gaelen T and Han, Kyuho and Jeng, Edwin E and others},
journal={Nature communications},
volume={8},
number={1},
pages={15178},
year={2017},
publisher={Nature Publishing Group UK London}
}

@Article{ching2018opportunities,
title={Opportunities and obstacles for deep learning in biology and medicine},
author={Ching, Travers and Himmelstein, Daniel S and Beaulieu-Jones, Brett K and Kalinin, Alexandr A and Do, Brian T and Way, Gregory P and Ferrero, Enrico and Agapow, Paul-Michael and Zietz, Michael and Hoffman, Michael M and others},
journal={Journal of the royal society interface},
volume={15},
number={141},
pages={20170387},
year={2018},
publisher={The Royal Society}
}

@Article{alexandari2017separable,
title={Separable fully connected layers improve deep learning models for genomics},
author={Alexandari, Amr Mohamed and Shrikumar, Avanti and Kundaje, Anshul},
journal={BioRxiv},
pages={146431},
year={2017},
publisher={Cold Spring Harbor Laboratory}
}

@Article{xu2017high,
title={High-throughput characterization of Cascade type IE CRISPR guide efficacy reveals unexpected PAM diversity and target sequence preferences},
author={Xu Hua Fu, Becky and Wainberg, Michael and Kundaje, Anshul and Fire, Andrew Z},
journal={Genetics},
volume={206},
number={4},
pages={1727--1738},
year={2017},
publisher={Oxford University Press}
}

@Article{arthur2014diverse,
title={Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster},
author={Arthur, Robert K and Kheradpour, Pouya and Kundaje, Anshul and N{`e}gre, Nicolas and Crofts, Alex and Ptashkin, Ryan and Zieba, Jennifer and Ostapenko, Alexander and Suchy, Sarah and Victorsen, Alec and others},
journal={Genome Research 7 (24), 1224-1235.(2014)},
year={2014}
}

@Article{wang2019network,
title={Network modelling of topological domains using Hi-C data},
author={Wang, YX Rachel and Sarkar, Purnamrita and Ursu, Oana and Kundaje, Anshul and Bickel, Peter J},
journal={The annals of applied statistics},
volume={13},
number={3},
pages={1511},
year={2019},
publisher={NIH Public Access}
}

@Article{greenside2017pyboost,
title={PyBoost: A parallelized Python implementation of 2D boosting with hierarchies},
author={Greenside, Peyton G and Hussami, Nadine and Chang, Jessica and Kundaje, Anshul},
journal={bioRxiv},
pages={170803},
year={2017},
publisher={Cold Spring Harbor Laboratory}
}

@Article{rubin2017lineage,
title={Lineage-specific dynamic and pre-established enhancer--promoter contacts cooperate in terminal differentiation},
author={Rubin, Adam J and Barajas, Brook C and Furlan-Magaril, Mayra and Lopez-Pajares, Vanessa and Mumbach, Maxwell R and Howard, Imani and Kim, Daniel S and Boxer, Lisa D and Cairns, Jonathan and Spivakov, Mikhail and others},
journal={Nature genetics},
volume={49},
number={10},
pages={1522--1528},
year={2017},
publisher={Nature Publishing Group US New York}
}

@Article{mumbach2017enhancer,
title={Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements},
author={Mumbach, Maxwell R and Satpathy, Ansuman T and Boyle, Evan A and Dai, Chao and Gowen, Benjamin G and Cho, Seung Woo and Nguyen, Michelle L and Rubin, Adam J and Granja, Jeffrey M and Kazane, Katelynn R and others},
journal={Nature genetics},
volume={49},
number={11},
pages={1602--1612},
year={2017},
publisher={Nature Publishing Group US New York}
}

@Article{corces2017improved,
title={An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues},
author={Corces, M Ryan and Trevino, Alexandro E and Hamilton, Emily G and Greenside, Peyton G and Sinnott-Armstrong, Nicholas A and Vesuna, Sam and Satpathy, Ansuman T and Rubin, Adam J and Montine, Kathleen S and Wu, Beijing and others},
journal={Nature methods},
volume={14},
number={10},
pages={959--962},
year={2017},
publisher={Nature Publishing Group UK London}
}

@Article{ursu2018genomedisco,
title={GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs},
author={Ursu, Oana and Boley, Nathan and Taranova, Maryna and Wang, YX Rachel and Yardimci, Galip Gurkan and Stafford Noble, William and Kundaje, Anshul},
journal={Bioinformatics},
volume={34},
number={16},
pages={2701--2707},
year={2018},
publisher={Oxford University Press}
}

@misc{shrikumar2017systems,
title={Systems and Methods for Holistic Extraction of Features from Neural Networks},
author={Shrikumar, Avanti and Greenside, Peyton Greis and Kundaje, Anshul},
year={2017},
month=aug # "~31",
note={US Patent App. 15/444,258}
}

@Article{blumberg2018common,
title={A common pattern of DNase I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization},
author={Blumberg, Amit and Danko, Charles G and Kundaje, Anshul and Mishmar, Dan},
journal={Genome Research},
volume={28},
number={8},
pages={1158--1168},
year={2018},
publisher={Cold Spring Harbor Lab}
}

@Article{wang2017vicus,
title={Vicus: Exploiting local structures to improve network-based analysis of biological data},
author={Wang, Bo and Huang, Lin and Zhu, Yuke and Kundaje, Anshul and Batzoglou, Serafim and Goldenberg, Anna},
journal={PLoS computational biology},
volume={13},
number={10},
pages={e1005621},
year={2017},
publisher={Public Library of Science San Francisco, CA USA}
}

@inproceedings{greenside2018prediction,
title={Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructures},
author={Greenside, Peyton and Hillenmeyer, Maureen and Kundaje, Anshul},
booktitle={Pacific Symposium on Biocomputing 2018: Proceedings of the Pacific Symposium},
pages={20--31},
year={2018}
}

@Article{bien2017enrichment,
title={Enrichment of colorectal cancer associations in functional regions: Insight for using epigenomics data in the analysis of whole genome sequence-imputed GWAS data},
author={Bien, Stephanie A and Auer, Paul L and Harrison, Tabitha A and Qu, Conghui and Connolly, Charles M and Greenside, Peyton G and Chen, Sai and Berndt, Sonja I and Bezieau, Stephane and Kang, Hyun M and others},
journal={PLoS One},
volume={12},
number={11},
pages={e0186518},
year={2017},
publisher={Public Library of Science San Francisco, CA USA}
}

@Article{carter2017challenges,
title={Challenges and recommendations for epigenomics in precision health},
author={Carter, Ava C and Chang, Howard Y and Church, George and Dombkowski, Ashley and Ecker, Joseph R and Gil, Elad and Giresi, Paul G and Greely, Henry and Greenleaf, William J and Hacohen, Nir and others},
journal={Nature biotechnology},
volume={35},
number={12},
pages={1128--1132},
year={2017},
publisher={Nature Publishing Group US New York}
}

@Article{kundaje2001modelling,
title={Modelling of the p53 pathway to cell cycle arrest and apoptosis: Relevance to cancer},
author={Kundaje, Anshul and Eisenman, Shane},
journal={Computational modeling of genetic and biochemical networks. Seattle: A Bradford book},
pages={1--19},
year={2001}
}

@Article{fisher2015integrative,
title={Integrative analysis of 111 reference human epigenomes},
author={Fisher, Susan and Tlsty, Thea and Costello, Joseph and Roadmap, EC and Kundaje, A and Meuleman, W and Ernst, J and Bilenky, M and Yen, A and Heravi-Moussavi, A and others},
year={2015}
}

@Article{stunnenberg2016international,
title={The International Human Epigenome Consortium: a blueprint for scientific collaboration and discovery},
author={Stunnenberg, Hendrik G and Abrignani, Sergio and Adams, David and de Almeida, Melanie and Altucci, Lucia and Amin, Viren and Amit, Ido and Antonarakis, Stylianos E and Aparicio, Samuel and Arima, Takahiro and others},
journal={Cell},
volume={167},
number={5},
pages={1145--1149},
year={2016},
publisher={Elsevier}
}

@Article{alexandari2018learning,
title={Learning to Abstain via Curve Optimization.},
author={Alexandari, Amr and Shrikumar, Avanti and Kundaje, Anshul},
journal={CoRR},
year={2018}
}

@Article{marinov2018chip,
title={ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation},
author={Marinov, Georgi K and Kundaje, Anshul},
journal={Briefings in functional genomics},
volume={17},
number={2},
pages={116--137},
year={2018},
publisher={Oxford University Press}
}

@Article{greenside2018discovering,
title={Discovering epistatic feature interactions from neural network models of regulatory DNA sequences},
author={Greenside, Peyton and Shimko, Tyler and Fordyce, Polly and Kundaje, Anshul},
journal={Bioinformatics},
volume={34},
number={17},
pages={i629--i637},
year={2018},
publisher={Oxford University Press}
}

@Article{liu2019multi,
title={A multi-modal neural network for learning cis and trans regulation of stress response in yeast},
author={Liu, Boxiang and Hussami, Nadine and Shrikumar, Avanti and Shimko, Tyler and Bhate, Salil and Longwell, Scott and Montgomery, Stephen and Kundaje, Anshul},
journal={arXiv preprint arXiv:1908.09426},
year={2019}
}

@Article{benayoun2019remodeling,
title={Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses},
author={Benayoun, B{'e}r{'e}nice A and Pollina, Elizabeth A and Singh, Param Priya and Mahmoudi, Salah and Harel, Itamar and Casey, Kerriann M and Dulken, Ben W and Kundaje, Anshul and Brunet, Anne},
journal={Genome research},
volume={29},
number={4},
pages={697--709},
year={2019},
publisher={Cold Spring Harbor Lab}
}

@Article{shrikumar2018computationally,
title={Computationally efficient measures of internal neuron importance},
author={Shrikumar, Avanti and Su, Jocelin and Kundaje, Anshul},
journal={arXiv preprint arXiv:1807.09946},
year={2018}
}

@Article{movva2019deciphering,
title={Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays},
author={Movva, Rajiv and Greenside, Peyton and Marinov, Georgi K and Nair, Surag and Shrikumar, Avanti and Kundaje, Anshul},
journal={PLoS One},
volume={14},
number={6},
pages={e0218073},
year={2019},
publisher={Public Library of Science San Francisco, CA USA}
}

@Article{fu2018differential,
title={Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers},
author={Fu, Shaliu and Wang, Qin and Moore, Jill E and Purcaro, Michael J and Pratt, Henry E and Fan, Kaili and Gu, Cuihua and Jiang, Cizhong and Zhu, Ruixin and Kundaje, Anshul and others},
journal={Nucleic acids research},
volume={46},
number={21},
pages={11184--11201},
year={2018},
publisher={Oxford University Press}
}

@Article{yang2018intertumoral,
title={Intertumoral heterogeneity in SCLC is influenced by the cell type of origin},
author={Yang, Dian and Denny, Sarah K and Greenside, Peyton G and Chaikovsky, Andrea C and Brady, Jennifer J and Ouadah, Youcef and Granja, Jeffrey M and Jahchan, Nadine S and Lim, Jing Shan and Kwok, Shirley and others},
journal={Cancer discovery},
volume={8},
number={10},
pages={1316--1331},
year={2018},
publisher={American Association for Cancer Research}
}

@Article{shrikumar2018technical,
title={Technical note on transcription factor motif discovery from importance scores (TF-MoDISco) version 0.5. 6.5},
author={Shrikumar, Avanti and Tian, Katherine and Avsec, {\v{Z}}iga and Shcherbina, Anna and Banerjee, Abhimanyu and Sharmin, Mahfuza and Nair, Surag and Kundaje, Anshul},
journal={arXiv preprint arXiv:1811.00416},
year={2018}
}

@Article{kohdata,
title={Data Descriptor: An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development},
author={Koh, Pang Wei and Sinha, Rahul and Barkal, Amira A and Morganti, Rachel M and Chen, Angela and Weissman, Irving L and Ang, Lay Teng and Kundaje, Anshul and Loh, Kyle M}
}

@Article{huyghe2019discovery,
title={Discovery of common and rare genetic risk variants for colorectal cancer},
author={Huyghe, Jeroen R and Bien, Stephanie A and Harrison, Tabitha A and Kang, Hyun Min and Chen, Sai and Schmit, Stephanie L and Conti, David V and Qu, Conghui and Jeon, Jihyoun and Edlund, Christopher K and others},
journal={Nature genetics},
volume={51},
number={1},
pages={76--87},
year={2019},
publisher={Nature Publishing Group US New York}
}

@Article{shipony2020long,
title={Long-range single-molecule mapping of chromatin accessibility in eukaryotes},
author={Shipony, Zohar and Marinov, Georgi K and Swaffer, Matthew P and Sinnott-Armstrong, Nicholas A and Skotheim, Jan M and Kundaje, Anshul and Greenleaf, William J},
journal={Nature methods},
volume={17},
number={3},
pages={319--327},
year={2020},
publisher={Nature Publishing Group US New York}
}

@Article{marom2019mtdna,
title={mtDNA chromatin-like organization is gradually established during mammalian embryogenesis},
author={Marom, Shani and Blumberg, Amit and Kundaje, Anshul and Mishmar, Dan},
journal={Iscience},
volume={12},
pages={141--151},
year={2019},
publisher={Elsevier}
}

@Article{tycko2019identification,
title={Identification and mitigation of pervasive off-target activity in CRISPR-Cas9 screens for essential non-coding elements},
author={Tycko, Josh and Wainberg, Michael and Marinov, Georgi K and Ursu, Oana and Hess, Gaelen T and Ego, Braeden K and Aradhana and Li, Amy and Truong, Alisa and Trevino, Alexandro E and others},
journal={bioRxiv},
pages={520569},
year={2019},
publisher={Cold Spring Harbor Laboratory}
}

@Article{fishmanunderstanding,
title={Understanding Transcriptional Regulatory Logic Using Convolutional and Generative Deep Learning Models},
author={Fishman, Nic and Marinov, Georgi K and Kundaje, Anshul}
}

@Article{fishmangenerating,
title={Generating Regulatory Sequence to Produce Target Expression},
author={Fishman, Nic and Marinov, Georgi and Kundaje, Anshul}
}

@Article{shcherbina2019brief,
title={Brief report: cell cycle dynamics of human pluripotent stem cells primed for differentiation},
author={Shcherbina, Anna and Li, Jingling and Narayanan, Cyndhavi and Greenleaf, William and Kundaje, Anshul and Chetty, Sundari},
journal={Stem Cells},
volume={37},
number={9},
pages={1151--1157},
year={2019},
publisher={Oxford University Press}
}

@Article{wainberg2019opportunities,
title={Opportunities and challenges for transcriptome-wide association studies},
author={Wainberg, Michael and Sinnott-Armstrong, Nasa and Mancuso, Nicholas and Barbeira, Alvaro N and Knowles, David A and Golan, David and Ermel, Raili and Ruusalepp, Arno and Quertermous, Thomas and Hao, Ke and others},
journal={Nature genetics},
volume={51},
number={4},
pages={592--599},
year={2019},
publisher={Nature Publishing Group US New York}
}

@Article{blumberg2019corrigendum,
title={Corrigendum: Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution},
author={Blumberg, Amit and Rice, Edward J and Kundaje, Anshul and Danko, Charles G and Mishmar, Dan},
journal={Genome Research},
volume={29},
number={4},
pages={710--1},
year={2019},
publisher={Cold Spring Harbor Laboratory Press}
}

@Article{shrikumar2018flexible,
title={A flexible and adaptive framework for abstention under class imbalance},
author={Shrikumar, Avanti and Alexandari, Amr and Kundaje, Anshul},
journal={arXiv e-prints},
pages={arXiv--1802},
year={2018}
}

@Article{yardimci2019measuring,
title={Measuring the reproducibility and quality of Hi-C data},
author={Yard{\i}mc{\i}, Galip G{"u}rkan and Ozadam, Hakan and Sauria, Michael EG and Ursu, Oana and Yan, Koon-Kiu and Yang, Tao and Chakraborty, Abhijit and Kaul, Arya and Lajoie, Bryan R and Song, Fan and others},
journal={Genome biology},
volume={20},
pages={1--19},
year={2019},
publisher={BioMed Central}
}

@Article{nair2019integrating,
title={Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts},
author={Nair, Surag and Kim, Daniel S and Perricone, Jacob and Kundaje, Anshul},
journal={Bioinformatics},
volume={35},
number={14},
pages={i108--i116},
year={2019},
publisher={Oxford University Press}
}

@Article{avsec2019kipoi,
title={The Kipoi repository accelerates community exchange and reuse of predictive models for genomics},
author={Avsec, {\v{Z}}iga and Kreuzhuber, Roman and Israeli, Johnny and Xu, Nancy and Cheng, Jun and Shrikumar, Avanti and Banerjee, Abhimanyu and Kim, Daniel S and Beier, Thorsten and Urban, Lara and others},
journal={Nature biotechnology},
volume={37},
number={6},
pages={592--600},
year={2019},
publisher={Nature Publishing Group US New York}
}

@Article{amemiya2019encode,
title={The ENCODE blacklist: identification of problematic regions of the genome},
author={Amemiya, Haley M and Kundaje, Anshul and Boyle, Alan P},
journal={Scientific reports},
volume={9},
number={1},
pages={9354},
year={2019},
publisher={Nature Publishing Group UK London}
}

@inproceedings{st2019predicting,
title={Predicting gene expression from plasma cell-free DNA using both the fragment length and fragment position},
author={St John, John and Gafni, Erik and White, Brandon and Kannan, Ajay and Hansen, Loren and Jaroszewicz, Artur and Kundaje, Anshul and Boley, Nathan},
booktitle={Cancer Research},
volume={79},
number={13},
year={2019},
organization={AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA~…}
}

@Article{stowers2019matrix,
title={Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility},
author={Stowers, Ryan S and Shcherbina, Anna and Israeli, Johnny and Gruber, Joshua J and Chang, Julie and Nam, Sungmin and Rabiee, Atefeh and Teruel, Mary N and Snyder, Michael P and Kundaje, Anshul and others},
journal={Nature biomedical engineering},
volume={3},
number={12},
pages={1009--1019},
year={2019},
publisher={Nature Publishing Group UK London}
}

@Article{shrikumar2019gkmexplain,
title={GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs},
author={Shrikumar, Avanti and Prakash, Eva and Kundaje, Anshul},
journal={Bioinformatics},
volume={35},
number={14},
pages={i173--i182},
year={2019},
publisher={Oxford University Press}
}

@Article{gupta2019targeted,
title={Targeted optimization of regulatory DNA sequences with neural editing architectures},
author={Gupta, Anvita and Kundaje, Anshul},
journal={BioRxiv},
pages={714402},
year={2019},
publisher={Cold Spring Harbor Laboratory}
}

@misc{curtis2024methods,
title={Methods using chromatin-related nucleic acid signals for performing clinical actions},
author={Curtis, Christina and Kundaje, Anshul Bharat and Probert, Chris},
year={2024},
month=sep # "~10",
note={US Patent 12,087,406}
}

@Article{tycko2019mitigation,
title={Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements},
author={Tycko, Josh and Wainberg, Michael and Marinov, Georgi K and Ursu, Oana and Hess, Gaelen T and Ego, Braeden K and Aradhana and Li, Amy and Truong, Alisa and Trevino, Alexandro E and others},
journal={Nature communications},
volume={10},
number={1},
pages={4063},
year={2019},
publisher={Nature Publishing Group UK London}
}

@Article{wainberg2021genome,
title={A genome-wide atlas of co-essential modules assigns function to uncharacterized genes},
author={Wainberg, Michael and Kamber, Roarke A and Balsubramani, Akshay and Meyers, Robin M and Sinnott-Armstrong, Nasa and Hornburg, Daniel and Jiang, Lihua and Chan, Joanne and Jian, Ruiqi and Gu, Mingxin and others},
journal={Nature genetics},
volume={53},
number={5},
pages={638--649},
year={2021},
publisher={Nature Publishing Group US New York}
}

@Article{liu2021learning,
title={Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis},
author={Liu, Xin and Sun, Tao and Shcherbina, Anna and Li, Qin and Jarmoskaite, Inga and Kappel, Kalli and Ramaswami, Gokul and Das, Rhiju and Kundaje, Anshul and Li, Jin Billy},
journal={Nature communications},
volume={12},
number={1},
pages={2165},
year={2021},
publisher={Nature Publishing Group UK London}
}

@Article{kundajenavigation,
title={Navigation Patterns for Scalable Internet Management},
author={Kundaje, Anshul and Stadler, Rolf and Lim, Koon Seng}
}

@Article{wainberg2019homogeneity,
title={Homogeneity in the association of body mass index with type 2 diabetes across the UK Biobank: a Mendelian randomization study},
author={Wainberg, Michael and Mahajan, Anubha and Kundaje, Anshul and McCarthy, Mark I and Ingelsson, Erik and Sinnott-Armstrong, Nasa and Rivas, Manuel A},
journal={PLoS medicine},
volume={16},
number={12},
pages={e1002982},
year={2019},
publisher={Public Library of Science San Francisco, CA USA}
}

@Article{bjorkegrentranscriptome,
title={Transcriptome-wide association studies: opportunities and challenges},
author={Bj{"o}rkegren, Johan LM and Im, Hae Kyung and Pasaniuc, Bogdan and Rivas, Manuel A and Kundaje, Anshul}
}

@Article{corces2020single,
title={Single-cell epigenomic identification of inherited risk loci in Alzheimer’s and Parkinson’s disease},
author={Corces, M Ryan and Shcherbina, Anna and Kundu, Soumya and Gloudemans, Michael J and Fr{'e}sard, Laure and Granja, Jeffrey M and Louie, Bryan H and Shams, Shadi and Bagdatli, S Tansu and Mumbach, Maxwell R and others},
journal={BioRxiv},
pages={2020--01},
year={2020},
publisher={Cold Spring Harbor Laboratory}
}

@Article{roadmap2015anshul,
title={Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, et al. Integrative analysis of 111 reference human epigenomes},
author={Roadmap Epigenomics Consortium and others},
journal={Nature},
volume={518},
pages={317--330},
year={2015}
}

@Article{haibe2020transparency,
title={Transparency and reproducibility in artificial intelligence},
author={Haibe-Kains, Benjamin and Adam, George Alexandru and Hosny, Ahmed and Khodakarami, Farnoosh and Massive Analysis Quality Control (MAQC) Society Board of Directors Shraddha Thakkar 35 Kusko Rebecca 36 Sansone Susanna-Assunta 37 Tong Weida 35 Wolfinger Russ D. 38 Mason Christopher E. 39 Jones Wendell 40 Dopazo Joaquin 41 Furlanello Cesare 42 and Waldron, Levi and Wang, Bo and McIntosh, Chris and Goldenberg, Anna and Kundaje, Anshul and others},
journal={Nature},
volume={586},
number={7829},
pages={E14--E16},
year={2020},
publisher={Nature Publishing Group UK London}
}

@Article{han2020crispr,
title={CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities},
author={Han, Kyuho and Pierce, Sarah E and Li, Amy and Spees, Kaitlyn and Anderson, Gray R and Seoane, Jose A and Lo, Yuan-Hung and Dubreuil, Michael and Olivas, Micah and Kamber, Roarke A and others},
journal={Nature},
volume={580},
number={7801},
pages={136--141},
year={2020},
publisher={Nature Publishing Group UK London}
}

@inproceedings{alexandari2020maximum,
title={Maximum likelihood with bias-corrected calibration is hard-to-beat at label shift adaptation},
author={Alexandari, Amr and Kundaje, Anshul and Shrikumar, Avanti},
booktitle={International Conference on Machine Learning},
pages={222--232},
year={2020},
organization={PMLR}
}

@Article{rozenblatt2020human,
title={The human tumor atlas network: charting tumor transitions across space and time at single-cell resolution},
author={Rozenblatt-Rosen, Orit and Regev, Aviv and Oberdoerffer, Philipp and Nawy, Tal and Hupalowska, Anna and Rood, Jennifer E and Ashenberg, Orr and Cerami, Ethan and Coffey, Robert J and Demir, Emek and others},
journal={Cell},
volume={181},
number={2},
pages={236--249},
year={2020},
publisher={Elsevier}
}

@Article{huyghe2021genetic,
title={Genetic architectures of proximal and distal colorectal cancer are partly distinct},
author={Huyghe, Jeroen R and Harrison, Tabitha A and Bien, Stephanie A and Hampel, Heather and Figueiredo, Jane C and Schmit, Stephanie L and Conti, David V and Chen, Sai and Qu, Conghui and Lin, Yi and others},
journal={Gut},
volume={70},
number={7},
pages={1325--1334},
year={2021},
publisher={BMJ Publishing Group}
}

@Article{cheng2021mtsplice,
title={MTSplice predicts effects of genetic variants on tissue-specific splicing},
author={Cheng, Jun and {\c{C}}elik, Muhammed Hasan and Kundaje, Anshul and Gagneur, Julien},
journal={Genome biology},
volume={22},
pages={1--19},
year={2021},
publisher={BioMed Central}
}

@Article{tseng2020fourier,
title={Fourier-transform-based attribution priors improve the interpretability and stability of deep learning models for genomics},
author={Tseng, Alex and Shrikumar, Avanti and Kundaje, Anshul},
journal={Advances in Neural Information Processing Systems},
volume={33},
pages={1913--1923},
year={2020}
}

@Article{kundaje2012assessment,
title={Assessment of ChIP-seq data quality using strand cross-correlation analysis},
author={Kundaje, Anshul and Jung, L and Kharchenko, P and Sidow, A and Batzoglou, S and Cherbas, P},
journal={Manuscript submitted},
year={2012}
}

@Article{wang2011genome,
title={Genome-wide mapping of the binding sites of 119 human transcription factors},
author={Wang, Jie and Zhuang, Jiali and Iyer, Sowmya and Lin, X and Whitfield, Troy and Greven, Melissa and Aldred, Shelley Force and Trinklein, Nathan and Dong, Xianjun and Kundaje, Anshul and others},
journal={Submitted, NCP010},
year={2011}
}

@Article{marinov2021transcription,
title={Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum},
author={Marinov, Georgi K and Trevino, Alexandro E and Xiang, Tingting and Kundaje, Anshul and Grossman, Arthur R and Greenleaf, William J},
journal={Nature Genetics},
volume={53},
number={5},
pages={613--617},
year={2021},
publisher={Nature Publishing Group US New York}
}

@Article{avsec2021base,
title={Base-resolution models of transcription-factor binding reveal soft motif syntax},
author={Avsec, {\v{Z}}iga and Weilert, Melanie and Shrikumar, Avanti and Krueger, Sabrina and Alexandari, Amr and Dalal, Khyati and Fropf, Robin and McAnany, Charles and Gagneur, Julien and Kundaje, Anshul and others},
journal={Nature genetics},
volume={53},
number={3},
pages={354--366},
year={2021},
publisher={Nature Publishing Group US New York}
}

@Article{grubert2020landscape,
title={Landscape of cohesin-mediated chromatin loops in the human genome},
author={Grubert, Fabian and Srivas, Rohith and Spacek, Damek V and Kasowski, Maya and Ruiz-Velasco, Mariana and Sinnott-Armstrong, Nasa and Greenside, Peyton and Narasimha, Anil and Liu, Qing and Geller, Benjamin and others},
journal={Nature},
volume={583},
number={7818},
pages={737--743},
year={2020},
publisher={Nature Publishing Group UK London}
}

@Article{encode2020expanded,
title={Expanded encyclopaedias of DNA elements in the human and mouse genomes},
author={Moore, Jill E and Purcaro, Michael J and Pratt, Henry E and Epstein, Charles B and Shoresh, Noam and Adrian, Jessika and Kawli, Trupti and Davis, Carrie A and Dobin, Alexander and others},
journal={Nature},
volume={583},
number={7818},
pages={699--710},
year={2020},
publisher={Nature Publishing Group UK London}
}

@Article{swaffer2020size,
title={Size-independent mRNA synthesis and chromatin-based partitioning mechanisms generate and maintain constant amounts of protein per cell},
author={Swaffer, MP and Chandler-Brown, D and Langhinrichs, M and Marinov, G and Greenleaf, W and Kundaje, A and Schmoller, KM and Skotheim, JM},
journal={bioRxiv},
year={2020}
}

@Article{nasser2020genome,
title={Genome-wide maps of enhancer regulation connect risk variants to disease genes},
author={Nasser, Joseph and Bergman, Drew T and Fulco, Charles P and Guckelberger, Philine and Doughty, Benjamin R and Patwardhan, Tejal A and Jones, Thouis R and Nguyen, Tung H and Ulirsch, Jacob C and Natri, Heini M and others},
journal={bioRxiv},
pages={2020--09},
year={2020},
publisher={Cold Spring Harbor Laboratory}
}

@Article{tycko2020high,
title={High-throughput discovery and characterization of human transcriptional effectors},
author={Tycko, Josh and DelRosso, Nicole and Hess, Gaelen T and Banerjee, Abhimanyu and Mukund, Aditya and Van, Mike V and Ego, Braeden K and Yao, David and Spees, Kaitlyn and Suzuki, Peter and others},
journal={Cell},
volume={183},
number={7},
year={2020},
publisher={Elsevier}
}

@Article{abascal2020perspectives,
title={Perspectives on ENCODE},
author={Abascal, Federico and Acosta, Reyes and Addleman, Nicholas J and Adrian, Jessika and Afzal, Veena and Aken, Bronwen and Akiyama, Jennifer A},
journal={Nature},
volume={583},
number={7818},
pages={693--699},
year={2020},
publisher={Nature Publishing Group}
}

@Article{nair2022fastism,
title={fastISM: performant in silico saturation mutagenesis for convolutional neural networks},
author={Nair, Surag and Shrikumar, Avanti and Schreiber, Jacob and Kundaje, Anshul},
journal={Bioinformatics},
volume={38},
number={9},
pages={2397--2403},
year={2022},
publisher={Oxford University Press}
}

@Article{kim2021dynamic,
title={The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation},
author={Kim, Daniel S and Risca, Viviana I and Reynolds, David L and Chappell, James and Rubin, Adam J and Jung, Namyoung and Donohue, Laura KH and Lopez-Pajares, Vanessa and Kathiria, Arwa and Shi, Minyi and others},
journal={Nature genetics},
volume={53},
number={11},
pages={1564--1576},
year={2021},
publisher={Nature Publishing Group US New York}
}

@Article{corces2020single,
title={Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases},
author={Corces, M Ryan and Shcherbina, Anna and Kundu, Soumya and Gloudemans, Michael J and Fr{'e}sard, Laure and Granja, Jeffrey M and Louie, Bryan H and Eulalio, Tiffany and Shams, Shadi and Bagdatli, S Tansu and others},
journal={Nature genetics},
volume={52},
number={11},
pages={1158--1168},
year={2020},
publisher={Nature Publishing Group US New York}
}

@Article{zhou2021towards,
title={Towards a better understanding of reverse-complement equivariance for deep learning models in regulatory genomics},
author={Zhou, Hannah and Shrikumar, Avanti and Kundaje, Anshul},
journal={BioRxiv},
pages={2020},
year={2021}
}

@inproceedings{koh2021wilds,
title={Wilds: A benchmark of in-the-wild distribution shifts},
author={Koh, Pang Wei and Sagawa, Shiori and Marklund, Henrik and Xie, Sang Michael and Zhang, Marvin and Balsubramani, Akshay and Hu, Weihua and Yasunaga, Michihiro and Phillips, Richard Lanas and Gao, Irena and others},
booktitle={International conference on machine learning},
pages={5637--5664},
year={2021},
organization={PMLR}
}

@Article{diez2020expression,
title={Expression and splicing quantitative trait locus (e/sQTLs) summary statistics from normal colon tissue},
author={Diez Obrero, Virginia and Dampier, Christopher H and Moratalla Navarro, Ferran and Devall, Matthew and Plummer, Sarah J and D{'\i}ez Villanueva, Anna and Peters, Ulrike and Bien, Stephanie A and Huyghe, Jeroen R and Kundaje, Anshul and others},
year={2020}
}

@Article{trevino2021chromatin,
title={Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution},
author={Trevino, Alexandro E and M{"u}ller, Fabian and Andersen, Jimena and Sundaram, Laksshman and Kathiria, Arwa and Shcherbina, Anna and Farh, Kyle and Chang, Howard Y and Pașca, Anca M and Kundaje, Anshul and others},
journal={Cell},
volume={184},
number={19},
pages={5053--5069},
year={2021},
publisher={Elsevier}
}

@Article{alexandari2020bias,
title={EM with Bias-Corrected Calibration is Hard-To-Beat at Label Shift Adaptation},
author={Alexandari, Amr and Kundaje, Anshul and Shrikumar, Avanti},
journal={arXiv preprint arXiv:1901.06852},
year={2020}
}

@Article{mumbach2017enhancer,
title={Enhancer connectome in primary human cells reveals target genes of disease-associated DNA elements},
author={Mumbach, Maxwell R and Satpathy, Ansuman T and Boyle, Evan A and Dai, Chao and Gowen, Benjamin G and Cho, Seung Woo and Nguyen, Michelle L and Rubin, Adam J and Granja, Jeffrey M and Kazane, Katelynn R and others},
journal={bioRxiv},
pages={178269},
year={2017},
publisher={Cold Spring Harbor Laboratory}
}

@Article{cochran2022domain,
title={Domain-adaptive neural networks improve cross-species prediction of transcription factor binding},
author={Cochran, Kelly and Srivastava, Divyanshi and Shrikumar, Avanti and Balsubramani, Akshay and Hardison, Ross C and Kundaje, Anshul and Mahony, Shaun},
journal={Genome research},
volume={32},
number={3},
pages={512--523},
year={2022},
publisher={Cold Spring Harbor Lab}
}

@Article{diez2021genetic,
title={Genetic effects on transcriptome profiles in colon epithelium provide functional insights for genetic risk loci},
author={D{'\i}ez-Obrero, Virginia and Dampier, Christopher H and Moratalla-Navarro, Ferran and Devall, Matthew and Plummer, Sarah J and D{'\i}ez-Villanueva, Anna and Peters, Ulrike and Bien, Stephanie and Huyghe, Jeroen R and Kundaje, Anshul and others},
journal={Cellular and molecular gastroenterology and hepatology},
volume={12},
number={1},
pages={181--197},
year={2021},
publisher={Elsevier}
}

@Article{becker2021single,
title={Single-cell analyses reveal a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer},
author={Becker, Winston R and Nevins, Stephanie A and Chen, Derek C and Chiu, Roxanne and Horning, Aaron and Laquindanum, Rozelle and Mills, Meredith and Chaib, Hassan and Ladabaum, Uri and Longacre, Teri and others},
journal={bioRxiv},
pages={2021--03},
year={2021},
publisher={Cold Spring Harbor Laboratory}
}

@Article{yeo2021chromatin,
title={Chromatin accessibility dynamics of neurogenic niche cells reveal a reversible decline in neural stem cell migration during aging},
author={Yeo, Robin W and Zhou, Olivia Y and Zhong, Brian and Sharmin, Mahfuza and Ruetz, Tyson J and Kundaje, Anshul and Dunn, Alexander R and Brunet, Anne},
journal={bioRxiv},
year={2021},
publisher={Cold Spring Harbor Laboratory}
}

@Article{nasser2021genome,
title={Genome-wide enhancer maps link risk variants to disease genes},
author={Nasser, Joseph and Bergman, Drew T and Fulco, Charles P and Guckelberger, Philine and Doughty, Benjamin R and Patwardhan, Tejal A and Jones, Thouis R and Nguyen, Tung H and Ulirsch, Jacob C and Lekschas, Fritz and others},
journal={Nature},
volume={593},
number={7858},
pages={238--243},
year={2021},
publisher={Nature Publishing Group UK London}
}

@Article{marinov2021direct,
title={Direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping (CasKAS)},
author={Marinov, Georgi K and Kim, Samuel H and Bagdatli, S Tansu and Trevino, Alexandro E and Tycko, Josh and Wu, Tong and Bintu, Lacramioara and Bassik, Michael C and He, Chuan and Kundaje, Anshul and others},
journal={bioRxiv},
pages={2021--04},
year={2021},
publisher={Cold Spring Harbor Laboratory}
}

@Article{snyder2021multi,
title={Multi-omic analysis of familial adenomatous polyposis reveals molecular pathways and polyclonal spreading associated with early tumorigenesis},
author={Snyder, Michael and Horning, Aaron and Esplin, Edward and Wu, Si and Hanson, Casey and Bararpour, Nasim and Nevins, Stephanie and Jiang, Lihua and Contrepoi, Kevin and Lee, Hayan and others},
journal={Res Square},
volume={10},
year={2021}
}

@Article{horning2021multi,
title={Multi-omic Analysis of Familial Adenomatous Polyposis Reveals Molecular Pathways and Polyclonal Spreading Associated with Early Tumorigenesis},
author={Horning, Aaron M and Esplin, Edward D and Wu, Si and Hanson, Casey and Bararpour, Nasim and Nevins, Stephanie A and Jiang, Lihua and Contrepois, K{'e}vin and Lee, Hayan and Guha, Tuhin K and others},
year={2021}
}

@Article{markov2021ap,
title={AP-1 is a temporally regulated dual gatekeeper of reprogramming to pluripotency},
author={Markov, Glenn J and Mai, Thach and Nair, Surag and Shcherbina, Anna and Wang, Yu Xin and Burns, David M and Kundaje, Anshul and Blau, Helen M},
journal={Proceedings of the National Academy of Sciences},
volume={118},
number={23},
pages={e2104841118},
year={2021},
publisher={National Academy of Sciences}
}

@Article{marklund2020wilds,
title={Wilds: A benchmark of in-the-wild distribution shifts},
author={Marklund, Henrik and Xie, Sang Michael and Zhang, Marvin and Balsubramani, Akshay and Hu, Weihua and Yasunaga, Michihiro and Phillips, Richard Lanas and Beery, Sara and Leskovec, Jure and Kundaje, Anshul and others},
journal={arXiv preprint arXiv:2012.07421},
year={2020}
}

@Article{turner2021cell,
title={Cell-specific chromatin landscape of human coronary artery resolves regulatory mechanisms of disease risk},
author={Turner, Adam W and Hu, Sheng’en and Mosquera, Jose Verdezoto and Ma, Wei Feng and Hodonsky, Chani J and Wong, Doris and Auguste, Ga{"e}lle and Sol-Church, Katia and Farber, Emily and Kundu, Soumya and others},
journal={Biorxiv},
pages={2021--06},
year={2021},
publisher={Cold Spring Harbor Laboratory}
}

@Article{gafni2021cell,
title={Cell-free DNA fragments inform epigenomic mechanisms for early detection of breast cancer},
author={Gafni, Erik and Harvey, Adam and Jaroszewicz, Artur and Solari, Omid Shams and Landolin, Jane and Barbirou, Mouadh and Miller, Amanda and Tonellato, Peter J and Kundaje, Anshul and Jeffrey, Stefanie S and others},
journal={Cancer Research},
volume={81},
number={13_Supplement},
pages={2105--2105},
year={2021},
publisher={The American Association for Cancer Research}
}

@Article{marinov2022chromatin,
title={The chromatin organization of a chlorarachniophyte nucleomorph genome},
author={Marinov, Georgi K and Chen, Xinyi and Wu, Tong and He, Chuan and Grossman, Arthur R and Kundaje, Anshul and Greenleaf, William James},
journal={Genome Biology},
volume={23},
number={1},
pages={65},
year={2022},
publisher={BioMed Central London}
}

@inproceedings{finkelstein2020look,
title={Look at the loss: Towards robust detection of false positive feature interactions learned by neural networks on genomic data},
author={Finkelstein, Mara and Shrikumar, Avanti and Kundaje, Anshul},
booktitle={Proceedings of the 37th International Conference on Machine Learning (ICML 2020), The 2020 ICML Workshop on Computational Biology},
year={2020}
}

@Article{swaffer2021rna,
title={RNA polymerase II dynamics and mRNA stability feedback determine mRNA scaling with cell size},
author={Swaffer, Matthew P and Marinov, Georgi K and Zheng, Huan and Jones, Andrew W and Greenwood, Jessica and Kundaje, Anshul and Snijders, Ambrosius P and Greenleaf, William J and Reyes-Lamothe, Rodrigo and Skotheim, Jan M},
journal={BioRxiv},
pages={2021--09},
year={2021},
publisher={Cold Spring Harbor Laboratory}
}

@Article{purmann2021direct,
title={Direct induction of human neurons from fibroblasts carrying the neuropsychiatric 22q11. 2 microdeletion reveals transcriptome-and epigenome-wide alterations},
author={Purmann, Carolin and Ang, Cheen Euong and Tanabe, Koji and Zhang, Yue and Kundu, Soumya and Danko, Tamas and Ma, Shining and Mitelpunkt, Alexis and Wong, Wing Hung and Bernstein, Jonathan and others},
journal={bioRxiv},
pages={2021--10},
year={2021},
publisher={Cold Spring Harbor Laboratory}
}

@Article{swaffer2021transcriptional,
title={Transcriptional and chromatin-based partitioning mechanisms uncouple protein scaling from cell size},
author={Swaffer, Matthew P and Kim, Jacob and Chandler-Brown, Devon and Langhinrichs, Maurice and Marinov, Georgi K and Greenleaf, William J and Kundaje, Anshul and Schmoller, Kurt M and Skotheim, Jan M},
journal={Molecular cell},
volume={81},
number={23},
pages={4861--4875},
year={2021},
publisher={Elsevier}
}

@Article{schreiber2022accelerating,
title={Accelerating in silico saturation mutagenesis using compressed sensing},
author={Schreiber, Jacob and Nair, Surag and Balsubramani, Akshay and Kundaje, Anshul},
journal={Bioinformatics},
volume={38},
number={14},
pages={3557--3564},
year={2022},
publisher={Oxford University Press}
}

@Article{addleman2020perspectives,
title={Perspectives on ENCODE},
author={Addleman, NJ and Adrian, J and Baymuradov, UK and Bhaskar, A and Boley, N and Cao, L and Chaib, H and Chan, ET and Chen, S and Cherry, JM and others},
journal={Nature},
volume={583},
number={7818},
pages={693--698},
year={2020},
publisher={Springer Nature}
}

@inproceedings{prakash2022towards,
title={Towards more realistic simulated datasets for benchmarking deep learning models in regulatory genomics},
author={Prakash, Eva I and Shrikumar, Avanti and Kundaje, Anshul},
booktitle={Machine Learning in Computational Biology},
pages={58--77},
year={2022},
organization={PMLR}
}

@Article{cheng2022zeb2,
title={ZEB2 shapes the epigenetic landscape of atherosclerosis},
author={Cheng, Paul and Wirka, Robert C and Shoa Clarke, Lee and Zhao, Quanyi and Kundu, Ramendra and Nguyen, Trieu and Nair, Surag and Sharma, Disha and Kim, Hyun-jung and Shi, Huitong and others},
journal={Circulation},
volume={145},
number={6},
pages={469--485},
year={2022},
publisher={Lippincott Williams & Wilkins Hagerstown, MD}
}

@inproceedings{zhou2022towards,
title={Towards a better understanding of reverse-complement equivariance for deep learning models in genomics},
author={Zhou, Hannah and Shrikumar, Avanti and Kundaje, Anshul},
booktitle={Machine Learning in Computational Biology},
pages={1--33},
year={2022},
organization={PMLR}
}

@Article{ludwig2022congenital,
title={Congenital anemia reveals distinct targeting mechanisms for master transcription factor GATA1},
author={Ludwig, Leif S and Lareau, Caleb A and Bao, Erik L and Liu, Nan and Utsugisawa, Taiju and Tseng, Alex M and Myers, Samuel A and Verboon, Jeffrey M and Ulirsch, Jacob C and Luo, Wendy and others},
journal={Blood, The Journal of the American Society of Hematology},
volume={139},
number={16},
pages={2534--2546},
year={2022},
publisher={American Society of Hematology Washington, DC}
}

@incollection{marinov2022single,
title={Single-molecule Multikilobase-scale profiling of chromatin accessibility using m6A-SMAC-Seq and m6A-CpG-GpC-SMAC-Seq},
author={Marinov, Georgi K and Shipony, Zohar and Kundaje, Anshul and Greenleaf, William J},
booktitle={Chromatin: Methods and Protocols},
pages={269--298},
year={2022},
publisher={Springer US New York, NY}
}

@Article{horton2022short,
title={Short tandem repeats recruit transcription factors to tune eukaryotic gene expression},
author={Horton, Connor A and Alexandari, Amr M and Hayes, Michael G and Schaepe, Julia M and Marklund, Emil and Shah, Nilay and Aditham, Arjun K and Shrikumar, Avanti and Afek, Ariel and Greenleaf, William J and others},
journal={Biophysical Journal},
volume={121},
number={3},
pages={287a--288a},
year={2022},
publisher={Elsevier}
}

@Article{jordahl2022beyond,
title={Beyond GWAS of colorectal cancer: evidence of Interaction with alcohol consumption and putative causal variant for the 10q24. 2 region},
author={Jordahl, Kristina M and Shcherbina, Anna and Kim, Andre E and Su, Yu-Ru and Lin, Yi and Wang, Jun and Qu, Conghui and Albanes, Demetrius and Arndt, Volker and Baurley, James W and others},
journal={Cancer Epidemiology, Biomarkers & Prevention},
volume={31},
number={5},
pages={1077--1089},
year={2022},
publisher={American Association for Cancer Research}
}

@Article{wang2022single,
title={Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases},
author={Wang, Sean K and Nair, Surag and Li, Rui and Kraft, Katerina and Pampari, Anusri and Patel, Aman and Kang, Joyce B and Luong, Christy and Kundaje, Anshul and Chang, Howard Y},
journal={Cell genomics},
volume={2},
number={8},
year={2022},
publisher={Elsevier}
}

@Article{moore2022author,
title={Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes},
author={Moore, Jill E and Purcaro, Michael J and Pratt, Henry E and Epstein, Charles B and Shoresh, Noam and Adrian, Jessika and Kawli, Trupti and Davis, Carrie A and Dobin, Alexander and Kaul, Rajinder and others},
journal={Nature},
volume={605},
number={7909},
pages={E3--E3},
year={2022},
publisher={Nature Publishing Group}
}

@Article{zaslavsky2022disease,
title={Disease diagnostics using machine learning of immune receptors},
author={Zaslavsky, Maxim E and Craig, Erin and Michuda, Jackson K and Sehgal, Nidhi and Ram-Mohan, Nikhil and Lee, Ji-Yeun and Nguyen, Khoa D and Hoh, Ramona A and Pham, Tho D and R{"o}ltgen, Katharina and others},
journal={Biorxiv},
pages={2022--04},
year={2022},
publisher={Cold Spring Harbor Laboratory}
}

@Article{tian2022genome,
title={Genome-wide interaction analysis of genetic variants with menopausal hormone therapy for colorectal cancer risk},
author={Tian, Yu and Kim, Andre E and Bien, Stephanie A and Lin, Yi and Qu, Conghui and Harrison, Tabitha A and Carreras-Torres, Robert and D{'\i}ez-Obrero, Virginia and Dimou, Niki and Drew, David A and others},
journal={Journal of the National Cancer Institute},
volume={114},
number={8},
pages={1135--1148},
year={2022},
publisher={Oxford University Press}
}

@Article{linder2022deciphering,
title={Deciphering the Impact of Genetic Variation on Human Polyadenylation},
author={Linder, Johannes and Kundaje, Anshul and Seelig, Georg},
journal={bioRxiv},
pages={2022--05},
year={2022},
publisher={Cold Spring Harbor Laboratory}
}

@Article{turner2022single,
title={Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk},
author={Turner, Adam W and Hu, Shengen Shawn and Mosquera, Jose Verdezoto and Ma, Wei Feng and Hodonsky, Chani J and Wong, Doris and Auguste, Ga{"e}lle and Song, Yipei and Sol-Church, Katia and Farber, Emily and others},
journal={Nature genetics},
volume={54},
number={6},
pages={804--816},
year={2022},
publisher={Nature Publishing Group US New York}
}

@Article{horton2023short,
title={Short tandem repeats bind transcription factors to tune eukaryotic gene expression},
author={Horton, Connor A and Alexandari, Amr M and Hayes, Michael GB and Marklund, Emil and Schaepe, Julia M and Aditham, Arjun K and Shah, Nilay and Suzuki, Peter H and Shrikumar, Avanti and Afek, Ariel and others},
journal={Science},
volume={381},
number={6664},
pages={eadd1250},
year={2023},
publisher={American Association for the Advancement of Science}
}

@Article{nair2022dynseq,
title={The dynseq genome browser track enables visualization of context-specific, dynamic DNA sequence features at single nucleotide resolution},
author={Nair, Surag and Barrett, Arjun and Li, Daofeng and Raney, Brian J and Lee, Brian T and Kerpedjiev, Peter and Ramalingam, Vivekanandan and Pampari, Anusri and Lekschas, Fritz and Wang, Ting and others},
journal={bioRxiv},
pages={2022--05},
year={2022},
publisher={Cold Spring Harbor Laboratory}
}

@Article{libbrecht2009transcription,
title={Transcription start site classification},
author={Libbrecht, Max and Fisher, Matt and Frostig, Roy and Papadakis, Hrysoula and Kundaje, Anshul and Batzoglou, Serafim},
year={2009}
}

@Article{wang2022single,
title={A single cell spatial temporal atlas of skeletal muscle reveals cellular neighborhoods that orchestrate regeneration and become disrupted in aging},
author={Wang, Yu Xin and Holbrook, Colin A and Hamilton, James N and Garoussian, Jasmin and Afshar, Mohsen and Su, Shiqi and Sch{"u}rch, Christian M and Lee, Michael Y and Goltsev, Yury and Kundaje, Anshul and others},
journal={BioRxiv},
pages={2022--06},
year={2022},
publisher={Cold Spring Harbor Laboratory}
}

@Article{becker2022single,
title={Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer},
author={Becker, Winston R and Nevins, Stephanie A and Chen, Derek C and Chiu, Roxanne and Horning, Aaron M and Guha, Tuhin K and Laquindanum, Rozelle and Mills, Meredith and Chaib, Hassan and Ladabaum, Uri and others},
journal={Nature genetics},
volume={54},
number={7},
pages={985--995},
year={2022},
publisher={Nature Publishing Group US New York}
}

@Article{ameen2022integrative,
title={Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease},
author={Ameen, Mohamed and Sundaram, Laksshman and Shen, Mengcheng and Banerjee, Abhimanyu and Kundu, Soumya and Nair, Surag and Shcherbina, Anna and Gu, Mingxia and Wilson, Kitchener D and Varadarajan, Avyay and others},
journal={Cell},
volume={185},
number={26},
pages={4937--4953},
year={2022},
publisher={Elsevier}
}

@Article{kundaje2022automated,
title={Automated sequence-based annotation and interpretation of the human genome},
author={Kundaje, Anshul and Meuleman, Wouter},
journal={Nature Genetics},
volume={54},
number={7},
pages={916--917},
year={2022},
publisher={Nature Publishing Group US New York}
}

@Article{marinov2023chromatin,
title={The chromatin landscape of the euryarchaeon Haloferax volcanii},
author={Marinov, Georgi K and Bagdatli, S Tansu and Wu, Tong and He, Chuan and Kundaje, Anshul and Greenleaf, William J},
journal={Genome Biology},
volume={24},
number={1},
pages={253},
year={2023},
publisher={BioMed Central London}
}

@Article{schreiber2023encode,
title={The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles},
author={Schreiber, Jacob and Boix, Carles and wook Lee, Jin and Li, Hongyang and Guan, Yuanfang and Chang, Chun-Chieh and Chang, Jen-Chien and Hawkins-Hooker, Alex and Sch{"o}lkopf, Bernhard and Schweikert, Gabriele and others},
journal={Genome biology},
volume={24},
number={1},
pages={79},
year={2023},
publisher={BioMed Central London}
}

@Article{lareau2022latent,
title={Latent human herpesvirus 6 is reactivated in chimeric antigen receptor T cells},
author={Lareau, Caleb A and Yin, Yajie and Maurer, Katie and Sandor, Katalin D and Yagnik, Garima and Pe{~n}a, Jos{'e} and Crawford, Jeremy Chase and Spanjaart, Anne M and Gutierrez, Jacob C and Haradhvala, Nicholas J and others},
journal={bioRxiv},
pages={2022--08},
year={2022},
publisher={Cold Spring Harbor Laboratory}
}

@Article{zhu2022global,
title={Global loss of fine-scale chromatin architecture and rebalancing of gene expression during early colorectal cancer development},
author={Zhu, Yizhou and Lee, Hayan and Weimer, Annika K and Horning, Aaron and Nevins, Stephanie A and Esplin, Edward D and Paul, Kristina and Krieger, Gat and Shipony, Zohar and Mills, Meredith and others},
year={2022}
}

@Article{turner2022author,
title={Author Correction: Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk},
author={Turner, Adam W and Hu, Shengen Shawn and Mosquera, Jose Verdezoto and Ma, Wei Feng and Hodonsky, Chani J and Wong, Doris and Auguste, Ga{"e}lle and Song, Yipei and Sol-Church, Katia and Farber, Emily and others},
journal={Nature genetics},
volume={54},
number={8},
pages={1259},
year={2022}
}

@Article{snyder2022global,
title={Global loss of fine-scale chromatin architecture and rebalancing of gene expression during early colorectal cancer development},
author={Snyder, Michael and Zhu, Yizhou and Lee, Hayan and Weimer, Annika and Horning, Aaron and Nevins, Stephanie and Esplin, Edward and Paul, Kristina and Krieger, Gat and Shipony, Zohar and others},
year={2022}
}

@Article{nigam2023tartarus,
title={Tartarus: A benchmarking platform for realistic and practical inverse molecular design},
author={Nigam, AkshatKumar and Pollice, Robert and Tom, Gary and Jorner, Kjell and Willes, John and Thiede, Luca and Kundaje, Anshul and Aspuru-Guzik, Al{'a}n},
journal={Advances in Neural Information Processing Systems},
volume={36},
pages={3263--3306},
year={2023}
}

@Article{nair2022dynseq,
title={The dynseq browser track shows context-specific features at nucleotide resolution},
author={Nair, Surag and Barrett, Arjun and Li, Daofeng and Raney, Brian J and Lee, Brian T and Kerpedjiev, Peter and Ramalingam, Vivekanandan and Pampari, Anusri and Lekschas, Fritz and Wang, Ting and others},
journal={Nature genetics},
volume={54},
number={11},
pages={1581--1583},
year={2022},
publisher={Nature Publishing Group US New York}
}

@Article{dimou2023probing,
title={Probing the diabetes and colorectal cancer relationship using gene--environment interaction analyses},
author={Dimou, Niki and Kim, Andre E and Flanagan, Orlagh and Murphy, Neil and Diez-Obrero, Virginia and Shcherbina, Anna and Aglago, Elom K and Bouras, Emmanouil and Campbell, Peter T and Casey, Graham and others},
journal={British journal of cancer},
volume={129},
number={3},
pages={511--520},
year={2023},
publisher={Nature Publishing Group UK London}
}

@Article{turner2022single,
title={Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk (vol 54, pg 804, 2022)},
author={Turner, Adam W and Hu, Shengen Shawn and Mosquera, Jose Verdezoto and Ma, Wei Feng and Hodonsky, Chani J and Wong, Doris and Auguste, Gaelle and Song, Yipei and Sol-Church, Katia and Farber, Emily and others},
journal={NATURE GENETICS},
volume={54},
number={8},
pages={1259--1259},
year={2022},
publisher={NATURE PORTFOLIO HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY}
}

@Article{linder2022deciphering,
title={Deciphering the impact of genetic variation on human polyadenylation using APARENT2},
author={Linder, Johannes and Koplik, Samantha E and Kundaje, Anshul and Seelig, Georg},
journal={Genome biology},
volume={23},
number={1},
pages={232},
year={2022},
publisher={BioMed Central London}
}

@Article{lareau2022single,
title={Single-cell multi-omics reveals dynamics of purifying selection of pathogenic mitochondrial DNA across human immune cells},
author={Lareau, Caleb A and Dubois, Sonia M and Buquicchio, Frank A and Hsieh, Yu-Hsin and Garg, Kopal and Kautz, Pauline and Nitsch, Lena and Praktiknjo, Samantha D and Maschmeyer, Patrick and Verboon, Jeffrey M and others},
journal={bioRxiv},
pages={2022--11},
year={2022},
publisher={Cold Spring Harbor Laboratory}
}

@Article{frankish2023gencode,
title={GENCODE: reference annotation for the human and mouse genomes in 2023},
author={Frankish, Adam and Carbonell-Sala, S{'\i}lvia and Diekhans, Mark and Jungreis, Irwin and Loveland, Jane E and Mudge, Jonathan M and Sisu, Cristina and Wright, James C and Arnan, Carme and Barnes, If and others},
journal={Nucleic acids research},
volume={51},
number={D1},
pages={D942--D949},
year={2023},
publisher={Oxford University Press}
}

@Article{brennan2022chromatin,
title={Chromatin accessibility is a two-tier process regulated by transcription factor pioneering and enhancer activation},
author={Brennan, Kaelan J and Weilert, Melanie and Krueger, Sabrina and Pampari, Anusri and Liu, Hsiao-Yun and Yang, Ally WH and Hughes, Timothy R and Rushlow, Christine A and Kundaje, Anshul and Zeitlinger, Julia},
journal={bioRxiv},
pages={2022--12},
year={2022},
publisher={Cold Spring Harbor Laboratory}
}

@Article{fernandez2023deciphering,
title={Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries},
author={Fernandez-Rozadilla, Ceres and Timofeeva, Maria and Chen, Zhishan and Law, Philip and Thomas, Minta and Schmit, Stephanie and D{'\i}ez-Obrero, Virginia and Hsu, Li and Fernandez-Tajes, Juan and Palles, Claire and others},
journal={Nature genetics},
volume={55},
number={1},
pages={89--99},
year={2023},
publisher={Nature Publishing Group US New York}
}

@Article{yao2024multicenter,
title={Multicenter integrated analysis of noncoding CRISPRi screens},
author={Yao, David and Tycko, Josh and Oh, Jin Woo and Bounds, Lexi R and Gosai, Sager J and Lataniotis, Lazaros and Mackay-Smith, Ava and Doughty, Benjamin R and Gabdank, Idan and Schmidt, Henri and others},
journal={Nature methods},
volume={21},
number={4},
pages={723--734},
year={2024},
publisher={Nature Publishing Group US New York}
}

@Article{carreras2023genome,
title={Genome-wide interaction study with smoking for colorectal cancer risk identifies novel genetic loci related to tumor suppression, inflammation, and immune response},
author={Carreras-Torres, Robert and Kim, Andre E and Lin, Yi and D{'\i}ez-Obrero, Virginia and Bien, Stephanie A and Qu, Conghui and Wang, Jun and Dimou, Niki and Aglago, Elom K and Albanes, Demetrius and others},
journal={Cancer Epidemiology, Biomarkers & Prevention},
volume={32},
number={3},
pages={315--328},
year={2023},
publisher={American Association for Cancer Research}
}

@Article{yeo2023chromatin,
title={Chromatin accessibility dynamics of neurogenic niche cells reveal defects in neural stem cell adhesion and migration during aging},
author={Yeo, Robin W and Zhou, Olivia Y and Zhong, Brian L and Sun, Eric D and Navarro Negredo, Paloma and Nair, Surag and Sharmin, Mahfuza and Ruetz, Tyson J and Wilson, Mikaela and Kundaje, Anshul and others},
journal={Nature Aging},
volume={3},
number={7},
pages={866--893},
year={2023},
publisher={Nature Publishing Group US New York}
}

@Article{alexandari2018general,
title={A General Framework for Abstention Under Label Shift},
author={Alexandari, Amr M and Kundaje, Anshul and Shrikumar, Avanti},
journal={arXiv preprint arXiv:1802.07024},
year={2018}
}

@Article{swaffer2021rna,
title={RNA polymerase II dynamics and mRNA stability feedback scale mRNA in proportion to cell size},
author={Swaffer, MP and Marinov, GK and Zheng, H and Tsui, CY and Jones, AW and Greenwood, J and Kundaje, A and Greenleaf, WJ and Reyes-Lamothe, R and Skotheim, JM},
year={2021}
}

@Article{kowalski2023cpa,
title={CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators},
author={Kowalski, Madeline H and Wessels, Hans-Hermann and Linder, Johannes and Choudhary, Saket and Hartman, Austin and Hao, Yuhan and Mascio, Isabella and Dalgarno, Carol and Kundaje, Anshul and Satija, Rahul},
journal={BioRxiv},
year={2023},
publisher={Cold Spring Harbor Laboratory Preprints}
}

@incollection{kim2022simultaneous,
title={Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-seq},
author={Kim, Samuel H and Marinov, Georgi K and Bagdatli, S Tansu and Higashino, Soon Il and Shipony, Zohar and Kundaje, Anshul and Greenleaf, William J},
booktitle={Chromatin Accessibility: Methods and Protocols},
pages={187--230},
year={2022},
publisher={Springer US New York, NY}
}

@incollection{marinov2022genome,
title={Genome-wide mapping of active regulatory elements using ATAC-seq},
author={Marinov, Georgi K and Shipony, Zohar and Kundaje, Anshul and Greenleaf, William J},
booktitle={Chromatin Accessibility: Methods and Protocols},
pages={3--19},
year={2022},
publisher={Springer US New York, NY}
}

@incollection{hinks2022single,
title={Single-molecule mapping of chromatin accessibility using NOMe-seq/dSMF},
author={Hinks, Michaela and Marinov, Georgi K and Kundaje, Anshul and Bintu, Lacramioara and Greenleaf, William J},
booktitle={Chromatin Accessibility: Methods and Protocols},
pages={101--119},
year={2022},
publisher={Springer US New York, NY}
}

@Article{boeynaems2023aberrant,
title={Aberrant phase separation is a common killing strategy of positively charged peptides in biology and human disease},
author={Boeynaems, Steven and Ma, X Rosa and Yeong, Vivian and Ginell, Garrett M and Chen, Jian-Hua and Blum, Jacob A and Nakayama, Lisa and Sanyal, Anushka and Briner, Adam and Van Haver, Delphi and others},
journal={bioRxiv},
year={2023},
publisher={Cold Spring Harbor Laboratory Preprints}
}

@Article{knowlesopportunities,
title={Opportunities and challenges for transcriptome-wide association studies},
author={Knowles, David A and Golan, David and Ermel, Raili and Ruusalepp, Arno and Quertermous, Thomas and Hao, Ke and Bj{"o}rkegren, Johan LM and Im, Hae Kyung and Pasaniuc, Bogdan and Rivas, Manuel A and others}
}

@Article{lin2015matters,
title={Matters Arising Response},
author={Lin, Haifan and Chen, Mengjie and Kundaje, Anshul and Valouev, Anton and Yin, Hang and Liu, Na and Neuenkirchen, Nils and Zhong, Mei and Snyder, Michael},
journal={Developmental Cell},
volume={32},
pages={772--774},
year={2015}
}

@Article{schenck2023polyclonal,
title={The polyclonal path to malignant transformation in familial adenomatous polyposis},
author={Schenck, Ryan O and Khan, Aziz and Horning, Aaron and Esplin, Edward D and Monte, Emma and Wu, Si and Hanson, Casey and Bararpour, Nasim and Neves, Stephanie and Jiang, Lihua and others},
journal={Cancer Research},
volume={83},
number={7_Supplement},
pages={3497--3497},
year={2023},
publisher={The American Association for Cancer Research}
}

@Article{hitz2023encode,
title={The ENCODE uniform analysis pipelines},
author={Hitz, Benjamin C and Jin-Wook, Lee and Jolanki, Otto and Kagda, Meenakshi S and Graham, Keenan and Sud, Paul and Gabdank, Idan and Strattan, J Seth and Sloan, Cricket A and Dreszer, Timothy and others},
journal={Biorxiv},
year={2023}
}

@Article{marinov2023caskas,
title={CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping},
author={Marinov, Georgi K and Kim, Samuel H and Bagdatli, S Tansu and Higashino, Soon Il and Trevino, Alexandro E and Tycko, Josh and Wu, Tong and Bintu, Lacramioara and Bassik, Michael C and He, Chuan and others},
journal={Genome Biology},
volume={24},
number={1},
pages={85},
year={2023},
publisher={BioMed Central London}
}

@Article{lareau2023codon,
title={Codon affinity in mitochondrial DNA shapes evolutionary and somatic fitness},
author={Lareau, Caleb A and Yin, Yajie and Gutierrez, Jacob C and Dhindsa, Ryan S and Gribling-Burrer, Anne-Sophie and Hsieh, Yu-Hsin and Nitsch, Lena and Buquicchio, Frank A and Abay, Tsion and Zielinski, Sebastian and others},
journal={bioRxiv},
pages={2023--04},
year={2023},
publisher={Cold Spring Harbor Laboratory}
}

@Article{alexandari2023novo,
title={De novo distillation of thermodynamic affinity from deep learning regulatory sequence models of in vivo protein-DNA binding},
author={Alexandari, Amr M and Horton, Connor A and Shrikumar, Avanti and Shah, Nilay and Li, Eileen and Weilert, Melanie and Pufall, Miles A and Zeitlinger, Julia and Fordyce, Polly M and Kundaje, Anshul},
journal={bioRxiv},
year={2023},
publisher={Cold Spring Harbor Laboratory Preprints}
}

@Article{levin2023slc12a9,
title={SLC12A9 is a lysosome-detoxifying ammonium--chloride co-transporter},
author={Levin-Konigsberg, Roni and Mitra, Koushambi and Nigam, AkshatKumar and Spees, Kaitlyn and Hivare, Pravin and Liu, Katherine and Kundaje, Anshul and Krishnan, Yamuna and Bassik, Michael C},
journal={bioRxiv},
pages={2023--05},
year={2023},
publisher={Cold Spring Harbor Laboratory}
}

@Article{aglago2023genetic,
title={A genetic locus within the FMN1/GREM1 gene region interacts with body mass index in colorectal cancer risk},
author={Aglago, Elom K and Kim, Andre and Lin, Yi and Qu, Conghui and Evangelou, Marina and Ren, Yu and Morrison, John and Albanes, Demetrius and Arndt, Volker and Barry, Elizabeth L and others},
journal={Cancer research},
volume={83},
number={15},
pages={2572--2583},
year={2023},
publisher={American Association for Cancer Research}
}

@Article{lareau2023single,
title={Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells},
author={Lareau, Caleb A and Dubois, Sonia M and Buquicchio, Frank A and Hsieh, Yu-Hsin and Garg, Kopal and Kautz, Pauline and Nitsch, Lena and Praktiknjo, Samantha D and Maschmeyer, Patrick and Verboon, Jeffrey M and others},
journal={Nature genetics},
volume={55},
number={7},
pages={1198--1209},
year={2023},
publisher={Nature Publishing Group US New York}
}

@Article{mahmood2023elucidating,
title={Elucidating the risk of colorectal cancer for variants in hereditary colorectal cancer genes},
author={Mahmood, Khalid and Thomas, Minta and Qu, Conghui and Wang, Xiaoliang and Huyghe, Jeroen R and Joo, Jihoon E and Georgeson, Peter and Arndt, Volker and Berndt, Sonja I and B{'e}zieau, St{'e}phane and others},
journal={Gastroenterology},
volume={165},
number={4},
pages={1070--1076},
year={2023},
publisher={WB Saunders}
}

@Article{brennan2023chromatin,
title={Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation},
author={Brennan, Kaelan J and Weilert, Melanie and Krueger, Sabrina and Pampari, Anusri and Liu, Hsiao-yun and Yang, Ally WH and Morrison, Jason A and Hughes, Timothy R and Rushlow, Christine A and Kundaje, Anshul and others},
journal={Developmental cell},
volume={58},
number={19},
pages={1898--1916},
year={2023},
publisher={Elsevier}
}

@Article{bouras2023genome,
title={Genome-wide interaction analysis of folate for colorectal cancer risk},
author={Bouras, Emmanouil and Kim, Andre E and Lin, Yi and Morrison, John and Du, Mengmeng and Albanes, Demetrius and Barry, Elizabeth L and Baurley, James W and Berndt, Sonja I and Bien, Stephanie A and others},
journal={The American journal of clinical nutrition},
volume={118},
number={5},
pages={881--891},
year={2023},
publisher={Elsevier}
}

@Article{nigam2024drug,
title={Drug Discovery in Low Data Regimes: Leveraging a Computational Pipeline for the Discovery of Novel SARS-CoV-2 Nsp14-MTase Inhibitors},
author={Nigam, AkshatKumar and Hurley, Matthew FD and Li, Fengling and Konkol'ov{'a}, Eva and Kl{'\i}ma, Martin and Tryl{\v{c}}ov{'a}, Jana and Pollice, Robert and {\c{C}}inaro{\u{g}}lu, S{"u}leyman Selim and Levin-Konigsberg, Roni and Handjaya, Jasemine and others},
journal={bioRxiv},
pages={2023--10},
year={2024}
}

@Article{nair2023transcription,
title={Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency},
author={Nair, Surag and Ameen, Mohamed and Sundaram, Laksshman and Pampari, Anusri and Schreiber, Jacob and Balsubramani, Akshay and Wang, Yu Xin and Burns, David and Blau, Helen M and Karakikes, Ioannis and others},
journal={bioRxiv},
year={2023},
publisher={Cold Spring Harbor Laboratory Preprints}
}

@Article{zhouautomatic,
title={Automatic Detection of Complex Structural Genome Variation Across Human Populations and in Brains of Individuals with Psychiatric Disorders},
author={Zhou, Bo and Arthur, Joseph G and Guo, Hanmin and Kim, Taeyoung and Huang, Yiling and Pattni, Reenal and Kundu, Soumya and Luo, Jay XJ and Lee, HoJoon and Wang, Tao and others}
}

@Article{marinov2023landscape,
title={The landscape of the histone-organized chromatin of Bdellovibrionota bacteria},
author={Marinov, Georgi K and Doughty, Benjamin and Kundaje, Anshul and Greenleaf, William J},
journal={bioRxiv},
year={2023},
publisher={Cold Spring Harbor Laboratory Preprints}
}

@Article{alexandarineural,
title={Neural networks can extract thermodynamic DNA sequence affinities from in vivo binding profiles of transcription factor binding},
author={Alexandari, Amr M and Horton, Connor and Shrikumar, Avanti and Fordyce, Polly and Kundaje, Anshul}
}

@Article{degorter2023transcriptomics,
title={Transcriptomics and chromatin accessibility in multiple African population samples},
author={DeGorter, Marianne K and Goddard, Pag{'e} C and Karakoc, Emre and Kundu, Soumya and Yan, Stephanie M and Nachun, Daniel and Abell, Nathan and Aguirre, Matthew and Carstensen, Tommy and Chen, Ziwei and others},
journal={bioRxiv},
year={2023},
publisher={Cold Spring Harbor Laboratory Preprints}
}

@Article{swaffer2023rna,
title={RNA polymerase II dynamics and mRNA stability feedback scale mRNA amounts with cell size},
author={Swaffer, Matthew P and Marinov, Georgi K and Zheng, Huan and Valenzuela, Lucas Fuentes and Tsui, Crystal Yee and Jones, Andrew W and Greenwood, Jessica and Kundaje, Anshul and Greenleaf, William J and Reyes-Lamothe, Rodrigo and others},
journal={Cell},
volume={186},
number={24},
pages={5254--5268},
year={2023},
publisher={Elsevier}
}

@Article{lareau2023latent,
title={Latent human herpesvirus 6 is reactivated in CAR T cells},
author={Lareau, Caleb A and Yin, Yajie and Maurer, Katie and Sandor, Katalin D and Daniel, Bence and Yagnik, Garima and Pe{~n}a, Jos{'e} and Crawford, Jeremy Chase and Spanjaart, Anne M and Gutierrez, Jacob C and others},
journal={Nature},
volume={623},
number={7987},
pages={608--615},
year={2023},
publisher={Nature Publishing Group UK London}
}

@Article{gschwind2023encyclopedia,
title={An encyclopedia of enhancer-gene regulatory interactions in the human genome},
author={Gschwind, Andreas R and Mualim, Kristy S and Karbalayghareh, Alireza and Sheth, Maya U and Dey, Kushal K and Jagoda, Evelyn and Nurtdinov, Ramil N and Xi, Wang and Tan, Anthony S and Jones, Hank and others},
journal={bioRxiv},
year={2023},
publisher={Cold Spring Harbor Laboratory Preprints}
}

@Article{kuderna2024identification,
title={Identification of constrained sequence elements across 239 primate genomes},
author={Kuderna, Lukas FK and Ulirsch, Jacob C and Rashid, Sabrina and Ameen, Mohamed and Sundaram, Laksshman and Hickey, Glenn and Cox, Anthony J and Gao, Hong and Kumar, Arvind and Aguet, Francois and others},
journal={Nature},
volume={625},
number={7996},
pages={735--742},
year={2024},
publisher={Nature Publishing Group UK London}
}

@Article{martyn2023rewriting,
title={Rewriting regulatory DNA to dissect and reprogram gene expression},
author={Martyn, Gabriella E and Montgomery, Michael T and Jones, Hank and Guo, Katherine and Doughty, Benjamin R and Linder, Johannes and Chen, Ziwei and Cochran, Kelly and Lawrence, Kathryn A and Munson, Glen and others},
journal={bioRxiv},
year={2023},
publisher={Cold Spring Harbor Laboratory Preprints}
}

@Article{stern2024genome,
title={Genome-Wide Gene--Environment Interaction Analyses to Understand the Relationship between Red Meat and Processed Meat Intake and Colorectal Cancer Risk},
author={Stern, Mariana C and Sanchez Mendez, Joel and Kim, Andre E and Ob{'o}n-Santacana, Mireia and Moratalla-Navarro, Ferran and Mart{'\i}n, Vicente and Moreno, Victor and Lin, Yi and Bien, Stephanie A and Qu, Conghui and others},
journal={Cancer Epidemiology, Biomarkers & Prevention},
volume={33},
number={3},
pages={400--410},
year={2024},
publisher={American Association for Cancer Research}
}

@Article{encode2020expanded,
title={Expanded encyclopaedias of DNA elements in the human and mouse genomes},
author={ENCODE Project Consortium and others},
journal={Nature},
volume={583},
number={7818},
pages={699--710},
year={2020},
publisher={Nature Publishing Group}
}

@Article{critical2024cagi,
title={CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods},
journal={Genome biology},
volume={25},
number={1},
pages={53},
year={2024},
publisher={BioMed Central London}
}

@inproceedings{carreras2024genome,
title={Genome-wide interaction study with smoking for colorectal cancer risk identifies novel genetic loci related to tumor suppression, inflammation and immune response},
author={Carreras-Torres, Robert and Kim, Andre E and Lin, Yi and Diez-Obrero, Virginia and Bien, Stephanie A and Qu, Conghui and Wang, Jun and Dimou, Niki and Aglago, Elom K and Bouras, Emmanouil and others},
booktitle={EUROPEAN JOURNAL OF HUMAN GENETICS},
volume={32},
pages={772--772},
year={2024},
organization={SPRINGERNATURE CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND}
}

@Article{marinov2024protocol,
title={Protocol for mapping the three-dimensional organization of dinoflagellate genomes},
author={Marinov, Georgi K and Kundaje, Anshul and Greenleaf, William J and Grossman, Arthur R},
journal={STAR protocols},
volume={5},
number={2},
pages={102941},
year={2024},
publisher={Elsevier}
}

@Article{jain2024critical,
title={Critical assessment of genome interpretation consortium. CAGI, the critical assessment of genome interpretation, establishes progress and pprospects for computational genetic variant interpretation methods.},
author={Jain, Shantanu and Bakolitsa, Constantina and Steven, E Brenner and Radivojac, Predrag and Moult, John and Repo, Susanna and Roger, A Hoskins and Andreoletti, Gaia and Barsky, Daniel and Chellapan, Ajithavalli and others},
journal={Genome Biology},
volume={22},
number={22; 25 (1): 53.},
pages={1--46},
year={2024},
publisher={Springer Nature}
}

@Article{tian2024genetic,
title={Genetic risk impacts the association of menopausal hormone therapy with colorectal cancer risk},
author={Tian, Yu and Lin, Yi and Qu, Conghui and Arndt, Volker and Baurley, James W and Berndt, Sonja I and Bien, Stephanie A and Bishop, D Timothy and Brenner, Hermann and Buchanan, Daniel D and others},
journal={British journal of cancer},
volume={130},
number={10},
pages={1687--1696},
year={2024},
publisher={Nature Publishing Group UK London}
}

@Article{min2024predicting,
title={Predicting chromatin conformation contact maps},
author={Min, Alan and Schreiber, Jacob and Kundaje, Anshul and Noble, William Stafford},
journal={bioRxiv},
year={2024},
publisher={Cold Spring Harbor Laboratory Preprints}
}

@Article{wojcik2023beyond,
title={Beyond the exome: what’s next in diagnostic testing for Mendelian conditions},
author={Wojcik, Monica H and Reuter, Chloe M and Marwaha, Shruti and Mahmoud, Medhat and Duyzend, Michael H and Barseghyan, Hayk and Yuan, Bo and Boone, Philip M and Groopman, Emily E and D{'e}lot, Emmanu{`e}le C and others},
journal={The American Journal of Human Genetics},
volume={110},
number={8},
pages={1229--1248},
year={2023},
publisher={Elsevier}
}

@misc{amemiya2019encode,
title={The ENCODE blacklist: identification of problematic regions of the genome. Sci. Rep. 9, 9354},
author={Amemiya, HM and Kundaje, A and Boyle, AP},
year={2019}
}

@Article{chen2024fine,
title={Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes},
author={Chen, Zhishan and Guo, Xingyi and Tao, Ran and Huyghe, Jeroen R and Law, Philip J and Fernandez-Rozadilla, Ceres and Ping, Jie and Jia, Guochong and Long, Jirong and Li, Chao and others},
journal={Nature Communications},
volume={15},
number={1},
pages={3557},
year={2024},
publisher={Nature Publishing Group UK London}
}

@Article{papadimitriou2024genome,
title={Genome-wide interaction study of dietary intake of fibre, fruits, and vegetables with risk of colorectal cancer},
author={Papadimitriou, Nikos and Kim, Andre and Kawaguchi, Eric S and Morrison, John and Diez-Obrero, Virginia and Albanes, Demetrius and Berndt, Sonja I and B{'e}zieau, St{'e}phane and Bien, Stephanie A and Bishop, D Timothy and others},
journal={EBioMedicine},
volume={104},
year={2024},
publisher={Elsevier}
}

@Article{nigam2024application,
title={Application of established computational techniques to identify potential SARS-CoV-2 Nsp14-MTase inhibitors in low data regimes},
author={Nigam, AkshatKumar and Hurley, Matthew FD and Li, Fengling and Konkol'ov{'a}, Eva and Kl{'\i}ma, Martin and Tryl{\v{c}}ov{'a}, Jana and Pollice, Robert and {\c{C}}inaroǧlu, S{"u}leyman Selim and Levin-Konigsberg, Roni and Handjaya, Jasemine and others},
journal={Digital Discovery},
year={2024},
publisher={Royal Society of Chemistry}
}

@Article{pratt2024using,
title={Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements},
author={Pratt, Henry E and Andrews, Gregory and Shedd, Nicole and Phalke, Nishigandha and Li, Tongxin and Pampari, Anusri and Jensen, Matthew and Wen, Cindy and Consortium, PsychENCODE and Gandal, Michael J and others},
journal={Science Advances},
volume={10},
number={21},
pages={eadj4452},
year={2024},
publisher={American Association for the Advancement of Science}
}

@Article{drew2024two,
title={Two genome-wide interaction loci modify the association of nonsteroidal anti-inflammatory drugs with colorectal cancer},
author={Drew, David A and Kim, Andre E and Lin, Yi and Qu, Conghui and Morrison, John and Lewinger, Juan Pablo and Kawaguchi, Eric and Wang, Jun and Fu, Yubo and Zemlianskaia, Natalia and others},
journal={Science Advances},
volume={10},
number={22},
pages={eadk3121},
year={2024},
publisher={American Association for the Advancement of Science}
}

@Article{naqvi2024transfer,
title={Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage},
author={Naqvi, Sahin and Kim, Seungsoo and Tabatabaee, Saman and Pampari, Anusri and Kundaje, Anshul and Pritchard, Jonathan K and Wysocka, Joanna},
journal={bioRxiv},
pages={2024--05},
year={2024},
publisher={Cold Spring Harbor Laboratory}
}

@Article{cochran2024dissecting,
title={Dissecting the cis-regulatory syntax of transcription initiation with deep learning},
author={Cochran, Kelly and Yin, Melody and Mantripragada, Anika and Schreiber, Jacob and Marinov, Georgi K and Shah, Sagar R and Yu, Haiyuan and T LIS, JOHN and Kundaje, Anshul},
journal={bioRxiv},
year={2024}
}

@Article{marinov2024updated,
title={An updated compendium and reevaluation of the evidence for nuclear transcription factor occupancy over the mitochondrial genome},
author={Marinov, Georgi K and Ramalingam, Vivekanandan and Greenleaf, William J and Kundaje, Anshul},
journal={bioRxiv},
year={2024}
}

@Article{myers2011user,
title={A user's guide to the encyclopedia of DNA elements (ENCODE)},
author={Myers, Richard M and Stamatoyannopoulos, John and Snyder, Michael and Dunham, Ian and Hardison, Ross C and Bernstein, Bradley E and Gingeras, Thomas R and Kent, W James and Birney, Ewan and Wold, Barbara and others},
journal={PLoS biology},
volume={9},
number={4},
year={2011}
}

@Article{zhu2024global,
title={Global loss of promoter--enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis},
author={Zhu, Yizhou and Lee, Hayan and White, Shannon and Weimer, Annika K and Monte, Emma and Horning, Aaron and Nevins, Stephanie A and Esplin, Edward D and Paul, Kristina and Krieger, Gat and others},
journal={Nature Cancer},
volume={5},
number={11},
pages={1697--1712},
year={2024},
publisher={Nature Publishing Group}
}

@Article{abrignani2016international,
title={The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery},
author={Abrignani, Sergio and Adams, David and de Almeida, Melanie and Altucci, Lucia and Amin, Viren and Amit, Ido and Stylianos, E and Aparicio, Samuel and Arima, Takahiro and Arrigoni, Laura and others},
journal={Cell},
volume={167},
number={5},
pages={1145--1149},
year={2016}
}

@Article{corces2017omni,
title={Omni-ATAC-seq: improved ATAC-seq protocol},
author={Corces, M Ryan and Cho, Seung Woo and Chang, Howard Y and Greenleaf, William J and Montine, Thomas J and Khavari, Paul A and Kundaje, Anshul and Risca, Viviana I and Orloff, Lisa A and Kasowski, Maya and others},
year={2017}
}

@misc{shrikumar2017proceedings,
title={Proceedings of the 34th International Conference on Machine Learning},
author={Shrikumar, Avanti and Greenside, Peyton and Kundaje, Anshul and Doina, Precup and Yee, WT},
journal={vol. 70 of Proceedings of Machine Learning Research},
pages={3145--3153},
year={2017},
publisher={PMLR}
}

@Article{dunham2012integrated,
title={An integrated encyclopedia of DNA elements in the human genome},
author={Dunham, Ian and Birney, Ewan and Lajoie, Bryan R and Sanyal, Amartya and Dong, Xianjun and Greven, Melissa and Lin, Xinying and Wang, Jie and Whitfield, Troy W and Zhuang, Jiali and others},
year={2012}
}

@Article{shrikumar2017learning,
title={Learning important features through propagating activation differences. arXiv},
author={Shrikumar, Avanti and Greenside, Peyton and Kundaje, Anshul},
journal={arXiv preprint arXiv:1704.02685},
volume={10},
year={2017}
}

@Article{kowalski2024multiplexed,
title={Multiplexed single-cell characterization of alternative polyadenylation regulators},
author={Kowalski, Madeline H and Wessels, Hans-Hermann and Linder, Johannes and Dalgarno, Carol and Mascio, Isabella and Choudhary, Saket and Hartman, Austin and Hao, Yuhan and Kundaje, Anshul and Satija, Rahul},
journal={Cell},
volume={187},
number={16},
pages={4408--4425},
year={2024},
publisher={Elsevier}
}

@Article{chong2024considerations,
title={Considerations for reporting variants in novel candidate genes identified during clinical genomic testing},
author={Chong, Jessica X and Berger, Seth I and Baxter, Samantha and Smith, Erica and Xiao, Changrui and Calame, Daniel G and Hawley, Megan H and Rivera-Munoz, E Andres and DiTroia, Stephanie and Abouhala, Siwaar and others},
journal={Genetics in Medicine},
volume={26},
number={10},
pages={101199},
year={2024},
publisher={Elsevier}
}

@Article{li2024multiomic,
title={A Multiomic Timecourse Atlas Of Murine Vascular Disease Smooth Muscle Cell Transition Phenotypes And Their Perturbation With Tcf21 Knockout},
author={Li, Daniel Y and Kundu, Soumya and Gu, Wenduo and Cheng, Paul and Jackson, William R and Zhao, Quanyi and Nguyen, Trieu and Ramste, Markus O and Monteiro, Jo{~a}o P and Li, Kevin and others},
journal={Arteriosclerosis, Thrombosis, and Vascular Biology},
volume={44},
number={Suppl_1},
pages={A2122--A2122},
year={2024},
publisher={Lippincott Williams & Wilkins Hagerstown, MD}
}

@Article{bahmani2024achieving,
title={Achieving Inclusive Healthcare through Integrating Education and Research with AI and Personalized Curricula},
author={Bahmani, Amir and Cha, Kexin and Alavi, Arash and Dixit, Amit and Ross, Antony and Park, Ryan and Goncalves, Francesca and Ma, Shirley and Saxman, Paul and Nair, Ramesh and others},
journal={medRxiv},
pages={2024--07},
year={2024},
publisher={Cold Spring Harbor Laboratory Press}
}

@Article{leedisease,
title={Disease diagnostics using machine learning of immune receptors},
author={Lee, Krishna M and Cunningham-Rundles, Charlotte and Moody10, M Anthony and Haynes11, Barton F and Pinsky, Benjamin A and Heath15, James R and James, Judith A and Yang, Samuel and Blish14, Catherine A and Tibshirani17, Robert and others}
}

@Article{alexandari2022novo,
title={De novo inference of thermodynamic binding energies using deep learning models of in vivo transcription factor binding},
author={Alexandari, Amr and Horton, Connor and Shrikumar, Avanti and Shah, Nilay and Li, Eileen and Weilert, Melanie and Pufall, Miles and Zeitlinger, Julia and Fordyce, Polly and Kundaje, Anshul},
year={2022},
publisher={Zenodo}
}

@Article{chai2024flexible,
title={Flexible use of conserved motif vocabularies constrains genome access in cell type evolution},
author={Chai, Chew and Gibson, Jesse and Li, Pengyang and Pampari, Anusri and Patel, Aman and Kundaje, Anshul and Wang, Bo},
journal={bioRxiv},
year={2024}
}

@Article{kosicki2024mutagenesis,
title={Mutagenesis Sensitivity Mapping of Human Enhancers In Vivo},
author={Kosicki, Michael and Zhang, Boyang and Pampari, Anusri and Akiyama, Jennifer A and Plajzer-Frick, Ingrid and Novak, Catherine S and Tran, Stella and Zhu, Yiwen and Kato, Momoe and Hunter, Riana D and others},
journal={bioRxiv},
year={2024}
}

@Article{zhao2024cell,
title={A cell and transcriptome atlas of the human arterial vasculature},
author={Zhao, Quanyi and Pedroza, Albert and Sharma, Disha and Gu, Wenduo and Dalal, Alex and Weldy, Chad and Jackson, William and Li, Daniel Yuhang and Ryan, Yana and Nguyen, Trieu and others},
journal={bioRxiv},
pages={2024--09},
year={2024},
publisher={Cold Spring Harbor Laboratory}
}

@Article{roadmap2015integrative,
title={Integrative analysis of 111 reference human epigenomes},
author={Roadmap Epigenomics, C and Kundaje, Anshul and Meuleman, Wouter and Ernst, Jason and Bilenky, Misha and Yen, Angela and Heravi-Moussavi, Alireza and Kheradpour, Pouya and Zhang, Zhizhuo and Wang, Jianrong and others},
journal={Nature},
volume={518},
number={7539},
pages={317--30},
year={2015}
}

@Article{coronado2024cxcl12,
title={CXCL12 drives natural variation in coronary artery anatomy across diverse populations},
author={Coronado, Pamela E Rios and Zanetti, Daniela and Zhou, Jiayan and Naftaly, Jeffrey A and Prabala, Pratima and Jaimes, Azalia M Mart{'\i}nez and Farah, Elie N and Fan, Xiaochen and Kundu, Soumya and Deshpande, Salil S and others},
journal={medRxiv},
pages={2023--10},
year={2024}
}

@Article{jha2024prediction,
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 Lieberman and Bertero, Alessandro and Noble, William Stafford},
journal={bioRxiv},
year={2024}
}

@Article{valbuena2024prediction,
title={Prediction and design of transcriptional repressor domains with large-scale mutational scans and deep learning},
author={Valbuena, Raeline and Nigam, AkshatKumar and Tycko, Josh and Suzuki, Peter and Spees, Kaitlyn and Aradhana, Aradhana and Arana, Sophia and Du, Peter and Patel, Roshni A and Bintu, Lacramioara and others},
journal={bioRxiv},
pages={2024--09},
year={2024},
publisher={Cold Spring Harbor Laboratory}
}

@Article{thomas2025characterization,
title={Characterization of additive gene--environment interactions for colorectal cancer risk},
author={Thomas, Claire E and Lin, Yi and Kim, Michelle and Kawaguchi, Eric S and Qu, Conghui and Um, Caroline Y and Lynch, Brigid M and Van Guelpen, Bethany and Tsilidis, Kostas and Carreras-Torres, Robert and others},
journal={Epidemiology},
volume={36},
number={1},
pages={126--138},
year={2025},
publisher={LWW}
}

@Article{zhou2024detection,
title={Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders},
author={Zhou, Bo and Arthur, Joseph G and Guo, Hanmin and Kim, Taeyoung and Huang, Yiling and Pattni, Reenal and Wang, Tao and Kundu, Soumya and Luo, Jay XJ and Lee, HoJoon and others},
journal={Cell},
volume={187},
number={23},
pages={6687--6706},
year={2024},
publisher={Elsevier}
}

@Article{ruzicka2024single,
title={Single-cell multi-cohort dissection of the schizophrenia transcriptome},
author={Ruzicka, W Brad and Mohammadi, Shahin and Fullard, John F and Davila-Velderrain, Jose and Subburaju, Sivan and Tso, Daniel Reed and Hourihan, Makayla and Jiang, Shan and Lee, Hao-Chih and Bendl, Jaroslav and others},
journal={Science},
volume={384},
number={6698},
pages={eadg5136},
year={2024},
publisher={American Association for the Advancement of Science}
}

@Article{zhou202480,
title={80. IMPLICATION OF COMPLEX STRUCTURAL GENOME VARIATION IN THE GENETIC ARCHITECTURE OF NEUROPSYCHIATRIC DISORDERS: INSIGHTS FROM HUMAN POPULATION ANALYSIS AND FROM POSTMORTEM BRAINS OF INDIVIDUALS WITH PSYCHIATRIC DISORDERS},
author={Zhou, Bo and Arthur, Joseph and Guo, Hanmin and Kim, Taeyoung and Huang, Yiling and Pattni, Reenal and Song, Giltae and Palejev, Dean and Dohna, Heinrich and Roussos, Panos and others},
journal={European Neuropsychopharmacology},
volume={87},
pages={93},
year={2024},
publisher={Elsevier}
}

@Article{levin2025slc12a9,
title={An SLC12A9-dependent ion transport mechanism maintains lysosomal osmolarity},
author={Levin-Konigsberg, Roni and Mitra, Koushambi and Spees, Kaitlyn and Nigam, AkshatKumar and Liu, Katherine and Januel, Camille and Hivare, Pravin and Arana, Sophia M and Prolo, Laura M and Kundaje, Anshul and others},
journal={Developmental Cell},
volume={60},
number={2},
pages={220--235},
year={2025},
publisher={Elsevier}
}

@Article{esplin2024multiomic,
title={Multiomic analysis of familial adenomatous polyposis reveals molecular pathways associated with early tumorigenesis},
author={Esplin, Edward D and Hanson, Casey and Wu, Si and Horning, Aaron M and Barapour, Nasim and Nevins, Stephanie A and Jiang, Lihua and Contrepois, K{'e}vin and Lee, Hayan and Guha, Tuhin K and others},
journal={Nature Cancer},
volume={5},
number={11},
pages={1737--1753},
year={2024},
publisher={Nature Publishing Group}
}

@Article{kundaje2015integrative,
title={Integrative analysis of 111 reference human epigenomes. Research Support, NIH, Extramural Research Support, Non-US Gov't Research Support, US Gov't, Non-PHS},
author={Kundaje, A and Meuleman, W and Ernst, J and others},
journal={Nature},
volume={518},
number={7539},
pages={317--330},
year={2015}
}

@Article{im2024sequence,
title={Sequence-based TCR-Peptide Representations Using Cross-Epitope Contrastive Fine-tuning of Protein Language Models},
author={Im, Chiho and Zhao, Ryan and Boyd, Scott D and Kundaje, Anshul},
journal={bioRxiv},
pages={2024--10},
year={2024},
publisher={Cold Spring Harbor Laboratory}
}

@Article{kaur2024gencode,
title={GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing},
author={Kaur, Gazaldeep and Perteghella, Tamara and Carbonell-Sala, Silvia and Gonzalez-Martinez, Jose and Hunt, Toby and Madry, Tomasz and Jungreis, Irwin and Arnan, Carme and Lagarde, Julien and Borsari, Beatrice and others},
journal={bioRxiv},
pages={2024--10},
year={2024},
publisher={Cold Spring Harbor Laboratory}
}

@Article{fabiha2024consensus,
title={A consensus variant-to-function score to functionally prioritize variants for disease},
author={Fabiha, Tabassum and Evergreen, Ivy and Kundu, Soumya and Pampari, Anusri and Abramov, Sergey and Boytsov, Alexandr and Strouse, Kari and Dura, Katherine and Fang, Weixiang and Kerner, Gaspard and others},
journal={bioRxiv},
pages={2024--11},
year={2024},
publisher={Cold Spring Harbor Laboratory}
}

@Article{patel2024dart,
title={DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA},
author={Patel, Aman and Singhal, Arpita and Wang, Austin and Pampari, Anusri and Kasowski, Maya and Kundaje, Anshul},
journal={arXiv preprint arXiv:2412.05430},
year={2024}
}

@Article{roadmap2015heravi,
title={Heravi-540 Moussavi},
author={Roadmap Epigenomics, C and Kundaje, A and Meuleman, W and Ernst, J and Bilenky, M and Yen, A},
journal={A., Kheradpour, P., Zhang, Z., Wang, J., et al},
pages={317--330},
year={2015}
}

@Article{encode2020813,
title={813 Shoresh},
author={ENCODE Project Consortium and Moore, JE and Purcaro, MJ and Pratt, HE and Epstein, CB and others},
journal={N., Adrian, J., Kawli, T., Davis, CA, Dobin, A., et al},
pages={699--710},
year={2020}
}

@Article{mudge2025gencode,
title={GENCODE 2025: reference gene annotation for human and mouse},
author={Mudge, Jonathan M and Carbonell-Sala, S{'\i}lvia and Diekhans, Mark and Martinez, Jose Gonzalez and Hunt, Toby and Jungreis, Irwin and Loveland, Jane E and Arnan, Carme and Barnes, If and Bennett, Ruth and others},
journal={Nucleic Acids Research},
volume={53},
number={D1},
pages={D966--D975},
year={2025},
publisher={Oxford University Press}
}

@Article{ma2024molecular,
title={Molecular convergence of risk variants for congenital heart defects leveraging a regulatory map of the human fetal heart},
author={Ma, X Rosa and Conley, Stephanie D and Kosicki, Michael and Bredikhin, Danila and Cui, Ran and Tran, Steven and Sheth, Maya U and Qiu, Wei-Lin and Chen, Sijie and Kundu, Soumya and others},
journal={medRxiv},
pages={2024--11},
year={2024},
publisher={Cold Spring Harbor Laboratory Press}
}

@Article{marinov2025chromatin,
title={The chromatin landscape of the histone-possessing Bacteriovorax bacteria},
author={Marinov, Georgi K and Doughty, Benjamin and Kundaje, Anshul and Greenleaf, William J},
journal={Genome Research},
volume={35},
number={1},
pages={109--123},
year={2025},
publisher={Cold Spring Harbor Lab}
}

@Article{sheth2024mapping,
title={Mapping enhancer-gene regulatory interactions from single-cell data},
author={Sheth, Maya U and Qiu, Wei-Lin and Ma, X Rosa and Gschwind, Andreas R and Jagoda, Evelyn and Tan, Anthony S and Einarsson, Hj{"o}rleifur and Gorissen, Bram L and Dubocanin, Danilo and McGinnis, Christopher S and others},
journal={bioRxiv},
pages={2024--11},
year={2024},
publisher={Cold Spring Harbor Laboratory}
}

@Article{chen2024directionality,
title={Directionality of transcriptional regulatory elements},
author={Chen, You and Shah, Sagar R and Leung, Alden and Paramo, Mauricio I and Cochran, Kelly and Kundaje, Anshul and Clark, Andrew G and Lis, John T and Yu, Haiyuan},
journal={bioRxiv},
pages={2024--12},
year={2024},
publisher={Cold Spring Harbor Laboratory}
}

@Article{mani2024deep,
title={Deep learning the cis-regulatory code of epigenomic rewiring by fusion transcription factors in pediatric leukemia},
author={Mani, Shouvik and Grubert, Fabian and Gratzinger, Dita and Kundaje, Anshul and Kasowski, Maya},
journal={Blood},
volume={144},
pages={4993},
year={2024},
publisher={Content Repository Only!}
}

@Article{white2024comparative,
title={Comparative atlas of genome-wide chromatin-associated protein co-occupancy},
author={White, Shannon M and Moyers, Belle A and Wang, Tao and Mackiewicz, Mark and Weimer, Annika K and Grubert, Fabian and Ramalingam, Vivekanandan and Luo, Jay XJ and Jiang, Lixia and Shi, Minyi and others},
journal={bioRxiv},
pages={2024--12},
year={2024},
publisher={Cold Spring Harbor Laboratory}
}

@Article{moore2024expanded,
title={An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation},
author={Moore, Jill E and Pratt, Henry E and Fan, Kaili and Phalke, Nishigandha and Fisher, Jonathan and Elhajjajy, Shaimae I and Andrews, Gregory and Gao, Mingshi and Shedd, Nicole and Fu, Yu and others},
journal={bioRxiv},
pages={2024--12},
year={2024},
publisher={Cold Spring Harbor Laboratory}
}

@Article{pampari2024chrombpnet,
title={ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants},
author={Pampari, Anusri and Shcherbina, Anna and Kvon, Evgeny Z and Kosicki, Michael and Nair, Surag and Kundu, Soumya and Kathiria, Arwa S and Risca, Viviana I and Kuningas, Kristiina and Alasoo, Kaur and others},
journal={bioRxiv},
pages={2024--12},
year={2024},
publisher={Cold Spring Harbor Laboratory}
}

@Article{kundaje2025artificial,
title={Artificial intelligence in molecular biology},
author={Kundaje, Anshul and Pollard, Katherine S and Ma, Jian and Chang, Xing and Chen, Mengjie and Rohs, Remo},
journal={Molecular Cell},
volume={85},
number={2},
pages={193--198},
year={2025},
publisher={Elsevier}
}

@Article{zhu2025author,
title={Author Correction: Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis},
author={Zhu, Yizhou and Lee, Hayan and White, Shannon and Weimer, Annika K and Monte, Emma and Horning, Aaron and Nevins, Stephanie A and Esplin, Edward D and Paul, Kristina and Krieger, Gat and others},
journal={Nature cancer},
year={2025}
}