arrow
Back
A

Anshul Kundaje

stanford university school of medicine

85H-index
620Paper Count
5.9WCitation Count
Published Papers 118
Publication Date
Mapping enhancer–gene regulatory interactions from single-cell data
err2026-08-03
err0
errOAAI
errMaya U. Sheth; Wei-Lin Qiu; X. Rosa Ma; Andreas R. Gschwind; Evelyn Jagoda; Anthony S. Tan; James Galante; Judhajeet Ray; Dulguun Amgalan; Hjörleifur Einarsson; Bram L. Gorissen; Danilo Dubocanin; Christopher S. McGinnis; Jacob Huang; Glen Munson; Kayla Brand; Ansuman T. Satpathy; Thouis R. Jones; Lars M. Steinmetz; Anshul Kundaje; Berk Ustun; Jesse M. Engreitz; Robin Andersson
errShare
errSave
An encyclopedia of human enhancer–gene regulatory interactions
errNature
IF48.5
err2026-07-15
err0
errOAAI
errAndreas R. Gschwind; Kristy S. Mualim; Alireza Karbalayghareh; Maya U. Sheth; Kushal K. Dey; Evelyn Jagoda; Ramil N. Nurtdinov; Wang Xi; Anthony S. Tan; James Galante; Hank Jones; X. Rosa Ma; David Yao; Dulguun Amgalan; Judhajeet Ray; Chad J. Munger; Joseph Nasser; Žiga Avsec; Benjamin T. James; Muhammad S. Shamim; Neva C. Durand; Suhas S. P. Rao; Ragini Mahajan; Benjamin R. Doughty; Kalina Andreeva; Jacob C. Ulirsch; Kaili Fan; Elizabeth M. Perez; Tri C. Nguyen; David R. Kelley; Hilary K. Finucane; Jill E. Moore; Zhiping Weng; Manolis Kellis; Michael C. Bassik; Berk Ustun; Alkes L. Price; Michael A. Beer; Roderic Guigó; John A. Stamatoyannopoulos; Erez Lieberman Aiden; William J. Greenleaf; Christina S. Leslie; Lars M. Steinmetz; Anshul Kundaje; Jesse M. Engreitz
errShare
errSave
Positional interpretation of cis-regulatory code and nucleosome organization with deep learning models
err2026-07-04
err0
errOAAI
errCharles E. McAnany; Melanie Weilert; Grishma Mehta; Fahad Kamulegeya; Jennifer M. Gardner; Jacob Schreiber; Anshul Kundaje; Julia Zeitlinger
errShare
errSave
Decoding common and rare noncoding variant effects across cellular and developmental contexts
err2026-06-15
err0
PREAI
errAndrew R. Marderstein; Soumya Kundu; Evin M. Padhi; Salil Deshpande; Austin Wang; Esther Robb; Ying Sun; Chang M. Yun; Diego Pomales-Matos; Yilin Xie; Serena H. Chang; Iris M. Chin; Aayushi J. Shah; Zachary A. Gardell; M. Ryan Corces; Daniel Nachun; Selin Jessa; Anshul Kundaje; Stephen B. Montgomery
errShare
errSave
Prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC
err2026-04-20
err0
errOAAI
errAnupama Jha; Borislav Hristov; Xiao Wang; Sheng Wang; William J. Greenleaf; Anshul Kundaje; Erez Lieberman Aiden; Alessandro Bertero; William Stafford Noble
errShare
errSave
Multiomics and deep learning dissect regulatory syntax in human development
errNature
IF48.5
err2026-04-08
err0
errOAAI
errBetty B. Liu; Selin Jessa; Samuel H. Kim; Yan Ting Ng; Soon Il Higashino; Georgi K. Marinov; Derek C. Chen; Benjamin E. Parks; Li Li; Tri C. Nguyen; Austin T. Wang; Sean K. Wang; Meng How Tan; Serena Y. Tan; Michael Kosicki; Len A. Pennacchio; Eyal Ben-David; Anca M. Pasca; Anshul Kundaje; Kyle K. H. Farh; William J. Greenleaf
errShare
errSave
Vascular smooth muscle cell state trajectories mediate molecular mechanisms of coronary disease risk
err2026-03-17
err0
errOAAI
errDaniel Y. Li; Soumya Kundu; Paul Cheng; Wenduo Gu; Matthew D. Worssam; William R. Jackson; Quanyi Zhao; Trieu Nguyen; Amelia M. Yu; João P. Monteiro; Roxanne D. Caceres; Stanley Dale; Brian T. Palmisano; Chad S. Weldy; Markus Ramste; Ramendra Kundu; Anshul Kundaje; Robert C. Wirka; Thomas Quertermous
errShare
errSave
An expanded registry of candidate cis-regulatory elements
errNature
IF48.5
err2026-01-07
err0
errOAAI
errJill E. Moore; Henry E. Pratt; Kaili Fan; Nishigandha Phalke; Jonathan Fisher; Shaimae I. Elhajjajy; Gregory Andrews; Mingshi Gao; Nicole Shedd; Yu Fu; Matthew C. Lacadie; Jair Meza; Mansi Khandpekar; Mohit Ganna; Eva Choudhury; Ross Swofford; Huong Phan; Christian C. Ramirez; Maxwell Campbell; Mary Likhite; Nina P. Farrell; Annika K. Weimer; Anusri Pampari; Vivekanandan Ramalingam; Fairlie Reese; Beatrice Borsari; Xuezhu Yu; Eve Wattenberg; Marina Ruiz-Romero; Milad Razavi-Mohseni; Jinrui Xu; Timur Galeev; Andres Colubri; Michael A. Beer; Roderic Guigó; Mark B. Gerstein; Jesse M. Engreitz; Mats Ljungman; Timothy E. Reddy; Michael P. Snyder; Charles B. Epstein; Elizabeth Gaskell; Bradley E. Bernstein; Diane E. Dickel; Axel Visel; Len A. Pennacchio; Ali Mortazavi; Anshul Kundaje; Zhiping Weng
errShare
errSave
JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models
err2025-12-01
err0
errOAAI
errOvek baydar, Damla; Rauluseviciute, Ieva; Aronsen, Dina R.; Blanc-Mathieu, Romain; Bonthuis, Ine; De beukelaer, Herman; Ferenc, Katalin; Jegou, Alice; Kumar, Vipin; Lemma, Roza Berhanu; Lucas, Jeremy; Pochon, Mathis; Yun, Chang M.; Ramalingam, Vivekanandan; Deshpande, Salil Sanjay; Patel, Aman; Marinov, Georgi k; Wang, Austin T.; Aguirre, Alejandro; Castro-Mondragon, Jaime a; Baranasic, Damir; Cheneby, Jeanne; Gundersen, Sveinung; Johansen, Morten; Khan, Aziz; Kuijjer, Marieke L.; Hovig, Eivind; Lenhard, Boris; Sandelin, Albin; Vandepoele, Klaas; Wasserman, Wyeth w; Parcy, Francois; Kundaje, Anshul; Mathelier, Anthony
errShare
errSave
Polyclonal origins of human premalignant colorectal lesions
errNature
IF48.5
err2025-11-25
err0
PREAI
errDebra Van Egeren; Ryan O. Schenck; Aziz Khan; Aaron M. Horning; Shanlan Mo; Clemens L. Weiß; Edward D. Esplin; Winston R. Becker; Si Wu; Casey Hanson; Nasim Barapour; Lihua Jiang; Kévin Contrepois; Hayan Lee; Stephanie A. Nevins; Tuhin K. Guha; Hao Zhang; Zhen He; Zhicheng Ma; Emma Monte; Thomas V. Karathanos; Rozelle Laquindanum; Meredith A. Mills; Hassan Chaib; Roxanne Chiu; Ruiqi Jian; Joanne Chan; Mathew Ellenberger; Bahareh Bahmani; Basil Michael; Annika K. Weimer; D. Glen Esplin; Samuel Lancaster; Jeanne Shen; Uri Ladabaum; Teri A. Longacre; Anshul Kundaje; William J. Greenleaf; Zheng Hu; James M. Ford; Michael P. Snyder; Christina Curtis
errShare
errSave
A cell and transcriptome atlas of human arterial vasculature
err2025-10-13
err0
errOAAI
errQuanyi Zhao; Albert Pedroza; Disha Sharma; Wenduo Gu; Alex Dalal; Chad Weldy; William Jackson; Daniel Yuhang Li; Yana Ryan; Trieu Nguyen; Rohan Shad; Brian T. Palmisano; João P. Monteiro; Matthew Worssam; Alexa Berezwitz; Meghana Iyer; Huitong Shi; Ramendra Kundu; Lasemahang Limbu; Juyong Brian Kim; Anshul Kundaje; Michael Fischbein; Robert Wirka; Thomas Quertermous; Paul Cheng
errShare
errSave
Using gene-environment interactions to explore pathways for colorectal cancer risk
err2025-10-01
err0
errOAAI
errBouras, Emmanouil; Yu, Ren; Kim, Andre E.; Markozannes, Georgios; Murphy, Neil; Albanes, Demetrius; Anderson, Laura N.; Barry, Elizabeth L.; Berndt, Sonja I.; Bishop, D. Timothy; Brenner, Hermann; Burnett-Hartman, Andrea; Campbell, Peter T.; Carreras-Torres, Robert; Chan, Andrew T.; Cheng, Iona; Devall, Matthew A.; Diez-Obrero, Virginia; Dimou, Niki; Drew, David A.; Gruber, Stephen B.; Gsur, Andrea; Hoffmeister, Michael; Hsu, Li; Huyghe, Jeroen R.; Kawaguchi, Eric; Keku, Temitope O.; Kundaje, Anshul; Kury, Sebastien; Le Marchand, Loic; Lewinger, Juan Pablo; Li, Li; Lynch, Brigid M.; Moreno, Victor; Morrison, John L.; Newton, Christina C.; Obon-Santacana, Mireia; Palmer, Julie R.; Papadimitriou, Nikos; Pellatt, Andrew J.; Peoples, Anita R.; Pharoah, Paul D. P.; Platz, Elizabeth A.; Qu, Conghui; Ruiz-Narvaez, Edward; Mendez, Joel Sanchez; Schoen, Robert E.; Stern, Mariana C.; Thomas, Claire E.; Tian, Yu; Um, Caroline Y.; Visvanathan, Kala; Vodicka, Pavel; Vymetalkova, Veronika; White, Emily; Wolk, Alicja; Woods, Michael O.; Wu, Anna H.; Gunter, Marc J.; Gauderman, W. James; Peters, Ulrike; Evangelou, Marina; Tsilidis, Konstantinos K.
errShare
errSave
Predicting chromatin conformation contact maps
err2025-09-29
err0
PREAI
errMin, Alan; Schreiber, Jacob; Kundaje, Anshul; Noble, William S.
errShare
errSave
Achieving inclusive healthcare through integrating education and research with AI and personalized curricula
err2025-08-16
err0
errOAAI
errAmir Bahmani; Kexin Cha; Arash Alavi; Amit Dixit; Antony Ross; Ryan Park; Francesca Goncalves; Shirley Ma; Paul Saxman; Ramesh Nair; Ramin Akhavan-Sarraf; Xin Zhou; Meng Wang; Kévin Contrepois; Jennifer Li-Pook-Than; Emma Monte; David Jose Florez Rodriguez; Jaslene Lai; Mohan Babu; Abtin Tondar; Sophia Miryam Schüssler-Fiorenza Rose; Ilya Akbari; Xinyue Zhang; Kritika Yegnashankaran; Joseph Yracheta; Kali Dale; Alison Derbenwick Miller; Scott Edmiston; Eva M. McGhee; Camille Nebeker; Joseph C. Wu; Anshul Kundaje; Michael Snyder
errShare
errSave
Multiomic profiling reveals that prostaglandin E2 reverses aged muscle stem cell dysfunction, leading to increased regeneration and strength
err2025-06-12
err0
PREAI
errYu Xin Wang; Adelaida R. Palla; Andrew T.V. Ho; Daniel C.L. Robinson; Meenakshi Ravichandran; Glenn J. Markov; Thach Mai; Chris Still; Akshay Balsubramani; Surag Nair; Colin A. Holbrook; Ann V. Yang; Peggy E. Kraft; Shiqi Su; David M. Burns; Nora D. Yucel; Lei S. Qi; Anshul Kundaje; Helen M. Blau
errShare
errSave
Predicting expression-altering promoter mutations with deep learning
errScience
IF45.8
err2025-05-29
err0
PREAI
errKishore Jaganathan; Nicole Ersaro; Gherman Novakovsky; Yuchuan Wang; Terena James; Jeremy Schwartzentruber; Petko Fiziev; Irfahan Kassam; Fan Cao; Johann Hawe; Henry Cavanagh; Ashley Lim; Grace Png; Jeremy McRae; Abhimanyu Banerjee; Arvind Kumar; Jacob Ulirsch; Yan Zhang; Francois Aguet; Pierrick Wainschtein; Laksshman Sundaram; Adriana Salcedo; Sofia Kyriazopoulou Panagiotopoulou; Delasa Aghamirzaie; Evin Padhi; Ziming Weng; Shan Dong; Damian Smedley; Mark Caulfield; Anne O’Donnell-Luria; Heidi L. Rehm; Stephan J. Sanders; Anshul Kundaje; Stephen B. Montgomery; Mark T. Ross; Kyle Kai-How Farh
errShare
errSave
Multiomic analysis of familial adenomatous polyposis reveals molecular pathways associated with early tumorigenesis
err2024-10-30
err1
errOAAI
errEsplin, Edward D.; Hanson, Casey; Wu, Si; Horning, Aaron M.; Barapour, Nasim; Nevins, Stephanie A.; Jiang, Lihua; Contrepois, Kevin; Lee, Hayan; Guha, Tuhin K.; Hu, Zheng; Laquindanum, Rozelle; Mills, Meredith A.; Chaib, Hassan; Chiu, Roxanne; Jian, Ruiqi; Chan, Joanne; Ellenberger, Mathew; Becker, Winston R.; Bahmani, Bahareh; Khan, Aziz; Michael, Basil; Weimer, Annika K.; Esplin, D. Glen; Shen, Jeanne; Lancaster, Samuel; Monte, Emma; Karathanos, Thomas V.; Ladabaum, Uri; Longacre, Teri A.; Kundaje, Anshul; Curtis, Christina; Greenleaf, William J.; Ford, James M.; Snyder, Michael P.
errShare
errSave
Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis
err2024-10-30
err2
errOAAI
errZhu, Yizhou; Lee, Hayan; White, Shannon; Weimer, Annika K.; Monte, Emma; Horning, Aaron; Nevins, Stephanie A.; Esplin, Edward D.; Paul, Kristina; Krieger, Gat; Shipony, Zohar; Chiu, Roxanne; Laquindanum, Rozelle; Karathanos, Thomas V.; Chua, Melissa W. Y.; Mills, Meredith; Ladabaum, Uri; Longacre, Teri; Shen, Jeanne; Jaimovich, Ariel; Lipson, Doron; Kundaje, Anshul; Greenleaf, William J.; Curtis, Christina; Ford, James M.; Snyder, Michael P.
errShare
errSave
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
err2024-10-01
err0
PREAI
errZhou, Bo; Arthur, Joseph; Guo, Hanmin; Kim, Taeyoung; Huang, Yiling; Pattni, Reenal; Song, Giltae; Palejev, Dean; Dohna, Heinrich; Roussos, Panos; Kundaje, Anshul; Hallmayer, Joachim; Snyder, Michael; Wong, Wing; Urban, Alexander
errShare
errSave
Genome-wide interaction study of dietary intake of fibre, fruits, and vegetables with risk of colorectal cancer
err2024-06-01
err1
errOAAI
errPapadimitriou, Nikos; Kim, Andre; Kawaguchi, Eric S.; Morrison, John; Diez-Obrero, Virginia; Albanes, Demetrius; Berndt, Sonja I.; Bezieau, Stephane; Bien, Stephanie A.; Bishop, D. Timothy; Bouras, Emmanouil; Brenner, Hermann; Buchanan, Daniel D.; Campbell, Peter T.; Carreras-Torres, Robert; Chan, Andrew T.; Chang-Claude, Jenny; Conti, David, V; Devall, Matthew A.; Dimou, Niki; Drew, David A.; Gruber, Stephen B.; Harrison, Tabitha A.; Hoffmeister, Michael; Huyghe, Jeroen R.; Joshi, Amit D.; Keku, Temitope O.; Kundaje, Anshul; Kury, Sebastien; Le Marchand, Loic; Lewinger, Juan Pablo; Li, Li; Lynch, Brigid M.; Moreno, Victor; Newton, Christina C.; Obon-Santacana, Mireia; Ose, Jennifer; Pellatt, Andrew J.; Peoples, Anita R.; Platz, Elizabeth A.; Qu, Conghui; Rennert, Gad; Ruiz-Narvaez, Edward; Shcherbina, Anna; Stern, Mariana C.; Su, Yu-Ru; Thomas, Duncan C.; Thomas, Claire E.; Tian, Yu; Tsilidis, Konstantinos K.; Ulrich, Cornelia M.; Um, Caroline Y.; Visvanathan, Kala; Wang, Jun; White, Emily; Woods, Michael O.; Schmit, Stephanie L.; Macrae, Finlay; Potter, John D.; Hopper, John L.; Peters, Ulrike; Murphy, Neil; Hsu, Li; Gunter, Marc J.; Gauderman, W. James
errShare
errSave