Anshul Kundaje

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2016-2023
Publications (10 Years): 80

Top Topics

Mitochondrial Dna

Genome Wide Association Study

Top Venues

Nature genetics

bioRxiv : the preprint server for biology

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

This page only lists publications with an associated author ORCID identifier.

Publications

Niki L Dimou, Andre E Kim, Orlagh Flanagan, Neil Murphy, Virginia Diez-Obrero, Anna Shcherbina, Elom Kouassivi Aglago, Emmanouil C Bouras, Peter T Campbell, Graham Casey, Steven Gallinger, Stephen B Gruber, Mark A Jenkins, Yi Lin, Victor Moreno, Edward A Ruiz-Narvaez, Mariana C Stern, Yu Tian, Kostas K Tsilidis, Volker Arndt, Elizabeth L Barry, James W Baurley, Sonja I Berndt, Stéphane Bézieau, Stephanie A Bien, D Timothy Bishop, Hermann Brenner, Arif Budiarto, Robert Carreras-Torres, Tjeng Wawan Cenggoro, Andrew T Chan, Jenny Chang-Claude, Stephen J Chanock, Xuechen Chen, David V Conti, Christopher H Dampier, Matthew Devall, David A Drew, Jane C Figueiredo, Graham G Giles, Andrea Gsur, Tabitha A Harrison, Akihisa Hidaka, Michael Hoffmeister, Jeroen R Huyghe, Kristina Jordahl, Eric Kawaguchi, Temitope O Keku, Susanna C Larsson, Loic Le Marchand, Juan Pablo Lewinger, Li Li, Bharuno Mahesworo, John Morrison, Polly A Newcomb, Christina C Newton, Mireia Obon-Santacana, Jennifer Ose, Rish K Pai, Julie R Palmer, Nikos Papadimitriou, Bens Pardamean, Anita R Peoples, Paul D P Pharoah, Elizabeth A Platz, John D Potter, Gad Rennert, Peter C Scacheri, Robert E Schoen, Yu-Ru Su, Catherine M Tangen, Stephen N Thibodeau, Duncan C Thomas, Cornelia M Ulrich, Caroline Y Um, Franzel J B van Duijnhoven, Kala Visvanathan, Pavel Vodicka, Ludmila Vodickova, Emily White, Alicja Wolk, Michael O Woods, Conghui Qu, Anshul Kundaje, Li Hsu, W James Gauderman, Marc J Gunter, Ulrike Peters
Probing the diabetes and colorectal cancer relationship using gene - environment interaction analyses. British journal of cancer (2023)
Andreas R Gschwind, Kristy S Mualim, Alireza Karbalayghareh, Maya U Sheth, Kushal K Dey, Evelyn Jagoda, Ramil N Nurtdinov, Wang Xi, Anthony S Tan, Hank Jones, X Rosa Ma, David Yao, Joseph Nasser, Žiga Avsec, Benjamin T James, Muhammad Saad 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, Nishigandha Phalke, Manolis Kellis, Michael C Bassik, Alkes L Price, Michael A Beer, Roderic Guigo, John A Stamatoyannopoulos, Erez Lieberman Aiden, William J Greenleaf, Christina S Leslie, Lars M Steinmetz, Anshul Kundaje, Jesse M Engreitz
An encyclopedia of enhancer-gene regulatory interactions in the human genome. bioRxiv : the preprint server for biology (2023)
Madeline H Kowalski, Hans-Hermann Wessels, Johannes Linder, Saket Choudhary, Austin Hartman, Yuhan Hao, Isabella Mascio, Carol Dalgarno, Anshul Kundaje, Rahul Satija
CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators. bioRxiv : the preprint server for biology (2023)
Ceres Fernández-Rozadilla, Maria N Timofeeva, Zhishan Chen, Philip J Law, Minta Thomas, Stephanie L Schmit, Virginia Díez-Obrero, Li Hsu, Juan Fernandez-Tajes, Claire Palles, Kitty Sherwood, Sarah Briggs, Victoria Svinti, Kevin Donnelly, Susan M Farrington, James Blackmur, Peter Vaughan-Shaw, Xiao-Ou Shu, Jirong Long, Qiuyin Cai, Xingyi Guo, Yingchang Lu, Peter Broderick, James B Studd, Jeroen R Huyghe, Tabitha A Harrison, David Conti, Christopher H Dampier, Mathew Devall, Fredrick R Schumacher, Marilena Melas, Gadi Rennert, Mireia Obón-Santacana, Vicente Martín-Sánchez, Ferran Moratalla-Navarro, Jae Hwan Oh, Jeong-Seon Kim, Sun Ha Jee, Keum Ji Jung, Sun-Seog Kweon, Min-Ho Shin, Aesun Shin, Yoon-Ok Ahn, Dong-Hyun Kim, Isao Oze, Wanqing Wen, Keitaro Matsuo, Koichi Matsuda, Chizu Tanikawa, Ze-Fang Ren, Yu-Tang Gao, Wei-Hua Jia, John Hopper, Mark E Jenkins, Aung-Ko Win, Rish Pai, Jane Figueiredo, Robert W Haile, Steven Gallinger, Michael Woods, Polly A Newcomb, David Duggan, Jeremy P Cheadle, Richard S Kaplan, Timothy Maughan, Rachel Kerr, David J Kerr, Iva Kirac, Jan Böhm, Lukka-Pekka Mecklin, Pekka Jousilahti, Paul Knekt, Lauri A Aaltonen, Harri Rissanen, Eero Pukkala, Johan Eriksson, Tatiana Cajuso, Ulrika Hänninen, Johanna Kondelin, Kimmo Palin, Tomas Tanskanen, Laura Renkonen-Sinisalo, Brent Zanke, Satu Männistö, Demetrius Albanes, Stephanie J Weinstein, Edward A Ruiz-Narvaez, Julie Palmer, Daniel D Buchanan, Elizabeth A Platz, Kala Visvanathan, Cornelia Ulrich, Erin M Siegel, Stefanie Brezina, Andrea Gsur, Peter Campbell, Jenny Chang-Claude, Michael Hoffmeister, Hermann Brenner, Martha Slattery, John D Potter, Konstantinos K Tsilidis, Matthias Bernd Schulze, Marc Gunter, Neil Murphy, Antoni Castells, Sergi Castellví-Bel, Leticia Moreira, Volker Arndt, Anna Shcherbina, Mariana Stern, Bens Pardamean, D Timothy Bishop, Graham G Giles, Melissa C Southey, Gregory Idos, Kevin McDonnell, Zomoroda Abu-Ful, Joel Greenson, Katerina Shulman, Flavio Lejbkowicz, Kenneth Offit, Yu-Ru Su, Robert Steinfelder, Temitope Keku, Bethany Van Guelpen, Thomas J Hudson, Heather Hampel, Rachel Pearlman, Sonja Berndt, Richard B Hayes, Marie Elena Martinez, Sushma Thomas, Douglas Corley, Paul D P Pharoah, Susanna C Larsson, Yun Yen, Heinz-Josef Lenz, Emily White, Li Li, Kimberly F Doheny, Elizabeth Pugh, Tameka Shelford, Andrew T Chan, Marcia Cruz-Correa, Annika Lindblom, David Hunter, Amit D Joshi, Clemens Schafmayer, Peter Scacheri, Anshul Kundaje, Deborah Nickerson, Robert E Schoen, Jochen Hampe, Zsofia Stadler, Pavel Vodicka, Ludmila Vodickova, Veronika Vymetalkova, Nickolas Papadopoulos, Chistopher Edlund, William Gauderman, Duncan C Thomas, David Shibata, Amanda Ewart Toland, Sanford Markowitz, Andre Kim, Stephen J Chanock, Franzel van Duijnhoven, Edith J M Feskens, Lori C Sakoda, Manuela Gago-Dominguez, Alicja Wolk, Alessio Naccarati, Barbara Pardini, Liesel M FitzGerald, Soo Chin Lee, Shuji Ogino, Stephanie Bien, Charles Kooperberg, Christopher Li, Yi Lin, Ross Prentice, Conghui Qu, Stéphane Bézieau, Catherine Tangen, Elaine R Mardis, Taiki Yamaji, Norie Sawada, Motoki Iwasaki, Christopher A Haiman, Loic Le Marchand, Anna Wu, Chenxu Qu, Caroline McNeil, Gerhard A Coetzee, Caroline Hayward, Ian J Deary, Sarah E Harris, Evropi Theodoratou, Stuart Reid, Marion Walker, Li Yin Ooi, Victor Moreno, Graham Casey, Stephen Gruber, Ian P M Tomlinson, Quan Long, Malcolm G Dunlop, Richard S Houlston, Ulrike Peters
Author Correction: Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries. Nature genetics (2023)
Robert Carreras-Torres, Andre E Kim, Yi Lin, Virginia Díez-Obrero, Stephanie A Bien, Conghui Qu, Jun Wang, Niki L Dimou, Elom Kouassivi Aglago, Demetrius Albanes, Volker Arndt, James W Baurley, Sonja I Berndt, Stéphane Bézieau, D Timothy Bishop, Emmanouil C Bouras, Hermann Brenner, Arif Budiarto, Peter T Campbell, Graham Casey, Andrew T Chan, Jenny Chang-Claude, Xuechen Chen, David V Conti, Christopher H Dampier, Matthew A M Devall, David A Drew, Jane C Figueiredo, Steven J Gallinger, Graham G Giles, Stephen B Gruber, Andrea Gsur, Marc J Gunter, Tabitha A Harrison, Akihisa Hidaka, Michael Hoffmeister, Jeroen R Huyghe, Mark E Jenkins, Kristina M Jordahl, Eric S Kawaguchi, Temitope O Keku, Anshul Kundaje, Loic Le Marchand, Juan Pablo Lewinger, Li Li, Bharuno Mahesworo, John L Morrison, Neil Murphy, Hongmei Nan, Rami Nassir, Polly A Newcomb, Mireia Obon-Santacana, Shuji Ogino, Jennifer Ose, Rish K Pai, Julie R Palmer, Nikos Papadimitriou, Bens Pardamean, Anita R Peoples, Paul D P Pharoah, Elizabeth A Platz, Gadi Rennert, Edward A Ruiz-Narvaez, Lori C Sakoda, Peter C Scacheri, Stephanie L Schmit, Robert E Schoen, Anna Shcherbina, Martha L Slattery, Mariana C Stern, Yu-Ru Su, Catherine M Tangen, Duncan C Thomas, Yu Tian, Konstantinos K Tsilidis, Cornelia M Ulrich, Franzel J B van Duijnhoven, Bethany Van Guelpen, Kala Visvanathan, Pavel Vodicka, Tjeng Wawan Cenggoro, Stephanie J Weinstein, Emily White, Alicja Wolk, Michael O Woods, Li Hsu, Ulrike Peters, Victor Moreno, W James Gauderman
Genome-wide Interaction Study with Smoking for Colorectal Cancer Risk Identifies Novel Genetic Loci Related to Tumor Suppression, Inflammation, and Immune Response. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 32 (3) (2023)
Robert Carreras-Torres, Andre E Kim, Yi Lin, Virginia Díez-Obrero, Stephanie A Bien, Conghui Qu, Jun Wang, Niki L Dimou, Elom Kouassivi Aglago, Demetrius Albanes, Volker Arndt, James W Baurley, Sonja I Berndt, Stéphane Bézieau, D Timothy Bishop, Emmanouil C Bouras, Hermann Brenner, Arif Budiarto, Peter T Campbell, Graham Casey, Andrew T Chan, Jenny Chang-Claude, Xuechen Chen, David V Conti, Christopher H Dampier, Matthew A M Devall, David A Drew, Jane C Figueiredo, Steven J Gallinger, Graham G Giles, Stephen B Gruber, Andrea Gsur, Marc J Gunter, Tabitha A Harrison, Akihisa Hidaka, Michael Hoffmeister, Jeroen R Huyghe, Mark E Jenkins, Kristina M Jordahl, Eric S Kawaguchi, Temitope O Keku, Anshul Kundaje, Loic Le Marchand, Juan Pablo Lewinger, Li Li, Bharuno Mahesworo, John L Morrison, Neil Murphy, Hongmei Nan, Rami Nassir, Polly A Newcomb, Mireia Obon-Santacana, Shuji Ogino, Jennifer Ose, Rish K Pai, Julie R Palmer, Nikos Papadimitriou, Bens Pardamean, Anita R Peoples, Paul D P Pharoah, Elizabeth A Platz, Gadi Rennert, Edward A Ruiz-Narvaez, Lori C Sakoda, Peter C Scacheri, Stephanie L Schmit, Robert E Schoen, Anna Shcherbina, Martha L Slattery, Mariana C Stern, Yu-Ru Su, Catherine M Tangen, Duncan C Thomas, Yu Tian, Konstantinos K Tsilidis, Cornelia M Ulrich, Franzel J B van Duijnhoven, Bethany Van Guelpen, Kala Visvanathan, Pavel Vodicka, Tjeng Wawan Cenggoro, Stephanie J Weinstein, Emily White, Alicja Wolk, Michael O Woods, Li Hsu, Ulrike Peters, Victor Moreno, W James Gauderman
Genome-wide Interaction Study with Smoking for Colorectal Cancer Risk Identifies Novel Genetic Loci Related to Tumor Suppression, Inflammation, and Immune Response. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 32 (3) (2023)
Amr M Alexandari, Connor A Horton, Avanti Shrikumar, Nilay Shah, Eileen Li, Melanie Weilert, Miles A Pufall, Julia Zeitlinger, Polly Morrell Fordyce, Anshul Kundaje
De novo distillation of thermodynamic affinity from deep learning regulatory sequence models of in vivo protein-DNA binding. bioRxiv : the preprint server for biology (2023)
Caleb A Lareau, Sonia M Dubois, Frank A Buquicchio, Yu-Hsin Hsieh, Kopal Garg, Pauline Kautz, Lena Nitsch, Samantha D Praktiknjo, Patrick Maschmeyer, Jeffrey M Verboon, Jacob C Gutierrez, Yajie Yin, Evgenij Fiskin, Wendy Luo, Eleni P Mimitou, Christoph Muus, Rhea Malhotra, Sumit Parikh, Mark D Fleming, Lena Oevermann, Johannes Hubertus Schulte, Cornelia Eckert, Anshul Kundaje, Peter Smibert, Santosha A Vardhana, Ansuman T Satpathy, Aviv Regev, Vijay G Sankaran, Suneet Agarwal, Leif S Ludwig
Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells. Nature genetics (2023)
Steven Boeynaems, X Rosa Ma, Vivian Yeong, Garrett M Ginell, Jian-Hua Chen, Jacob A Blum, Lisa Nakayama, Anushka Sanyal, Adam Briner, Delphi Van Haver, Jarne Pauwels, Axel Ekman, Hermann Broder Schmidt, Kousik Sundararajan, Lucas Porta, Keren Lasker, Carolyn A Larabell, Mirian A F Hayashi, Anshul Kundaje, Francis Impens, Allie C Obermeyer, Alex S Holehouse, Aaron D Gitler
Aberrant phase separation is a common killing strategy of positively charged peptides in biology and human disease. bioRxiv : the preprint server for biology (2023)
Robert Carreras-Torres, Andre E Kim, Yi Lin, Virginia Díez-Obrero, Stephanie A Bien, Conghui Qu, Jun Wang, Niki L Dimou, Elom Kouassivi Aglago, Demetrius Albanes, Volker Arndt, James W Baurley, Sonja I Berndt, Stéphane Bézieau, D Timothy Bishop, Emmanouil C Bouras, Hermann Brenner, Arif Budiarto, Peter T Campbell, Graham Casey, Andrew T Chan, Jenny Chang-Claude, Xuechen Chen, David V Conti, Christopher H Dampier, Matthew A M Devall, David A Drew, Jane C Figueiredo, Steven J Gallinger, Graham G Giles, Stephen B Gruber, Andrea Gsur, Marc J Gunter, Tabitha A Harrison, Akihisa Hidaka, Michael Hoffmeister, Jeroen R Huyghe, Mark E Jenkins, Kristina M Jordahl, Eric S Kawaguchi, Temitope O Keku, Anshul Kundaje, Loic Le Marchand, Juan Pablo Lewinger, Li Li, Bharuno Mahesworo, John L Morrison, Neil Murphy, Hongmei Nan, Rami Nassir, Polly A Newcomb, Mireia Obon-Santacana, Shuji Ogino, Jennifer Ose, Rish K Pai, Julie R Palmer, Nikos Papadimitriou, Bens Pardamean, Anita R Peoples, Paul D P Pharoah, Elizabeth A Platz, Gadi Rennert, Edward A Ruiz-Narvaez, Lori C Sakoda, Peter C Scacheri, Stephanie L Schmit, Robert E Schoen, Anna Shcherbina, Martha L Slattery, Mariana C Stern, Yu-Ru Su, Catherine M Tangen, Duncan C Thomas, Yu Tian, Konstantinos K Tsilidis, Cornelia M Ulrich, Franzel J B van Duijnhoven, Bethany Van Guelpen, Kala Visvanathan, Pavel Vodicka, Tjeng Wawan Cenggoro, Stephanie J Weinstein, Emily White, Alicja Wolk, Michael O Woods, Li Hsu, Ulrike Peters, Victor Moreno, W James Gauderman
Genome-wide Interaction Study with Smoking for Colorectal Cancer Risk Identifies Novel Genetic Loci Related to Tumor Suppression, Inflammation, and Immune Response. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 32 (3) (2023)
Robin W Yeo, Olivia Y Zhou, Brian L Zhong, Eric D Sun, Paloma Navarro Negredo, Surag Nair, Mahfuza Sharmin, Tyson J Ruetz, Mikaela Wilson, Anshul Kundaje, Alexander R Dunn, Anne Brunet
Chromatin accessibility dynamics of neurogenic niche cells reveal defects in neural stem cell adhesion and migration during aging. Nature aging (2023)
Surag Nair, Mohamed Ameen, Laksshman Sundaram, Anusri Pampari, Jacob Schreiber, Akshay Balsubramani, Yu Xin Wang, David Burns, Helen M Blau, Ioannis Karakikes, Kevin C Wang, Anshul Kundaje
Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency. bioRxiv : the preprint server for biology (2023)
Caleb A Lareau, Yajie Yin, Katie Maurer, Katalin D Sandor, Bence Daniel, Garima Yagnik, José Peña, Jeremy Chase Crawford, Stephan Mielke, Jacob C Gutierrez, Nicholas J Haradhvala, Janice M Riberdy, Tsion Abay, Robert R Stickels, Jeffrey M Verboon, Vincent Liu, Frank A Buquicchio, Fangyi Wang, Jackson Southard, Ren Song, Wenjing Li, Aastha Shrestha, Laxmi Parida, Gad A Getz, Marcela V Maus, Shuqiang Li, Alison Moore, Zachary J Roberts, Leif S Ludwig, Aimee C Talleur, Paul Glyndwr Thomas, Houman Dehghani, Thomas Pertel, Anshul Kundaje, Stephen Gottschalk, Theodore L Roth, Marie José Kersten, Catherine J Wu, Robbie G Majzner, Ansuman T Satpathy
Latent human herpesvirus 6 is reactivated in CAR T cells. Nature (2023)
Madeline H Kowalski, Hans-Hermann Wessels, Johannes Linder, Saket Choudhary, Austin Hartman, Yuhan Hao, Isabella Mascio, Carol Dalgarno, Anshul Kundaje, Rahul Satija
CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators. bioRxiv : the preprint server for biology (2023)
Ceres Fernández-Rozadilla, Maria N Timofeeva, Zhishan Chen, Philip J Law, Minta Thomas, Stephanie L Schmit, Virginia Díez-Obrero, Li Hsu, Juan Fernandez-Tajes, Claire Palles, Kitty Sherwood, Sarah Briggs, Victoria Svinti, Kevin Donnelly, Susan M Farrington, James Blackmur, Peter Vaughan-Shaw, Xiao-Ou Shu, Jirong Long, Qiuyin Cai, Xingyi Guo, Yingchang Lu, Peter Broderick, James B Studd, Jeroen R Huyghe, Tabitha A Harrison, David Conti, Christopher H Dampier, Mathew Devall, Fredrick R Schumacher, Marilena Melas, Gadi Rennert, Mireia Obón-Santacana, Vicente Martín-Sánchez, Ferran Moratalla-Navarro, Jae Hwan Oh, Jeong-Seon Kim, Sun Ha Jee, Keum Ji Jung, Sun-Seog Kweon, Min-Ho Shin, Aesun Shin, Yoon-Ok Ahn, Dong-Hyun Kim, Isao Oze, Wanqing Wen, Keitaro Matsuo, Koichi Matsuda, Chizu Tanikawa, Ze-Fang Ren, Yu-Tang Gao, Wei-Hua Jia, John Hopper, Mark E Jenkins, Aung-Ko Win, Rish Pai, Jane Figueiredo, Robert W Haile, Steven Gallinger, Michael Woods, Polly A Newcomb, David Duggan, Jeremy P Cheadle, Richard S Kaplan, Timothy Maughan, Rachel Kerr, David J Kerr, Iva Kirac, Jan Böhm, Lukka-Pekka Mecklin, Pekka Jousilahti, Paul Knekt, Lauri A Aaltonen, Harri Rissanen, Eero Pukkala, Johan Eriksson, Tatiana Cajuso, Ulrika Hänninen, Johanna Kondelin, Kimmo Palin, Tomas Tanskanen, Laura Renkonen-Sinisalo, Brent Zanke, Satu Männistö, Demetrius Albanes, Stephanie J Weinstein, Edward A Ruiz-Narvaez, Julie Palmer, Daniel D Buchanan, Elizabeth A Platz, Kala Visvanathan, Cornelia Ulrich, Erin M Siegel, Stefanie Brezina, Andrea Gsur, Peter Campbell, Jenny Chang-Claude, Michael Hoffmeister, Hermann Brenner, Martha Slattery, John D Potter, Konstantinos K Tsilidis, Matthias Bernd Schulze, Marc Gunter, Neil Murphy, Antoni Castells, Sergi Castellví-Bel, Leticia Moreira, Volker Arndt, Anna Shcherbina, Mariana Stern, Bens Pardamean, D Timothy Bishop, Graham G Giles, Melissa C Southey, Gregory Idos, Kevin McDonnell, Zomoroda Abu-Ful, Joel Greenson, Katerina Shulman, Flavio Lejbkowicz, Kenneth Offit, Yu-Ru Su, Robert Steinfelder, Temitope Keku, Bethany Van Guelpen, Thomas J Hudson, Heather Hampel, Rachel Pearlman, Sonja Berndt, Richard B Hayes, Marie Elena Martinez, Sushma Thomas, Douglas Corley, Paul D P Pharoah, Susanna C Larsson, Yun Yen, Heinz-Josef Lenz, Emily White, Li Li, Kimberly F Doheny, Elizabeth Pugh, Tameka Shelford, Andrew T Chan, Marcia Cruz-Correa, Annika Lindblom, David Hunter, Amit D Joshi, Clemens Schafmayer, Peter Scacheri, Anshul Kundaje, Deborah Nickerson, Robert E Schoen, Jochen Hampe, Zsofia Stadler, Pavel Vodicka, Ludmila Vodickova, Veronika Vymetalkova, Nickolas Papadopoulos, Chistopher Edlund, William Gauderman, Duncan C Thomas, David Shibata, Amanda Ewart Toland, Sanford Markowitz, Andre Kim, Stephen J Chanock, Franzel van Duijnhoven, Edith J M Feskens, Lori C Sakoda, Manuela Gago-Dominguez, Alicja Wolk, Alessio Naccarati, Barbara Pardini, Liesel M FitzGerald, Soo Chin Lee, Shuji Ogino, Stephanie Bien, Charles Kooperberg, Christopher Li, Yi Lin, Ross Prentice, Conghui Qu, Stéphane Bézieau, Catherine Tangen, Elaine R Mardis, Taiki Yamaji, Norie Sawada, Motoki Iwasaki, Christopher A Haiman, Loic Le Marchand, Anna Wu, Chenxu Qu, Caroline McNeil, Gerhard A Coetzee, Caroline Hayward, Ian J Deary, Sarah E Harris, Evropi Theodoratou, Stuart Reid, Marion Walker, Li Yin Ooi, Victor Moreno, Graham Casey, Stephen Gruber, Ian P M Tomlinson, Quan Long, Malcolm G Dunlop, Richard S Houlston, Ulrike Peters
Author Correction: Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries. Nature genetics (2023)
Connor A Horton, Amr M Alexandari, Michael G B Hayes, Emil Marklund, Julia M Schaepe, Arjun K Aditham, Nilay Shah, Peter H Suzuki, Avanti Shrikumar, Ariel Afek, William J Greenleaf, Raluca Gordân, Julia Zeitlinger, Anshul Kundaje, Polly Morrell Fordyce
Short tandem repeats bind transcription factors to tune eukaryotic gene expression. Science (New York, N.Y.) 381 (6664) (2023)
Elom Kouassivi Aglago, Andre E Kim, Yi Lin, Conghui Qu, Marina Evangelou, Yu Ren, John L Morrison, Demetrius Albanes, Volker Arndt, Elizabeth L Barry, James W Baurley, Sonja I Berndt, Stephanie A Bien, D Timothy Bishop, Emmanouil C Bouras, Hermann Brenner, Daniel D Buchanan, Arif Budiarto, Robert Carreras-Torres, Graham Casey, Tjeng Wawan Cenggoro, Andrew T Chan, Jenny Chang-Claude, Xuechen Chen, David V Conti, Matthew A M Devall, Virginia Díez-Obrero, Niki L Dimou, David A Drew, Jane C Figueiredo, Steven J Gallinger, Graham G Giles, Stephen B Gruber, Andrea Gsur, Marc J Gunter, Heather Hampel, Sophia Harlid, Akihisa Hidaka, Tabitha A Harrison, Michael Hoffmeister, Jeroen R Huyghe, Mark E Jenkins, Kristina M Jordahl, Amit D Joshi, Eric S Kawaguchi, Temitope O Keku, Anshul Kundaje, Susanna C Larsson, Loic Le Marchand, Juan Pablo Lewinger, Li Li, Brigid M Lynch, Bharuno Mahesworo, Marko Mandic, Mireia Obon-Santacana, Victor Moreno, Neil Murphy, Hongmei Nan, Rami Nassir, Polly A Newcomb, Shuji Ogino, Jennifer Ose, Rish K Pai, Julie R Palmer, Nikos Papadimitriou, Bens Pardamean, Anita R Peoples, Elizabeth A Platz, John D Potter, Ross L Prentice, Gadi Rennert, Edward A Ruiz-Narvaez, Lori C Sakoda, Peter C Scacheri, Stephanie L Schmit, Robert E Schoen, Anna Shcherbina, Martha L Slattery, Mariana C Stern, Yu-Ru Su, Catherine M Tangen, Stephen N Thibodeau, Duncan C Thomas, Yu Tian, Cornelia M Ulrich, Franzel J B van Duijnhoven, Bethany Van Guelpen, Kala Visvanathan, Pavel Vodicka, Jun Wang, Emily White, Alicja Wolk, Michael O Woods, Anna H Wu, Natalia Zemlianskaia, Li Hsu, W James Gauderman, Ulrike Peters, Konstantinos K Tsilidis, Peter T Campbell
A genetic locus within the FMN1/GREM1 gene region interacts with body mass index in colorectal cancer risk. Cancer research (2023)
Niki L Dimou, Andre E Kim, Orlagh Flanagan, Neil Murphy, Virginia Diez-Obrero, Anna Shcherbina, Elom Kouassivi Aglago, Emmanouil C Bouras, Peter T Campbell, Graham Casey, Steven Gallinger, Stephen B Gruber, Mark A Jenkins, Yi Lin, Victor Moreno, Edward A Ruiz-Narvaez, Mariana C Stern, Yu Tian, Kostas K Tsilidis, Volker Arndt, Elizabeth L Barry, James W Baurley, Sonja I Berndt, Stéphane Bézieau, Stephanie A Bien, D Timothy Bishop, Hermann Brenner, Arif Budiarto, Robert Carreras-Torres, Tjeng Wawan Cenggoro, Andrew T Chan, Jenny Chang-Claude, Stephen J Chanock, Xuechen Chen, David V Conti, Christopher H Dampier, Matthew Devall, David A Drew, Jane C Figueiredo, Graham G Giles, Andrea Gsur, Tabitha A Harrison, Akihisa Hidaka, Michael Hoffmeister, Jeroen R Huyghe, Kristina Jordahl, Eric Kawaguchi, Temitope O Keku, Susanna C Larsson, Loic Le Marchand, Juan Pablo Lewinger, Li Li, Bharuno Mahesworo, John Morrison, Polly A Newcomb, Christina C Newton, Mireia Obon-Santacana, Jennifer Ose, Rish K Pai, Julie R Palmer, Nikos Papadimitriou, Bens Pardamean, Anita R Peoples, Paul D P Pharoah, Elizabeth A Platz, John D Potter, Gad Rennert, Peter C Scacheri, Robert E Schoen, Yu-Ru Su, Catherine M Tangen, Stephen N Thibodeau, Duncan C Thomas, Cornelia M Ulrich, Caroline Y Um, Franzel J B van Duijnhoven, Kala Visvanathan, Pavel Vodicka, Ludmila Vodickova, Emily White, Alicja Wolk, Michael O Woods, Conghui Qu, Anshul Kundaje, Li Hsu, W James Gauderman, Marc J Gunter, Ulrike Peters
Probing the diabetes and colorectal cancer relationship using gene - environment interaction analyses. British journal of cancer (2023)
Benjamin Hitz, Jin-Wook Lee, Otto Jolanki, Meenakshi S Kagda, Keenan Graham, Paul Sud, Idan Gabdank, J Seth Strattan, Cricket Sloan, Timothy Dreszer, Laurence Rowe, Nikhil Podduturi, Venkat Malladi, Esther T Chan, Jean Davidson, Marcus Ho, Stuart Miyasato, Matt Simison, Forrest Tanaka, Yunhai Luo, Ian Wahling, Khine Zin Lin, Jennifer Jou, Eurie Hong, Laurence D Rowe, Richard Sandstrom, Eric Rynes, Jemma Nelson, Andrew Nishida, Alyssa Ingersoll, Michael Buckley, Mark Frerker, Daniel Kim, Nathan Boley, Diane Trout, Alexander Dobin, Sorena Rahmanian, Dana Wyman, Gabriela Balderrama-Gutierrez, Fairlie Reese, Neva C Durand, Olga Dudchenko, David Weisz, Suhas Rao, Alyssa Blackburn, Dimos Gkountaroulis, Mahdi Sadr, Moshe Olshansky, Yossi Eliaz, Dat Nguyen, Ivan Bochkov, Muhammad Saad Shamim, Ragini Mahajan, Erez Aiden, Thomas Gingeras, Simon Heath, Martin Hirst, W James Kent, Anshul Kundaje, Ali Mortazavi, Barbara J Wold, J Michael Cherry
The ENCODE Uniform Analysis Pipelines. Research square (2023)
Benjamin C Hitz, Jin-Wook Lee, Otto Jolanki, Meenakshi S Kagda, Keenan Graham, Paul Sud, Aditi K Narayanan, Benjamin C Hitz, Cricket A Sloan, Timothy Dreszer, Laurence D Rowe, Nikhil R Podduturi, Venkat S Malladi, Esther T Chan, Jean M Davidson, Brian T Lee, Stuart Miyasato, Matt Simison, Forrest Tanaka, Yunhai Luo, Ian Whaling, Eurie L Hong, Laurence D Rowe, Richard S Sandstrom, Eric Rynes, Jemma Nelson, Andrew Nishida, Alyssa Ingersoll, Michael Buckley, Mark Frerker, Daniel S Kim, Nathan Boley, Diane Trout, Alexander Dobin, Sorena Rahmanian, Dana Wyman, Gabriela Balderrama-Gutierrez, Fairlie Reese, Neva C Durand, Olga Dudchenko, David Weisz, Suhas S P Rao, Alyssa Blackburn, Dimos Gkountaroulis, Mahdi Sadr, Moshe Olshansky, Yossi Eliaz, Dat Nguyen, Ivan Bochkov, Muhammad Saad Shamim, Ragini Mahajan, Erez Lieberman Aiden, Thomas R Gingeras, Simon Charles Heath, Martin Hirst, W James Kent, Anshul Kundaje, Ali Mortazavi, Barbara J Wold, J Michael Cherry
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Kelly Cochran, Divyanshi Srivastava, Avanti Shrikumar, Akshay Balsubramani, Ross Cameron Hardison, Anshul Kundaje, Shaun Mahony
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Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries. Nature genetics 55 (1) (2022)
Robert Carreras-Torres, Andre E Kim, Yi Lin, Virginia Díez-Obrero, Stephanie A Bien, Conghui Qu, Jun Wang, Niki L Dimou, Elom Kouassivi Aglago, Demetrius Albanes, Volker Arndt, James W Baurley, Sonja I Berndt, Stéphane Bézieau, D Timothy Bishop, Emmanouil C Bouras, Hermann Brenner, Arif Budiarto, Peter T Campbell, Graham Casey, Andrew T Chan, Jenny Chang-Claude, Xuechen Chen, David V Conti, Christopher H Dampier, Matthew A M Devall, David A Drew, Jane C Figueiredo, Steven J Gallinger, Graham G Giles, Stephen B Gruber, Andrea Gsur, Marc J Gunter, Tabitha A Harrison, Akihisa Hidaka, Michael Hoffmeister, Jeroen R Huyghe, Mark E Jenkins, Kristina M Jordahl, Eric S Kawaguchi, Temitope O Keku, Anshul Kundaje, Loic Le Marchand, Juan Pablo Lewinger, Li Li, Bharuno Mahesworo, John L Morrison, Neil Murphy, Hongmei Nan, Rami Nassir, Polly A Newcomb, Mireia Obon-Santacana, Shuji Ogino, Jennifer Ose, Rish K Pai, Julie R Palmer, Nikos Papadimitriou, Bens Pardamean, Anita R Peoples, Paul D P Pharoah, Elizabeth A Platz, Gadi Rennert, Edward A Ruiz-Narvaez, Lori C Sakoda, Peter C Scacheri, Stephanie L Schmit, Robert E Schoen, Anna Shcherbina, Martha L Slattery, Mariana C Stern, Yu-Ru Su, Catherine M Tangen, Duncan C Thomas, Yu Tian, Konstantinos K Tsilidis, Cornelia M Ulrich, Franzel J B van Duijnhoven, Bethany Van Guelpen, Kala Visvanathan, Pavel Vodicka, Tjeng Wawan Cenggoro, Stephanie J Weinstein, Emily White, Alicja Wolk, Michael O Woods, Li Hsu, Ulrike Peters, Victor Moreno, W James Gauderman
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Winston R Becker, Stephanie A Nevins, Derek C Chen, Roxanne Chiu, Aaron M Horning, Tuhin K Guha, Rozelle Laquindanum, Meredith Mills, Hassan Chaib, Uri Ladabaum, Teri Longacre, Jeanne Shen, Edward D Esplin, Anshul Kundaje, James M Ford, Christina Curtis, Michael Paul Snyder, William J Greenleaf
Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer. Nature genetics 54 (7) (2022)
Ceres Fernández-Rozadilla, Maria N Timofeeva, Zhishan Chen, Philip J Law, Minta Thomas, Stephanie L Schmit, Virginia Díez-Obrero, Li Hsu, Juan Fernandez-Tajes, Claire Palles, Kitty Sherwood, Sarah Briggs, Victoria Svinti, Kevin Donnelly, Susan M Farrington, James Blackmur, Peter Vaughan-Shaw, Xiao-Ou Shu, Jirong Long, Qiuyin Cai, Xingyi Guo, Yingchang Lu, Peter Broderick, James B Studd, Jeroen R Huyghe, Tabitha A Harrison, David Conti, Christopher H Dampier, Mathew Devall, Fredrick R Schumacher, Marilena Melas, Gadi Rennert, Mireia Obón-Santacana, Vicente Martín-Sánchez, Ferran Moratalla-Navarro, Jae Hwan Oh, Jeong-Seon Kim, Sun Ha Jee, Keum Ji Jung, Sun-Seog Kweon, Min-Ho Shin, Aesun Shin, Yoon-Ok Ahn, Dong-Hyun Kim, Isao Oze, Wanqing Wen, Keitaro Matsuo, Koichi Matsuda, Chizu Tanikawa, Ze-Fang Ren, Yu-Tang Gao, Wei-Hua Jia, John Hopper, Mark E Jenkins, Aung-Ko Win, Rish Pai, Jane Figueiredo, Robert W Haile, Steven Gallinger, Michael Woods, Polly A Newcomb, David Duggan, Jeremy P Cheadle, Richard S Kaplan, Timothy Maughan, Rachel Kerr, David J Kerr, Iva Kirac, Jan Böhm, Lukka-Pekka Mecklin, Pekka Jousilahti, Paul Knekt, Lauri A Aaltonen, Harri Rissanen, Eero Pukkala, Johan Eriksson, Tatiana Cajuso, Ulrika Hänninen, Johanna Kondelin, Kimmo Palin, Tomas Tanskanen, Laura Renkonen-Sinisalo, Brent Zanke, Satu Männistö, Demetrius Albanes, Stephanie J Weinstein, Edward A Ruiz-Narvaez, Julie Palmer, Daniel D Buchanan, Elizabeth A Platz, Kala Visvanathan, Cornelia Ulrich, Erin M Siegel, Stefanie Brezina, Andrea Gsur, Peter Campbell, Jenny Chang-Claude, Michael Hoffmeister, Hermann Brenner, Martha Slattery, John D Potter, Konstantinos K Tsilidis, Matthias Bernd Schulze, Marc Gunter, Neil Murphy, Antoni Castells, Sergi Castellví-Bel, Leticia Moreira, Volker Arndt, Anna Shcherbina, Mariana Stern, Bens Pardamean, D Timothy Bishop, Graham G Giles, Melissa C Southey, Gregory Idos, Kevin McDonnell, Zomoroda Abu-Ful, Joel Greenson, Katerina Shulman, Flavio Lejbkowicz, Kenneth Offit, Yu-Ru Su, Robert Steinfelder, Temitope Keku, Bethany Van Guelpen, Thomas J Hudson, Heather Hampel, Rachel Pearlman, Sonja Berndt, Richard B Hayes, Marie Elena Martinez, Sushma Thomas, Douglas Corley, Paul D P Pharoah, Susanna C Larsson, Yun Yen, Heinz-Josef Lenz, Emily White, Li Li, Kimberly F Doheny, Elizabeth Pugh, Tameka Shelford, Andrew T Chan, Marcia Cruz-Correa, Annika Lindblom, David Hunter, Amit D Joshi, Clemens Schafmayer, Peter Scacheri, Anshul Kundaje, Deborah Nickerson, Robert E Schoen, Jochen Hampe, Zsofia Stadler, Pavel Vodicka, Ludmila Vodickova, Veronika Vymetalkova, Nickolas Papadopoulos, Chistopher Edlund, William Gauderman, Duncan C Thomas, David Shibata, Amanda Ewart Toland, Sanford Markowitz, Andre Kim, Stephen J Chanock, Franzel van Duijnhoven, Edith J M Feskens, Lori C Sakoda, Manuela Gago-Dominguez, Alicja Wolk, Alessio Naccarati, Barbara Pardini, Liesel M FitzGerald, Soo Chin Lee, Shuji Ogino, Stephanie Bien, Charles Kooperberg, Christopher Li, Yi Lin, Ross Prentice, Conghui Qu, Stéphane Bézieau, Catherine Tangen, Elaine R Mardis, Taiki Yamaji, Norie Sawada, Motoki Iwasaki, Christopher A Haiman, Loic Le Marchand, Anna Wu, Chenxu Qu, Caroline McNeil, Gerhard A Coetzee, Caroline Hayward, Ian J Deary, Sarah E Harris, Evropi Theodoratou, Stuart Reid, Marion Walker, Li Yin Ooi, Victor Moreno, Graham Casey, Stephen Gruber, Ian P M Tomlinson, Quan Long, Malcolm G Dunlop, Richard S Houlston, Ulrike Peters
Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries. Nature genetics 55 (1) (2022)
Surag Nair, Arjun Barrett, Daofeng Li, Brian J Raney, Brian T Lee, Peter Kerpedjiev, Vivekanandan Ramalingam, Anusri Pampari, Fritz Lekschas, Ting Wang, Maximilian Haeussler, Anshul Kundaje
The dynseq browser track shows context-specific features at nucleotide resolution. Nature genetics 54 (11) (2022)
Ceres Fernández-Rozadilla, Maria N Timofeeva, Zhishan Chen, Philip J Law, Minta Thomas, Stephanie L Schmit, Virginia Díez-Obrero, Li Hsu, Juan Fernandez-Tajes, Claire Palles, Kitty Sherwood, Sarah Briggs, Victoria Svinti, Kevin Donnelly, Susan M Farrington, James Blackmur, Peter Vaughan-Shaw, Xiao-Ou Shu, Jirong Long, Qiuyin Cai, Xingyi Guo, Yingchang Lu, Peter Broderick, James B Studd, Jeroen R Huyghe, Tabitha A Harrison, David Conti, Christopher H Dampier, Mathew Devall, Fredrick R Schumacher, Marilena Melas, Gadi Rennert, Mireia Obón-Santacana, Vicente Martín-Sánchez, Ferran Moratalla-Navarro, Jae Hwan Oh, Jeong-Seon Kim, Sun Ha Jee, Keum Ji Jung, Sun-Seog Kweon, Min-Ho Shin, Aesun Shin, Yoon-Ok Ahn, Dong-Hyun Kim, Isao Oze, Wanqing Wen, Keitaro Matsuo, Koichi Matsuda, Chizu Tanikawa, Ze-Fang Ren, Yu-Tang Gao, Wei-Hua Jia, John Hopper, Mark E Jenkins, Aung-Ko Win, Rish Pai, Jane Figueiredo, Robert W Haile, Steven Gallinger, Michael Woods, Polly A Newcomb, David Duggan, Jeremy P Cheadle, Richard S Kaplan, Timothy Maughan, Rachel Kerr, David J Kerr, Iva Kirac, Jan Böhm, Lukka-Pekka Mecklin, Pekka Jousilahti, Paul Knekt, Lauri A Aaltonen, Harri Rissanen, Eero Pukkala, Johan Eriksson, Tatiana Cajuso, Ulrika Hänninen, Johanna Kondelin, Kimmo Palin, Tomas Tanskanen, Laura Renkonen-Sinisalo, Brent Zanke, Satu Männistö, Demetrius Albanes, Stephanie J Weinstein, Edward A Ruiz-Narvaez, Julie Palmer, Daniel D Buchanan, Elizabeth A Platz, Kala Visvanathan, Cornelia Ulrich, Erin M Siegel, Stefanie Brezina, Andrea Gsur, Peter Campbell, Jenny Chang-Claude, Michael Hoffmeister, Hermann Brenner, Martha Slattery, John D Potter, Konstantinos K Tsilidis, Matthias Bernd Schulze, Marc Gunter, Neil Murphy, Antoni Castells, Sergi Castellví-Bel, Leticia Moreira, Volker Arndt, Anna Shcherbina, Mariana Stern, Bens Pardamean, D Timothy Bishop, Graham G Giles, Melissa C Southey, Gregory Idos, Kevin McDonnell, Zomoroda Abu-Ful, Joel Greenson, Katerina Shulman, Flavio Lejbkowicz, Kenneth Offit, Yu-Ru Su, Robert Steinfelder, Temitope Keku, Bethany Van Guelpen, Thomas J Hudson, Heather Hampel, Rachel Pearlman, Sonja Berndt, Richard B Hayes, Marie Elena Martinez, Sushma Thomas, Douglas Corley, Paul D P Pharoah, Susanna C Larsson, Yun Yen, Heinz-Josef Lenz, Emily White, Li Li, Kimberly F Doheny, Elizabeth Pugh, Tameka Shelford, Andrew T Chan, Marcia Cruz-Correa, Annika Lindblom, David Hunter, Amit D Joshi, Clemens Schafmayer, Peter Scacheri, Anshul Kundaje, Deborah Nickerson, Robert E Schoen, Jochen Hampe, Zsofia Stadler, Pavel Vodicka, Ludmila Vodickova, Veronika Vymetalkova, Nickolas Papadopoulos, Chistopher Edlund, William Gauderman, Duncan C Thomas, David Shibata, Amanda Ewart Toland, Sanford Markowitz, Andre Kim, Stephen J Chanock, Franzel van Duijnhoven, Edith J M Feskens, Lori C Sakoda, Manuela Gago-Dominguez, Alicja Wolk, Alessio Naccarati, Barbara Pardini, Liesel M FitzGerald, Soo Chin Lee, Shuji Ogino, Stephanie Bien, Charles Kooperberg, Christopher Li, Yi Lin, Ross Prentice, Conghui Qu, Stéphane Bézieau, Catherine Tangen, Elaine R Mardis, Taiki Yamaji, Norie Sawada, Motoki Iwasaki, Christopher A Haiman, Loic Le Marchand, Anna Wu, Chenxu Qu, Caroline McNeil, Gerhard A Coetzee, Caroline Hayward, Ian J Deary, Sarah E Harris, Evropi Theodoratou, Stuart Reid, Marion Walker, Li Yin Ooi, Victor Moreno, Graham Casey, Stephen Gruber, Ian P M Tomlinson, Quan Long, Malcolm G Dunlop, Richard S Houlston, Ulrike Peters
Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries. Nature genetics 55 (1) (2022)
Robert Carreras-Torres, Andre E Kim, Yi Lin, Virginia Díez-Obrero, Stephanie A Bien, Conghui Qu, Jun Wang, Niki L Dimou, Elom Kouassivi Aglago, Demetrius Albanes, Volker Arndt, James W Baurley, Sonja I Berndt, Stéphane Bézieau, D Timothy Bishop, Emmanouil C Bouras, Hermann Brenner, Arif Budiarto, Peter T Campbell, Graham Casey, Andrew T Chan, Jenny Chang-Claude, Xuechen Chen, David V Conti, Christopher H Dampier, Matthew A M Devall, David A Drew, Jane C Figueiredo, Steven J Gallinger, Graham G Giles, Stephen B Gruber, Andrea Gsur, Marc J Gunter, Tabitha A Harrison, Akihisa Hidaka, Michael Hoffmeister, Jeroen R Huyghe, Mark E Jenkins, Kristina M Jordahl, Eric S Kawaguchi, Temitope O Keku, Anshul Kundaje, Loic Le Marchand, Juan Pablo Lewinger, Li Li, Bharuno Mahesworo, John L Morrison, Neil Murphy, Hongmei Nan, Rami Nassir, Polly A Newcomb, Mireia Obon-Santacana, Shuji Ogino, Jennifer Ose, Rish K Pai, Julie R Palmer, Nikos Papadimitriou, Bens Pardamean, Anita R Peoples, Paul D P Pharoah, Elizabeth A Platz, Gadi Rennert, Edward A Ruiz-Narvaez, Lori C Sakoda, Peter C Scacheri, Stephanie L Schmit, Robert E Schoen, Anna Shcherbina, Martha L Slattery, Mariana C Stern, Yu-Ru Su, Catherine M Tangen, Duncan C Thomas, Yu Tian, Konstantinos K Tsilidis, Cornelia M Ulrich, Franzel J B van Duijnhoven, Bethany Van Guelpen, Kala Visvanathan, Pavel Vodicka, Tjeng Wawan Cenggoro, Stephanie J Weinstein, Emily White, Alicja Wolk, Michael O Woods, Li Hsu, Ulrike Peters, Victor Moreno, W James Gauderman
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Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries. Nature genetics 55 (1) (2022)
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Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries. Nature genetics 55 (1) (2022)
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Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk. Nature genetics 54 (6) (2022)
Ceres Fernández-Rozadilla, Maria N Timofeeva, Zhishan Chen, Philip J Law, Minta Thomas, Stephanie L Schmit, Virginia Díez-Obrero, Li Hsu, Juan Fernandez-Tajes, Claire Palles, Kitty Sherwood, Sarah Briggs, Victoria Svinti, Kevin Donnelly, Susan M Farrington, James Blackmur, Peter Vaughan-Shaw, Xiao-Ou Shu, Jirong Long, Qiuyin Cai, Xingyi Guo, Yingchang Lu, Peter Broderick, James B Studd, Jeroen R Huyghe, Tabitha A Harrison, David Conti, Christopher H Dampier, Mathew Devall, Fredrick R Schumacher, Marilena Melas, Gadi Rennert, Mireia Obón-Santacana, Vicente Martín-Sánchez, Ferran Moratalla-Navarro, Jae Hwan Oh, Jeong-Seon Kim, Sun Ha Jee, Keum Ji Jung, Sun-Seog Kweon, Min-Ho Shin, Aesun Shin, Yoon-Ok Ahn, Dong-Hyun Kim, Isao Oze, Wanqing Wen, Keitaro Matsuo, Koichi Matsuda, Chizu Tanikawa, Ze-Fang Ren, Yu-Tang Gao, Wei-Hua Jia, John Hopper, Mark E Jenkins, Aung-Ko Win, Rish Pai, Jane Figueiredo, Robert W Haile, Steven Gallinger, Michael Woods, Polly A Newcomb, David Duggan, Jeremy P Cheadle, Richard S Kaplan, Timothy Maughan, Rachel Kerr, David J Kerr, Iva Kirac, Jan Böhm, Lukka-Pekka Mecklin, Pekka Jousilahti, Paul Knekt, Lauri A Aaltonen, Harri Rissanen, Eero Pukkala, Johan Eriksson, Tatiana Cajuso, Ulrika Hänninen, Johanna Kondelin, Kimmo Palin, Tomas Tanskanen, Laura Renkonen-Sinisalo, Brent Zanke, Satu Männistö, Demetrius Albanes, Stephanie J Weinstein, Edward A Ruiz-Narvaez, Julie Palmer, Daniel D Buchanan, Elizabeth A Platz, Kala Visvanathan, Cornelia Ulrich, Erin M Siegel, Stefanie Brezina, Andrea Gsur, Peter Campbell, Jenny Chang-Claude, Michael Hoffmeister, Hermann Brenner, Martha Slattery, John D Potter, Konstantinos K Tsilidis, Matthias Bernd Schulze, Marc Gunter, Neil Murphy, Antoni Castells, Sergi Castellví-Bel, Leticia Moreira, Volker Arndt, Anna Shcherbina, Mariana Stern, Bens Pardamean, D Timothy Bishop, Graham G Giles, Melissa C Southey, Gregory Idos, Kevin McDonnell, Zomoroda Abu-Ful, Joel Greenson, Katerina Shulman, Flavio Lejbkowicz, Kenneth Offit, Yu-Ru Su, Robert Steinfelder, Temitope Keku, Bethany Van Guelpen, Thomas J Hudson, Heather Hampel, Rachel Pearlman, Sonja Berndt, Richard B Hayes, Marie Elena Martinez, Sushma Thomas, Douglas Corley, Paul D P Pharoah, Susanna C Larsson, Yun Yen, Heinz-Josef Lenz, Emily White, Li Li, Kimberly F Doheny, Elizabeth Pugh, Tameka Shelford, Andrew T Chan, Marcia Cruz-Correa, Annika Lindblom, David Hunter, Amit D Joshi, Clemens Schafmayer, Peter Scacheri, Anshul Kundaje, Deborah Nickerson, Robert E Schoen, Jochen Hampe, Zsofia Stadler, Pavel Vodicka, Ludmila Vodickova, Veronika Vymetalkova, Nickolas Papadopoulos, Chistopher Edlund, William Gauderman, Duncan C Thomas, David Shibata, Amanda Ewart Toland, Sanford Markowitz, Andre Kim, Stephen J Chanock, Franzel van Duijnhoven, Edith J M Feskens, Lori C Sakoda, Manuela Gago-Dominguez, Alicja Wolk, Alessio Naccarati, Barbara Pardini, Liesel M FitzGerald, Soo Chin Lee, Shuji Ogino, Stephanie Bien, Charles Kooperberg, Christopher Li, Yi Lin, Ross Prentice, Conghui Qu, Stéphane Bézieau, Catherine Tangen, Elaine R Mardis, Taiki Yamaji, Norie Sawada, Motoki Iwasaki, Christopher A Haiman, Loic Le Marchand, Anna Wu, Chenxu Qu, Caroline McNeil, Gerhard A Coetzee, Caroline Hayward, Ian J Deary, Sarah E Harris, Evropi Theodoratou, Stuart Reid, Marion Walker, Li Yin Ooi, Victor Moreno, Graham Casey, Stephen Gruber, Ian P M Tomlinson, Quan Long, Malcolm G Dunlop, Richard S Houlston, Ulrike Peters
Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries. Nature genetics 55 (1) (2022)
Surag Nair, Avanti Shrikumar, Jacob Schreiber, Anshul Kundaje
fastISM: performant in silico saturation mutagenesis for convolutional neural networks. Bioinformatics (Oxford, England) 38 (9) (2022)
Johannes Linder, Samantha E Koplik, Anshul Kundaje, Georg Seelig
Deciphering the impact of genetic variation on human polyadenylation using APARENT2. Genome biology 23 (1) (2022)
Glenn J Markov, Thach Mai, Surag Nair, Anna Shcherbina, Yu Xin Wang, David M Burns, Anshul Kundaje, Helen M Blau
AP-1 is a temporally regulated dual gatekeeper of reprogramming to pluripotency. Proceedings of the National Academy of Sciences of the United States of America 118 (23) (2021)
Michael Wainberg, Roarke A Kamber, Akshay Balsubramani, Robin M Meyers, Nicholas A Sinnott-Armstrong, Daniel Hornburg, Lihua Jiang, Joanne Chan, Ruiqi Jian, Mingxin Gu, Anna Shcherbina, Michael M Dubreuil, Kaitlyn Spees, Wouter Meuleman, Michael Paul Snyder, Michael C Bassik, Anshul Kundaje
A genome-wide atlas of co-essential modules assigns function to uncharacterized genes. Nature genetics 53 (5) (2021)
Joseph Nasser, Drew T Bergman, Charles P Fulco, Philine Guckelberger, Benjamin R Doughty, Tejal A Patwardhan, Thouis R Jones, Tung H Nguyen, Jacob C Ulirsch, Fritz Lekschas, Kristy Mualim, Heini M Natri, Elle M Weeks, Glen Munson, Michael Kane, Helen Y Kang, Ang Cui, John P Ray, Thomas M Eisenhaure, Ryan L Collins, Kushal Dey, Hanspeter Pfister, Alkes L Price, Charles B Epstein, Anshul Kundaje, Ramnik J Xavier, Mark J Daly, Hailiang Huang, Hilary K Finucane, Nir Hacohen, Eric S Lander, Jesse M Engreitz
Genome-wide enhancer maps link risk variants to disease genes. Nature 593 (7858) (2021)
Georgi K Marinov, Alexandro E Trevino, Tingting Xiang, Anshul Kundaje, Arthur R Grossman, William J Greenleaf
Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum. Nature genetics 53 (5) (2021)
Xin Liu, Tao Sun, Anna Shcherbina, Qin Li, Inga Jarmoskaite, Kalli Kappel, Gokul Ramaswami, Rachel J Hagey, Anshul Kundaje, Jin Billy Li
Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis. Nature communications 12 (1) (2021)
Žiga Avsec, Melanie Weilert, Avanti Shrikumar, Sabrina Krueger, Amr Alexandari, Khyati Dalal, Robin Fropf, Charles McAnany, Julien Gagneur, Anshul Kundaje, Julia Zeitlinger
Base-resolution models of transcription-factor binding reveal soft motif syntax. Nature genetics 53 (3) (2021)
M Ryan Corces, Anna Shcherbina, Soumya Kundu, Michael J Gloudemans, Laure Frésard, Jeffrey M Granja, Bryan H Louie, Tiffany Eulalio, Shadi Shams, S Tansu Bagdatli, Maxwell R Mumbach, Boxiang Liu, Kathleen S Montine, William J Greenleaf, Anshul Kundaje, Stephen B Montgomery, Howard Y Chang, Thomas J Montine
Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases. Nature genetics 52 (11) (2020)
Benjamin Haibe-Kains, George Alexandru Adam, Ahmed Hosny, Farnoosh Khodakarami, null null, Levi Waldron, Bo Wang, Chris McIntosh, Anna Goldenberg, Anshul Kundaje, Casey S Greene, Tamara Broderick, Michael M Hoffman, Jeffrey T Leek, Keegan Korthauer, Wolfgang Huber, Alvis Brazma, Joelle Pineau, Robert Tibshirani, Trevor Hastie, John P A Ioannidis, John Quackenbush, Hugo J W L Aerts
Transparency and reproducibility in artificial intelligence. Nature 586 (7829) (2020)
null null, Jill E Moore, Michael J Purcaro, Henry E Pratt, Charles B Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A Davis, Alexander Dobin, Rajinder Kaul, Jessica Halow, Eric L Van Nostrand, Peter Freese, David U Gorkin, Yin Shen, Yupeng He, Mark Mackiewicz, Florencia Pauli-Behn, Brian A Williams, Ali Mortazavi, Cheryl A Keller, Xiao-Ou Zhang, Shaimae I Elhajjajy, Jack Huey, Diane E Dickel, Valentina Snetkova, Xintao Wei, Xiaofeng Wang, Juan Carlos Rivera-Mulia, Joel Rozowsky, Jing Zhang, Surya B Chhetri, Jialing Zhang, Alec Victorsen, Kevin P White, Axel Visel, Gene W Yeo, Christopher B Burge, Eric Lécuyer, David M Gilbert, Job Dekker, John L Rinn, Eric M Mendenhall, Joseph R Ecker, Manolis Kellis, Robert J Klein, William S Noble, Anshul Kundaje, Roderic Guigó, Peggy J Farnham, J Michael Cherry, Richard M Myers, Bing Ren, Brenton R Graveley, Mark B Gerstein, Len A Pennacchio, Michael Paul Snyder, Bradley E Bernstein, Barbara Wold, Ross Cameron Hardison, Thomas R Gingeras, John A Stamatoyannopoulos, Nishigandha Phalke
Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583 (7818) (2020)
Fabian Grubert, Rohith Srivas, Damek V Spacek, Maya Kasowski, Mariana Ruiz-Velasco, Nasa Sinnott-Armstrong, Peyton Greenside, Anil Narasimha, Qing Liu, Benjamin Geller, Akshay Sanghi, Michael Kulik, Silin Sa, Marlene Rabinovitch, Anshul Kundaje, Stephen Dalton, Judith Barbara Zaugg, Michael Paul Snyder
Landscape of cohesin-mediated chromatin loops in the human genome. Nature 583 (7818) (2020)
Michael Wainberg, Nicholas A Sinnott-Armstrong, Nicholas Mancuso, Alvaro N Barbeira, David A Knowles, David Golan, Raili Ermel, Arno Ruusalepp, Thomas Quertermous, Ke Hao, Johan L M Bjorkegren, Hae Kyung Im, Bogdan Pasaniuc, Manuel A Rivas, Anshul Kundaje
Opportunities and challenges for transcriptome-wide association studies. Nature genetics 51 (4) (2019)
Berenice Anath Benayoun, Elizabeth A Pollina, Param Priya Singh, Salah Mahmoudi, Itamar Harel, Kerriann M Casey, Ben W Dulken, Anshul Kundaje, Anne Brunet
Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses. Genome research 29 (4) (2019)
Rajiv Movva, Peyton Greenside, Georgi K Marinov, Surag Nair, Avanti Shrikumar, Anshul Kundaje
Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays. PloS one 14 (6) (2019)
Haley M Amemiya, Anshul Kundaje, Alan P Boyle
The ENCODE Blacklist: Identification of Problematic Regions of the Genome. Scientific reports 9 (1) (2019)
Žiga Avsec, Roman Kreuzhuber, Johnny Israeli, Nancy Xu, Jun Cheng, Avanti Shrikumar, Abhimanyu Banerjee, Daniel S Kim, Thorsten Beier, Lara Urban, Anshul Kundaje, Oliver Stegle, Julien Gagneur
The Kipoi repository accelerates community exchange and reuse of predictive models for genomics. Nature biotechnology 37 (6) (2019)
Travers Ching, Daniel Scott Himmelstein, Brett K Beaulieu-Jones, Alexandr A Kalinin, Brian T Do, Gregory P Way, Enrico Ferrero, Paul-Michael Agapow, Michael Zietz, Michael M Hoffman, Wei Xie, Gail L Rosen, Benjamin J Lengerich, Johnny Israeli, Jack Lanchantin, Stephen Woloszynek, Anne E Carpenter, Avanti Shrikumar, Jinbo Xu, Evan M Cofer, Christopher A Lavender, Srinivas C Turaga, Amr M Alexandari, Zhiyong Lu, David J Harris, Dave DeCaprio, Yanjun Qi, Anshul Kundaje, Yifan Peng, Laura K Wiley, Marwin H S Segler, Simina M Boca, S Joshua Swamidass, Austin Huang, Anthony Gitter, Casey S Greene
Opportunities and obstacles for deep learning in biology and medicine. Journal of the Royal Society, Interface 15 (141) (2019)
Ryan S Stowers, Anna Shcherbina, Johnny Israeli, Joshua J Gruber, Julie Chang, Sungmin Nam, Atefeh Rabiee, Mary N Teruel, Michael P Snyder, Anshul Kundaje, Ovijit Chaudhuri
Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility. Nature biomedical engineering 3 (12) (2019)
Michael Wainberg, Anubha Mahajan, Anshul Kundaje, Mark I McCarthy, Erik Ingelsson, Nicholas A Sinnott-Armstrong, Manuel A Rivas
Homogeneity in the association of body mass index with type 2 diabetes across the UK Biobank: A Mendelian randomization study. PLoS medicine 16 (12) (2019)
Dian Yang, Sarah K Denny, Peyton G Greenside, Andrea C Chaikovsky, Jennifer J Brady, Youcef Ouadah, Jeffrey M Granja, Nadine S Jahchan, Jing Shan Lim, Shirley Kwok, Christina S Kong, Anna S Berghoff, Anna Schmitt, H Christian Reinhardt, Kwon-Sik Park, Matthias Preusser, Anshul Kundaje, William J Greenleaf, Julien Sage, Monte M Winslow
Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin. Cancer discovery 8 (10) (2018)
Amit Blumberg, Charles G Danko, Anshul Kundaje, Dan Mishmar
A common pattern of DNase I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization. Genome research 28 (8) (2018)
Bo Wang, Lin Huang, Yuke Zhu, Anshul Kundaje, Serafim Batzoglou, Anna Goldenberg
Vicus: Exploiting local structures to improve network-based analysis of biological data. PLoS computational biology 13 (10) (2017)
Stephanie A Bien, Paul L Auer, Tabitha A Harrison, Conghui Qu, Charles M Connolly, Peyton G Greenside, Sai Chen, Sonja I Berndt, Stéphane Bézieau, Hyun M Kang, Jeroen Huyghe, Hermann Brenner, Graham Casey, Andrew T Chan, John L Hopper, Barbara L Banbury, Jenny Chang-Claude, Stephen J Chanock, Robert W Haile, Michael Hoffmeister, Christian Fuchsberger, Mark E Jenkins, Suzanne M Leal, Mathieu Lemire, Polly A Newcomb, Steven Gallinger, John D Potter, Robert E Schoen, Martha L Slattery, Joshua D Smith, Loic Le Marchand, Emily White, Brent W Zanke, Goncalo R Abeçasis, Christopher S Carlson, Ulrike Peters, Deborah A Nickerson, Anshul Kundaje, Li Hsu, null null
Enrichment of colorectal cancer associations in functional regions: Insight for using epigenomics data in the analysis of whole genome sequence-imputed GWAS data. PloS one 12 (11) (2017)
Maxwell R Mumbach, Ansuman T Satpathy, Evan August Boyle, Chao Dai, Benjamin G Gowen, Seung Woo Cho, Michelle L Nguyen, Adam J Rubin, Jeffrey M Granja, Katelynn R Kazane, Yuning Wei, Trieu Nguyen, Peyton G Greenside, M Ryan Corces, Josh Tycko, Dimitre R Simeonov, Nabeela Suliman, Rui Li, Jin Xu, Ryan A Flynn, Anshul Kundaje, Paul A Khavari, Alexander Marson, Jacob E Corn, Thomas Quertermous, William J Greenleaf, Howard Y Chang
Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Nature genetics 49 (11) (2017)
M Ryan Corces, Alexandro E Trevino, Emily G Hamilton, Peyton G Greenside, Nicholas A Sinnott-Armstrong, Sam Vesuna, Ansuman T Satpathy, Adam J Rubin, Kathleen S Montine, Beijing Wu, Arwa Kathiria, Seung Woo Cho, Maxwell R Mumbach, Ava C Carter, Maya Kasowski, Lisa A Orloff, Viviana I Risca, Anshul Kundaje, Paul A Khavari, Thomas J Montine, William J Greenleaf, Howard Y Chang
An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature methods 14 (10) (2017)
Adam J Rubin, Brook C Barajas, Mayra Furlan-Magaril, Vanessa Lopez-Pajares, Maxwell R Mumbach, Imani Howard, Daniel S Kim, Lisa D Boxer, Jonathan Cairns, Mikhail Spivakov, Steven W Wingett, Minyi Shi, Zhixin Zhao, William J Greenleaf, Anshul Kundaje, Michael Snyder, Howard Y Chang, Peter Fraser, Paul A Khavari
Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation. Nature genetics 49 (10) (2017)
Amit Blumberg, Edward J Rice, Anshul Kundaje, Charles G Danko, Dan Mishmar
Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution. Genome research 27 (3) (2017)
David W Morgens, Michael Wainberg, Evan August Boyle, Oana Ursu, Carlos L Araya, C Kimberly Tsui, Michael S Haney, Gaelen T Hess, Kyuho Han, Edwin E Jeng, Amy Li, Michael P Snyder, William J Greenleaf, Anshul Kundaje, Michael C Bassik
Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens. Nature communications 8 (2017)
M Ryan Corces, Jason D Buenrostro, Beijing Wu, Peyton G Greenside, Steven M Chan, Julie L Koenig, Michael P Snyder, Jonathan K Pritchard, Anshul Kundaje, William J Greenleaf, Ravindra Majeti, Howard Y Chang
Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nature genetics 48 (10) (2016)