Anshul Kundaje

Affiliations

Department of Computer Science, Stanford University, Stanford, California, United States of America.
Department of Genetics, Stanford University, Stanford, California, United States of America.

Publications (98)

Homogeneity in the association of body mass index with type 2 diabetes across the UK Biobank: A Mendelian randomization study.

PLoS medicine

Avec: Michael Wainberg , Anubha Mahajan , Anshul Kundaje , Mark I McCarthy , Erik Ingelsson , Nasa Sinnott-Armstrong , Manuel A Rivas

Opportunities and challenges for transcriptome-wide association studies.

Nature genetics

Avec: Michael Wainberg , Nasa Sinnott-Armstrong , Nicholas Mancuso , Alvaro N Barbeira , David A Knowles , David Golan , Raili Ermel , Arno Ruusalepp , Thomas Quertermous , Ke Hao , Johan L M Björkegren , Hae Kyung Im , Bogdan Pasaniuc , Manuel A Rivas , Anshul Kundaje

CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities.

Nature

Avec: Kyuho Han , Sarah E Pierce , Amy Li , Kaitlyn Spees , Gray R Anderson , Jose A Seoane , Yuan-Hung Lo , Michael Dubreuil , Micah Olivas , Roarke A Kamber , Michael Wainberg , Kaja Kostyrko , Marcus R Kelly , Maryam Yousefi , Scott W Simpkins , David Yao , Keonil Lee , Calvin J Kuo , Peter K Jackson , Alejandro Sweet-Cordero , Anshul Kundaje , Andrew J Gentles , Christina Curtis , Monte M Winslow , Michael C Bassik

Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays.

PloS one

Avec: Rajiv Movva , Peyton Greenside , Georgi K Marinov , Surag Nair , Avanti Shrikumar , Anshul Kundaje

Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum.

Nature genetics

Avec: Georgi K Marinov , Alexandro E Trevino , Tingting Xiang , Anshul Kundaje , Arthur R Grossman , William J Greenleaf

Domain-adaptive neural networks improve cross-species prediction of transcription factor binding.

Genome research

Avec: Kelly Cochran , Divyanshi Srivastava , Avanti Shrikumar , Akshay Balsubramani , Ross C Hardison , Anshul Kundaje , Shaun Mahony

Congenital anemia reveals distinct targeting mechanisms for master transcription factor GATA1.

Blood

Avec: Leif S Ludwig , Caleb A Lareau , Erik L Bao , Nan Liu , Taiju Utsugisawa , Alex M Tseng , Samuel A Myers , Jeffrey M Verboon , Jacob C Ulirsch , Wendy Luo , Christoph Muus , Claudia Fiorini , Meagan E Olive , Christopher M Vockley , Mathias Munschauer , Abigail Hunter , Hiromi Ogura , Toshiyuki Yamamoto , Hiroko Inada , Shinichiro Nakagawa , Shuichi Ohzono , Vidya Subramanian , Roberto Chiarle , Bertil Glader , Steven A Carr , Martin J Aryee , Anshul Kundaje , Stuart H Orkin , Aviv Regev , Timothy L McCavit , Hitoshi Kanno , Vijay G Sankaran

CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping.

Genome biology

Avec: Georgi K Marinov , Samuel H Kim , S Tansu Bagdatli , Soon Il Higashino , Alexandro E Trevino , Josh Tycko , Tong Wu , Lacramioara Bintu , Michael C Bassik , Chuan He , Anshul Kundaje , William J Greenleaf

Multicenter integrated analysis of noncoding CRISPRi screens.

Nature methods

Avec: David Yao , Josh Tycko , Jin Woo Oh , Lexi R Bounds , Sager J Gosai , Lazaros Lataniotis , Ava Mackay-Smith , Benjamin R Doughty , Idan Gabdank , Henri Schmidt , Tania Guerrero-Altamirano , Keith Siklenka , Katherine Guo , Alexander D White , Ingrid Youngworth , Kalina Andreeva , Xingjie Ren , Alejandro Barrera , Yunhai Luo , Galip Gürkan Yardımcı , Ryan Tewhey , Anshul Kundaje , William J Greenleaf , Pardis C Sabeti , Christina Leslie , Yuri Pritykin , Jill E Moore , Michael A Beer , Charles A Gersbach , Timothy E Reddy , Yin Shen , Jesse M Engreitz , Michael C Bassik , Steven K Reilly

Genetic risk impacts the association of menopausal hormone therapy with colorectal cancer risk.

British journal of cancer

Avec: Yu Tian , Yi Lin , Conghui Qu , Volker Arndt , James W Baurley , Sonja I Berndt , Stephanie A Bien , D Timothy Bishop , Hermann Brenner , Daniel D Buchanan , Arif Budiarto , Peter T Campbell , Robert Carreras-Torres , Graham Casey , Andrew T Chan , Rui Chen , Xuechen Chen , David V Conti , Virginia Díez-Obrero , Niki Dimou , David A Drew , Jane C Figueiredo , Steven Gallinger , Graham G Giles , Stephen B Gruber , Marc J Gunter , Sophia Harlid , Tabitha A Harrison , Akihisa Hidaka , Michael Hoffmeister , Jeroen R Huyghe , Mark A Jenkins , Kristina M Jordahl , Amit D Joshi , Temitope O Keku , Eric Kawaguchi , Andre E Kim , Anshul Kundaje , Susanna C Larsson , Loic Le Marchand , Juan Pablo Lewinger , Li Li , Victor Moreno , John Morrison , Neil Murphy , Hongmei Nan , Rami Nassir , Polly A Newcomb , Mireia Obón-Santacana , Shuji Ogino , Jennifer Ose , Bens Pardamean , Andrew J Pellatt , Anita R Peoples , Elizabeth A Platz , John D Potter , Ross L Prentice , Gad Rennert , Edward A Ruiz-Narvaez , Lori C Sakoda , Robert E Schoen , Anna Shcherbina , Mariana C Stern , Yu-Ru Su , Stephen N Thibodeau , Duncan C Thomas , Konstantinos K Tsilidis , Franzel J B van Duijnhoven , Bethany Van Guelpen , Kala Visvanathan , Emily White , Alicja Wolk , Michael O Woods , Anna H Wu , Ulrike Peters , W James Gauderman , Li Hsu , Jenny Chang-Claude

Protocol for mapping the three-dimensional organization of dinoflagellate genomes.

STAR protocols

Avec: Georgi K Marinov , Anshul Kundaje , William J Greenleaf , Arthur R Grossman

Accelerating in silico saturation mutagenesis using compressed sensing.

Bioinformatics (Oxford, England)

Avec: Jacob Schreiber , Surag Nair , Akshay Balsubramani , Anshul Kundaje

Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases.

Cell genomics

Avec: Sean K Wang , Surag Nair , Rui Li , Katerina Kraft , Anusri Pampari , Aman Patel , Joyce B Kang , Christy Luong , Anshul Kundaje , Howard Y Chang

Deciphering the impact of genetic variation on human polyadenylation using APARENT2.

Genome biology

Avec: Johannes Linder , Samantha E Koplik , Anshul Kundaje , Georg Seelig

The chromatin landscape of the euryarchaeon Haloferax volcanii.

Genome biology

Avec: Georgi K Marinov , S Tansu Bagdatli , Tong Wu , Chuan He , Anshul Kundaje , William J Greenleaf

Transcriptomics and chromatin accessibility in multiple African population samples.

bioRxiv : the preprint server for biology

Avec: Marianne K DeGorter , Page C Goddard , Emre Karakoc , Soumya Kundu , Stephanie M Yan , Daniel Nachun , Nathan Abell , Matthew Aguirre , Tommy Carstensen , Ziwei Chen , Matthew Durrant , Vikranth R Dwaracherla , Karen Feng , Michael J Gloudemans , Naiomi Hunter , Mohana P S Moorthy , Cristina Pomilla , Kameron B Rodrigues , Courtney J Smith , Kevin S Smith , Rachel A Ungar , Brunilda Balliu , Jacques Fellay , Paul Flicek , Paul J McLaren , Brenna Henn , Rajiv C McCoy , Lauren Sugden , Anshul Kundaje , Manjinder S Sandhu , Deepti Gurdasani , Stephen B Montgomery

Two genome-wide interaction loci modify the association of nonsteroidal anti-inflammatory drugs with colorectal cancer.

Science advances

Avec: David A Drew , Andre E Kim , Yi Lin , Conghui Qu , John Morrison , Juan Pablo Lewinger , Eric Kawaguchi , Jun Wang , Yubo Fu , Natalia Zemlianskaia , Virginia Díez-Obrero , Stephanie A Bien , Niki Dimou , Demetrius Albanes , James W Baurley , Anna H Wu , Daniel D Buchanan , John D Potter , Ross L Prentice , Sophia Harlid , Volker Arndt , Elizabeth L Barry , Sonja I Berndt , Emmanouil Bouras , Hermann Brenner , Arif Budiarto , Andrea Burnett-Hartman , Peter T Campbell , Robert Carreras-Torres , Graham Casey , Jenny Chang-Claude , David V Conti , Matthew A M Devall , Jane C Figueiredo , Stephen B Gruber , Andrea Gsur , Marc J Gunter , Tabitha A Harrison , Akihisa Hidaka , Michael Hoffmeister , Jeroen R Huyghe , Mark A Jenkins , Kristina M Jordahl , Anshul Kundaje , Loic Le Marchand , Li Li , Brigid M Lynch , Neil Murphy , Rami Nassir , Polly A Newcomb , Christina C Newton , Mireia Obón-Santacana , Shuji Ogino , Jennifer Ose , Rish K Pai , Julie R Palmer , Nikos Papadimitriou , Bens Pardamean , Andrew J Pellatt , Anita R Peoples , Elizabeth A Platz , Gad Rennert , Edward Ruiz-Narvaez , Lori C Sakoda , Peter C Scacheri , Stephanie L Schmit , Robert E Schoen , Mariana C Stern , Yu-Ru Su , Duncan C Thomas , Yu Tian , Konstantinos K Tsilidis , Cornelia M Ulrich , Caroline Y Um , Fränzel J B van Duijnhoven , Bethany Van Guelpen , Emily White , Li Hsu , Victor Moreno , Ulrike Peters , Andrew T Chan , W James Gauderman

Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts.

Bioinformatics (Oxford, England)

Avec: Surag Nair , Daniel S Kim , Jacob Perricone , Anshul Kundaje

A genome-wide atlas of co-essential modules assigns function to uncharacterized genes.

Nature genetics

Avec: Michael Wainberg , Roarke A Kamber , Akshay Balsubramani , Robin M Meyers , Nasa Sinnott-Armstrong , Daniel Hornburg , Lihua Jiang , Joanne Chan , Ruiqi Jian , Mingxin Gu , Anna Shcherbina , Michael M Dubreuil , Kaitlyn Spees , Wouter Meuleman , Michael P Snyder , Michael C Bassik , Anshul Kundaje

Base-resolution models of transcription-factor binding reveal soft motif syntax.

Nature genetics

Avec: Žiga Avsec , Melanie Weilert , Avanti Shrikumar , Sabrina Krueger , Amr Alexandari , Khyati Dalal , Robin Fropf , Charles McAnany , Julien Gagneur , Anshul Kundaje , Julia Zeitlinger

High-Throughput Discovery and Characterization of Human Transcriptional Effectors.

Cell

Avec: Josh Tycko , Nicole DelRosso , Gaelen T Hess , Aradhana , Abhimanyu Banerjee , Aditya Mukund , Mike V Van , Braeden K Ego , David Yao , Kaitlyn Spees , Peter Suzuki , Georgi K Marinov , Anshul Kundaje , Michael C Bassik , Lacramioara Bintu

Genome-Wide Interaction Analysis of Genetic Variants With Menopausal Hormone Therapy for Colorectal Cancer Risk.

Journal of the National Cancer Institute

Avec: Yu Tian , Andre E Kim , Stephanie A Bien , Yi Lin , Conghui Qu , Tabitha A Harrison , Robert Carreras-Torres , Virginia Díez-Obrero , Niki Dimou , David A Drew , Akihisa Hidaka , Jeroen R Huyghe , Kristina M Jordahl , John Morrison , Neil Murphy , Mireia Obón-Santacana , Cornelia M Ulrich , Jennifer Ose , Anita R Peoples , Edward A Ruiz-Narvaez , Anna Shcherbina , Mariana C Stern , Yu-Ru Su , Franzel J B van Duijnhoven , Volker Arndt , James W Baurley , Sonja I Berndt , D Timothy Bishop , Hermann Brenner , Daniel D Buchanan , Andrew T Chan , Jane C Figueiredo , Steven Gallinger , Stephen B Gruber , Sophia Harlid , Michael Hoffmeister , Mark A Jenkins , Amit D Joshi , Temitope O Keku , Susanna C Larsson , Loic Le Marchand , Li Li , Graham G Giles , Roger L Milne , Hongmei Nan , Rami Nassir , Shuji Ogino , Arif Budiarto , Elizabeth A Platz , John D Potter , Ross L Prentice , Gad Rennert , Lori C Sakoda , Robert E Schoen , Martha L Slattery , Stephen N Thibodeau , Bethany Van Guelpen , Kala Visvanathan , Emily White , Alicja Wolk , Michael O Woods , Anna H Wu , Peter T Campbell , Graham Casey , David V Conti , Marc J Gunter , Anshul Kundaje , Juan Pablo Lewinger , Victor Moreno , Polly A Newcomb , Bens Pardamean , Duncan C Thomas , Konstantinos K Tsilidis , Ulrike Peters , W James Gauderman , Li Hsu , Jenny Chang-Claude

Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk.

Nature genetics

Avec: Adam W Turner , Shengen Shawn Hu , Jose Verdezoto Mosquera , Wei Feng Ma , Chani J Hodonsky , Doris Wong , Gaëlle Auguste , Yipei Song , Katia Sol-Church , Emily Farber , Soumya Kundu , Anshul Kundaje , Nicolas G Lopez , Lijiang Ma , Saikat Kumar B Ghosh , Suna Onengut-Gumuscu , Euan A Ashley , Thomas Quertermous , Aloke V Finn , Nicholas J Leeper , Jason C Kovacic , Johan L M Björkegren , Chongzhi Zang , Clint L Miller

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

Avec: Glenn J Markov , Thach Mai , Surag Nair , Anna Shcherbina , Yu Xin Wang , David M Burns , Anshul Kundaje , Helen M Blau

Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer.

Nature genetics

Avec: 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 P Snyder , William J Greenleaf

Probing the diabetes and colorectal cancer relationship using gene - environment interaction analyses.

British journal of cancer

Avec: Niki Dimou , Andre E Kim , Orlagh Flanagan , Neil Murphy , Virginia Diez-Obrero , Anna Shcherbina , Elom K Aglago , Emmanouil Bouras , Peter T Campbell , Graham Casey , Steven Gallinger , Stephen B Gruber , Mark A Jenkins , Yi Lin , Victor Moreno , Edward 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

bioRxiv : the preprint server for biology

Avec: Amr M Alexandari , Connor A Horton , Avanti Shrikumar , Nilay Shah , Eileen Li , Melanie Weilert , Miles A Pufall , Julia Zeitlinger , Polly M Fordyce , 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

Avec: 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

Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease.

Cell

Avec: Mohamed Ameen , Laksshman Sundaram , Mengcheng Shen , Abhimanyu Banerjee , Soumya Kundu , Surag Nair , Anna Shcherbina , Mingxia Gu , Kitchener D Wilson , Avyay Varadarajan , Nirmal Vadgama , Akshay Balsubramani , Joseph C Wu , Jesse M Engreitz , Kyle Farh , Ioannis Karakikes , Kevin C Wang , Thomas Quertermous , William J Greenleaf , Anshul Kundaje

CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators.

bioRxiv : the preprint server for biology

Avec: Madeline H Kowalski , Hans-Hermann Wessels , Johannes Linder , Saket Choudhary , Austin Hartman , Yuhan Hao , Isabella Mascio , Carol Dalgarno , Anshul Kundaje , Rahul Satija

Dissecting the cis-regulatory syntax of transcription initiation with deep learning.

bioRxiv : the preprint server for biology

Avec: Kelly Cochran , Melody Yin , Anika Mantripragada , Jacob Schreiber , Georgi K Marinov , Anshul Kundaje

Flexible use of conserved motif vocabularies constrains genome access in cell type evolution.

bioRxiv : the preprint server for biology

Avec: Chew Chai , Jesse Gibson , Pengyang Li , Anusri Pampari , Aman Patel , Anshul Kundaje , Bo Wang

Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders.

Cell

Avec: Bo Zhou , Joseph G Arthur , Hanmin Guo , Taeyoung Kim , Yiling Huang , Reenal Pattni , Tao Wang , Soumya Kundu , Jay X J Luo , HoJoon Lee , Daniel C Nachun , Carolin Purmann , Emma M Monte , Annika K Weimer , Ping-Ping Qu , Minyi Shi , Lixia Jiang , Xinqiong Yang , John F Fullard , Jaroslav Bendl , Kiran Girdhar , Minsu Kim , Xi Chen , Auteur inconnu , William J Greenleaf , Laramie Duncan , Hanlee P Ji , Xiang Zhu , Giltae Song , Stephen B Montgomery , Dean Palejev , Heinrich Zu Dohna , Panos Roussos , Anshul Kundaje , Joachim F Hallmayer , Michael P Snyder , Wing H Wong , Alexander E Urban

Prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC.

bioRxiv : the preprint server for biology

Avec: Anupama Jha , Borislav Hristov , Xiao Wang , Sheng Wang , William J Greenleaf , Anshul Kundaje , Erez Lieberman Aiden , Alessandro Bertero , William Stafford Noble

A cell and transcriptome atlas of the human arterial vasculature.

bioRxiv : the preprint server for biology

Avec: Quanyi 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

Prediction and design of transcriptional repressor domains with large-scale mutational scans and deep learning.

bioRxiv : the preprint server for biology

Avec: Raeline Valbuena , AkshatKumar Nigam , Josh Tycko , Peter Suzuki , Kaitlyn Spees , Aradhana , Sophia Arana , Peter Du , Roshni A Patel , Lacramiora Bintu , Anshul Kundaje , Michael C Bassik

An SLC12A9-dependent ion transport mechanism maintains lysosomal osmolarity.

Developmental cell

Avec: Roni Levin-Konigsberg , Koushambi Mitra , Kaitlyn Spees , AkshatKumar Nigam , Katherine Liu , Camille Januel , Pravin Hivare , Sophia M Arana , Laura M Prolo , Anshul Kundaje , Manuel D Leonetti , Yamuna Krishnan , Michael C Bassik

Long-range single-molecule mapping of chromatin accessibility in eukaryotes.

Nature methods

Avec: Zohar Shipony , Georgi K Marinov , Matthew P Swaffer , Nicholas A Sinnott-Armstrong , Jan M Skotheim , Anshul Kundaje , William J Greenleaf

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses.

Genome research

Avec: Bérénice A Benayoun , Elizabeth A Pollina , Param Priya Singh , Salah Mahmoudi , Itamar Harel , Kerriann M Casey , Ben W Dulken , Anshul Kundaje , Anne Brunet

Measuring the reproducibility and quality of Hi-C data.

Genome biology

Avec: Galip Gürkan Yardımcı , Hakan Ozadam , Michael E G Sauria , Oana Ursu , Koon-Kiu Yan , Tao Yang , Abhijit Chakraborty , Arya Kaul , Bryan R Lajoie , Fan Song , Ye Zhan , Ferhat Ay , Mark Gerstein , Anshul Kundaje , Qunhua Li , James Taylor , Feng Yue , Job Dekker , William S Noble

mtDNA Chromatin-like Organization Is Gradually Established during Mammalian Embryogenesis.

iScience

Avec: Shani Marom , Amit Blumberg , Anshul Kundaje , Dan Mishmar

Landscape of cohesin-mediated chromatin loops in the human genome.

Nature

Avec: 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 B Zaugg , Michael Snyder

Expanded encyclopaedias of DNA elements in the human and mouse genomes.

Nature

Avec: Auteur inconnu , 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 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 P Snyder , Bradley E Bernstein , Barbara Wold , Ross C Hardison , Thomas R Gingeras , John A Stamatoyannopoulos , Zhiping Weng

GENCODE: reference annotation for the human and mouse genomes in 2023.

Nucleic acids research

Avec: Adam Frankish , Sílvia Carbonell-Sala , Mark Diekhans , Irwin Jungreis , Jane E Loveland , Jonathan M Mudge , Cristina Sisu , James C Wright , Carme Arnan , If Barnes , Abhimanyu Banerjee , Ruth Bennett , Andrew Berry , Alexandra Bignell , Carles Boix , Ferriol Calvet , Daniel Cerdán-Vélez , Fiona Cunningham , Claire Davidson , Sarah Donaldson , Cagatay Dursun , Reham Fatima , Stefano Giorgetti , Carlos Garcıa Giron , Jose Manuel Gonzalez , Matthew Hardy , Peter W Harrison , Thibaut Hourlier , Zoe Hollis , Toby Hunt , Benjamin James , Yunzhe Jiang , Rory Johnson , Mike Kay , Julien Lagarde , Fergal J Martin , Laura Martínez Gómez , Surag Nair , Pengyu Ni , Fernando Pozo , Vivek Ramalingam , Magali Ruffier , Bianca M Schmitt , Jacob M Schreiber , Emily Steed , Marie-Marthe Suner , Dulika Sumathipala , Irina Sycheva , Barbara Uszczynska-Ratajczak , Elizabeth Wass , Yucheng T Yang , Andrew Yates , Zahoor Zafrulla , Jyoti S Choudhary , Mark Gerstein , Roderic Guigo , Tim J P Hubbard , Manolis Kellis , Anshul Kundaje , Benedict Paten , Michael L Tress , Paul Flicek

Single-Molecule Mapping of Chromatin Accessibility Using NOMe-seq/dSMF.

Methods in molecular biology (Clifton, N.J.)

Avec: Michaela Hinks , Georgi K Marinov , Anshul Kundaje , Lacramioara Bintu , William J Greenleaf

Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-seq.

Methods in molecular biology (Clifton, N.J.)

Avec: Samuel H Kim , Georgi K Marinov , S Tansu Bagdatli , Soon Il Higashino , Zohar Shipony , Anshul Kundaje , William J Greenleaf

The ENCODE Uniform Analysis Pipelines.

bioRxiv : the preprint server for biology

Avec: Benjamin C Hitz , Lee Jin-Wook , Otto Jolanki , Meenakshi S Kagda , Keenan Graham , Paul Sud , Idan Gabdank , J Seth Strattan , Cricket A Sloan , Timothy Dreszer , Laurence D Rowe , Nikhil R Podduturi , Venkat S Malladi , Esther T Chan , Jean M Davidson , Marcus Ho , Stuart Miyasato , Matt Simison , Forrest Tanaka , Yunhai Luo , Ian Whaling , Eurie L Hong , Brian T Lee , Richard Sandstrom , Eric Rynes , Jemma Nelson , Andrew Nishida , Alyssa Ingersoll , Michael Buckley , Mark Frerker , Daniel S Kim , Nathan Boley , Diane Trout , Alex 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 Aiden , Tom Gingeras , Simon Heath , Martin Hirst , W James Kent , Anshul Kundaje , Ali Mortazavi , Barbara Wold , J Michael Cherry

Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells.

Nature genetics

Avec: 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 Schulte , Cornelia Eckert , Anshul Kundaje , Peter Smibert , Santosha A Vardhana , Ansuman T Satpathy , Aviv Regev , Vijay G Sankaran , Suneet Agarwal , Leif S Ludwig

Genome-wide interaction analysis of folate for colorectal cancer risk.

The American journal of clinical nutrition

Avec: Emmanouil Bouras , Andre E Kim , Yi Lin , John Morrison , Mengmeng Du , Demetrius Albanes , Elizabeth L Barry , James W Baurley , Sonja I Berndt , Stephanie A Bien , Timothy D Bishop , Hermann Brenner , Arif Budiarto , Andrea Burnett-Hartman , Peter T Campbell , Robert Carreras-Torres , Graham Casey , Tjeng Wawan Cenggoro , Andrew T Chan , Jenny Chang-Claude , David V Conti , Michelle Cotterchio , Matthew Devall , Virginia Diez-Obrero , Niki Dimou , David A Drew , Jane C Figueiredo , Graham G Giles , Stephen B Gruber , Marc J Gunter , Tabitha A Harrison , Akihisa Hidaka , Michael Hoffmeister , Jeroen R Huyghe , Amit D Joshi , Eric S Kawaguchi , Temitope O Keku , Anshul Kundaje , Loic Le Marchand , Juan Pablo Lewinger , Li Li , Brigid M Lynch , Bharuno Mahesworo , Satu Männistö , Victor Moreno , Neil Murphy , Polly A Newcomb , Mireia Obón-Santacana , Jennifer Ose , Julie R Palmer , Nikos Papadimitriou , Bens Pardamean , Andrew J Pellatt , Anita R Peoples , Elizabeth A Platz , John D Potter , Lihong Qi , Conghui Qu , Gad Rennert , Edward Ruiz-Narvaez , Lori C Sakoda , Stephanie L Schmit , Anna Shcherbina , Mariana C Stern , Yu-Ru Su , Catherine M Tangen , Duncan C Thomas , Yu Tian , Caroline Y Um , Franzel Jb van Duijnhoven , Bethany Van Guelpen , Kala Visvanathan , Jun Wang , Emily White , Alicja Wolk , Michael O Woods , Cornelia M Ulrich , Li Hsu , W James Gauderman , Ulrike Peters , Konstantinos K Tsilidis

Drug Discovery in Low Data Regimes: Leveraging a Computational Pipeline for the Discovery of Novel SARS-CoV-2 Nsp14-MTase Inhibitors.

bioRxiv : the preprint server for biology

Avec: AkshatKumar Nigam , Matthew F D Hurley , Fengling Li , Eva Konkoǐová , Martin Klíma , Jana Trylčová , Robert Pollice , Süleyman Selim Çinaroǧlu , Roni Levin-Konigsberg , Jasemine Handjaya , Matthieu Schapira , Irene Chau , Sumera Perveen , Ho-Leung Ng , H Ümit Kaniskan , Yulin Han , Sukrit Singh , Christoph Gorgulla , Anshul Kundaje , Jian Jin , Vincent A Voelz , Jan Weber , Radim Nencka , Evzen Boura , Masoud Vedadi , Alán Aspuru-Guzik

Short tandem repeats bind transcription factors to tune eukaryotic gene expression.

Science (New York, N.Y.)

Avec: 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 M Fordyce

Rewriting regulatory DNA to dissect and reprogram gene expression.

bioRxiv : the preprint server for biology

Avec: Gabriella E Martyn , Michael T Montgomery , Hank Jones , Katherine Guo , Benjamin R Doughty , Johannes Linder , Ziwei Chen , Kelly Cochran , Kathryn A Lawrence , Glen Munson , Anusri Pampari , Charles P Fulco , David R Kelley , Eric S Lander , Anshul Kundaje , Jesse M Engreitz

Predicting chromatin conformation contact maps.

bioRxiv : the preprint server for biology

Avec: Alan Min , Jacob Schreiber , Anshul Kundaje , William Stafford Noble

The landscape of the histone-organized chromatin of Bdellovibrionota bacteria.

bioRxiv : the preprint server for biology

Avec: Georgi K Marinov , Benjamin Doughty , Anshul Kundaje , William J Greenleaf

RNA polymerase II dynamics and mRNA stability feedback scale mRNA amounts with cell size.

Cell

Avec: Matthew P Swaffer , Georgi K Marinov , Huan Zheng , Lucas Fuentes Valenzuela , Crystal Yee Tsui , Andrew W Jones , Jessica Greenwood , Anshul Kundaje , William J Greenleaf , Rodrigo Reyes-Lamothe , Jan M Skotheim

Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements.

Science advances

Avec: Henry E Pratt , Gregory Andrews , Nicole Shedd , Nishigandha Phalke , Tongxin Li , Anusri Pampari , Matthew Jensen , Cindy Wen , PsychENCODE Consortium , Michael J Gandal , Daniel H Geschwind , Mark Gerstein , Jill Moore , Anshul Kundaje , Andrés Colubri , Zhiping Weng

Achieving Inclusive Healthcare through Integrating Education and Research with AI and Personalized Curricula.

medRxiv : the preprint server for health sciences

Avec: Amir 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

Mutagenesis Sensitivity Mapping of Human Enhancers In Vivo.

bioRxiv : the preprint server for biology

Avec: Michael Kosicki , Boyang Zhang , Anusri Pampari , Jennifer A Akiyama , Ingrid Playzer-Frick , Catherine S Novak , Stella Tran , Yiwen Zhu , Momoe Kato , Riana D Hunter , Kianna von Maydell , Sarah Barton , Erik Beckman , Anshul Kundaje , Diane E Dickel , Axel Visel , Len A Pennacchio

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements.

Nature communications

Avec: Josh Tycko , Michael Wainberg , Georgi K Marinov , Oana Ursu , Gaelen T Hess , Braeden K Ego , Aradhana , Amy Li , Alisa Truong , Alexandro E Trevino , Kaitlyn Spees , David Yao , Irene M Kaplow , Peyton G Greenside , David W Morgens , Douglas H Phanstiel , Michael P Snyder , Lacramioara Bintu , William J Greenleaf , Anshul Kundaje , Michael C Bassik

GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs.

Bioinformatics (Oxford, England)

Avec: Avanti Shrikumar , Eva Prakash , Anshul Kundaje

Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility.

Nature biomedical engineering

Avec: 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

Discovery of common and rare genetic risk variants for colorectal cancer.

Nature genetics

Avec: Jeroen R Huyghe , Stephanie A Bien , Tabitha A Harrison , Hyun Min Kang , Sai Chen , Stephanie L Schmit , David V Conti , Conghui Qu , Jihyoun Jeon , Christopher K Edlund , Peyton Greenside , Michael Wainberg , Fredrick R Schumacher , Joshua D Smith , David M Levine , Sarah C Nelson , Nasa A Sinnott-Armstrong , Demetrius Albanes , M Henar Alonso , Kristin Anderson , Coral Arnau-Collell , Volker Arndt , Christina Bamia , Barbara L Banbury , John A Baron , Sonja I Berndt , Stéphane Bézieau , D Timothy Bishop , Juergen Boehm , Heiner Boeing , Hermann Brenner , Stefanie Brezina , Stephan Buch , Daniel D Buchanan , Andrea Burnett-Hartman , Katja Butterbach , Bette J Caan , Peter T Campbell , Christopher S Carlson , Sergi Castellví-Bel , Andrew T Chan , Jenny Chang-Claude , Stephen J Chanock , Maria-Dolores Chirlaque , Sang Hee Cho , Charles M Connolly , Amanda J Cross , Katarina Cuk , Keith R Curtis , Albert de la Chapelle , Kimberly F Doheny , David Duggan , Douglas F Easton , Sjoerd G Elias , Faye Elliott , Dallas R English , Edith J M Feskens , Jane C Figueiredo , Rocky Fischer , Liesel M FitzGerald , David Forman , Manish Gala , Steven Gallinger , W James Gauderman , Graham G Giles , Elizabeth Gillanders , Jian Gong , Phyllis J Goodman , William M Grady , John S Grove , Andrea Gsur , Marc J Gunter , Robert W Haile , Jochen Hampe , Heather Hampel , Sophia Harlid , Richard B Hayes , Philipp Hofer , Michael Hoffmeister , John L Hopper , Wan-Ling Hsu , Wen-Yi Huang , Thomas J Hudson , David J Hunter , Gemma Ibañez-Sanz , Gregory E Idos , Roxann Ingersoll , Rebecca D Jackson , Eric J Jacobs , Mark A Jenkins , Amit D Joshi , Corinne E Joshu , Temitope O Keku , Timothy J Key , Hyeong Rok Kim , Emiko Kobayashi , Laurence N Kolonel , Charles Kooperberg , Tilman Kühn , Sébastien Küry , Sun-Seog Kweon , Susanna C Larsson , Cecelia A Laurie , Loic Le Marchand , Suzanne M Leal , Soo Chin Lee , Flavio Lejbkowicz , Mathieu Lemire , Christopher I Li , Li Li , Wolfgang Lieb , Yi Lin , Annika Lindblom , Noralane M Lindor , Hua Ling , Tin L Louie , Satu Männistö , Sanford D Markowitz , Vicente Martín , Giovanna Masala , Caroline E McNeil , Marilena Melas , Roger L Milne , Lorena Moreno , Neil Murphy , Robin Myte , Alessio Naccarati , Polly A Newcomb , Kenneth Offit , Shuji Ogino , N Charlotte Onland-Moret , Barbara Pardini , Patrick S Parfrey , Rachel Pearlman , Vittorio Perduca , Paul D P Pharoah , Mila Pinchev , Elizabeth A Platz , Ross L Prentice , Elizabeth Pugh , Leon Raskin , Gad Rennert , Hedy S Rennert , Elio Riboli , Miguel Rodríguez-Barranco , Jane Romm , Lori C Sakoda , Clemens Schafmayer , Robert E Schoen , Daniela Seminara , Mitul Shah , Tameka Shelford , Min-Ho Shin , Katerina Shulman , Sabina Sieri , Martha L Slattery , Melissa C Southey , Zsofia K Stadler , Christa Stegmaier , Yu-Ru Su , Catherine M Tangen , Stephen N Thibodeau , Duncan C Thomas , Sushma S Thomas , Amanda E Toland , Antonia Trichopoulou , Cornelia M Ulrich , David J Van Den Berg , Franzel J B van Duijnhoven , Bethany Van Guelpen , Henk van Kranen , Joseph Vijai , Kala Visvanathan , Pavel Vodicka , Ludmila Vodickova , Veronika Vymetalkova , Korbinian Weigl , Stephanie J Weinstein , Emily White , Aung Ko Win , C Roland Wolf , Alicja Wolk , Michael O Woods , Anna H Wu , Syed H Zaidi , Brent W Zanke , Qing Zhang , Wei Zheng , Peter C Scacheri , John D Potter , Michael C Bassik , Anshul Kundaje , Graham Casey , Victor Moreno , Goncalo R Abecasis , Deborah A Nickerson , Stephen B Gruber , Li Hsu , Ulrike Peters

Brief Report: Cell Cycle Dynamics of Human Pluripotent Stem Cells Primed for Differentiation.

Stem cells (Dayton, Ohio)

Avec: Anna Shcherbina , Jingling Li , Cyndhavi Narayanan , William Greenleaf , Anshul Kundaje , Sundari Chetty

Transcriptional and chromatin-based partitioning mechanisms uncouple protein scaling from cell size.

Molecular cell

Avec: Matthew P Swaffer , Jacob Kim , Devon Chandler-Brown , Maurice Langhinrichs , Georgi K Marinov , William J Greenleaf , Anshul Kundaje , Kurt M Schmoller , Jan M Skotheim

Circulation

Avec: Paul Cheng , Robert C Wirka , Lee Shoa Clarke , Quanyi Zhao , Ramendra Kundu , Trieu Nguyen , Surag Nair , Disha Sharma , Hyun-Jung Kim , Huitong Shi , Themistocles Assimes , Juyong Brian Kim , Anshul Kundaje , Thomas Quertermous

Genetic Effects on Transcriptome Profiles in Colon Epithelium Provide Functional Insights for Genetic Risk Loci.

Cellular and molecular gastroenterology and hepatology

Avec: Virginia Díez-Obrero , Christopher H Dampier , Ferran Moratalla-Navarro , Matthew Devall , Sarah J Plummer , Anna Díez-Villanueva , Ulrike Peters , Stephanie Bien , Jeroen R Huyghe , Anshul Kundaje , Gemma Ibáñez-Sanz , Elisabeth Guinó , Mireia Obón-Santacana , Robert Carreras-Torres , Graham Casey , Víctor Moreno

Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis.

Nature communications

Avec: Xin Liu , Tao Sun , Anna Shcherbina , Qin Li , Inga Jarmoskaite , Kalli Kappel , Gokul Ramaswami , Rhiju Das , Anshul Kundaje , Jin Billy Li

Genome-wide gene-environment interaction analyses to understand the relationship between red meat and processed meat intake and colorectal cancer risk.

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

Avec: Mariana C Stern , Joel Sanchez Mendez , Andre E Kim , Mireia Obón-Santacana , Ferran Moratalla-Navarro , Vicente Martín , Victor Moreno , Yi Lin , Stephanie A Bien , Conghui Qu , Yu-Ru Su , Emily White , Tabitha A Harrison , Jeroen R Huyghe , Catherine M Tangen , Polly A Newcomb , Amanda I Phipps , Claire E Thomas , Eric S Kawaguchi , Juan Pablo Lewinger , John L Morrison , David V Conti , Jun Wang , Duncan C Thomas , Elizabeth A Platz , Kala Visvanathan , Temitope O Keku , Christina C Newton , Caroline Y Um , Anshul Kundaje , Anna Shcherbina , Neil Murphy , Marc J Gunter , Niki Dimou , Nikos Papadimitriou , Stéphane Bézieau , Fränzel Jb van Duijnhoven , Satu Männistö , Gad Rennert , Alicja Wolk , Michael Hoffmeister , Hermann Brenner , Jenny Chang-Claude , Yu Tian , Loïc Le Marchand , Michelle Cotterchio , Konstantinos K Tsilidis , D Timothy Timothy Bishop , Yohannes Adama Melaku , Brigid M Lynch , Daniel D Buchanan , Cornelia M Ulrich , Jennifer Ose , Anita R Peoples , Andrew J Pellatt , Li Li , Matthew Am Devall , Peter T Campbell , Demetrius Albanes , Stephanie J Weinstein , Sonja I Berndt , Stephen B Gruber , Edward Ruiz-Narvaez , Mingyang Song , Amit D Joshi , David A Drew , Jessica L Petrick , Andrew T Chan , Marios Giannakis , Ulrike Peters , Li Hsu , W James Gauderman

Latent human herpesvirus 6 is reactivated in CAR T cells.

Nature

Avec: Caleb A Lareau , Yajie Yin , Katie Maurer , Katalin D Sandor , Bence Daniel , Garima Yagnik , José Peña , Jeremy Chase Crawford , Anne M Spanjaart , 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 Getz , Marcela V Maus , Shuqiang Li , Alison Moore , Zachary J Roberts , Leif S Ludwig , Aimee C Talleur , Paul G Thomas , Houman Dehghani , Thomas Pertel , Anshul Kundaje , Stephen Gottschalk , Theodore L Roth , Marie J Kersten , Catherine J Wu , Robbie G Majzner , Ansuman T Satpathy

An encyclopedia of enhancer-gene regulatory interactions in the human genome.

bioRxiv : the preprint server for biology

Avec: 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 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 , 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

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

Avec: Robert Carreras-Torres , Andre E Kim , Yi Lin , Virginia Díez-Obrero , Stephanie A Bien , Conghui Qu , Jun Wang , Niki Dimou , Elom K Aglago , Demetrius Albanes , Volker Arndt , James W Baurley , Sonja I Berndt , Stéphane Bézieau , D Timothy Bishop , Emmanouil 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 Gallinger , Graham G Giles , Stephen B Gruber , Andrea Gsur , Marc J Gunter , Tabitha A Harrison , Akihisa Hidaka , Michael Hoffmeister , Jeroen R Huyghe , Mark A Jenkins , Kristina M Jordahl , Eric 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 Obón-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 , Gad Rennert , Edward 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 , Fränzel 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

Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries.

Nature genetics

Avec: Ceres Fernandez-Rozadilla , Maria Timofeeva , Zhishan Chen , Philip Law , Minta Thomas , Stephanie Schmit , Virginia Díez-Obrero , Li Hsu , Juan Fernandez-Tajes , Claire Palles , Kitty Sherwood , Sarah Briggs , Victoria Svinti , Kevin Donnelly , Susan Farrington , James Blackmur , Peter Vaughan-Shaw , Xiao-Ou Shu , Jirong Long , Qiuyin Cai , Xingyi Guo , Yingchang Lu , Peter Broderick , James Studd , Jeroen Huyghe , Tabitha Harrison , David Conti , Christopher Dampier , Mathew Devall , Fredrick Schumacher , Marilena Melas , Gad Rennert , Mireia Obón-Santacana , Vicente Martín-Sánchez , Ferran Moratalla-Navarro , Jae Hwan Oh , Jeongseon 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 , Zefang Ren , Yu-Tang Gao , Wei-Hua Jia , John Hopper , Mark Jenkins , Aung Ko Win , Rish Pai , Jane Figueiredo , Robert Haile , Steven Gallinger , Michael Woods , Polly Newcomb , David Duggan , Jeremy Cheadle , Richard Kaplan , Timothy Maughan , Rachel Kerr , David Kerr , Iva Kirac , Jan Böhm , Lukka-Pekka Mecklin , Pekka Jousilahti , Paul Knekt , Lauri 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 Weinstein , Edward Ruiz-Narvaez , Julie Palmer , Daniel Buchanan , Elizabeth Platz , Kala Visvanathan , Cornelia Ulrich , Erin Siegel , Stefanie Brezina , Andrea Gsur , Peter Campbell , Jenny Chang-Claude , Michael Hoffmeister , Hermann Brenner , Martha Slattery , John Potter , Konstantinos Tsilidis , Matthias Schulze , Marc Gunter , Neil Murphy , Antoni Castells , Sergi Castellví-Bel , Leticia Moreira , Volker Arndt , Anna Shcherbina , Mariana Stern , Bens Pardamean , Timothy Bishop , Graham Giles , Melissa 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 Hudson , Heather Hampel , Rachel Pearlman , Sonja Berndt , Richard Hayes , Marie Elena Martinez , Sushma Thomas , Douglas Corley , Paul Pharoah , Susanna Larsson , Yun Yen , Heinz-Josef Lenz , Emily White , Li Li , Kimberly Doheny , Elizabeth Pugh , Tameka Shelford , Andrew Chan , Marcia Cruz-Correa , Annika Lindblom , David Hunter , Amit Joshi , Clemens Schafmayer , Peter Scacheri , Anshul Kundaje , Deborah Nickerson , Robert Schoen , Jochen Hampe , Zsofia Stadler , Pavel Vodicka , Ludmila Vodickova , Veronika Vymetalkova , Nickolas Papadopoulos , Chistopher Edlund , William Gauderman , Duncan Thomas , David Shibata , Amanda Toland , Sanford Markowitz , Andre Kim , Stephen Chanock , Franzel van Duijnhoven , Edith Feskens , Lori Sakoda , Manuela Gago-Dominguez , Alicja Wolk , Alessio Naccarati , Barbara Pardini , Liesel FitzGerald , Soo Chin Lee , Shuji Ogino , Stephanie Bien , Charles Kooperberg , Christopher Li , Yi Lin , Ross Prentice , Conghui Qu , Stéphane Bézieau , Catherine Tangen , Elaine Mardis , Taiki Yamaji , Norie Sawada , Motoki Iwasaki , Christopher Haiman , Loic Le Marchand , Anna Wu , Chenxu Qu , Caroline McNeil , Gerhard Coetzee , Caroline Hayward , Ian Deary , Sarah Harris , Evropi Theodoratou , Stuart Reid , Marion Walker , Li Yin Ooi , Victor Moreno , Graham Casey , Stephen Gruber , Ian Tomlinson , Wei Zheng , Malcolm Dunlop , Richard Houlston , Ulrike Peters

Genome-Wide Mapping of Active Regulatory Elements Using ATAC-seq.

Methods in molecular biology (Clifton, N.J.)

Avec: Georgi K Marinov , Zohar Shipony , Anshul Kundaje , William J Greenleaf

Aberrant phase separation is a common killing strategy of positively charged peptides in biology and human disease.

bioRxiv : the preprint server for biology

Avec: 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 , H Broder Schmidt , Kousik Sundararajan , Lucas Porta , Keren Lasker , Carolyn Larabell , Mirian A F Hayashi , Anshul Kundaje , Francis Impens , Allie Obermeyer , Alex S Holehouse , Aaron D Gitler

A Genetic Locus within the FMN1/GREM1 Gene Region Interacts with Body Mass Index in Colorectal Cancer Risk.

Cancer research

Avec: Elom K Aglago , Andre Kim , Yi Lin , Conghui Qu , Marina Evangelou , Yu Ren , John Morrison , Demetrius Albanes , Volker Arndt , Elizabeth L Barry , James W Baurley , Sonja I Berndt , Stephanie A Bien , D Timothy Bishop , Emmanouil 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 Devall , Virginia Diez-Obrero , Niki Dimou , David Drew , Jane C Figueiredo , Steven 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 A Jenkins , Kristina 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 Obón-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 , Gad Rennert , Edward 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 Jb 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

Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation.

Developmental cell

Avec: Kaelan J Brennan , Melanie Weilert , Sabrina Krueger , Anusri Pampari , Hsiao-Yun Liu , Ally W H Yang , Jason A Morrison , Timothy R Hughes , Christine A Rushlow , Anshul Kundaje , Julia Zeitlinger

The ENCODE Uniform Analysis Pipelines.

Research square

Avec: Benjamin C Hitz , Jin-Wook Lee , Otto Jolanki , Meenakshi S Kagda , Keenan Graham , Paul Sud , Idan Gabdank , J Seth Strattan , Cricket A Sloan , Timothy Dreszer , Laurence D Rowe , Nikhil R Podduturi , Venkat S Malladi , Esther T Chan , Jean M Davidson , Marcus Ho , Stuart Miyasato , Matt Simison , Forrest Tanaka , Yunhai Luo , Ian Whaling , Eurie L Hong , Brian T Lee , Richard Sandstrom , Eric Rynes , Jemma Nelson , Andrew Nishida , Alyssa Ingersoll , Michael Buckley , Mark Frerker , Daniel S Kim , Nathan Boley , Diane Trout , Alex 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 Aiden , Tom Gingeras , Simon Heath , Martin Hirst , W James Kent , Anshul Kundaje , Ali Mortazavi , Barbara Wold , J Michael Cherry

Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage.

bioRxiv : the preprint server for biology

Avec: Sahin Naqvi , Seungsoo Kim , Saman Tabatabaee , Anusri Pampari , Anshul Kundaje , Jonathan K Pritchard , Joanna Wysocka

Characterization of additive gene-environment interactions for colorectal cancer risk.

Epidemiology (Cambridge, Mass.)

Avec: Claire E Thomas , Yi Lin , Michelle Kim , Eric S Kawaguchi , Conghui Qu , Caroline Y Um , Brigid M Lynch , Bethany Van Guelpen , Kostas Tsilidis , Robert Carreras-Torres , Franzel Jb van Duijnhoven , Lori C Sakoda , Peter T Campbell , Yu Tian , Jenny Chang-Claude , Stéphane Bézieau , Arif Budiarto , Julie R Palmer , Polly A Newcomb , Graham Casey , Loic Le Marchand , Marios Giannakis , Christopher I Li , Andrea Gsur , Christina Newton , Mireia Obón-Santacana , Victor Moreno , Pavel Vodicka , Hermann Brenner , Michael Hoffmeister , Andrew J Pellatt , Robert E Schoen , Niki Dimou , Neil Murphy , Marc J Gunter , Sergi Castellví-Bel , Jane C Figueiredo , Andrew T Chan , Mingyang Song , Li Li , D Timothy Bishop , Stephen B Gruber , James W Baurley , Stephanie A Bien , David V Conti , Jeroen R Huyghe , Anshul Kundaje , Yu-Ru Su , Jun Wang , Temitope O Keku , Michael O Woods , Sonja I Berndt , Stephen J Chanock , Catherine M Tangen , Alicja Wolk , Andrea Burnett-Hartman , Anna H Wu , Emily White , Matthew A Devall , Virginia Díez-Obrero , David A Drew , Edward Giovannucci , Akihisa Hidaka , Andre E Kim , Juan Pablo Lewinger , John Morrison , Jennifer Ose , Nikos Papadimitriou , Bens Pardamean , Anita R Peoples , Edward A Ruiz-Narvaez , Anna Shcherbina , Mariana C Stern , Xuechen Chen , Duncan C Thomas , Elizabeth A Platz , W James Gauderman , Ulrike Peters , Li Hsu

Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases.

Nature genetics

Avec: 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

Genetic architectures of proximal and distal colorectal cancer are partly distinct.

Gut

Avec: Jeroen R Huyghe , Tabitha A Harrison , Stephanie A Bien , Heather Hampel , Jane C Figueiredo , Stephanie L Schmit , David V Conti , Sai Chen , Conghui Qu , Yi Lin , Richard Barfield , John A Baron , Amanda J Cross , Brenda Diergaarde , David Duggan , Sophia Harlid , Liher Imaz , Hyun Min Kang , David M Levine , Vittorio Perduca , Aurora Perez-Cornago , Lori C Sakoda , Fredrick R Schumacher , Martha L Slattery , Amanda E Toland , Fränzel J B van Duijnhoven , Bethany Van Guelpen , Antonio Agudo , Demetrius Albanes , M Henar Alonso , Kristin Anderson , Coral Arnau-Collell , Volker Arndt , Barbara L Banbury , Michael C Bassik , Sonja I Berndt , Stéphane Bézieau , D Timothy Bishop , Juergen Boehm , Heiner Boeing , Marie-Christine Boutron-Ruault , Hermann Brenner , Stefanie Brezina , Stephan Buch , Daniel D Buchanan , Andrea Burnett-Hartman , Bette J Caan , Peter T Campbell , Prudence R Carr , Antoni Castells , Sergi Castellví-Bel , Andrew T Chan , Jenny Chang-Claude , Stephen J Chanock , Keith R Curtis , Albert de la Chapelle , Douglas F Easton , Dallas R English , Edith J M Feskens , Manish Gala , Steven J Gallinger , W James Gauderman , Graham G Giles , Phyllis J Goodman , William M Grady , John S Grove , Andrea Gsur , Marc J Gunter , Robert W Haile , Jochen Hampe , Michael Hoffmeister , John L Hopper , Wan-Ling Hsu , Wen-Yi Huang , Thomas J Hudson , Mazda Jenab , Mark A Jenkins , Amit D Joshi , Temitope O Keku , Charles Kooperberg , Tilman Kühn , Sébastien Küry , Loic Le Marchand , Flavio Lejbkowicz , Christopher I Li , Li Li , Wolfgang Lieb , Annika Lindblom , Noralane M Lindor , Satu Männistö , Sanford D Markowitz , Roger L Milne , Lorena Moreno , Neil Murphy , Rami Nassir , Kenneth Offit , Shuji Ogino , Salvatore Panico , Patrick S Parfrey , Rachel Pearlman , Paul D P Pharoah , Amanda I Phipps , Elizabeth A Platz , John D Potter , Ross L Prentice , Lihong Qi , Leon Raskin , Gad Rennert , Hedy S Rennert , Elio Riboli , Clemens Schafmayer , Robert E Schoen , Daniela Seminara , Mingyang Song , Yu-Ru Su , Catherine M Tangen , Stephen N Thibodeau , Duncan C Thomas , Antonia Trichopoulou , Cornelia M Ulrich , Kala Visvanathan , Pavel Vodicka , Ludmila Vodickova , Veronika Vymetalkova , Korbinian Weigl , Stephanie J Weinstein , Emily White , Alicja Wolk , Michael O Woods , Anna H Wu , Goncalo R Abecasis , Deborah A Nickerson , Peter C Scacheri , Anshul Kundaje , Graham Casey , Stephen B Gruber , Li Hsu , Victor Moreno , Richard B Hayes , Polly A Newcomb , Ulrike Peters

Genome-wide enhancer maps link risk variants to disease genes.

Nature

Avec: 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

MTSplice predicts effects of genetic variants on tissue-specific splicing.

Genome biology

Avec: Jun Cheng , Muhammed Hasan Çelik , Anshul Kundaje , Julien Gagneur

The ENCODE Blacklist: Identification of Problematic Regions of the Genome.

Scientific reports

Avec: Haley M Amemiya , Anshul Kundaje , Alan P Boyle

NETWORK MODELLING OF TOPOLOGICAL DOMAINS USING HI-C DATA.

The annals of applied statistics

Avec: Y X Rachel Wang , Purnamrita Sarkar , Oana Ursu , Anshul Kundaje , Peter J Bickel

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution.

Cell

Avec: Alexandro E Trevino , Fabian Müller , Jimena Andersen , Laksshman Sundaram , Arwa Kathiria , Anna Shcherbina , Kyle Farh , Howard Y Chang , Anca M Pașca , Anshul Kundaje , Sergiu P Pașca , William J Greenleaf

The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation.

Nature genetics

Avec: Daniel S Kim , Viviana I Risca , David L Reynolds , James Chappell , Adam J Rubin , Namyoung Jung , Laura K H Donohue , Vanessa Lopez-Pajares , Arwa Kathiria , Minyi Shi , Zhixin Zhao , Harsh Deep , Mahfuza Sharmin , Deepti Rao , Shin Lin , Howard Y Chang , Michael P Snyder , William J Greenleaf , Anshul Kundaje , Paul A Khavari

Single-Molecule Multikilobase-Scale Profiling of Chromatin Accessibility Using m6A-SMAC-Seq and m6A-CpG-GpC-SMAC-Seq.

Methods in molecular biology (Clifton, N.J.)

Avec: Georgi K Marinov , Zohar Shipony , Anshul Kundaje , William J Greenleaf

The chromatin organization of a chlorarachniophyte nucleomorph genome.

Genome biology

Avec: Georgi K Marinov , Xinyi Chen , Tong Wu , Chuan He , Arthur R Grossman , Anshul Kundaje , William James Greenleaf

fastISM: performant in silico saturation mutagenesis for convolutional neural networks.

Bioinformatics (Oxford, England)

Avec: Surag Nair , Avanti Shrikumar , Jacob Schreiber , Anshul Kundaje

Disease diagnostics using machine learning of immune receptors.

bioRxiv : the preprint server for biology

Avec: Maxim E Zaslavsky , Erin Craig , Jackson K Michuda , Nikhil Ram-Mohan , Ji-Yeun Lee , Khoa D Nguyen , Ramona A Hoh , Tho D Pham , Ella S Parsons , Susan R Macwana , Wade DeJager , Krishna M Roskin , Charlotte Cunningham-Rundles , M Anthony Moody , Barton F Haynes , Jason D Goldman , James R Heath , Imelda Balboni , Paul J Utz , Kari C Nadeau , Benjamin A Pinsky , Catherine A Blish , Joan T Merrill , Joel M Guthridge , Judith A James , Samuel Yang , Robert Tibshirani , Anshul Kundaje , Scott D Boyd

Beyond GWAS of Colorectal Cancer: Evidence of Interaction with Alcohol Consumption and Putative Causal Variant for the 10q24.2 Region.

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

Avec: Kristina M Jordahl , Anna Shcherbina , Andre E Kim , Yu-Ru Su , Yi Lin , Jun Wang , Conghui Qu , Demetrius Albanes , Volker Arndt , James W Baurley , Sonja I Berndt , Stephanie A Bien , D Timothy Bishop , Emmanouil Bouras , Hermann Brenner , Daniel D Buchanan , Arif Budiarto , Peter T Campbell , Robert Carreras-Torres , Graham Casey , Tjeng Wawan Cenggoro , Andrew T Chan , David V Conti , Christopher H Dampier , Matthew A Devall , Virginia Díez-Obrero , Niki Dimou , David A Drew , Jane C Figueiredo , Steven Gallinger , Graham G Giles , Stephen B Gruber , Andrea Gsur , Marc J Gunter , Heather Hampel , Sophia Harlid , Tabitha A Harrison , Akihisa Hidaka , Michael Hoffmeister , Jeroen R Huyghe , Mark A Jenkins , Amit D Joshi , Temitope O Keku , Susanna C Larsson , Loic Le Marchand , Juan Pablo Lewinger , Li Li , Bharuno Mahesworo , Victor Moreno , John L Morrison , Neil Murphy , Hongmei Nan , Rami Nassir , Polly A Newcomb , Mireia Obón-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 , John D Potter , Ross L Prentice , Gad Rennert , Edward Ruiz-Narvaez , Lori C Sakoda , Peter C Scacheri , Stephanie L Schmit , Robert E Schoen , Martha L Slattery , Mariana C Stern , Catherine M Tangen , Stephen N Thibodeau , Duncan C Thomas , Yu Tian , Konstantinos K Tsilidis , Cornelia M Ulrich , Franzel J B van Duijnhoven , Bethany Van Guelpen , Kala Visvanathan , Pavel Vodicka , Emily White , Alicja Wolk , Michael O Woods , Anna H Wu , Natalia Zemlianskaia , Jenny Chang-Claude , W James Gauderman , Li Hsu , Anshul Kundaje , Ulrike Peters

Genome-wide interaction study of dietary intake of fibre, fruits, and vegetables with risk of colorectal cancer.

EBioMedicine

Avec: Nikos Papadimitriou , Andre Kim , Eric S Kawaguchi , John Morrison , Virginia Diez-Obrero , Demetrius Albanes , Sonja I Berndt , Stéphane Bézieau , Stephanie A Bien , D Timothy Bishop , Emmanouil Bouras , Hermann Brenner , Daniel D Buchanan , Peter T Campbell , Robert Carreras-Torres , Andrew T Chan , Jenny Chang-Claude , David V Conti , Matthew A Devall , Niki Dimou , David A Drew , Stephen B Gruber , Tabitha A Harrison , Michael Hoffmeister , Jeroen R Huyghe , Amit D Joshi , Temitope O Keku , Anshul Kundaje , Sébastien Küry , Loic Le Marchand , Juan Pablo Lewinger , Li Li , Brigid M Lynch , Victor Moreno , Christina C Newton , Mireia Obón-Santacana , Jennifer Ose , Andrew J Pellatt , Anita R Peoples , Elizabeth A Platz , Conghui Qu , Gad Rennert , Edward Ruiz-Narvaez , Anna Shcherbina , Mariana C Stern , Yu-Ru Su , Duncan C Thomas , Claire E Thomas , Yu Tian , Konstantinos K Tsilidis , Cornelia M Ulrich , Caroline Y Um , Kala Visvanathan , Jun Wang , Emily White , Michael O Woods , Stephanie L Schmit , Finlay Macrae , John D Potter , John L Hopper , Ulrike Peters , Neil Murphy , Li Hsu , Marc J Gunter , W James Gauderman

Multiplexed single-cell characterization of alternative polyadenylation regulators.

Cell

Avec: Madeline H Kowalski , Hans-Hermann Wessels , Johannes Linder , Carol Dalgarno , Isabella Mascio , Saket Choudhary , Austin Hartman , Yuhan Hao , Anshul Kundaje , Rahul Satija

Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes.

Nature communications

Avec: Zhishan Chen , Xingyi Guo , Ran Tao , Jeroen R Huyghe , Philip J Law , Ceres Fernandez-Rozadilla , Jie Ping , Guochong Jia , Jirong Long , Chao Li , Quanhu Shen , Yuhan Xie , Maria N Timofeeva , Minta Thomas , Stephanie L Schmit , Virginia Díez-Obrero , Matthew Devall , Ferran Moratalla-Navarro , Juan Fernandez-Tajes , Claire Palles , Kitty Sherwood , Sarah E W Briggs , Victoria Svinti , Kevin Donnelly , Susan M Farrington , James Blackmur , Peter G Vaughan-Shaw , Xiao-Ou Shu , Yingchang Lu , Peter Broderick , James Studd , Tabitha A Harrison , David V Conti , Fredrick R Schumacher , Marilena Melas , Gad Rennert , Mireia Obón-Santacana , Vicente Martín-Sánchez , Jae Hwan Oh , Jeongseon 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 , Zefang Ren , Yu-Tang Gao , Wei-Hua Jia , John L Hopper , Mark A Jenkins , Aung Ko Win , Rish K Pai , Jane C Figueiredo , Robert W Haile , Steven Gallinger , Michael O Woods , Polly A Newcomb , David Duggan , Jeremy P Cheadle , Richard Kaplan , Rachel Kerr , David Kerr , Iva Kirac , Jan Böhm , Jukka-Pekka Mecklin , Pekka Jousilahti , Paul Knekt , Lauri A Aaltonen , Harri Rissanen , Eero Pukkala , Johan G Eriksson , Tatiana Cajuso , Ulrika Hänninen , Johanna Kondelin , Kimmo Palin , Tomas Tanskanen , Laura Renkonen-Sinisalo , Satu Männistö , Demetrius Albanes , Stephanie J Weinstein , Edward Ruiz-Narvaez , Julie R Palmer , Daniel D Buchanan , Elizabeth A Platz , Kala Visvanathan , Cornelia M Ulrich , Erin Siegel , Stefanie Brezina , Andrea Gsur , Peter T Campbell , Jenny Chang-Claude , Michael Hoffmeister , Hermann Brenner , Martha L Slattery , John D Potter , Kostas K Tsilidis , Matthias B Schulze , Marc J Gunter , Neil Murphy , Antoni Castells , Sergi Castellví-Bel , Leticia Moreira , Volker Arndt , Anna Shcherbina , D Timothy Bishop , Graham G Giles , Melissa C Southey , Gregory E Idos , Kevin J McDonnell , Zomoroda Abu-Ful , Joel K Greenson , Katerina Shulman , Flavio Lejbkowicz , Kenneth Offit , Yu-Ru Su , Robert Steinfelder , Temitope O Keku , Bethany van Guelpen , Thomas J Hudson , Heather Hampel , Rachel Pearlman , Sonja I Berndt , Richard B Hayes , Marie Elena Martinez , Sushma S Thomas , 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 J Hunter , Amit D Joshi , Clemens Schafmayer , Peter C Scacheri , Anshul Kundaje , Robert E Schoen , Jochen Hampe , Zsofia K Stadler , Pavel Vodicka , Ludmila Vodickova , Veronika Vymetalkova , Christopher K Edlund , W James Gauderman , David Shibata , Amanda Toland , Sanford Markowitz , Andre Kim , Stephen J Chanock , Franzel van Duijnhoven , Edith J M Feskens , Lori C Sakoda , Manuela Gago-Dominguez , Alicja Wolk , Barbara Pardini , Liesel M FitzGerald , Soo Chin Lee , Shuji Ogino , Stephanie A Bien , Charles Kooperberg , Christopher I Li , Yi Lin , Ross Prentice , Conghui Qu , Stéphane Bézieau , Taiki Yamaji , Norie Sawada , Motoki Iwasaki , Loic Le Marchand , Anna H Wu , Chenxu Qu , Caroline E McNeil , Gerhard Coetzee , Caroline Hayward , Ian J Deary , Sarah E Harris , Evropi Theodoratou , Stuart Reid , Marion Walker , Li Yin Ooi , Ken S Lau , Hongyu Zhao , Li Hsu , Qiuyin Cai , Malcolm G Dunlop , Stephen B Gruber , Richard S Houlston , Victor Moreno , Graham Casey , Ulrike Peters , Ian Tomlinson , Wei Zheng

An updated compendium and reevaluation of the evidence for nuclear transcription factor occupancy over the mitochondrial genome.

bioRxiv : the preprint server for biology

Avec: Georgi K Marinov , Vivekanandan Ramalingam , William J Greenleaf , Anshul Kundaje

The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles.

Genome biology

Avec: Jacob Schreiber , Carles Boix , Jin Wook Lee , Hongyang Li , Yuanfang Guan , Chun-Chieh Chang , Jen-Chien Chang , Alex Hawkins-Hooker , Bernhard Schölkopf , Gabriele Schweikert , Mateo Rojas Carulla , Arif Canakoglu , Francesco Guzzo , Luca Nanni , Marco Masseroli , Mark James Carman , Pietro Pinoli , Chenyang Hong , Kevin Y Yip , Jeffrey P Spence , Sanjit Singh Batra , Yun S Song , Shaun Mahony , Zheng Zhang , Wuwei Tan , Yang Shen , Yuanfei Sun , Minyi Shi , Jessika Adrian , Richard Sandstrom , Nina Farrell , Jessica Halow , Kristen Lee , Lixia Jiang , Xinqiong Yang , Charles Epstein , J Seth Strattan , Bradley Bernstein , Michael Snyder , Manolis Kellis , William Stafford , Anshul Kundaje , Auteur inconnu

SLC12A9 is a lysosome-detoxifying ammonium - chloride co-transporter.

bioRxiv : the preprint server for biology

Avec: Roni Levin-Konigsberg , Koushambi Mitra , AkshatKumar Nigam , Kaitlyn Spees , Pravin Hivare , Katherine Liu , Anshul Kundaje , Yamuna Krishnan , Michael C Bassik

Réseau de co-auteurs

William J Greenleaf 24 collaborations

Anna Shcherbina 20 collaborations

Georgi K Marinov 18 collaborations

Ulrike Peters 16 collaborations

Conghui Qu 15 collaborations

Hermann Brenner 15 collaborations

Michael Hoffmeister 15 collaborations

Jeroen R Huyghe 15 collaborations

Li Li 15 collaborations

Victor Moreno 15 collaborations

Neil Murphy 15 collaborations

Yu-Ru Su 15 collaborations

Emily White 15 collaborations

Li Hsu 15 collaborations

Jenny Chang-Claude 15 collaborations

Yi Lin 14 collaborations

Sonja I Berndt 14 collaborations

Stephanie A Bien 14 collaborations

Peter T Campbell 14 collaborations

Graham Casey 14 collaborations

Andrew T Chan 14 collaborations

David V Conti 14 collaborations

Stephen B Gruber 14 collaborations

Marc J Gunter 14 collaborations

Loic Le Marchand 14 collaborations

Elizabeth A Platz 14 collaborations

Gad Rennert 14 collaborations

W James Gauderman 14 collaborations

Tabitha A Harrison 13 collaborations

Temitope O Keku 13 collaborations

Polly A Newcomb 13 collaborations

Mireia Obón-Santacana 13 collaborations

Duncan C Thomas 13 collaborations

Kala Visvanathan 13 collaborations

Alicja Wolk 13 collaborations

Michael C Bassik 12 collaborations

Jane C Figueiredo 12 collaborations

Michael O Woods 12 collaborations

Cornelia M Ulrich 12 collaborations

Yu Tian 11 collaborations

Volker Arndt 11 collaborations

D Timothy Bishop 11 collaborations

Robert Carreras-Torres 11 collaborations

Niki Dimou 11 collaborations

Juan Pablo Lewinger 11 collaborations

Jennifer Ose 11 collaborations

Anita R Peoples 11 collaborations

John D Potter 11 collaborations

Lori C Sakoda 11 collaborations

Robert E Schoen 11 collaborations

Mariana C Stern 11 collaborations

Demetrius Albanes 11 collaborations

Surag Nair 10 collaborations

Daniel D Buchanan 10 collaborations

David A Drew 10 collaborations

Graham G Giles 10 collaborations

Mark A Jenkins 10 collaborations

Amit D Joshi 10 collaborations

Shuji Ogino 10 collaborations

Bens Pardamean 10 collaborations

Bethany Van Guelpen 10 collaborations

Andrea Gsur 10 collaborations

Edward Ruiz-Narvaez 10 collaborations

James W Baurley 9 collaborations

Arif Budiarto 9 collaborations

Virginia Díez-Obrero 9 collaborations

Steven Gallinger 9 collaborations

Akihisa Hidaka 9 collaborations

Andre E Kim 9 collaborations

Konstantinos K Tsilidis 9 collaborations

Anna H Wu 9 collaborations

Nikos Papadimitriou 9 collaborations

Stephanie L Schmit 9 collaborations

Stéphane Bézieau 9 collaborations

Catherine M Tangen 9 collaborations

Pavel Vodicka 9 collaborations

John Morrison 8 collaborations

Anusri Pampari 8 collaborations

Jun Wang 8 collaborations

Julie R Palmer 8 collaborations

Peter C Scacheri 8 collaborations

Kaitlyn Spees 7 collaborations

Avanti Shrikumar 7 collaborations

Sophia Harlid 7 collaborations

Susanna C Larsson 7 collaborations

Rami Nassir 7 collaborations

Ross L Prentice 7 collaborations

Stephen N Thibodeau 7 collaborations

Emmanouil Bouras 7 collaborations

Michael P Snyder 7 collaborations

Martha L Slattery 7 collaborations

Michael Wainberg 6 collaborations

Andrew J Pellatt 6 collaborations

Jacob Schreiber 6 collaborations

Brigid M Lynch 6 collaborations

Rish K Pai 6 collaborations

Caroline Y Um 6 collaborations

Paul D P Pharoah 6 collaborations

Satu Männistö 6 collaborations

Heather Hampel 6 collaborations

Thomas Quertermous 5 collaborations

David Yao 5 collaborations

Akshay Balsubramani 5 collaborations

Josh Tycko 5 collaborations

Jesse M Engreitz 5 collaborations

Xuechen Chen 5 collaborations

Kristina M Jordahl 5 collaborations

Hongmei Nan 5 collaborations

Franzel J B van Duijnhoven 5 collaborations

Soumya Kundu 5 collaborations

Andrea Burnett-Hartman 5 collaborations

Tjeng Wawan Cenggoro 5 collaborations

Stephen J Chanock 5 collaborations

Matthew Devall 5 collaborations

Bharuno Mahesworo 5 collaborations

Ludmila Vodickova 5 collaborations

Eric S Kawaguchi 5 collaborations

Sergi Castellví-Bel 5 collaborations

Stephanie J Weinstein 5 collaborations

Nasa Sinnott-Armstrong 4 collaborations

Alexandro E Trevino 4 collaborations

S Tansu Bagdatli 4 collaborations

Lacramioara Bintu 4 collaborations

Benjamin R Doughty 4 collaborations

Eric Kawaguchi 4 collaborations

Howard Y Chang 4 collaborations

Johannes Linder 4 collaborations

Elizabeth L Barry 4 collaborations

Christina C Newton 4 collaborations

Daniel S Kim 4 collaborations

Julia Zeitlinger 4 collaborations

Virginia Diez-Obrero 4 collaborations

Christopher H Dampier 4 collaborations

AkshatKumar Nigam 4 collaborations

Zohar Shipony 4 collaborations

Manolis Kellis 4 collaborations

Stefanie Brezina 4 collaborations

David Duggan 4 collaborations

Jochen Hampe 4 collaborations

John L Hopper 4 collaborations

Charles Kooperberg 4 collaborations

Flavio Lejbkowicz 4 collaborations

Christopher I Li 4 collaborations

Annika Lindblom 4 collaborations

Kenneth Offit 4 collaborations

Rachel Pearlman 4 collaborations

Clemens Schafmayer 4 collaborations

Veronika Vymetalkova 4 collaborations

Ferran Moratalla-Navarro 4 collaborations

Andre Kim 4 collaborations

Peyton Greenside 3 collaborations

Arthur R Grossman 3 collaborations

Kelly Cochran 3 collaborations

Leif S Ludwig 3 collaborations

Caleb A Lareau 3 collaborations

Jeffrey M Verboon 3 collaborations

Jacob C Ulirsch 3 collaborations

Tong Wu 3 collaborations

Chuan He 3 collaborations

Idan Gabdank 3 collaborations

Yunhai Luo 3 collaborations

Jill E Moore 3 collaborations

Edward A Ruiz-Narvaez 3 collaborations

Stephen B Montgomery 3 collaborations

Natalia Zemlianskaia 3 collaborations

Fränzel J B van Duijnhoven 3 collaborations

Melanie Weilert 3 collaborations

None Aradhana 3 collaborations

Abhimanyu Banerjee 3 collaborations

Roger L Milne 3 collaborations

Elom K Aglago 3 collaborations

Laksshman Sundaram 3 collaborations

Minyi Shi 3 collaborations

None None 3 collaborations

Roni Levin-Konigsberg 3 collaborations

Matthew P Swaffer 3 collaborations

Jan M Skotheim 3 collaborations

Oana Ursu 3 collaborations

Mark Gerstein 3 collaborations

Michael Snyder 3 collaborations

Ali Mortazavi 3 collaborations

J Michael Cherry 3 collaborations

Barbara Wold 3 collaborations

Zhiping Weng 3 collaborations

J Seth Strattan 3 collaborations

Richard Sandstrom 3 collaborations

Neva C Durand 3 collaborations

Suhas S P Rao 3 collaborations

Ragini Mahajan 3 collaborations

Franzel Jb van Duijnhoven 3 collaborations

Fredrick R Schumacher 3 collaborations

Edith J M Feskens 3 collaborations

Robert W Haile 3 collaborations

Richard B Hayes 3 collaborations

Thomas J Hudson 3 collaborations

Sébastien Küry 3 collaborations

Sun-Seog Kweon 3 collaborations

Soo Chin Lee 3 collaborations

Marilena Melas 3 collaborations

Barbara Pardini 3 collaborations

Elizabeth Pugh 3 collaborations

Tameka Shelford 3 collaborations

Min-Ho Shin 3 collaborations

Katerina Shulman 3 collaborations

Aung Ko Win 3 collaborations

Wei Zheng 3 collaborations

Claire E Thomas 3 collaborations

John L Morrison 3 collaborations

Mingyang Song 3 collaborations

Antoni Castells 3 collaborations

Matthew A Devall 3 collaborations

Manuel A Rivas 2 collaborations

Johan L M Björkegren 2 collaborations

Amy Li 2 collaborations

Roarke A Kamber 2 collaborations

Christina Curtis 2 collaborations

Ross C Hardison 2 collaborations

Shaun Mahony 2 collaborations

Wendy Luo 2 collaborations

Christoph Muus 2 collaborations

Aviv Regev 2 collaborations

Vijay G Sankaran 2 collaborations

Samuel H Kim 2 collaborations

Soon Il Higashino 2 collaborations

Katherine Guo 2 collaborations

Kalina Andreeva 2 collaborations

Galip Gürkan Yardımcı 2 collaborations

Michael A Beer 2 collaborations

Yin Shen 2 collaborations

Aman Patel 2 collaborations

Ziwei Chen 2 collaborations

Michael J Gloudemans 2 collaborations

Paul Flicek 2 collaborations

Matthew A M Devall 2 collaborations

Žiga Avsec 2 collaborations

Sabrina Krueger 2 collaborations

Julien Gagneur 2 collaborations

Gaelen T Hess 2 collaborations

Braeden K Ego 2 collaborations

Peter Suzuki 2 collaborations

Yu Xin Wang 2 collaborations

Helen M Blau 2 collaborations

Kostas K Tsilidis 2 collaborations

Kristina Jordahl 2 collaborations

Amr M Alexandari 2 collaborations

Connor A Horton 2 collaborations

Nilay Shah 2 collaborations

Polly M Fordyce 2 collaborations

Mohamed Ameen 2 collaborations

Ioannis Karakikes 2 collaborations

Kevin C Wang 2 collaborations

Joseph C Wu 2 collaborations

Kyle Farh 2 collaborations

Madeline H Kowalski 2 collaborations

Hans-Hermann Wessels 2 collaborations

Saket Choudhary 2 collaborations

Austin Hartman 2 collaborations

Yuhan Hao 2 collaborations

Isabella Mascio 2 collaborations

Carol Dalgarno 2 collaborations

Rahul Satija 2 collaborations

Lixia Jiang 2 collaborations

Xinqiong Yang 2 collaborations

Erez Lieberman Aiden 2 collaborations

William Stafford Noble 2 collaborations

Quanyi Zhao 2 collaborations

Disha Sharma 2 collaborations

Trieu Nguyen 2 collaborations

Huitong Shi 2 collaborations

Ramendra Kundu 2 collaborations

Juyong Brian Kim 2 collaborations

Paul Cheng 2 collaborations

Koushambi Mitra 2 collaborations

Katherine Liu 2 collaborations

Pravin Hivare 2 collaborations

Yamuna Krishnan 2 collaborations

Job Dekker 2 collaborations

William S Noble 2 collaborations

Henry E Pratt 2 collaborations

Charles B Epstein 2 collaborations

Jessika Adrian 2 collaborations

Jessica Halow 2 collaborations

Diane E Dickel 2 collaborations

Axel Visel 2 collaborations

Roderic Guigó 2 collaborations

Len A Pennacchio 2 collaborations

John A Stamatoyannopoulos 2 collaborations

Carles Boix 2 collaborations

Benjamin C Hitz 2 collaborations

Otto Jolanki 2 collaborations

Meenakshi S Kagda 2 collaborations

Keenan Graham 2 collaborations

Paul Sud 2 collaborations

Cricket A Sloan 2 collaborations

Timothy Dreszer 2 collaborations

Laurence D Rowe 2 collaborations

Nikhil R Podduturi 2 collaborations

Venkat S Malladi 2 collaborations

Esther T Chan 2 collaborations

Jean M Davidson 2 collaborations

Marcus Ho 2 collaborations

Stuart Miyasato 2 collaborations

Matt Simison 2 collaborations

Forrest Tanaka 2 collaborations

Ian Whaling 2 collaborations

Eurie L Hong 2 collaborations

Brian T Lee 2 collaborations

Eric Rynes 2 collaborations

Jemma Nelson 2 collaborations

Andrew Nishida 2 collaborations

Alyssa Ingersoll 2 collaborations

Michael Buckley 2 collaborations

Mark Frerker 2 collaborations

Nathan Boley 2 collaborations

Diane Trout 2 collaborations

Alex Dobin 2 collaborations

Sorena Rahmanian 2 collaborations

Dana Wyman 2 collaborations

Gabriela Balderrama-Gutierrez 2 collaborations

Fairlie Reese 2 collaborations

Olga Dudchenko 2 collaborations

David Weisz 2 collaborations

Alyssa Blackburn 2 collaborations

Dimos Gkountaroulis 2 collaborations

Mahdi Sadr 2 collaborations

Moshe Olshansky 2 collaborations

Yossi Eliaz 2 collaborations

Dat Nguyen 2 collaborations

Ivan Bochkov 2 collaborations

Muhammad Saad Shamim 2 collaborations

Erez Aiden 2 collaborations

Tom Gingeras 2 collaborations

Simon Heath 2 collaborations

Martin Hirst 2 collaborations

W James Kent 2 collaborations

Frank A Buquicchio 2 collaborations

Jacob C Gutierrez 2 collaborations

Yajie Yin 2 collaborations

Ansuman T Satpathy 2 collaborations

Michelle Cotterchio 2 collaborations

Lihong Qi 2 collaborations

Hank Jones 2 collaborations

Glen Munson 2 collaborations

Charles P Fulco 2 collaborations

David R Kelley 2 collaborations

Eric S Lander 2 collaborations

Hyun Min Kang 2 collaborations

Sai Chen 2 collaborations

Christopher K Edlund 2 collaborations

David M Levine 2 collaborations

M Henar Alonso 2 collaborations

Kristin Anderson 2 collaborations

Coral Arnau-Collell 2 collaborations

Barbara L Banbury 2 collaborations

John A Baron 2 collaborations

Juergen Boehm 2 collaborations

Heiner Boeing 2 collaborations

Stephan Buch 2 collaborations

Bette J Caan 2 collaborations

Amanda J Cross 2 collaborations

Keith R Curtis 2 collaborations

Albert de la Chapelle 2 collaborations

Kimberly F Doheny 2 collaborations

Douglas F Easton 2 collaborations

Dallas R English 2 collaborations

Liesel M FitzGerald 2 collaborations

Manish Gala 2 collaborations

Phyllis J Goodman 2 collaborations

William M Grady 2 collaborations

John S Grove 2 collaborations

Wan-Ling Hsu 2 collaborations

Wen-Yi Huang 2 collaborations

David J Hunter 2 collaborations

Gregory E Idos 2 collaborations

Tilman Kühn 2 collaborations

Wolfgang Lieb 2 collaborations

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