ENGREITZLAB

Publications

Selected

An encyclopedia of human enhancer–gene regulatory interactions

Andreas R. Gschwind*, Kristy S. Mualim*, Alireza Karbalayghareh*, Maya U. Sheth*, Kushal K. Dey*, Evelyn Jagoda*, Ramil N. Nurtdinov*, Wang Xi*, Anthony S. Tan, James Galante, Hank Jones, X. Rosa Ma, David Yao, Dulguun Amgalan, Judhajeet Ray, Chad J. Munger, Joseph Nasser, Žiga Avsec, Benjamin T. James, Muhammad S. Shamim, Neva C. Durand, Suhas S. P. Rao, Ragini Mahajan, Benjamin R. Doughty, Kalina Andreeva, Jacob C. Ulirsch, Kaili Fan, Elizabeth M. Perez, Tri C. Nguyen, David R. Kelley, Hilary K. Finucane, Jill E. Moore, Zhiping Weng, Manolis Kellis, Michael C. Bassik, Berk Ustun, Alkes L. Price†, Michael A. Beer†, Roderic Guigó†, John A. Stamatoyannopoulos†, Erez Lieberman Aiden†, William J. Greenleaf†, Christina S. Leslie†, Lars M. Steinmetz†, Anshul Kundaje†, Jesse M. Engreitz†

Nature 2026

Article Preprint Code Blog

Mapping enhancer–gene regulatory interactions from single-cell data

Maya U. Sheth*, Wei-Lin Qiu*, X. Rosa Ma, Andreas R. Gschwind, Evelyn Jagoda, Anthony S. Tan, James Galante, Judhajeet Ray, Dulguun Amgalan, Hjörleifur Einarsson, Bram L. Gorissen, Danilo Dubocanin, Christopher S. McGinnis, Jacob Huang, Glen Munson, Kayla Brand, Ansuman T. Satpathy, Thouis R. Jones, Lars M. Steinmetz, Anshul Kundaje, Berk Ustun, Jesse M. Engreitz†, Robin Andersson†

Nature Genetics 2026

Article Preprint Code Blog

Convergence of coronary artery disease genes onto endothelial cell programs

Gavin R Schnitzler*, Helen Kang*, Shi Fang, Ramcharan S Angom, Vivian S Lee-Kim, X Rosa Ma, Tony Zeng, Ronghao Zhou, Katherine Guo, Martin S. Taylor, Shamsudheen Karuthedath Vellarikkal, Aurelie E. Barry, Oscar Sias-Garcia, Alex Bloemendal, Glen Munson, Philine Guckelberger, Tung H Nguyen, Drew T Bergman, Stephen Hinshaw, Nathan Cheng, Brian Cleary, Krishna Aragam, Eric S Lander, Hilary K Finucane, Debabrata Mukhopadhyay, Rajat M Gupta†, Jesse M. Engreitz†

Nature 2024

Article Blog

Rewriting regulatory DNA to dissect and reprogram gene expression

Gabriella E Martyn*, Michael T Montgomery*, Hank Jones, Katherine Guo, Benjamin R Doughty, Johannes Linder, Deepa Bisht, Fan Xia, Xiangmeng S Cai, Ziwei Chen, Kelly Cochran, Kathryn A Lawrence, Glen Munson, Anusri Pampari, Charles P Fulco, Nidhi Sahni, David R Kelley, Eric S Lander, Anshul Kundaje, Jesse M Engreitz

Cell 2025

Article Blog

A Perturb-seq screen guided by species divergence uncovers pathways for collateral artery formation

Xiaochen Fan*, Ronghao Zhou*, Brian C. Raftrey, Pamela E. Rios Coronado, Emily Trimm, Erin Clancy, Xinhong Chen, Jamie Bozeman, Maggie S. Chen, Shoxruxxon Alimukhamedov, Juan Alcocer, Idalina Bonham, Stuti Agarwal, Alina Isakova, Vinicio A. de Jesus Perez, Chong Y. Park, Timothy F. Shay, Viviana Gradinaru, Thomas Quertermous, Jesse M. Engreitz†, Kristy Red-Horse†

bioRxiv 2026

Preprint Blog

A systematic survey of distal element-gene regulatory interactions with Direct-Capture Targeted Perturb-seq

Judhajeet Ray, Evelyn Jagoda*, Maya U Sheth*, James Galante*, Dulguun Amgalan*, Andreas R Gschwind, Chad J. Munger, Jacob Huang, Glen Munson, Madeleine Murphy, Eugenio Mattei, Timothy Barry, Vasundhara Singh, Aarthee Baskaran, Helen Kang, Eugene Katsevich, Lars M. Steinmetz, Jesse M. Engreitz

bioRxiv 2025

Preprint Blog

Interpreting variants associated with congenital heart disease with a regulatory map of the human fetal heart

X. Rosa Ma*, Stephanie D. Conley*, Maggie S. Chen*, Michael Kosicki, Yifan Lu, Danila Bredikhin, Ran Cui, Maya U. Sheth, Wei-Lin Qiu, Dulguun Amgalan, Sijie Chen, Robin M. Perelli, Neil Slaven, Michael T. Montgomery, Sarah Fan Xia, Zhainib Amir-Ugokwe, Charu Balamurugan, Steven Tran, Soumya Kundu, Helen Y. Kang, Xiangmeng Shawn Cai, Chad J. Munger, Yannick C. Lee-Yow, Tony Zeng, Yanyan Alexandra Mo, Julia Vahey, Tri Nguyen, Chloe V. McCreery, Sidney Vermeulen, Lauren Duan, Katherine Dang, Jan-Renier Moonen, Oriane Matthys Rubio, Shinwan Kany, Siavash Zamirpour, John DePaolo, Arun Padmanabhan, Birth Defects Research Laboratory, Jeffrey Olgin, Scott M. Damrauer, Robin Andersson, Mingxia Gu, James R. Priest, Thomas Quertermous, Marlene Rabinovitch, Kristy Red-Horse, Axel Visel, Len A. Pennacchio, Xiaojie Qiu, Anshul Kundaje, Ian A. Glass, Casey A. Gifford, James P. Pirruccello, William R. Goodyer†, Jesse M. Engreitz†

medRxiv 2024

Article Preprint Browser Blog

Genome-wide enhancer maps link risk variants to disease genes

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, Tom 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†

Nature 2021

Article

2026

An expanded registry of candidate cis-regulatory elements

Jill E. Moore, Henry E. Pratt, Kaili Fan, Nishigandha Phalke, Jonathan Fisher, Shaimae I. Elhajjajy, Gregory Andrews, Mingshi Gao, Nicole Shedd, Yu Fu, Matthew C Lacadie, Jair Meza, Mansi Khandpekar, Mohit Ganna, Eva Choudhury, Ross Swofford, Huong Phan, Christian C. Ramirez, Maxwell Campbell, Mary Likhite, Nina P. Farrell, Annika K. Weimer, Anusri Pampari, Vivekanandan Ramalingam, Fairlie Reese, Beatrice Borsari, Xuezhu Yu, Eve Wattenberg, Marina Ruiz-Romero, Milad Razavi-Mohseni, Jinrui Xu, Timur Galeev, Andres Colubri, Michael A. Beer, Roderic Guigó, Mark B. Gerstein, Jesse M. Engreitz, Mats Ljungman, Timothy E. Reddy, Michael P. Snyder, Charles B. Epstein, Elizabeth Gaskell, Bradley E. Bernstein, Diane E. Dickel, Axel Visel, Len A. Pennacchio, Ali Mortazavi, Anshul Kundaje, Zhiping Weng

Nature 2026

Article Preprint

Genome-scale mapping of variant, enhancer and gene function in primary human CD4+ T cells

Dewi P I Moonen, Annique Claringbould, Andreas R Gschwind, Stefan Schrod, Jana Braunger, Claudia Feng, Benedikt Rauscher, Jia Yi, Shirley Z Bi, Yves Matthess, Manuel Kaulich, Ricelle A Acob, Aruna Ayer, Jesse M Engreitz, Britta Velten, Oliver Stegle, Gosia Trynka, Judith B Zaugg, Daniel Schraivogel, Lars M Steinmetz

bioRxiv 2026

Preprint

Mapping active cis-regulatory elements from transcription initiation events

Hjörleifur Einarsson, Natsuda Navamajiti, Christian Skov Vaagensø, Stefano Pellegrini, Lykke Jirström, Nicolas Alcaraz, Malte Thodberg, Daniel A. Solvie, Wei-Lin Qiu, Maya U. Sheth, Marta Greedy Escudero, Bram L. Gorissen, Marco Salvatore, Takeya Kasukawa, Hazuki Takahashi, Piero Carninci, Bradley E. Bernstein, Albin Sandelin, Jesse M. Engreitz, Robert Krautz, Robin Andersson

bioRxiv 2026

Article Preprint

PantheonOS: An Evolvable Multi-Agent Framework for Automatic Genomics Discovery

Weize Xu, Erwin Poussi, Quan Zhong, Zehua Zeng, Christopher Zou, Xuehai Wang, Yifan Lu, Miao Cui, Daiji Okamura, Cinlong Huang, Jiayuan Ding, Zhe Zhao, Yuheng Yang, Xinhai Pan, Varshini Vijay, Naoki Konno, Nianping Liu, Lei Li, X. Rosa Ma, Stephanie D. Conley, Colin Kern, William R. Goodyer, Bogdan Bintu, Quan Zhu, Neil C. Chi, Jiang He, Lorenz Rognoni, Xiuwei Zhang, Jun Wu, David Ellison, Marlene Rabinovitch, Jesse M. Engreitz, Xiaojie Qiu

bioRxiv 2026

Article Preprint

PerturbPlan: An analytical framework for designing Perturb-seq experiments

Ziang Niu, Yihui He, James Galante, Andreas R Gschwind, Judhajeet Ray, Lars M Steinmetz, Jesse M Engreitz, Eugene Katsevich

bioRxiv 2026

Preprint

Quantitative changes in 3D contact predict changes in enhancer-promoter regulation upon cohesin depletion

Philine Guckelberger, Benjamin R. Doughty, Suhas S. P. Rao, Glen Munson, Yingxuan Tan, Xiangmeng Shawn Cai, Charles P. Fulco, Joseph Nasser, Drew T. Bergman, Judhajeet Ray, Evelyn Jagoda, Andreas R. Gschwind, Maya U. Sheth, Chad J. Munger, Anthony S. Tan, Kristy S. Mualim, Saul Godinez Pulido, Namita Mitra, David Weisz, Muhammad Saad Shamim, Neva C. Durand, Ragini Mahajan, Ruqayya Khan, Lars M. Steinmetz, Masato T. Kanemaki, Eric S. Lander, Erez Lieberman Aiden, Jesse M. Engreitz

Nature Communications 2026

Article Preprint

The IGVF catalog—from genetic variation to function

Daofeng Li*, Shane Liu*, Pedro R Assis*, Mingjie Li*, Shengcheng Dong, Ian Whaling, Otto Jolanki, Meenakshi Kagda, Wenjin Zhang, Juan F Macias-Velasco, Tianjie Liu, Sarah Cody, Lucinda Antonacci-Fulton, Yuanhao Huang, Jie Liu, Michael T Montgomery, Daniel Zeiberg, Shantanu Jain, Vikas Pejaver, Timothy Bergquist, Yile Chen, Predrag Radivojac, Charles A Gersbach, Rintsen N Sherpa, Christopher P Castro, Alan P Boyle, Lea M Starita, Douglas M Fowler, Nadav Ahituv, Kushal K Dey, William H Majoros, Timothy E Reddy, Mark Craven, Riya Sinha, Yuriy Sverchkov, Xiangmeng Cai, Mpathi Z Nzima, Michael A Calderwood, Joel Rozowsky, Mark Gerstein, Jian Ma, Feng Yue, J Michael Cherry, Michael I Love, Jesse M Engreitz, Benjamin C Hitz†, Ting Wang†

Nucleic Acids Research 2026

Article

2025

Decoding Chromatin Dynamics in Cardiac Organoids Reveals Genetic Drivers of Human Heart Development and Disease

Eyal Metzl-Raz*, Ryan Zhao*, Salil Deshpande*, Jackson Powell, Elizabeth G. Porter, Yassine Zouaghi, Betty B. Liu, Samuel H. Kim, Immanuel Abdi, Ivy Evergreen, Megha Agarwal, Maya U. Sheth, Joshua Rico, Matthew Miyamoto, Julie M. Sanchez, Jesse M. Engreitz, Anshul Kundaje†, William J. Greenleaf†, Casey A. Gifford†

bioRxiv 2025

Preprint

Disease-linked regulatory DNA variants and homeostatic transcription factors in epidermis

Douglas F Porter, Robin M Meyers, Weili Miao, David L Reynolds, Audrey W Hong, Xue Yang, Suhas Srinivasan, Smarajit Mondal, Zurab Siprashvili, Tania Fabo, Ronghao Zhou, Tri Nguyen, Luca Ducoli, Jordan M Meyers, Duy T Nguyen, Lisa A Ko, Laura N Kellman, Ibtihal Elfaki, Margaret Guo, Mårten CG Winge, Leandra V Jackrazi, Vanessa Lopez-Pajares, Betty B Liu, Yuanhao Qu, Imani E Porter, Samuel H Kim, Gyuhyeon Kim, Shiying Tao, Jesse M Engreitz, Paul A Khavari

Nature Communications 2025

Article

Enhancer-targeting CRISPR screens at coronary artery disease loci suggest shared mechanisms of disease risk

Markus Ramste, Chad Weldy, Soumya Kundu, Quanyi Zhao, Daniel Li, Kayla Brand, Disha Sharma, Amanda Ramste, Evelyn Jagoda, Judhajeet Ray, Roxanne Diaz Caceres, James Galante, Andreas R Gschwind, Nuutti Lahtinen, Trieu Nguyen, Junedh M Amrute, Chong Yong Park, Juyong Brian Kim, Minna U Kaikkonen, Nathan O Stitziel, Lars Steinmetz, Anshul Kundaje, Jesse M Engreitz†, Thomas Quertermous†

medRxiv 2025

Preprint

MorPhiC Consortium: towards functional characterization of all human genes

Mazhar Adli, Laralynne Przybyla, Tony Burdett, Paul W. Burridge, Pilar Cacheiro, Howard Y. Chang, Jesse M. Engreitz, Luke A. Gilbert, William J. Greenleaf, Li Hsu, Danwei Huangfu, Ling-Hong Hung, Anshul Kundaje, Sheng Li, Helen Parkinson, Xiaojie Qiu, Paul Robson, Stephan C. Schürer, Ali Shojaie, William C. Skarnes, Damian Smedley, Lorenz Studer, Wei Sun, Dušica Vidović, The MorPhiC Consortium

Nature 2025

Article

Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma

Ashwin R Iyer, Aishwarya Gurumurthy, Shih-Chun A Chu, Rohan Kodgule, Athalee R Aguilar, Travis Saari, Abdullah Ramzan, Jan Rosa, Juhi Gupta, Arvind Emmanuel, Cody N Hall, John S Runge, Anna B Owczarczyk, Jang W Cho, Matthew B Weiss, Rockwell Anyoha, Kristin Sikkink, Savanna Gemus, Charles P Fulco, Anamarija M Perry, Anthony D Schmitt, Jesse M Engreitz, Noah A Brown, Marcin P Cieslik, Russell J H Ryan

Blood Cancer Discovery 2025

Article

Targeting RUNX1 in Macrophages Facilitates Cardiac Recovery

Junedh M. Amrute, Ada Zhu, Yun-Ling Pai, Melissa Hector-Greene, Yuqian An, Kenji Rowell Kim, Maya U. Sheth, Arun Padmanabhan, Clara Youngna Lee, Tracy Yamawaki, Florian Sicklinger, Niklas Hartman, Andrea Bredemeyer, Chang Jie Mick Lee, Vee Xu, Lauren Bell, Tyler Harmon, Haewon Shin, Alekhya Parvathaneni, Lei Liu, Amal K. Dutta, Danielle Pruitt, Jose Barreda, Jing Chen, Urvi Nikhil Shroff, Rangarajan Nadadur, Jess Nigro, Carla Weinheimer, Atilla Kovacs, Jixin Cui, Chen Wang, Chi-Ming Li, Daniel Kreisel, Yongjian Liu, Roger S-Y Foo, Rebekka K Schneider, Jesse M. Engreitz, Douglas L. Mann, Ingrid Rulifson, Simon Jackson, Brandon Ason, Rafael Kramann, Stavros G. Drakos, Florian Leuschner, Michael Alexanian, Kory J. Lavine

bioRxiv 2025

Article Preprint

2024

A consensus variant-to-function score to functionally prioritize variants for disease

Tabassum Fabiha, Ivy Evergreen, Soumya Kundu, Anusri Pampari, Sergey Abramov, Alexandr Boytsov, Kari Strouse, Katherine Dura, Weixiang Fang, Gaspard Kerner, John Butts, Thahmina Ali, Andreas R. Gschwind, Kristy S Mualim, Jill E Moore, Zhiping Weng, Jacob Ulirsch, Hongkai E Ji, Jeff Vierstra, Timothy E. Reddy, Stephen B Montgomery, Jesse M. Engreitz, Anshul Kundaje, Ryan Tewhey, Alkes Price, Kushal Dey

bioRxiv 2024

Preprint

Genetic and functional analysis of Raynaud's syndrome implicates loci in vasculature and immunity

Anniina Tervi, Markus Ramste, Erik Abner, Paul Cheng, Jacqueline M Lane, Matthew Maher, Jesse Valliere, Vilma Lammi, Satu Strausz, Juha Riikonen, Trieu Nguyen, Gabriella E Martyn, Maya U Sheth, Fan (Sarah) Xia, Mauro Lago Docampo, Wenduo Gu, Tõnu Esko, Richa Saxena, Matti Pirinen, Aarno Palotie, Samuli Ripatti, Nasa Sinnott-Armstrong, Mark Daly, Jesse M Engreitz, Marlene Rabinovitch, Caroline A Heckman, Thomas Quertermous, Samuel E Jones, Hanna M Ollila

Cell Genomics 2024

Article

High Shear Stress Reduces ERG Causing Endothelial-Mesenchymal Transition and Pulmonary Arterial Hypertension

Tsutomu Shinohara, Jan-Renier AJ Moonen, Yoon Hong Chun, Yannick C Lee-Yow, Kenichi Okamura, Jason M Szafron, Jordan Kaplan, Aiqin Cao, Lingli Wang, Shalina Taylor, Sarasa Isobe, Melody Dong, Weiguang Yang, Katherine Guo, Benjamin D Franco, Cholawat Pacharinsak, Laura J Pisani, Shinji Saitoh, Yoshihide Mitani, Alison L Marsden, Jesse M. Engreitz, Jakob Korbelin, Marlene Rabinovitch

Arterioscler Thromb Vasc Biol 2024

Article

Multicenter integrated analysis of noncoding CRISPR screens

David Yao*, Josh Tycko*, 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 Gersbach+, Timothy E Reddy+, Yin Shen+, Jesse M Engreitz+, Michael C Bassik+, Steven K Reilly

Nature Methods 2024

Article Preprint

Single cell variant to enhancer to gene map for coronary artery disease

Junedh M. Amrute, Paul C. Lee, Ittai Eres, Chang Jie Mick Lee, Andrea Bredemeyer, Maya U. Sheth, Tracy Yamawaki, Rijan Gurung, Chukwuemeka Anene-Nzelu, Wei-Lin Qiu, Soumya Kundu, Daniel Y. Li, Markus Ramste, Daniel Lu, Anthony Tan, Chul-Joo Kang, Ryan E. Wagoner, Arturo Alisio, Paul Cheng, Quanyi Zhao, Clint L. Miller, Ira M. Hall, Rajat M. Gupta, Yi-Hsiang Hsu, Saptarsi M. Haldar, Kory J. Lavine, Simon Jackson, Robin Andersson, Jesse M. Engreitz, Roger S-Y Foo, Chi-Ming Li, Brandon Ason, Thomas Quertermous, Nathan O. Stitziel

medRxiv 2024

Preprint

Small-cohort GWAS discovery with AI over massive functional genomics knowledge graph

Kexin Huang, Tony Zeng, Soner Koc, Alexandra Pettet, Jingtian Zhou, Mika Jain, Dongbo Sun, Camilo Ruiz, Hongyu Ren, Laurence Howe, Tom G Richardson, Adrian Cortes, Katie Aiello, Kim Branson, Andreas Pfenning, Jesse M Engreitz, Martin Jinye Zhang, Jure Leskovec

medRxiv 2024

Preprint

2023

Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases

Elle M Weeks, Jacob C Ulirsch, Nathan Y Cheng, Brian L Trippe, Rebecca S Fine, Jenkai Miao, Tejal A Patwardhan, Masahiro Kanai, Joseph Nasser, Charles P Fulco, Katherine C Tashman, Francois Aguet, Taibo Li, Jose Ordovas-Montanes, Christopher S Smillie, Moshe Biton, Alex K Shalek, Ashwin N Ananthakrishnan, Ramnik J Xavier, Aviv Regev, Rajat M Gupta, Kasper Lage, Kristin G Ardlie, Joel N Hirschhorn, Eric S Lander, Jesse M Engreitz, Hilary K Finucane

Nature Genetics 2023

Article Preprint

Oligogenic Architecture of Rare Noncoding Variants Distinguishes 4 Congenital Heart Disease Phenotypes

Mengyao Yu, Matthew Aguirre, Meiwen Jia, Ketrin Gjoni, Aldo Cordova-Palomera, Chad Munger, Dulguun Amgalan, X. Rosa Ma, Alexandre Pereira, Catherine Tcheandjieu, Christine Seidman, Jonathan Seidman, Martin Tristani-Firousti, Wendy Chung, Elizabeth Goldmuntz, Deepak Srivastava, Ruth J.F. Loos, Nathalie Chami, Heather Cordell, Martina Dreßen, Bertram Mueller-Myhsok, Harald Lahm, Markus Krane, Katherine S. Pollard, Jesse M. Engreitz, Sarah A. Gagliano Taliun, Bruce D. Gelb, James R. Priest

Circulation: Genomic and Precision Medicine 2023

Article

2022

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

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 Greenleaf†, Anshul Kundaje†

Cell 2022

Article

2021

2020

Inherited causes of clonal haematopoiesis in 97,691 whole genomes

Alexander G Bick*, Joshua S Weinstock*, Satish K Nandakumar, Charles P Fulco, Erik L Bao, Seyedeh M Zekavat, Mindy D Szeto, Xiaotian Liao, Matthew J Leventhal, Joseph Nasser, Eric S Lander, Jesse M Engreitz, Benjamin L Ebert, Alexander P Reiner, Siddhartha Jaiswal, Goncalo Abecasis, Vijay G Sankaran, Pradeep Natarajan, Sekar Kathiresan

Nature 2020

Article

Integrative approaches to improve the informativeness of deep learning models for human complex diseases

Kushal K. Dey, Samuel S. Kim, Steven Gazal, Joseph Nasser, Jesse M. Engreitz, Alkes L. Price

bioRxiv 2020

Preprint

2019

2018

Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries

SM Zekavat, S Ruotsalainen, RE Handsaker, M Alver, J Bloom, T Poterba, C Seed, J Ernst, M Chaffin, J Engreitz, GM Peloso, A Manichaikul, C Yang, KA Ryan, M Fu, WC Johnson, M Tsai, M Budoff, RS Vasan, LA Cupples, JI Rotter, SS Rich, W Post, BD Mitchell, A Correa, A Metspalu, JG Wilson, V Salomaa, M Kellis, MJ Daly, BM Neale, S McCarroll, I Surakka, T Esko, A Ganna, S Ripatti, S Kathiresan, P Natarajan

Nature Communications 2018

Article

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals

P Natarajan, GM Peloso, SM Zekavat, M Montasser, A Ganna, M Chaffin, AV Khera, W Zhou, JM Bloom, JM Engreitz, J Ernst, JR O'Connell, SE Ruotsalainen, M Alver, A Manichaikul, WC Johnson, JA Perry, T Poterba, C Seed, IL Surakka, T Esko, S Ripatti, V Salomaa, A Correa, RS Vasan, M Kellis, BM Neale, ES Lander, G Abecasis, B Mitchell, SS Rich, JG Wilson, LA Cupples, JI Rotter, CJ Willer, S Kathiresan

Nature Communications 2018

Article

2017

Cohesin loss eliminates all loop domains

SSP Rao, SC Huang, BT St. Hilaire, JM Engreitz, EM Perez, KR Kieffer-Kwon, AL Sanborn, SE Johnstone, GD Bascom, ID Bochkov, X Huang, MS Shamim, J Shin, D Turner, Z Ye, AD Omer, JT Robinson, T Schlick, BE Bernstein, R Casellas, ES Lander, EL Aiden

Cell 2017

Article

Recurrent and functional regulatory mutations in breast cancer

E Rheinbay, P Parasuraman, J Grimsb, G Tiao, JM Engreitz, J Kim, MS Lawrence, A Taylor-Weiner, S Rodriguez-Cuevas, M Rosenberg, J Hess, C Stewart, YE Maruvka, P Stojanov, ML Cortes, S Seepo, C Cibulskis, A Tracy, TJ Pugh, J Lee, Z Zheng, LW Ellisen, AJ Iafrate, JA Boehm, SB Gabriel, ML Meyerson, TR Golub, J Baselga, A Hidalgo-Miranda, T Shioda, A Bernards, ES Lander, G Getz

Nature 2017

Article

2010–2016

For the complete, continuously updated list, see Google Scholar.