Publications

106 Results (Filters Applied)
  • Computational Biology x
The American Journal of Surgical Pathology. 2023 Dec 4.

NIPBL::NACC1 Fusion Hepatic Carcinoma.

Erika Hissong, Majd Al Assaad, Munita Bal, Katelyn A Reed, Adele Fornelli, Max F Levine, Gunes Gundem, Alissa Semaan, Christine E Orr, Uma Sakhadeo, Jyothi Manohar, Michael Sigouros, David Wilkes, Andrea Sboner, Elizabeth A Montgomery, Rondell P Graham, Juan S Medina-Martínez, Nicolas Robine, Jiayun M Fang, Eun-Young K Choi, Maria Westerhoff, Jesús Delgado-de la Mora, Patricia Caudell, Rhonda K Yantiss, Elli Papaemmanuil, Olivier Elemento, Carlie Sigel, José Jessurun, Juan Miguel Mosquera

Frontiers in Immunology. 2023 Oct. 24.

Heterozygote advantage at HLA class I and II loci and reduced risk of colorectal cancer.

Ya-Yu Tsai, Chenxu Qu, Joseph D Bonner, Rebeca Sanz-Pamplona, Sidney S Lindsey, Marilena Melas, Kevin J McDonnell, Gregory E Idos, Christopher P Walker, Kevin K Tsang, Diane M Da Silva, Ferran Moratalla-Navarro, Asaf Maoz, Hedy S Rennert, W Martin Kast, Joel K Greenson, Victor Moreno, Gad Rennert, Stephen B Gruber, Stephanie L Schmit

NPJ Precision Oncology. 2023 Sept. 13.

Evolution of structural rearrangements in prostate cancer intracranial metastases.

Francesca Khani, William F. Hooper, Xiaofei Wang, Timothy R. Chu, Minita Shah, Lara Winterkorn, Michael Sigouros, Vincenza Conteduca, David Pisapia, Sara Wobker, Sydney Walker, Julie N. Graff, Brian Robinson, Juan Miguel Mosquera, Andrea Sboner, Olivier Elemento, Nicolas Robine & Himisha Beltran

Cell Reports. 2023 Aug. 2.

Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma.

Miriam I Rosenberg, Erez Greenstein, Martin Buchkovich, Ayelet Peres, Eric Santoni-Rugiu, Lei Yang, Martin Mikl, Zalman Vaksman, David L Gibbs, Dan Reshef, Amy Salovin, Meredith S Irwin, Arlene Naranjo, Igor Ulitsky, Pedro A de Alarcon, Katherine K Matthay, Victor Weigman, Gur Yaari, Jessica A Panzer, Nir Friedman, John M Maris

Neuro-Oncology. 2023 May 29.

Significant increase of high-risk chromosome 1q gain and 6q loss at recurrence in posterior fossa group A ependymoma: a multicenter study.

Andrew M Donson, Kelsey C Bertrand, Kent A Riemondy, Dexiang Gao, Yonghua Zhuang, Bridget Sanford, Gregory A Norris, Rebecca J Chapman, Rui Fu, Nicholas Willard, Andrea M Griesinger, Graziella Ribeiro de Sousa, Vladimir Amani, Enrique Grimaldo, Todd C Hankinson, Ffyona Booker, Martin Sill, Richard G Grundy, Kristian W Pajtler, David W Ellison, Nicholas K Foreman, Timothy A Ritzmann

Nature. 2022 Dec. 14.

Recurrent repeat expansions in human cancer genomes.

Graham S. Erwin, Gamze Gürsoy, Rashid Al-Abri, Ashwini Suriyaprakash, Egor Dolzhenko, Kevin Zhu, Christian R. Hoerner, Shannon M. White, Lucia Ramirez, Ananya Vadlakonda, Alekhya Vadlakonda, Konor von Kraut, Julia Park, Charlotte M. Brannon, Daniel A. Sumano, Raushun A. Kirtikar, Alicia A. Erwin, Thomas J. Metzner, Ryan K. C. Yuen, Alice C. Fan, John T. Leppert, Michael A. Eberle, Mark Gerstein & Michael P. Snyder

Nature Communications. 2022 Oct. 11

Whole genome sequence analysis of blood lipid levels in >66,000 individuals.

Margaret Sunitha Selvaraj, Xihao Li, Zilin Li, Akhil Pampana, David Y. Zhang, Joseph Park, Stella Aslibekyan, Joshua C. Bis, Jennifer A. Brody, Brian E. Cade, Lee-Ming Chuang, Ren-Hua Chung, Joanne E. Curran, Lisa de las Fuentes, Paul S. de Vries, Ravindranath Duggirala, Barry I. Freedman, Mariaelisa Graff, Xiuqing Guo, Nancy Heard-Costa, Bertha Hidalgo, Chii-Min Hwu, Marguerite R. Irvin, Tanika N. Kelly, Brian G. Kral, Leslie Lange, Xiaohui Li, Martin Lisa, Steven A. Lubitz, Ani W. Manichaikul, Preuss Michael, May E. Montasser, Alanna C. Morrison, Take Naseri, Jeffrey R. O’Connell, Nicholette D. Palmer, Patricia A. Peyser, Muagututia S. Reupena, Jennifer A. Smith, Xiao Sun, Kent D. Taylor, Russell P. Tracy, Michael Y. Tsai, Zhe Wang, Yuxuan Wang, Wei Bao, John T. Wilkins, Lisa R. Yanek, Wei Zhao, Donna K. Arnett, John Blangero, Eric Boerwinkle, Donald W. Bowden, Yii-Der Ida Chen, Adolfo Correa, L. Adrienne Cupples, Susan K. Dutcher, Patrick T. Ellinor, Myriam Fornage, Stacey Gabriel, Soren Germer, Richard Gibbs, Jiang He, Robert C. Kaplan, Sharon L. R. Kardia, Ryan Kim, Charles Kooperberg, Ruth J. F. Loos, Karine A Viaud-Martinez, Rasika A. Mathias, Stephen T. McGarvey, Braxton D. Mitchell, Deborah Nickerson, Kari E. North, Bruce M. Psaty, Susan Redline, Alexander P. Reiner, Ramachandran S. Vasan, Stephen S. Rich, Cristen Willer, Jerome I. Rotter, Daniel J. Rader, Xihong Lin, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Gina M. Peloso & Pradeep Natarajan

AACR Journals. 2022 Sept. 19.

African Ancestry Associated Gene Expression Profiles in Triple Negative Breast Cancer Underlie Altered Tumor Biology and Clinical Outcome in Women of African Descent.

Rachel Martini, Princesca Delpe, Timothy R. Chu, Kanika Arora, Brittany Lord, Akanksha Verma, Yalei Chen, Endale Gebregzabher, Joseph K. Oppong, Ernest K. Adjei, Aisha Jibril, Baffour Awuah, Mahteme Bekele, Engida Abebe, Ishmael Kyei, Frances S. Aitpillah, Michael O. Adinku, Kwasi Ankomah, Ernest B. Osei-Bonsu, Dhananjay Chitale, Jessica M. Bensenhaver, Saul David Nathanson, LaToya Jackson, Evelyn Jiagge, Lindsay F. Petersen, Erica Proctor, Kofi K. Gyan, Lee Gibbs, Zarko Monojlovic, Rick Kittles, Jason White, Clayton Yates, Upender Manne, Kevin Gardner, Nigel Mongan, Esther Cheng, Paula Ginter, Syed Hoda, Olivier Elemento, Nicolas Robine, Andrea Sboner, John Carpten, Lisa Newman, Melissa B. Davis

npj Genomic Medicine. 2022 Sept. 5.

A translational genomics approach identifies IL10RB as the top candidate gene target for COVID-19 susceptibility.

Georgios Voloudakis, James M. Vicari, Sanan Venkatesh, Gabriel E. Hoffman, Kristina Dobrindt, Wen Zhang, Noam D. Beckmann, Christina A. Higgins, Stathis Argyriou, Shan Jiang, Daisy Hoagland, Lina Gao, André Corvelo, Kelly Cho, Kyung Min Lee, Jiantao Bian, Jennifer S. Lee, Sudha K. Iyengar, Shiuh-Wen Luoh, Schahram Akbarian, Robert Striker, Themistocles L. Assimes, Eric E. Schadt, Julie A. Lynch, Miriam Merad, Benjamin R. tenOever, Alexander W. Charney, Mount Sinai COVID-19 Biobank, VA Million Veteran Program COVID-19 Science Initiative, Kristen J. Brennand, John F. Fullard & Panos Roussos

Cell. 2022 Sept. 1.

High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios.

Marta Byrska-Bishop, Uday S. Evani, Xuefang Zhao, Anna O. Basile, Haley J. Abel, Allison A. Regier, André Corvelo, Wayne E. Clarke, Rajeeva Musunuri, Kshithija Nagulapalli, Susan Fairley, Alexi Runnels, Lara Winterkorn, Ernesto Lowy-Gallego, The Human Genome Structural Variation Consortium, Paul Flicek, Soren Germer, Harrison Brand, Ira M. Hall, Michael E. Talkowski, Giuseppe Narzisi, Michael C. Zody

PNAS Nexus. 2022 June 24.

Retromer dysfunction in amyotrophic lateral sclerosis.

Eduardo J Pérez-Torres, Irina Utkina-Sosunova, Vartika Mishra, Peter Barbuti, Mariangels De Planell-Saguer, Georgia Dermentzaki , Heather Geiger, Anna O Basile, Nicolas Robine, Delphine Fagegaltier, Kristin A Politi, Paola Rinchetti, Vernice Jackson-Lewis, NYGC ALS Consortium; Matthew Harms, Hemali Phatnani, Francesco Lotti, Serge Przedborski

Nature Biotechnology. 2022 May 30.

Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing.

Aditya S. Deshpande, Netha Ulahannan, Matthew Pendleton, Xiaoguang Dai, Lynn Ly, Julie M. Behr, Stefan Schwenk, Will Liao, Michael A. Augello, Carly Tyer, Priyesh Rughani, Sarah Kudman, Huasong Tian, Hannah G. Otis, Emily Adney, David Wilkes, Juan Miguel Mosquera, Christopher E. Barbieri, Ari Melnick, David Stoddart, Daniel J. Turner, Sissel Juul, Eoghan Harrington & Marcin Imieliński

This work was partially supported by a gift from the Simons Foundation.