Publications

94 Results (Filters Applied)
  • Computational Biology x
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

Nature Communications. 2022 Apr. 28.

Somatic whole genome dynamics of precancer in Barrett’s esophagus reveals features associated with disease progression.

Thomas G. Paulson, Patricia C. Galipeau, Kenji M. Oman, Carissa A. Sanchez, Mary K. Kuhner, Lucian P. Smith, Kevin Hadi, Minita Shah, Kanika Arora, Jennifer Shelton, Molly Johnson, Andre Corvelo, Carlo C. Maley, Xiaotong Yao, Rashesh Sanghvi, Elisa Venturini, Anne-Katrin Emde, Benjamin Hubert, Marcin Imielinski, Nicolas Robine, Brian J. Reid & Xiaohong Li

Cell Genomics. 2022 Apr. 28.

Benchmarking challenging small variants with linked and long reads.

Justin Wagner, Nathan D Olson, Lindsay Harris, Ziad Khan, Jesse Farek, Medhat Mahmoud, Ana Stankovic, Vladimir Kovacevic, Aaron M Wenger, William J Rowell, Chunlin Xiao, Byunggil Yoo, Neil Miller, Jeffrey A Rosenfeld, Bohan Ni, Samantha Zarate, Melanie Kirsche, Sergey Aganezov, Michael Schatz, Giuseppe Narzisi, Marta Byrska-Bishop, Wayne Clarke, Uday S Evani, Charles Markello, Kishwar Shafin, Xin Zhou, Arend Sidow, Vikas Bansal, Alvaro Martinez Barrio, Ian T Fiddes, Arkarachai Fungtammasan, Chen-Shan Chin, Fritz J Sedlazeck, Andrew Carroll, Marc Salit, Justin M Zook, Genome in a Bottle Consortium
Nature Communications. 2022 March 28.

Nasal airway transcriptome-wide association study of asthma reveals genetically driven mucus pathobiology.

Satria P Sajuthi, Jamie L Everman, Nathan D Jackson, Benjamin Saef, Cydney L Rios, Camille M Moore, Angel C Y Mak, Celeste Eng, Ana Fairbanks-Mahnke, Sandra Salazar, Jennifer Elhawary, Scott Huntsman, Vivian Medina, Deborah A Nickerson, Soren Germer, Michael C Zody, Gonçalo Abecasis, Hyun Min Kang, Kenneth M Rice, Rajesh Kumar, Noah A Zaitlen, Sam Oh, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; José Rodríguez-Santana, Esteban G Burchard, Max A Seibold

Cell Reports Medicine. 2022 Feb. 15.

System-wide transcriptome damage and tissue identity loss in COVID-19 patients.

Jiwoon Park, Jonathan Foox, Tyler Hether, David C. Danko, Sarah Warren, Youngmi Kim, Jason Reeves, Daniel J. Butler, Christopher Mozsary, Joel Rosiene, Alon Shaiber, Evan E. Afshin, Matthew MacKay, Andre´ F. Rendeiro, Yaron Bram, Vasuretha Chandar, Heather Geiger, Arryn Craney, Priya Velu, Ari M. Melnick, Iman Hajirasouliha, Afshin Beheshti, Deanne Taylor, Amanda Saravia-Butler, Urminder Singh, Eve Syrkin Wurtele, Jonathan Schisler, Samantha Fennessey, Andre´ Corvelo, Michael C. Zody, Soren Germer, Steven Salvatore, Shawn Levy, Shixiu Wu, Nicholas P. Tatonetti, Sagi Shapira,22 Mirella Salvatore,8,23 Lars F. Westblade,7,8 Melissa Cushing,7 Hanna Rennert,7 Alison J. Kriegel,24 Olivier Elemento, Marcin Imielinski, Charles M. Rice, Alain C. Borczuk, Cem Meydan, Robert E. Schwartz, and Christopher E. Mason

Nature Biotechnology. 2022 Feb. 7.

Curated variation benchmarks for challenging medically relevant autosomal genes.

Justin Wagner, Nathan D Olson, Lindsay Harris, Jennifer McDaniel, Haoyu Cheng, Arkarachai Fungtammasan, Yih-Chii Hwang, Richa Gupta, Aaron M Wenger, William J Rowell, Ziad M Khan, Jesse Farek, Yiming Zhu, Aishwarya Pisupati, Medhat Mahmoud, Chunlin Xiao, Byunggil Yoo, Sayed Mohammad Ebrahim Sahraeian, Danny E Miller, David Jaspez, Jose M Lorenzo-Salazar, Adrian Munoz-Barrera, Luis A Rubio-Rodriguez, Carlos Flores, Giuseppe Narzisi, Uday Shanker Evani, Wayne E Clarke, Joyce Lee, Christopher E Mason, Stephen E Lincoln, Karen H. Miga, Mark TW Ebbert, Alaina Shumate, Heng Li, Chen-Shan Chin, Justin M Zook, Fritz J Sedlazeck

Genome Biology. 2021 Dec. 6.

The SEQC2 epigenomics quality control (EpiQC) study.

Foox J, Nordlund J, Lalancette C, Gong T, Lacey M, Lent S, Langhorst BW, Ponnaluri VKC, Williams L, Padmanabhan KR, Cavalcante R, Lundmark A, Butler D, Mozsary C, Gurvitch J, Greally JM, Suzuki M, Menor M, Nasu M, Alonso A, Sheridan C, Scherer A, Bruinsma S, Golda G, Muszynska A, Łabaj PP, Campbell MA, Wos F, Raine A, Liljedahl U, Axelsson T, Wang C, Chen Z, Yang Z, Li J, Yang X, Wang H, Melnick A, Guo S, Blume A, Franke V, Ibanez de Caceres I, Rodriguez-Antolin C, Rosas R, Davis JW, Ishii J, Megherbi DB, Xiao W, Liao W, Xu J, Hong H, Ning B, Tong W, Akalin A, Wang Y, Deng Y, Mason CE.

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