Modeling ChIP sequencing in silico with applications.

by Zhengdong D Zhang, Joel Rozowsky, Michael Snyder, Joseph Chang, Mark Gerstein
Published 2008-08-01

Fast and Scalable Private Genotype Imputation Using Machine Learning and Partially Homomorphic Encryption

by Esha Sarkar, Eduardo Chielle, Gamze Gursoy, Oleg Mazonka, Mark Gerstein, Michail Maniatakos
Published 2021-01-01

Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms.

by Rajini R Haraksingh, Alexej Abyzov, Mark Gerstein, Alexander E Urban, Michael Snyder
Published 2011-01-01

Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients

by Shaoke Lou, Tianxiao Li, Daniel Spakowicz, Xiting Yan, Geoffrey Lowell Chupp, Mark Gerstein
Published 2020-10-01

IQSeq: integrated isoform quantification analysis based on next-generation sequencing.

by Jiang Du, Jing Leng, Lukas Habegger, Andrea Sboner, Drew McDermott, Mark Gerstein
Published 2012-01-01

An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits.

by Yang Liu, Jianrong Li, Lee Sam, Chern-Sing Goh, Mark Gerstein, Yves A Lussier
Published 2006-11-01

DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring

by Jing Zhang, Jason Liu, Donghoon Lee, Shaoke Lou, Zhanlin Chen, Gamze Gürsoy, Mark Gerstein
Published 2020-07-01

NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis

by Jing Zhang, Jason Liu, Patrick McGillivray, Caroline Yi, Lucas Lochovsky, Donghoon Lee, Mark Gerstein
Published 2020-10-01

Genomics and data science: an application within an umbrella

by Fábio C. P. Navarro, Hussein Mohsen, Chengfei Yan, Shantao Li, Mengting Gu, William Meyerson, Mark Gerstein
Published 2019-05-01

RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins

by Jing Zhang, Jason Liu, Donghoon Lee, Jo-Jo Feng, Lucas Lochovsky, Shaoke Lou, Michael Rutenberg-Schoenberg, Mark Gerstein
Published 2020-07-01

A Comprehensive Nuclear Receptor Network for Breast Cancer Cells

by Ralf Kittler, Jie Zhou, Sujun Hua, Lijia Ma, Yuwen Liu, Elisha Pendleton, Chao Cheng, Mark Gerstein, Kevin P. White
Published 2013-02-01

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals

by Jieming Chen, Joel Rozowsky, Timur R. Galeev, Arif Harmanci, Robert Kitchen, Jason Bedford, Alexej Abyzov, Yong Kong, Lynne Regan, Mark Gerstein
Published 2016-04-01

Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes

by Suganthi Balasubramanian, Yao Fu, Mayur Pawashe, Patrick McGillivray, Mike Jin, Jeremy Liu, Konrad J. Karczewski, Daniel G. MacArthur, Mark Gerstein
Published 2017-08-01

STARRPeaker: uniform processing and accurate identification of STARR-seq active regions

by Donghoon Lee, Manman Shi, Jennifer Moran, Martha Wall, Jing Zhang, Jason Liu, Dominic Fitzgerald, Yasuhiro Kyono, Lijia Ma, Kevin P. White, Mark Gerstein
Published 2020-12-01

Discordant Expression of Circulating microRNA from Cellular and Extracellular Sources.

by Ravi Shah, Kahraman Tanriverdi, Daniel Levy, Martin Larson, Mark Gerstein, Eric Mick, Joel Rozowsky, Robert Kitchen, Venkatesh Murthy, Ekaterina Mikalev, Jane E Freedman
Published 2016-01-01

Cellular superspreaders: an epidemiological perspective on HIV infection inside the body.

by Kristina Talbert-Slagle, Katherine E Atkins, Koon-Kiu Yan, Ekta Khurana, Mark Gerstein, Elizabeth H Bradley, David Berg, Alison P Galvani, Jeffrey P Townsend
Published 2014-05-01

Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden

by Tao Qing, Hussein Mohsen, Michal Marczyk, Yixuan Ye, Tess O’Meara, Hongyu Zhao, Jeffrey P. Townsend, Mark Gerstein, Christos Hatzis, Yuval Kluger, Lajos Pusztai
Published 2020-05-01

Transcriptional activity and strain-specific history of mouse pseudogenes

by Cristina Sisu, Paul Muir, Adam Frankish, Ian Fiddes, Mark Diekhans, David Thybert, Duncan T. Odom, Paul Flicek, Thomas M. Keane, Tim Hubbard, Jennifer Harrow, Mark Gerstein
Published 2020-07-01

GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner.

by Shaoke Lou, Kellie A Cotter, Tianxiao Li, Jin Liang, Hussein Mohsen, Jason Liu, Jing Zhang, Sandra Cohen, Jinrui Xu, Haiyuan Yu, Mark A Rubin, Mark Gerstein
Published 2019-08-01

Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients

by Daniel Spakowicz, Shaoke Lou, Brian Barron, Jose L. Gomez, Tianxiao Li, Qing Liu, Nicole Grant, Xiting Yan, Rebecca Hoyd, George Weinstock, Geoffrey L. Chupp, Mark Gerstein
Published 2020-06-01