Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data.

by Chao Cheng, Koon-Kiu Yan, Woochang Hwang, Jiang Qian, Nitin Bhardwaj, Joel Rozowsky, Zhi John Lu, Wei Niu, Pedro Alves, Masaomi Kato, Michael Snyder, Mark Gerstein
Published 2011-11-01

Global identification and characterization of transcriptionally active regions in the rice genome.

by Lei Li, Xiangfeng Wang, Rajkumar Sasidharan, Viktor Stolc, Wei Deng, Hang He, Jan Korbel, Xuewei Chen, Waraporn Tongprasit, Pamela Ronald, Runsheng Chen, Mark Gerstein, Xing Wang Deng
Published 2007-01-01

Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line.

by Jia Qian Wu, Montrell Seay, Vincent P Schulz, Manoj Hariharan, David Tuck, Jin Lian, Jiang Du, Minyi Shi, Zhijia Ye, Mark Gerstein, Michael P Snyder, Sherman Weissman
Published 2012-01-01

Identification of Genes Critical for Resistance to Infection by West Nile Virus Using RNA-Seq Analysis

by Mark Gerstein, Erol Fikrig, Sebastian Kurscheid, Hongyu Zhao, Xiaomei Wang, Zhong Wang, Roger P. Alexander, Vincent Bruno, Wei Zheng, Lisa Chung, Feng Qian, Michael Snyder, Ruth R. Montgomery
Published 2013-07-01

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

by Jethro S. Johnson, Daniel J. Spakowicz, Bo-Young Hong, Lauren M. Petersen, Patrick Demkowicz, Lei Chen, Shana R. Leopold, Blake M. Hanson, Hanako O. Agresta, Mark Gerstein, Erica Sodergren, George M. Weinstock
Published 2019-11-01

Pollen-derived RNAs Are Found in the Human Circulation

by Milka Koupenova, Eric Mick, Heather A. Corkrey, Anupama Singh, Selim E. Tanriverdi, Olga Vitseva, Daniel Levy, Allison M. Keeler, Marzieh Ezzaty Mirhashemi, Mai K. ElMallah, Mark Gerstein, Joel Rozowsky, Kahraman Tanriverdi, Jane E. Freedman
Published 2019-09-01

Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers

by Xiaotong Li, Sushant Kumar, Arif Harmanci, Shantao Li, Robert R. Kitchen, Yan Zhang, Vikram B. Wali, Sangeetha M. Reddy, Wendy A. Woodward, James M. Reuben, Joel Rozowsky, Christos Hatzis, Naoto T. Ueno, Savitri Krishnamurthy, Lajos Pusztai, Mark Gerstein
Published 2021-04-01

Measuring the reproducibility and quality of Hi-C data

by 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
Published 2019-03-01

FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods

by Timothy Becker, Wan-Ping Lee, Joseph Leone, Qihui Zhu, Chengsheng Zhang, Silvia Liu, Jack Sargent, Kritika Shanker, Adam Mil-homens, Eliza Cerveira, Mallory Ryan, Jane Cha, Fabio C. P. Navarro, Timur Galeev, Mark Gerstein, Ryan E. Mills, Dong-Guk Shin, Charles Lee, Ankit Malhotra
Published 2018-03-01

Correction: Corrigendum: Diverse human extracellular RNAs are widely detected in human plasma

by Jane E. Freedman, Mark Gerstein, Eric Mick, Joel Rozowsky, Daniel Levy, Robert Kitchen, Saumya Das, Ravi Shah, Kirsty Danielson, Lea Beaulieu, Fabio C. P. Navarro, Yaoyu Wang, Timur R. Galeev, Alex Holman, Raymond Y. Kwong, Venkatesh Murthy, Selim E. Tanriverdi, Milka Koupenova, Ekaterina Mikhalev, Kahraman Tanriverdi
Published 2016-06-01

Diverse human extracellular RNAs are widely detected in human plasma

by Jane E. Freedman, Mark Gerstein, Eric Mick, Joel Rozowsky, Daniel Levy, Robert Kitchen, Saumya Das, Ravi Shah, Kirsty Danielson, Lea Beaulieu, Fabio C. P. Navarro, Yaoyu Wang, Timur R. Galeev, Alex Holman, Raymond Y. Kwong, Venkatesh Murthy, Selim E. Tanriverdi, Milka Koupenova, Ekaterina Mikhalev, Kahraman Tanriverdi
Published 2016-04-01

Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response.

by Mei Zhong, Wei Niu, Zhi John Lu, Mihail Sarov, John I Murray, Judith Janette, Debasish Raha, Karyn L Sheaffer, Hugo Y K Lam, Elicia Preston, Cindie Slightham, LaDeana W Hillier, Trisha Brock, Ashish Agarwal, Raymond Auerbach, Anthony A Hyman, Mark Gerstein, Susan E Mango, Stuart K Kim, Robert H Waterston, Valerie Reinke, Michael Snyder
Published 2010-02-01

An integrative ENCODE resource for cancer genomics

by Jing Zhang, Donghoon Lee, Vineet Dhiman, Peng Jiang, Jie Xu, Patrick McGillivray, Hongbo Yang, Jason Liu, William Meyerson, Declan Clarke, Mengting Gu, Shantao Li, Shaoke Lou, Jinrui Xu, Lucas Lochovsky, Matthew Ung, Lijia Ma, Shan Yu, Qin Cao, Arif Harmanci, Koon-Kiu Yan, Anurag Sethi, Gamze Gürsoy, Michael Rutenberg Schoenberg, Joel Rozowsky, Jonathan Warrell, Prashant Emani, Yucheng T. Yang, Timur Galeev, Xiangmeng Kong, Shuang Liu, Xiaotong Li, Jayanth Krishnan, Yanlin Feng, Juan Carlos Rivera-Mulia, Jessica Adrian, James R Broach, Michael Bolt, Jennifer Moran, Dominic Fitzgerald, Vishnu Dileep, Tingting Liu, Shenglin Mei, Takayo Sasaki, Claudia Trevilla-Garcia, Su Wang, Yanli Wang, Chongzhi Zang, Daifeng Wang, Robert J. Klein, Michael Snyder, David M. Gilbert, Kevin Yip, Chao Cheng, Feng Yue, X. Shirley Liu, Kevin P. White, Mark Gerstein
Published 2020-07-01