Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood

by Shantao Li, Forrest W. Crawford, Mark B. Gerstein
Published 2020

Integrated assessment of genomic correlates of protein evolutionary rate.

by Yu Xia, Eric A Franzosa, Mark B Gerstein
Published 2009

Getting started in gene orthology and functional analysis.

by Gang Fang, Nitin Bhardwaj, Rebecca Robilotto, Mark B Gerstein
Published 2010

Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin

by Guan Wang, Traci Kitaoka, Ali Crawford, Qian Mao, Andrew Hesketh, Fergus M. Guppy, Garrett I. Ash, Jason Liu, Mark B. Gerstein, Yannis P. Pitsiladis
Published 2021

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

by Sayed Mohammad Ebrahim Sahraeian, Marghoob Mohiyuddin, Robert Sebra, Hagen Tilgner, Pegah T. Afshar, Kin Fai Au, Narges Bani Asadi, Mark B. Gerstein, Wing Hung Wong, Michael P. Snyder, Eric Schadt, Hugo Y. K. Lam
Published 2017

Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis.

by Younghee Lee, Xinan Yang, Yong Huang, Hanli Fan, Qingbei Zhang, Youngfei Wu, Jianrong Li, Rifat Hasina, Chao Cheng, Mark W Lingen, Mark B Gerstein, Ralph R Weichselbaum, H Rosie Xing, Yves A Lussier
Published 2010

The reality of pervasive transcription.

by Michael B Clark, Paulo P Amaral, Felix J Schlesinger, Marcel E Dinger, Ryan J Taft, John L Rinn, Chris P Ponting, Peter F Stadler, Kevin V Morris, Antonin Morillon, Joel S Rozowsky, Mark B Gerstein, Claes Wahlestedt, Yoshihide Hayashizaki, Piero Carninci, Thomas R Gingeras, John S Mattick
Published 2011

Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins.

by Raffi Tonikian, Xiaofeng Xin, Christopher P Toret, David Gfeller, Christiane Landgraf, Simona Panni, Serena Paoluzi, Luisa Castagnoli, Bridget Currell, Somasekar Seshagiri, Haiyuan Yu, Barbara Winsor, Marc Vidal, Mark B Gerstein, Gary D Bader, Rudolf Volkmer, Gianni Cesareni, David G Drubin, Philip M Kim, Sachdev S Sidhu, Charles Boone
Published 2009

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

by Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Gordon Saksena, Kyle Ellrott, Michael C. Wendl, David A. Wheeler, Gad Getz, Jared T. Simpson, Mark B. Gerstein, Li Ding, PCAWG Consortium
Published 2020

Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

by Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Gordon Saksena, Kyle Ellrott, Michael C. Wendl, David A. Wheeler, Gad Getz, Jared T. Simpson, Mark B. Gerstein, Li Ding, PCAWG Consortium
Published 2020

Multi-platform discovery of haplotype-resolved structural variation in human genomes

by Mark J. P. Chaisson, Ashley D. Sanders, Xuefang Zhao, Ankit Malhotra, David Porubsky, Tobias Rausch, Eugene J. Gardner, Oscar L. Rodriguez, Li Guo, Ryan L. Collins, Xian Fan, Jia Wen, Robert E. Handsaker, Susan Fairley, Zev N. Kronenberg, Xiangmeng Kong, Fereydoun Hormozdiari, Dillon Lee, Aaron M. Wenger, Alex R. Hastie, Danny Antaki, Thomas Anantharaman, Peter A. Audano, Harrison Brand, Stuart Cantsilieris, Han Cao, Eliza Cerveira, Chong Chen, Xintong Chen, Chen-Shan Chin, Zechen Chong, Nelson T. Chuang, Christine C. Lambert, Deanna M. Church, Laura Clarke, Andrew Farrell, Joey Flores, Timur Galeev, David U. Gorkin, Madhusudan Gujral, Victor Guryev, William Haynes Heaton, Jonas Korlach, Sushant Kumar, Jee Young Kwon, Ernest T. Lam, Jong Eun Lee, Joyce Lee, Wan-Ping Lee, Sau Peng Lee, Shantao Li, Patrick Marks, Karine Viaud-Martinez, Sascha Meiers, Katherine M. Munson, Fabio C. P. Navarro, Bradley J. Nelson, Conor Nodzak, Amina Noor, Sofia Kyriazopoulou-Panagiotopoulou, Andy W. C. Pang, Yunjiang Qiu, Gabriel Rosanio, Mallory Ryan, Adrian Stütz, Diana C. J. Spierings, Alistair Ward, AnneMarie E. Welch, Ming Xiao, Wei Xu, Chengsheng Zhang, Qihui Zhu, Xiangqun Zheng-Bradley, Ernesto Lowy, Sergei Yakneen, Steven McCarroll, Goo Jun, Li Ding, Chong Lek Koh, Bing Ren, Paul Flicek, Ken Chen, Mark B. Gerstein, Pui-Yan Kwok, Peter M. Lansdorp, Gabor T. Marth, Jonathan Sebat, Xinghua Shi, Ali Bashir, Kai Ye, Scott E. Devine, Michael E. Talkowski, Ryan E. Mills, Tobias Marschall, Jan O. Korbel, Evan E. Eichler, Charles Lee
Published 2019