Shane J. Neph

According to our database, Shane J. Neph authored at least 6 papers between 2006 and 2019.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2019

eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data.

Charles E. Breeze, Alex P. Reynolds, Jenny van Dongen, Ian Dunham, John Lazar, Shane J. Neph, Jeff Vierstra, Guillaume Bourque, Andrew E. Teschendorff, John A. Stamatoyannopoulos, Stephan Beck

Bioinform., 2019

2016

Operating on Genomic Ranges Using BEDOPS.

Shane J. Neph, Alex P. Reynolds, Scott Kuehn, John A. Stamatoyannopoulos

Proceedings of the Statistical Genomics - Methods and Protocols, 2016

2015

Integrative analysis of 111 reference human epigenomes Open.

Roadmap Epigenomics Consortium, Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi Moussavi, Pouya Kheradpour, ZhiZhuo Zhang, Jianrong Wang, Michael J. Ziller, Viren Amin, John W. Whitaker, Matthew D. Schultz, Lucas D. Ward, Abhishek Sarkar, Gerald T. Quon, Richard S. Sandstrom, Matthew L. Eaton, Yi-Chieh Wu, Andreas R. Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R. Alan Harris, Noam Shoresh, Charles B. Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R. David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J. Mungall, Richard A. Moore, Eric Chuah, Angela Tam, Theresa K. Canfield, R. Scott Hansen, Rajinder Kaul, Peter J. Sabo, Mukul S. Bansal, Annaick Carles, Jesse R. Dixon, Kyle Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca F. Lowdon, GiNell Elliott, Tim R. Mercer, Shane J. Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C. Sallari, Kyle T. Siebenthall, Nicholas A. Sinnott-Armstrong, Michael Stevens, Robert E. Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E. Beaudet, Laurie A. Boyer, Philip L. De Jager, Peggy J. Farnham, Susan J. Fisher, David Haussler, Steven J. M. Jones, Wei Li, Marco A. Marra, Michael T. McManus, Shamil R. Sunyaev, James A. Thomson, Thea D. Tlsty, Li-Huei Tsai, Wei Wang, Robert A. Waterland, Michael Q. Zhang, Lisa H. Chadwick, Bradley E. Bernstein, Joseph F. Costello, Joseph R. Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A. Stamatoyannopoulos, Ting Wang, Manolis Kellis

Nat., 2015

2012

BEDOPS: high-performance genomic feature operations.

Shane J. Neph, Scott Kuehn, Alex P. Reynolds, Eric Haugen, Robert E. Thurman, Audra K. Johnson, Eric Rynes, Matthew T. Maurano, Jeff Vierstra, Sean Thomas, Richard S. Sandstrom, Richard Humbert, John A. Stamatoyannopoulos

Bioinform., 2012

2007

A Computational Pipeline for High- Throughput Discovery of <i>cis</i>-Regulatory Noncoding RNA in Prokaryotes.

Zizhen Yao, Jeffrey E. Barrick, Zasha Weinberg, Shane J. Neph, Ronald R. Breaker, Martin Tompa, Walter L. Ruzzo

PLoS Comput. Biol., 2007

2006

MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes.

Shane J. Neph, Martin Tompa

Nucleic Acids Res., 2006