John A. Stamatoyannopoulos

According to our database, John A. Stamatoyannopoulos authored at least 14 papers between 2005 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

2014

Topologically associating domains are stable units of replication-timing regulation Open.

Benjamin D. Pope, Tyrone Ryba, Vishnu Dileep, Feng Yue, Wei-Sheng Wu, Olgert Denas, Daniel L. Vera, Yanli Wang, R. Scott Hansen, Theresa K. Canfield, Robert E. Thurman, Yong Cheng, Günhan Gülsoy, Jonathan H. Dennis, Michael P. Snyder, John A. Stamatoyannopoulos, James Taylor, Ross C. Hardison, Tamer Kahveci, Bing Ren, David M. Gilbert

Nat., 2014

2013

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State.

Nisha Rajagopal, Wei Xie, Yan Li, Uli Wagner, Wei Wang, John A. Stamatoyannopoulos, Jason Ernst, Manolis Kellis, Bing Ren

PLoS Comput. Biol., 2013

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

2008

Predicting Human Nucleosome Occupancy from Primary Sequence.

Shobhit Gupta, Jonathan H. Dennis, Robert E. Thurman, Robert E. Kingston, John A. Stamatoyannopoulos, William Stafford Noble

PLoS Comput. Biol., 2008

Automated mapping of large-scale chromatin structure in ENCODE.

Heng Lian, William A. Thompson, Robert E. Thurman, John A. Stamatoyannopoulos, William Stafford Noble, Charles E. Lawrence

Bioinform., 2008

Multi-Scale Correlations in Continuous Genomic Data.

Robert E. Thurman, William Stafford Noble, John A. Stamatoyannopoulos

Proceedings of the Biocomputing 2008, 2008

2007

Analysis of Sequence Conservation at Nucleotide Resolution.

Saurabh Asthana, Mikhail A. Roytberg, John A. Stamatoyannopoulos, Shamil R. Sunyaev

PLoS Comput. Biol., 2007

Unsupervised segmentation of continuous genomic data.

Nathan Day, Andrew Hemmaplardh, Robert E. Thurman, John A. Stamatoyannopoulos, William Stafford Noble

Bioinform., 2007

2006

Automated Validation of Polymerase Chain Reaction Amplicon Melting Curves.

Tobias P. Mann, Richard Humbert, John A. Stamatoyannopoulos, William Stafford Noble

J. Bioinform. Comput. Biol., 2006

2005

Predicting the <i>in vivo</i> signature of human gene regulatory sequence.

William Stafford Noble, Scott Kuehn, Robert E. Thurman, Man Yu, John A. Stamatoyannopoulos

Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

Automated Validation of Polymerase Chain Reactions Using Amplicon Melting Curves.

Tobias P. Mann, Richard Humbert, John A. Stamatoyannopoulos, William Stafford Noble

Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005