Automated Validation of Polymerase Chain Reactions Using Amplicon Melting Curves. - Tobias P. Mann; Richard Humbert; John A. Stamatoyannopoulos; William Stafford Noble (CSB, 2005)

Predicting the in vivo signature of human gene regulatory sequence. - William Stafford Noble; Scott Kuehn; Robert E. Thurman; Man Yu; John A. Stamatoyannopoulos (ISMB (Supplement of Bioinformatics), 2005)

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)

Unsupervised segmentation of continuous genomic data. - Nathan Day; Andrew Hemmaplardh; Robert E. Thurman; John A. Stamatoyannopoulos; William Stafford Noble (Bioinform., 2007)

Analysis of Sequence Conservation at Nucleotide Resolution. - Saurabh Asthana; Mikhail A. Roytberg; John A. Stamatoyannopoulos; Shamil R. Sunyaev (PLoS Comput. Biol., 2007)

Multi-Scale Correlations in Continuous Genomic Data. - Robert E. Thurman; William Stafford Noble; John A. Stamatoyannopoulos (Pacific Symposium on Biocomputing, 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)

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)

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; et al. (Bioinform., 2012)

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State. - Nisha Rajagopal; Wei Xie; Yan Li; Uli Wagner 002; Wei Wang 051; John A. Stamatoyannopoulos; Jason Ernst; Manolis Kellis; Bing Ren (PLoS Comput. Biol., 2013)

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; et al. (Nat., 2014)

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; et al. (Nat., 2015)

Operating on Genomic Ranges Using BEDOPS. - Shane J. Neph; Alex P. Reynolds; Scott Kuehn; John A. Stamatoyannopoulos (Statistical Genomics, 2016)

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 002 (Bioinform., 2019)