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Results for: Publications | Epigenome-based Phenotyping Project


Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes. Roy S, Sridharan R. Genome Research, 2017.

Annotation regression for genome-wide association studies with an application to psychiatric genomic consortium data. Shin S, Keles S. Statistics in Biosciences, 2016.

Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq. Liu P, Sanalkumar R, Bresnick E, Keles S, Dewey C. Genome Research 26:1124–1133, 2016.

A hierarchical framework for state space matrix inference and clustering. Zuo C, Chen K, Hewitt K, Bresnick EH, Keles S. Annals of Applied Statistics 10(3):1348-1372, 2016.

A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions. Siahpirani A, Ay F, Roy S. Genome Biology 17:114, 2016.

A MAD-Bayes algorithm for state-space inference and clustering with application to querying large collections of ChIP-seq data sets. Zuo C, Chen K, Keles S. Proceedings of the 20th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2016.

A predictive modeling approach for cell line-specific long-range regulatory interactions. Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R. Nucleic Acids Research 43(18):8694-8712, 2015.

atSNP: transcription factor binding affinity testing for regulatory SNP detection. Zuo C, Shin S, Keles S. Bioinformatics 31(20):3353-5, 2015.

Hematopoietic signaling mechanism revealed from a stem/progenitor cell cistrome. Hewitt KJ, Kim DH, Devadas P, Prathibha R, Zuo C, Sanalkumar R, Johnson D, Kang Y-A, Kim J-S, Dewey CN, Keles S, Bresnick EH. Molecular Cell 9(1):62–74, 2015.