We propose to develop statistical and computational methods for interpreting data on gene regulation in a variety of cell types from the ENCODE Project. Our work will focus on (i) developing methods for integrating diverse data types in many tissues to infer chromatin architecture; (ii) inferring the sequence determinants and regulatory consequences of differences in chromatin across cell types; and (iii) empirical tests of our predictions using both natural genetic variation and experimental approaches.
The purpose of this project is to develop new statistical and computational tools for analyzing and interpreting data from the ENCODE project. These data relate to the controls of gene regulation in a wide variety of cell types.
|Sharon, Eilon; Sibener, Leah V; Battle, Alexis et al. (2016) Genetic variation in MHC proteins is associated with T cell receptor expression biases. Nat Genet 48:995-1002|
|Raj, Anil; Wang, Sidney H; Shim, Heejung et al. (2016) Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. Elife 5:|
|Li, Yang I; van de Geijn, Bryce; Raj, Anil et al. (2016) RNA splicing is a primary link between genetic variation and disease. Science 352:600-4|
|van de Geijn, Bryce; McVicker, Graham; Gilad, Yoav et al. (2015) WASP: allele-specific software for robust molecular quantitative trait locus discovery. Nat Methods 12:1061-3|
|Raj, Anil; Shim, Heejung; Gilad, Yoav et al. (2015) msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding. PLoS One 10:e0138030|
|Battle, Alexis; Khan, Zia; Wang, Sidney H et al. (2015) Genomic variation. Impact of regulatory variation from RNA to protein. Science 347:664-7|
|Nalabothula, Narasimharao; McVicker, Graham; Maiorano, John et al. (2014) The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation. BMC Genomics 15:92|
|Raj, Anil; Stephens, Matthew; Pritchard, Jonathan K (2014) fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics 197:573-89|
|Banovich, Nicholas E; Lan, Xun; McVicker, Graham et al. (2014) Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. PLoS Genet 10:e1004663|
|McVicker, Graham; van de Geijn, Bryce; Degner, Jacob F et al. (2013) Identification of genetic variants that affect histone modifications in human cells. Science 342:747-9|