Raychaudhuri S, Plenge RM, Rossin E, Ng A. et al. Identifying Relationships Among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions. PLoS Genetics. 5:e1000534, 2009. [PubMed][PDF]

Raychaudhuri S. VIZ-GRAIL: Visualizing Functional Connections Across Disease Loci. Bioinformatics. 27:1589-90, 2011. [Pubmed][PDF]

Chromatin marks identify critical cell-types for fine-mapping complex trait variants.  Trynka G,  Sandor C,  Han B,  Xu H, Strange BE,   Liu XS,   Raychaudhuri S. Nature Genetics. 45: 124-30, 2013. [Pubmed][PDF]

Jia X, Han B, Onengut-Gumuscu S, Chen W-M, Concannon PJ, Rich S, Raychaudhuri S ,and de Bakker PIW. Imputing amino acid polymorphisms in human leukocyte antigens. PLoS One. 8:e64683. 2013 [PubMed][PDF]

Hu X, Kim H, Brennan P,  Han B, Baecher-Allan C, de Jager PL, Brenner M, Raychaudhuri S. User-guided cytometric data analysis for large-scale immunoprofiling studies: application to invariant natural killer T cells. Proc Natl Acad Sci. 110:19030–19035, 2013. [PubMed][PDF]

Slowikowski K, Hu X, Raychaudhuri S. SNPsea: an algorithm to identify cell types, tissues and pathways affected by risk loci. Bioinformatics. 30:2496-7, 2014. [Pubmed][PDF]