Cell Subset Prediction for Blood Genomic Studies. - Christopher R. Bolen; Mohamed Uduman; Steven H. Kleinstein (BMC Bioinform., 2011)

Detecting selection in immunoglobulin sequences. - Mohamed Uduman; Gur Yaari; Uri Hershberg; Jacob A. Stern; Mark J. Shlomchik; Steven H. Kleinstein (Nucleic Acids Res., 2011)

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. - Jason A. Vander Heiden; Gur Yaari; Mohamed Uduman; Joel N. H. Stern; Kevin C. O'Connor; David A. Hafler; Francois Vigneault; Steven H. Kleinstein (Bioinform., 2014)

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. - Namita T. Gupta; Jason A. Vander Heiden; Mohamed Uduman; Daniel Gadala-Maria; Gur Yaari; Steven H. Kleinstein (Bioinform., 2015)

VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. - Inimary T. Toby; Mikhail K. Levin; Edward Salinas; Scott Christley; Sanchita Bhattacharya; Felix Breden; Adam Buntzman; Brian Corrie; John M. Fonner; Namita T. Gupta; Uri Hershberg; Nishanth Marthandan; et al. (BMC Bioinform., 2016)