owl_cpp, a C++ Library for Working with OWL Ontologies. - Mikhail K. Levin; Alan Ruttenberg; Anna Maria Masci; Lindsay G. Cowell (ICBO, 2011)

Connecting Ontologies for the Representation of Biological Pathways. - Anna Maria Masci; Mikhail K. Levin; Alan Ruttenberg; Lindsay G. Cowell (ICBO, 2011)

owlcpp: a C++ library for working with OWL ontologies. - Mikhail K. Levin; Lindsay G. Cowell (J. Biomed. Semant., 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)

VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data. - Scott Christley; Mikhail K. Levin; Inimary T. Toby; John M. Fonner; Nancy Monson; William Rounds; Florian Rubelt; Walter Scarborough; Richard H. Scheuermann; Lindsay G. Cowell (BMC Bioinform., 2017)