GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. - Bing Zhang 003; Denise Schmoyer; Stefan Kirov; Jay Snoddy (BMC Bioinform., 2004)

WebGestalt: an integrated system for exploring gene sets in various biological contexts. - Bing Zhang 003; Stefan Kirov; Jay Snoddy (Nucleic Acids Res., 2005)

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. - Elodie Portales-Casamar; David J. Arenillas; Jonathan S. Lim; Magdalena I. Swanson; Steven Jiang; Anthony McCallum; Stefan Kirov; Wyeth W. Wasserman (Nucleic Acids Res., 2009)

CRISPR-DAV: CRISPR NGS data analysis and visualization pipeline. - Xuning Wang; Charles Tilford; Isaac Neuhaus; Gabe Mintier; Qi Guo; John N. Feder; Stefan Kirov (Bioinform., 2017)

Bayesian Hierarchical Modelling for Antimicrobial Resistance. - Maya Zhelyazkova; Roumyana Yordanova; Iliyan Mihaylov; Stefan Kirov; Stefan Tsonev; David Danko; Dimitar Vassilev (BioInfoMed, 2020)