CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. - Roded Sharan; Ivan Ovcharenko; Asa Ben-Hur; Richard M. Karp (ISMB (Supplement of Bioinformatics), 2003)

rVISTA 2.0: evolutionary analysis of transcription factor binding sites. - Gabriela G. Loots; Ivan Ovcharenko (Nucleic Acids Res., 2004)

ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. - Ivan Ovcharenko; Marcelo A. Nobrega; Gabriela G. Loots; Lisa Stubbs (Nucleic Acids Res., 2004)

CREME: Cis-Regulatory Module Explorer for the human genome. - Roded Sharan; Asa Ben-Hur; Gabriela G. Loots; Ivan Ovcharenko (Nucleic Acids Res., 2004)

Dcode.org anthology of comparative genomic tools. - Gabriela G. Loots; Ivan Ovcharenko (Nucleic Acids Res., 2005)

Identifying synonymous regulatory elements in vertebrate genomes. - Ivan Ovcharenko; Marcelo A. Nobrega (Nucleic Acids Res., 2005)

Array2BIO: from microarray expression data to functional annotation of co-regulated genes. - Gabriela G. Loots; Patrick S. G. Chain; Shalini Mabery; Amy Rasley; Emilio Garcia; Ivan Ovcharenko (BMC Bioinform., 2006)

ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes. - Gabriela G. Loots; Ivan Ovcharenko (Bioinform., 2007)

DiRE: identifying distant regulatory elements of co-expressed genes. - Valer Gotea; Ivan Ovcharenko (Nucleic Acids Res., 2008)

Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. - Leila Taher; Ivan Ovcharenko (Bioinform., 2009)

Structure of Proximal and Distant Regulatory Elements in the Human Genome. - Ivan Ovcharenko (ISBRA, 2010)

CLARE: Cracking the LAnguage of Regulatory Elements. - Leila Taher; Leelavati Narlikar; Ivan Ovcharenko (Bioinform., 2012)

Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs. - Hani Z. Girgis; Ivan Ovcharenko (BMC Bioinform., 2012)

SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome. - Roberto Vera Alvarez; Shan Li; David Landsman; Ivan Ovcharenko (Bioinform., 2018)

Enhancer reprogramming in mammalian genomes. - Mario A. Flores; Ivan Ovcharenko (BMC Bioinform., 2018)

ChromDL: a next-generation regulatory DNA classifier. - Christopher Hill; Sanjarbek Hudaiberdiev; Ivan Ovcharenko (Bioinform., 2023)