Comparative Analysis of Regulatory Patterns in Bacterial Genomes. - Mikhail S. Gelfand; Pavel S. Novichkov; Elena S. Novichkova; Andrey A. Mironov (Briefings Bioinform., 2000)

Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors. - Andrey A. Mironov; Pavel S. Novichkov; Mikhail S. Gelfand (Bioinform., 2001)

Gene recognition in eukaryotic DNA by comparison of genomic sequences. - Pavel S. Novichkov; Mikhail S. Gelfand; Andrey A. Mironov (Bioinform., 2001)

SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins. - Olga V. Kalinina; Pavel S. Novichkov; Andrey A. Mironov; Mikhail S. Gelfand; Aleksandra B. Rakhmaninova (Nucleic Acids Res., 2004)

RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. - Alexei E. Kazakov; Michael J. Cipriano; Pavel S. Novichkov; Simon Minovitsky; Dmitry V. Vinogradov; Adam P. Arkin; Andrey A. Mironov; Mikhail S. Gelfand; Inna Dubchak (Nucleic Acids Res., 2007)

ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. - Pavel S. Novichkov; Igor Ratnere; Yuri I. Wolf; Eugene V. Koonin; Inna Dubchak (Nucleic Acids Res., 2009)

MicrobesOnline: an integrated portal for comparative and functional genomics. - Paramvir S. Dehal; Marcin P. Joachimiak; Morgan N. Price; John T. Bates; Jason K. Baumohl; Dylan Chivian; Greg D. Friedland; Katherine H. Huang; Keith Keller; Pavel S. Novichkov; Inna Dubchak; Eric J. Alm; et al. (Nucleic Acids Res., 2010)

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. - Pavel S. Novichkov; Olga N. Laikova; Elena S. Novichkova; Mikhail S. Gelfand; Adam P. Arkin; Inna Dubchak; Dmitry A. Rodionov (Nucleic Acids Res., 2010)

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. - Pavel S. Novichkov; Dmitry A. Rodionov; Elena D. Stavrovskaya; Elena S. Novichkova; Alexei E. Kazakov; Mikhail S. Gelfand; Adam P. Arkin; Andrey A. Mironov; Inna Dubchak (Nucleic Acids Res., 2010)

VISTA Region Viewer (RViewer) - a computational system for prioritizing genomic intervals for biomedical studies. - Igor Lukashin; Pavel S. Novichkov; Dario Boffelli; Alex R. Paciorkowski; Simon Minovitsky; Song Yang; Inna Dubchak (Bioinform., 2011)

Automated Regulon Content Prediction and Estimation of PWM Quality. - Elena D. Stavrovskaya; Andrey A. Mironov; Dmitry A. Rodionov; Inna Dubchak; Pavel S. Novichkov (BIOINFORMATICS, 2012)

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. - Pavel S. Novichkov; Thomas S. Brettin; Elena S. Novichkova; Paramvir S. Dehal; Adam P. Arkin; Inna Dubchak; Dmitry A. Rodionov (Nucleic Acids Res., 2012)

Network portal: a database for storage, analysis and visualization of biological networks. - Serdar Turkarslan; Elisabeth J. Wurtmann; Wei-Ju Wu; Ning Jiang; J. Christopher Bare; Karen Foley; David J. Reiss; Pavel S. Novichkov; Nitin S. Baliga (Nucleic Acids Res., 2014)

Large Scale Comparative Visualisation of Regulatory Networks with TRNDiff. - Xin-Yi Chua; Lawrence Buckingham; James M. Hogan; Pavel S. Novichkov (ICCS, 2015)