PHOG: a database of supergenomes built from proteome complements

Por Merkeev, Igor V, Novichkov, Pavel S, Mironov, Andrey A
Publicado em 2006

Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes

Por Novichkov, Pavel S., Wolf, Yuri I., Dubchak, Inna, Koonin, Eugene V.
Publicado em 2009

ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

Por Novichkov, Pavel S., Ratnere, Igor, Wolf, Yuri I., Koonin, Eugene V., Dubchak, Inna
Publicado em 2009

SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins

Por Kalinina, Olga V., Novichkov, Pavel S., Mironov, Andrey A., Gelfand, Mikhail S., Rakhmaninova, Aleksandra B.
Publicado em 2004

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

Por Makarova, Kira S, Sorokin, Alexander V, Novichkov, Pavel S, Wolf, Yuri I, Koonin, Eugene V
Publicado em 2007

The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

Por Wolf, Yuri I., Novichkov, Pavel S., Karev, Georgy P., Koonin, Eugene V., Lipman, David J.
Publicado em 2009

VISTA Region Viewer (RViewer)—a computational system for prioritizing genomic intervals for biomedical studies

Por Lukashin, Igor, Novichkov, Pavel, Boffelli, Dario, Paciorkowski, Alex R., Minovitsky, Simon, Yang, Song, Dubchak, Inna
Publicado em 2011

Genome-Wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution

Por Novichkov, Pavel S., Omelchenko, Marina V., Gelfand, Mikhail S., Mironov, Andrei A., Wolf, Yuri I., Koonin, Eugene V.
Publicado em 2004

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics

Por Novichkov, Pavel S., Brettin, Thomas S., Novichkova, Elena S., Dehal, Paramvir S., Arkin, Adam P., Dubchak, Inna, Rodionov, Dmitry A.
Publicado em 2012

Transcription Factor Family-Based Reconstruction of Singleton Regulons and Study of the Crp/Fnr, ArsR, and GntR Families in Desulfovibrionales Genomes

Por Kazakov, Alexey E., Rodionov, Dmitry A., Price, Morgan N., Arkin, Adam P., Dubchak, Inna, Novichkov, Pavel S.
Publicado em 2013

σ(54)-dependent regulome in Desulfovibrio vulgaris Hildenborough

Por Kazakov, Alexey E., Rajeev, Lara, Chen, Amy, Luning, Eric G., Dubchak, Inna, Mukhopadhyay, Aindrila, Novichkov, Pavel S.
Publicado no BMC Genomics (2015)

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

Por Novichkov, Pavel S., Laikova, Olga N., Novichkova, Elena S., Gelfand, Mikhail S., Arkin, Adam P., Dubchak, Inna, Rodionov, Dmitry A.
Publicado em 2010

Distinct Patterns of Expression and Evolution of Intronless and Intron-Containing Mammalian Genes

Por Shabalina, Svetlana A., Ogurtsov, Aleksey Y., Spiridonov, Alexey N., Novichkov, Pavel S., Spiridonov, Nikolay A., Koonin, Eugene V.
Publicado em 2010

Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria

Por Ravcheev, Dmitry A, Best, Aaron A, Sernova, Natalia V, Kazanov, Marat D, Novichkov, Pavel S, Rodionov, Dmitry A
Publicado em 2013

Genomic Reconstruction of the Transcriptional Regulatory Network in Bacillus subtilis

Por Leyn, Semen A., Kazanov, Marat D., Sernova, Natalia V., Ermakova, Ekaterina O., Novichkov, Pavel S., Rodionov, Dmitry A.
Publicado em 2013

Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria

Por Sun, Eric I, Leyn, Semen A, Kazanov, Marat D, Saier, Milton H, Novichkov, Pavel S, Rodionov, Dmitry A
Publicado em 2013

Activation of Phenotypic Subpopulations in Response to Ciprofloxacin Treatment in Acinetobacter baumannii

Por MacGuire, Ashley E., Ching, Meining Carly, Diamond, Brett H., Kazakov, Alexey, Novichkov, Pavel, Godoy, Veronica G.
Publicado em 2014

Comparative Genomics of Transcriptional Regulation of Methionine Metabolism in Proteobacteria

Por Leyn, Semen A., Suvorova, Inna A., Kholina, Tatiana D., Sherstneva, Sofia S., Novichkov, Pavel S., Gelfand, Mikhail S., Rodionov, Dmitry A.
Publicado no PLoS One (2014)

Inference of the Transcriptional Regulatory Network in Staphylococcus aureus by Integration of Experimental and Genomics-Based Evidence

Por Ravcheev, Dmitry A., Best, Aaron A., Tintle, Nathan, DeJongh, Matthew, Osterman, Andrei L., Novichkov, Pavel S., Rodionov, Dmitry A.
Publicado em 2011

RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes

Por Cipriano, Michael J, Novichkov, Pavel N, Kazakov, Alexey E, Rodionov, Dmitry A, Arkin, Adam P, Gelfand, Mikhail S, Dubchak, Inna
Publicado em 2013