Comparison of Two Variations of Neural Network Approaches to the Prediction of Protein Folding Pattern. - Inna Dubchak; Stephen R. Holbrook; Sung-Hou Kim (ISMB, 1993)

Relation Between Protein Structure, Sequence Homology and Composition of Amino Acids. - Eddy Mayoraz; Inna Dubchak; Ilya B. Muchnik (ISMB, 1995)

Protein Folding Class Predictor for SCOP: Approach Based on Global Descriptors. - Inna Dubchak; Ilya B. Muchnik; Sung-Hou Kim (ISMB, 1997)

Analysis of Ribosomal RNA Sequences by Combinatorial Clustering. - Poe Xing; Casimir A. Kulikowski; Ilya B. Muchnik; Inna Dubchak; Denise M. Wolf; Sylvia Spengler; Manfred Zorn (ISMB, 1999)

ASDB: database of alternatively spliced genes. - Mikhail S. Gelfand; Inna Dubchak; I. Dralyuk; Manfred Zorn (Nucleic Acids Res., 1999)

VISTA : visualizing global DNA sequence alignments of arbitrary length. - Chris Mayor; Michael Brudno; Jody R. Schwartz; Alexander Poliakov; Edward M. Rubin; Kelly A. Frazer; Lior Pachter; Inna Dubchak (Bioinform., 2000)

Representing and Reasoning about Protein Families Using Generative and Discriminative Methods. - I. Saira Mian; Inna Dubchak (J. Comput. Biol., 2000)

ASDB: database of alternatively spliced genes. - I. Dralyuk; Michael Brudno; Mikhail S. Gelfand; Manfred Zorn; Inna Dubchak (Nucleic Acids Res., 2000)

Multi-class protein fold recognition using support vector machines and neural networks. - Chris H. Q. Ding; Inna Dubchak (Bioinform., 2001)

Genome-Wide Analysis and Comparative Genomics - Session Introduction. - Inna Dubchak; Lior Pachter; Liping Wei (Pacific Symposium on Biocomputing, 2002)

The computational challenges of applying comparative-based computational methods to whole genomes. - Inna Dubchak; Lior Pachter (Briefings Bioinform., 2002)

Comparative genomics approaches to study organism similarities and differences. - Liping Wei; Yueyi Liu; Inna Dubchak; John Shon; John Park (J. Biomed. Informatics, 2002)

Glocal alignment: finding rearrangements during alignment. - Michael Brudno; Sanket Malde; Alexander Poliakov; Chuong B. Do; Olivier Couronne; Inna Dubchak; Serafim Batzoglou (ISMB (Supplement of Bioinformatics), 2003)

Genome-wide Analysis and Comparative Genomics - Session Introduction. - Liping Wei; Inna Dubchak; Victor V. Solovyev (Pacific Symposium on Biocomputing, 2003)

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. - Nameeta Y. Shah; Olivier Couronne; Len A. Pennacchio; Michael Brudno; Serafim Batzoglou; E. Wes Bethel; Edward M. Rubin; Bernd Hamann; Inna Dubchak (Bioinform., 2004)

VISTA: computational tools for comparative genomics. - Kelly A. Frazer; Lior Pachter; Alexander Poliakov; Edward M. Rubin; Inna Dubchak (Nucleic Acids Res., 2004)

SNP-VISTA: An interactive SNP visualization tool. - Nameeta Y. Shah; Michael V. Teplitsky; Simon Minovitsky; Len A. Pennacchio; Philip Hugenholtz; Bernd Hamann; Inna Dubchak (BMC Bioinform., 2005)

Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks. - Dmitry A. Rodionov; Inna Dubchak; Adam P. Arkin; Eric J. Alm; Mikhail S. Gelfand (PLoS Comput. Biol., 2005)

An experimental metagenome data management and analysis system. - Victor M. Markowitz; Natalia Ivanova; Krishna Palaniappan; Ernest Szeto; Frank Korzeniewski; Athanasios Lykidis; Iain Anderson; Konstantinos Mavrommatis; Victor Kunin; Héctor García Martín; Inna Dubchak; Philip Hugenholtz; et al. (ISMB (Supplement of Bioinformatics), 2006)

The integrated microbial genomes (IMG) system. - Victor M. Markowitz; Frank Korzeniewski; Krishna Palaniappan; Ernest Szeto; Greg Werner; Anu Padki; Xueling Zhao; Inna Dubchak; Philip Hugenholtz; Iain Anderson; Athanasios Lykidis; Konstantinos Mavrommatis; et al. (Nucleic Acids Res., 2006)

TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities. - Shengyin Gu; Iain Anderson; Victor Kunin; Michael J. Cipriano; Simon Minovitsky; Gunther H. Weber; Nina Amenta; Bernd Hamann; Inna Dubchak (Bioinform., 2007)

Multiple whole genome alignments and novel biomedical applications at the VISTA portal. - Michael Brudno; Alexander Poliakov; Simon Minovitsky; Igor Ratnere; Inna Dubchak (Nucleic Acids Res., 2007)

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)

VISTA Enhancer Browser - a database of tissue-specific human enhancers. - Axel Visel; Simon Minovitsky; Inna Dubchak; Len A. Pennacchio (Nucleic Acids Res., 2007)

IMG/M: a data management and analysis system for metagenomes. - Victor M. Markowitz; Natalia Ivanova; Ernest Szeto; Krishna Palaniappan; Ken Chu; Daniel Dalevi; I-Min A. Chen; Yuri Grechkin; Inna Dubchak; Iain Anderson; Athanasios Lykidis; Konstantinos Mavrommatis; et al. (Nucleic Acids Res., 2008)

The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. - Victor M. Markowitz; Ernest Szeto; Krishna Palaniappan; Yuri Grechkin; Ken Chu; I-Min A. Chen; Inna Dubchak; Iain Anderson; Athanasios Lykidis; Konstantinos Mavrommatis; Natalia Ivanova; Nikos Kyrpides (Nucleic Acids Res., 2008)

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)

The Genome Portal of the Department of Energy Joint Genome Institute. - Igor V. Grigoriev; Henrik Nordberg; Igor Shabalov; Andrea Aerts; Mike Cantor; David M. Goodstein; Alan Kuo; Simon Minovitsky; Roman Nikitin; Robin A. Ohm; Robert Otillar; Alexander Poliakov; et al. (Nucleic Acids Res., 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)

Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data. - Inna Dubchak; Matthew Munoz; Alexander Poliakov; Nathan Salomonis; Simon Minovitsky; Rolf Bodmer; Alexander C. Zambon (Bioinform., 2013)

GenomeVISTA - an integrated software package for whole-genome alignment and visualization. - Alexander Poliakov; Justin Foong; Michael Brudno; Inna Dubchak (Bioinform., 2014)

MycoCosm portal: gearing up for 1000 fungal genomes. - Igor V. Grigoriev; Roman Nikitin; Sajeet Haridas; Alan Kuo; Robin A. Ohm; Robert Otillar; Robert Riley 002; Asaf A. Salamov; Xueling Zhao; Frank Korzeniewski; Tatyana Smirnova; Henrik Nordberg; et al. (Nucleic Acids Res., 2014)

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates. - Henrik Nordberg; Michael Cantor; Serge Dusheyko; Susan Hua; Alexander Poliakov; Igor Shabalov; Tatyana Smirnova; Igor V. Grigoriev; Inna Dubchak (Nucleic Acids Res., 2014)

Elviz - exploration of metagenome assemblies with an interactive visualization tool. - Michael Cantor; Henrik Nordberg; Tatyana Smirnova; Matthias Hess; Susannah Tringe; Inna Dubchak (BMC Bioinform., 2015)

Rice SNP-seek database update: new SNPs, indels, and queries. - Locedie Mansueto; Roven Rommel Fuentes; Frances Nikki Borja; Jeffery Detras; Juan Miguel Abriol-Santos; Dmytro Chebotarov; Millicent Sanciangco; Kevin Palis; Dario Copetti; Alexandre Poliakov; Inna Dubchak; Victor V. Solovyev; et al. (Nucleic Acids Res., 2017)