Inna Dubchak

Igor V. Grigoriev, Henrik Nordberg, Igor Shabalov, Andrea Aerts, Mike Cantor, David Goodstein, Alan Kuo, Simon Minovitsky, Roman Nikitin, Robin A. Ohm, Robert Otillar, Alexander Poliakov, Igor Ratnere, Robert Riley, Tatyana Smirnova, Daniel Rokhsar, Inna Dubchak: The Genome Portal of the Department of Energy Joint Genome Institute. Nucleic Acids Research 40(Database-Issue): 26-32 (2012)

Pavel S. Novichkov, Thomas S. Brettin, Elena S. Novichkova, Paramvir S. Dehal, Adam P. Arkin, Inna Dubchak, Dmitry A. Rodionov: RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. Nucleic Acids Research 40(Web-Server-Issue): 604-608 (2012)

Elena D. Stavrovskaya, Andrey A. Mironov, Dmitry A. Rodionov, Inna Dubchak, Pavel S. Novichkov: Automated Regulon Content Prediction and Estimation of PWM Quality. BIOINFORMATICS 2012: 322-325

Igor Lukashin, Pavel S. Novichkov, Dario Boffelli, Alex R. Paciorkowski, Simon Minovitsky, Song Yang, Inna Dubchak: VISTA Region Viewer (RViewer) - a computational system for prioritizing genomic intervals for biomedical studies. Bioinformatics 27(18): 2595-2597 (2011)

Pavel S. Novichkov, Olga N. Laikova, Elena S. Novichkova, Mikhail S. Gelfand, Adam P. Arkin, Inna Dubchak, Dmitry A. Rodionov: RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Research 38(Database-Issue): 111-118 (2010)

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, Adam P. Arkin: MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Research 38(Database-Issue): 396-400 (2010)

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: RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Research 38(Web-Server-Issue): 299-307 (2010)

Pavel S. Novichkov, Igor Ratnere, Yuri I. Wolf, Eugene V. Koonin, Inna Dubchak: ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. Nucleic Acids Research 37(Database-Issue): 448-454 (2009)

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: The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Research 36(Database-Issue): 528-533 (2008)

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, Philip Hugenholtz, Nikos Kyrpides: IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Research 36(Database-Issue): 534-538 (2008)

Shengyin Gu, Iain Anderson, Victor Kunin, Michael J. Cipriano, Simon Minovitsky, Gunther H. Weber, Nina Amenta, Bernd Hamann, Inna Dubchak: TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities. Bioinformatics 23(6): 764-766 (2007)

Axel Visel, Simon Minovitsky, Inna Dubchak, Len A. Pennacchio: VISTA Enhancer Browser - a database of tissue-specific human enhancers. Nucleic Acids Research 35(Database-Issue): 88-92 (2007)

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: RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Research 35(Database-Issue): 407-412 (2007)

Michael Brudno, Alexander Poliakov, Simon Minovitsky, Igor Ratnere, Inna Dubchak: Multiple whole genome alignments and novel biomedical applications at the VISTA portal. Nucleic Acids Research 35(Web-Server-Issue): 669-674 (2007)

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, Natalia Ivanova, Nikos Kyrpides: The integrated microbial genomes (IMG) system. Nucleic Acids Research 34(Database-Issue): 344-348 (2006)

Victor M. Markowitz, Natalia Ivanova, Krishna Palaniappan, Ernest Szeto, Frank Korzeniewski, Athanasios Lykidis, Iain Anderson, Konstantinos Mavrommatis, Victor Kunin, Hector Garcia Martin, Inna Dubchak, Philip Hugenholtz, Nikos Kyrpides: An experimental metagenome data management and analysis system. ISMB (Supplement of Bioinformatics) 2006: 359-367

Nameeta Shah, Michael V. Teplitsky, Simon Minovitsky, Len A. Pennacchio, Philip Hugenholtz, Bernd Hamann, Inna Dubchak: SNP-VISTA: An interactive SNP visualization tool. BMC Bioinformatics 6: 292 (2005)

Dmitry A. Rodionov, Inna Dubchak, Adam P. Arkin, Eric J. Alm, Mikhail S. Gelfand: Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks. PLoS Computational Biology 1(5) (2005)

Nameeta Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, E. Wes Bethel, Edward M. Rubin, Bernd Hamann, Inna Dubchak: Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinformatics 20(5): 636-643 (2004)

Kelly A. Frazer, Lior Pachter, Alexander Poliakov, Edward M. Rubin, Inna Dubchak: VISTA: computational tools for comparative genomics. Nucleic Acids Research 32(Web-Server-Issue): 273-279 (2004)

Michael Brudno, Sanket Malde, Alexander Poliakov, Chuong B. Do, Olivier Couronne, Inna Dubchak, Serafim Batzoglou: Glocal alignment: finding rearrangements during alignment. ISMB (Supplement of Bioinformatics) 2003: 54-62

Liping Wei, Inna Dubchak, Victor V. Solovyev: Genome-wide Analysis and Comparative Genomics - Session Introduction. Pacific Symposium on Biocomputing 2003: 276-278

Inna Dubchak, Lior Pachter: The computational challenges of applying comparative-based computational methods to whole genomes. Briefings in Bioinformatics 3(1): 18-22 (2002)

Liping Wei, Yueyi Liu, Inna Dubchak, John Shon, John Park: Comparative genomics approaches to study organism similarities and differences. Journal of Biomedical Informatics 35(2): 142-150 (2002)

Inna Dubchak, Lior Pachter, Liping Wei: Genome-Wide Analysis and Comparative Genomics - Session Introduction. Pacific Symposium on Biocomputing 2002: 112-114

Chris H. Q. Ding, Inna Dubchak: Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics 17(4): 349-358 (2001)

Chris Mayor, Michael Brudno, Jody R. Schwartz, Alexander Poliakov, Edward M. Rubin, Kelly A. Frazer, Lior Pachter, Inna Dubchak: VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16(11): 1046-1047 (2000)

I. Saira Mian, Inna Dubchak: Representing and Reasoning about Protein Families Using Generative and Discriminative Methods. Journal of Computational Biology 7(6): 849-862 (2000)

I. Dralyuk, Michael Brudno, Mikhail S. Gelfand, Manfred Zorn, Inna Dubchak: ASDB: database of alternatively spliced genes. Nucleic Acids Research 28(1): 296-297 (2000)

Mikhail S. Gelfand, Inna Dubchak, I. Dralyuk, Manfred Zorn: ASDB: database of alternatively spliced genes. Nucleic Acids Research 27(1): 301-302 (1999)

Poe Xing, Casimir A. Kulikowski, Ilya B. Muchnik, Inna Dubchak, Denise M. Wolf, Sylvia Spengler, Manfred Zorn: Analysis of Ribosomal RNA Sequences by Combinatorial Clustering. ISMB 1999: 287-296

Inna Dubchak, Ilya B. Muchnik, Sung-Hou Kim: Protein Folding Class Predictor for SCOP: Approach Based on Global Descriptors. ISMB 1997: 104-107

Eddy Mayoraz, Inna Dubchak, Ilya B. Muchnik: Relation Between Protein Structure, Sequence Homology and Composition of Amino Acids. ISMB 1995: 240-248

Inna Dubchak, Stephen R. Holbrook, Sung-Hou Kim: Comparison of Two Variations of Neural Network Approaches to the Prediction of Protein Folding Pattern. ISMB 1993: 118-126