Inna Dubchak

Publication Activity (10 Years)

Years Active: 1993-2017
Publications (10 Years): 2

Top Topics

Genotype Phenotype

Visualization Tools

Transcriptional Regulatory

Top Venues

Nucleic Acids Res.

Publications

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, Rod A. Wing, Ruaraidh Sackville Hamilton, Ramil Mauleon, Kenneth L. McNally, Nickolai Alexandrov
Rice SNP-seek database update: new SNPs, indels, and queries. Nucleic Acids Res. 45 (Database-Issue) (2017)
Michael Cantor, Henrik Nordberg, Tatyana Smirnova, Matthias Hess, Susannah Tringe, Inna Dubchak
Elviz - exploration of metagenome assemblies with an interactive visualization tool. BMC Bioinform. 16 (2015)
Igor V. Grigoriev, Roman Nikitin, Sajeet Haridas, Alan Kuo, Robin A. Ohm, Robert Otillar, Robert Riley, Asaf A. Salamov, Xueling Zhao, Frank Korzeniewski, Tatyana Smirnova, Henrik Nordberg, Inna Dubchak, Igor Shabalov
MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res. 42 (Database-Issue) (2014)
Henrik Nordberg, Michael Cantor, Serge Dusheyko, Susan Hua, Alexander Poliakov, Igor Shabalov, Tatyana Smirnova, Igor V. Grigoriev, Inna Dubchak
The genome portal of the Department of Energy Joint Genome Institute: 2014 updates. Nucleic Acids Res. 42 (Database-Issue) (2014)
Alexander Poliakov, Justin Foong, Michael Brudno, Inna Dubchak
GenomeVISTA - an integrated software package for whole-genome alignment and visualization. Bioinform. 30 (18) (2014)
Inna Dubchak, Matthew Munoz, Alexander Poliakov, Nathan Salomonis, Simon Minovitsky, Rolf Bodmer, Alexander C. Zambon
Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data. Bioinform. 29 (16) (2013)
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, Igor Ratnere, Robert Riley, Tatyana Smirnova, Daniel Rokhsar, Inna Dubchak
The Genome Portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res. 40 (Database-Issue) (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 Res. 40 (Web-Server-Issue) (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)
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. Bioinform. 27 (18) (2011)
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 Res. 38 (Web-Server-Issue) (2010)
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 Res. 38 (Database-Issue) (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 Res. 38 (Database-Issue) (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 Res. 37 (Database-Issue) (2009)
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 Res. 36 (Database-Issue) (2008)
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 Res. 36 (Database-Issue) (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. Bioinform. 23 (6) (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 Res. 35 (Database-Issue) (2007)
Axel Visel, Simon Minovitsky, Inna Dubchak, Len A. Pennacchio
VISTA Enhancer Browser - a database of tissue-specific human enhancers. Nucleic Acids Res. 35 (Database-Issue) (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 Res. 35 (Web-Server-Issue) (2007)
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, Nikos Kyrpides
An experimental metagenome data management and analysis system. ISMB (Supplement of Bioinformatics) (2006)
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 Res. 34 (Database-Issue) (2006)
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 Comput. Biol. 1 (5) (2005)
Nameeta Y. Shah, Michael V. Teplitsky, Simon Minovitsky, Len A. Pennacchio, Philip Hugenholtz, Bernd Hamann, Inna Dubchak
SNP-VISTA: An interactive SNP visualization tool. BMC Bioinform. 6 (2005)
Nameeta Y. 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. Bioinform. 20 (5) (2004)
Kelly A. Frazer, Lior Pachter, Alexander Poliakov, Edward M. Rubin, Inna Dubchak
VISTA: computational tools for comparative genomics. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Liping Wei, Inna Dubchak, Victor V. Solovyev
Genome-wide Analysis and Comparative Genomics - Session Introduction. Pacific Symposium on Biocomputing (2003)
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)
Inna Dubchak, Lior Pachter, Liping Wei
Genome-Wide Analysis and Comparative Genomics - Session Introduction. Pacific Symposium on Biocomputing (2002)
Inna Dubchak, Lior Pachter
The computational challenges of applying comparative-based computational methods to whole genomes. Briefings Bioinform. 3 (1) (2002)
Liping Wei, Yueyi Liu, Inna Dubchak, John Shon, John Park
Comparative genomics approaches to study organism similarities and differences. J. Biomed. Informatics 35 (2) (2002)
Chris H. Q. Ding, Inna Dubchak
Multi-class protein fold recognition using support vector machines and neural networks. Bioinform. 17 (4) (2001)
I. Saira Mian, Inna Dubchak
Representing and Reasoning about Protein Families Using Generative and Discriminative Methods. J. Comput. Biol. 7 (6) (2000)
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. Bioinform. 16 (11) (2000)
I. Dralyuk, Michael Brudno, Mikhail S. Gelfand, Manfred Zorn, Inna Dubchak
ASDB: database of alternatively spliced genes. Nucleic Acids Res. 28 (1) (2000)
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)
Mikhail S. Gelfand, Inna Dubchak, I. Dralyuk, Manfred Zorn
ASDB: database of alternatively spliced genes. Nucleic Acids Res. 27 (1) (1999)
Inna Dubchak, Ilya B. Muchnik, Sung-Hou Kim
Protein Folding Class Predictor for SCOP: Approach Based on Global Descriptors. ISMB (1997)
Eddy Mayoraz, Inna Dubchak, Ilya B. Muchnik
Relation Between Protein Structure, Sequence Homology and Composition of Amino Acids. ISMB (1995)
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)