Inna Dubchak

40 papers A 4Misc 2Journal 31Unranked 3
YearRankTypeTitle / Venue / Authors
2017 J jnl
Rice SNP-seek database update: new SNPs, indels, and queries.
Nucleic Acids Res.
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
2015 J jnl
Elviz - exploration of metagenome assemblies with an interactive visualization tool.
BMC Bioinform.
Michael Cantor, Henrik Nordberg, Tatyana Smirnova, Matthias Hess, Susannah Tringe, Inna Dubchak
2014 J jnl
GenomeVISTA - an integrated software package for whole-genome alignment and visualization.
Bioinform.
Alexander Poliakov, Justin Foong, Michael Brudno, Inna Dubchak
2014 J jnl
MycoCosm portal: gearing up for 1000 fungal genomes.
Nucleic Acids Res.
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
2014 J jnl
The genome portal of the Department of Energy Joint Genome Institute: 2014 updates.
Nucleic Acids Res.
Henrik Nordberg, Michael Cantor, Serge Dusheyko, Susan Hua, Alexander Poliakov, Igor Shabalov, Tatyana Smirnova, Igor V. Grigoriev, Inna Dubchak
2013 J jnl
Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data.
Bioinform.
Inna Dubchak, Matthew Munoz, Alexander Poliakov, Nathan Salomonis, Simon Minovitsky, Rolf Bodmer, Alexander C. Zambon
2012 — conf
Automated Regulon Content Prediction and Estimation of PWM Quality.
BIOINFORMATICS
Elena D. Stavrovskaya, Andrey A. Mironov, Dmitry A. Rodionov, Inna Dubchak, Pavel S. Novichkov
2012 J jnl
RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.
Nucleic Acids Res.
Pavel S. Novichkov, Thomas S. Brettin, Elena S. Novichkova, Paramvir S. Dehal, Adam P. Arkin, Inna Dubchak, Dmitry A. Rodionov
2012 J jnl
The Genome Portal of the Department of Energy Joint Genome Institute.
Nucleic Acids Res.
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
2011 J jnl
VISTA Region Viewer (RViewer) - a computational system for prioritizing genomic intervals for biomedical studies.
Bioinform.
Igor Lukashin, Pavel S. Novichkov, Dario Boffelli, Alex R. Paciorkowski, Simon Minovitsky, Song Yang, Inna Dubchak
2010 J jnl
MicrobesOnline: an integrated portal for comparative and functional genomics.
Nucleic Acids Res.
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
2010 J jnl
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.
Nucleic Acids Res.
Pavel S. Novichkov, Olga N. Laikova, Elena S. Novichkova, Mikhail S. Gelfand, Adam P. Arkin, Inna Dubchak, Dmitry A. Rodionov
2010 J jnl
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach.
Nucleic Acids Res.
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
2009 J jnl
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes.
Nucleic Acids Res.
Pavel S. Novichkov, Igor Ratnere, Yuri I. Wolf, Eugene V. Koonin, Inna Dubchak
2008 J jnl
IMG/M: a data management and analysis system for metagenomes.
Nucleic Acids Res.
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
2008 J jnl
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.
Nucleic Acids Res.
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
2007 J jnl
Multiple whole genome alignments and novel biomedical applications at the VISTA portal.
Nucleic Acids Res.
Michael Brudno, Alexander Poliakov, Simon Minovitsky, Igor Ratnere, Inna Dubchak
2007 J jnl
RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes.
Nucleic Acids Res.
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
2007 J jnl
TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities.
Bioinform.
Shengyin Gu, Iain Anderson, Victor Kunin, Michael J. Cipriano, Simon Minovitsky, Gunther H. Weber, Nina Amenta, Bernd Hamann, Inna Dubchak
2007 J jnl
VISTA Enhancer Browser - a database of tissue-specific human enhancers.
Nucleic Acids Res.
Axel Visel, Simon Minovitsky, Inna Dubchak, Len A. Pennacchio
2006 — conf
An experimental metagenome data management and analysis system.
ISMB (Supplement of Bioinformatics)
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
2006 J jnl
The integrated microbial genomes (IMG) system.
Nucleic Acids Res.
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
2005 J jnl
Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks.
PLoS Comput. Biol.
Dmitry A. Rodionov, Inna Dubchak, Adam P. Arkin, Eric J. Alm, Mikhail S. Gelfand
2005 J jnl
SNP-VISTA: An interactive SNP visualization tool.
BMC Bioinform.
Nameeta Y. Shah, Michael V. Teplitsky, Simon Minovitsky, Len A. Pennacchio, Philip Hugenholtz, Bernd Hamann, Inna Dubchak
2004 J jnl
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.
Bioinform.
Nameeta Y. Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, E. Wes Bethel, Edward M. Rubin, Bernd Hamann, Inna Dubchak
2004 J jnl
VISTA: computational tools for comparative genomics.
Nucleic Acids Res.
Kelly A. Frazer, Lior Pachter, Alexander Poliakov, Edward M. Rubin, Inna Dubchak
2003 Misc conf
Genome-wide Analysis and Comparative Genomics - Session Introduction.
Pacific Symposium on Biocomputing
Liping Wei, Inna Dubchak, Victor V. Solovyev
2003 — conf
Glocal alignment: finding rearrangements during alignment.
ISMB (Supplement of Bioinformatics)
Michael Brudno, Sanket Malde, Alexander Poliakov, Chuong B. Do, Olivier Couronne, Inna Dubchak, Serafim Batzoglou
2002 J jnl
Comparative genomics approaches to study organism similarities and differences.
J. Biomed. Informatics
Liping Wei, Yueyi Liu, Inna Dubchak, John Shon, John Park
2002 Misc conf
Genome-Wide Analysis and Comparative Genomics - Session Introduction.
Pacific Symposium on Biocomputing
Inna Dubchak, Lior Pachter, Liping Wei
2002 J jnl
The computational challenges of applying comparative-based computational methods to whole genomes.
Briefings Bioinform.
Inna Dubchak, Lior Pachter
2001 J jnl
Multi-class protein fold recognition using support vector machines and neural networks.
Bioinform.
Chris H. Q. Ding, Inna Dubchak
2000 J jnl
ASDB: database of alternatively spliced genes.
Nucleic Acids Res.
I. Dralyuk, Michael Brudno, Mikhail S. Gelfand, Manfred Zorn, Inna Dubchak
2000 J jnl
Representing and Reasoning about Protein Families Using Generative and Discriminative Methods.
J. Comput. Biol.
I. Saira Mian, Inna Dubchak
2000 J jnl
VISTA : visualizing global DNA sequence alignments of arbitrary length.
Bioinform.
Chris Mayor, Michael Brudno, Jody R. Schwartz, Alexander Poliakov, Edward M. Rubin, Kelly A. Frazer, Lior Pachter, Inna Dubchak
1999 J jnl
ASDB: database of alternatively spliced genes.
Nucleic Acids Res.
Mikhail S. Gelfand, Inna Dubchak, I. Dralyuk, Manfred Zorn
1999 A conf
Analysis of Ribosomal RNA Sequences by Combinatorial Clustering.
ISMB
Poe Xing, Casimir A. Kulikowski, Ilya B. Muchnik, Inna Dubchak, Denise M. Wolf, Sylvia Spengler, Manfred Zorn
1997 A conf
Protein Folding Class Predictor for SCOP: Approach Based on Global Descriptors.
ISMB
Inna Dubchak, Ilya B. Muchnik, Sung-Hou Kim
1995 A conf
Relation Between Protein Structure, Sequence Homology and Composition of Amino Acids.
ISMB
Eddy Mayoraz, Inna Dubchak, Ilya B. Muchnik
1993 A conf
Comparison of Two Variations of Neural Network Approaches to the Prediction of Protein Folding Pattern.
ISMB
Inna Dubchak, Stephen R. Holbrook, Sung-Hou Kim