Inna Dubchak

According to our database, Inna Dubchak authored at least 40 papers between 1993 and 2017.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2017

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, Rod A. Wing, Ruaraidh Sackville Hamilton, Ramil Mauleon, Kenneth L. McNally, Nickolai Alexandrov

Nucleic Acids Res., 2017

2015

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

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

MycoCosm portal: gearing up for 1000 fungal genomes.

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

Nucleic Acids Res., 2014

GenomeVISTA - an integrated software package for whole-genome alignment and visualization.

Alexander Poliakov, Justin Foong, Michael Brudno, Inna Dubchak

Bioinform., 2014

2013

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

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

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, Igor Ratnere, Robert Riley, Tatyana Smirnova, Daniel Rokhsar, Inna Dubchak

Nucleic Acids Res., 2012

Automated Regulon Content Prediction and Estimation of PWM Quality.

Elena D. Stavrovskaya, Andrey A. Mironov, Dmitry A. Rodionov, Inna Dubchak, Pavel S. Novichkov

Proceedings of the BIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Vilamoura, Algarve, Portugal, 1, 2012

2011

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

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

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

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, Adam P. Arkin

Nucleic Acids Res., 2010

2009

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

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

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, Philip Hugenholtz, Nikos Kyrpides

Nucleic Acids Res., 2008

2007

VISTA Enhancer Browser - a database of tissue-specific human enhancers.

Axel Visel, Simon Minovitsky, Inna Dubchak, Len A. Pennacchio

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

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

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

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, Natalia Ivanova, Nikos Kyrpides

Nucleic Acids Res., 2006

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, Nikos Kyrpides

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

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

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

2004

VISTA: computational tools for comparative genomics.

Kelly A. Frazer, Lior Pachter, Alexander Poliakov, Edward M. Rubin, Inna Dubchak

Nucleic Acids Res., 2004

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

2003

Genome-wide Analysis and Comparative Genomics - Session Introduction.

Liping Wei, Inna Dubchak, Victor V. Solovyev

Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

Glocal alignment: finding rearrangements during alignment.

Michael Brudno, Sanket Malde, Alexander Poliakov, Chuong B. Do, Olivier Couronne, Inna Dubchak, Serafim Batzoglou

Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

2002

Comparative genomics approaches to study organism similarities and differences.

Liping Wei, Yueyi Liu, Inna Dubchak, John Shon, John Park

J. Biomed. Informatics, 2002

The computational challenges of applying comparative-based computational methods to whole genomes.

Inna Dubchak, Lior Pachter

Briefings Bioinform., 2002

Genome-Wide Analysis and Comparative Genomics - Session Introduction.

Inna Dubchak, Lior Pachter, Liping Wei

Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

2001

Multi-class protein fold recognition using support vector machines and neural networks.

Chris H. Q. Ding, Inna Dubchak

Bioinform., 2001

2000

ASDB: database of alternatively spliced genes.

I. Dralyuk, Michael Brudno, Mikhail S. Gelfand, Manfred Zorn, Inna Dubchak

Nucleic Acids Res., 2000

Representing and Reasoning about Protein Families Using Generative and Discriminative Methods.

I. Saira Mian, Inna Dubchak

J. Comput. Biol., 2000

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

1999

ASDB: database of alternatively spliced genes.

Mikhail S. Gelfand, Inna Dubchak, I. Dralyuk, Manfred Zorn

Nucleic Acids Res., 1999

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

Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, 1999

1997

Protein Folding Class Predictor for SCOP: Approach Based on Global Descriptors.

Inna Dubchak, Ilya B. Muchnik, Sung-Hou Kim

Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

1995

Relation Between Protein Structure, Sequence Homology and Composition of Amino Acids.

Eddy Mayoraz, Inna Dubchak, Ilya B. Muchnik

Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, 1995

1993

Comparison of Two Variations of Neural Network Approaches to the Prediction of Protein Folding Pattern.

Inna Dubchak, Stephen R. Holbrook, Sung-Hou Kim

Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology, 1993