Inna Dubchak

发表

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

Lior Pachter, Inna Dubchak, L. Pachter, 2002, Briefings Bioinform..

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

Inna Dubchak, Michael Brudno, Alexander Poliakov, 2014, Bioinform..

An experimental metagenome data management and analysis system (vol 22, pg 359, 2006)

Inna Dubchak, Nikos C. Kyrpides, Krishna Palaniappan, 2006 .

MycoCosm portal: gearing up for 1000 fungal genomes

Inna Dubchak, Henrik Nordberg, Tatyana Smirnova, 2013, Nucleic Acids Res..

IMG/M: a data management and analysis system for metagenomes

I-Min A. Chen, Inna Dubchak, Natalia Ivanova, 2007, Nucleic Acids Res..

VISTA : visualizing global DNA sequence alignments of arbitrary length

Lior Pachter, Inna Dubchak, Michael Brudno, 2000, Bioinform..

RegTransBase—a database of regulatory sequences and interactions in a wide range of prokaryotic genomes

Inna Dubchak, Mikhail S. Gelfand, Adam P. Arkin, 2006, Nucleic Acids Res..

Representing and Reasoning about Protein Families Using Generative and Discriminative Methods

Inna Dubchak, I. Saira Mian, I. Mian, 2000, J. Comput. Biol..

VISTA tools for interactive visualization and analysis of multiple alignments of DNA sequences and whole genomes

Bernd Hamann, Inna Dubchak, Nameeta Shah, 2004 .

Glocal alignment: finding rearrangements during alignment

Inna Dubchak, Michael Brudno, Serafim Batzoglou, 2003, ISMB.

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics

Inna Dubchak, Thomas S. Brettin, Adam P. Arkin, 2012, Nucleic Acids Res..

The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions

I-Min A. Chen, Inna Dubchak, Natalia Ivanova, 2007, Nucleic Acids Res..

SNP-VISTA: An interactive SNP visualization tool

Bernd Hamann, Inna Dubchak, Nameeta Shah, 2005, BMC Bioinformatics.

Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks.

Inna Dubchak, Bing Xie, Dinanath Sulakhe, 2017, Methods in molecular biology.

Elviz – exploration of metagenome assemblies with an interactive visualization tool

Inna Dubchak, Matthias Hess, Henrik Nordberg, 2015, BMC Bioinformatics.

The integrated microbial genomes (IMG) system

Inna Dubchak, Natalia Ivanova, Victor M. Markowitz, 2005, Nucleic Acids Res..

Automated Regulon Content Prediction and Estimation of PWM Quality

Inna Dubchak, Elena D. Stavrovskaya, Andrey A. Mironov, 2012, BIOINFORMATICS.

Genome-Wide Analysis and Comparative Genomics - Session Introduction

Lior Pachter, Inna Dubchak, Liping Wei, 2002, Pacific Symposium on Biocomputing.

Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks

Inna Dubchak, Mikhail S. Gelfand, Adam P. Arkin, 2005, PLoS Comput. Biol..

Comparative analysis and visualization of genomic sequences using VISTA browser and associated computational tools.

Inna Dubchak, I. Dubchak, 2007, Methods in molecular biology.

benchNGS : An approach to benchmark short reads alignment tools

Inna Dubchak, Alona Kryshchenko, Mehedi Hassan, 2015 .

Alignathon: A competitive assessment of whole genome alignment methods

David Haussler, Inna Dubchak, Brian J. Raney, 2014 .

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

Inna Dubchak, Mikhail S. Gelfand, Adam P. Arkin, 2010, Nucleic Acids Res..

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

Inna Dubchak, Mikhail S. Gelfand, Adam P. Arkin, 2009, Nucleic Acids Res..

benchNGS : An approach to benchmark short reads alignment tools

Inna Dubchak, Alona Kryshchenko, Mehedi Hassan, 2015, bioRxiv.

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

Inna Dubchak, Susan Hua, Henrik Nordberg, 2013, Nucleic Acids Res..

Analysis of Ribosomal RNA Sequences by Combinatorial Clustering

Inna Dubchak, Casimir A. Kulikowski, Ilya B. Muchnik, 1999, ISMB.

Multiple whole genome alignments and novel biomedical applications at the VISTA portal

Inna Dubchak, Michael Brudno, Alexander Poliakov, 2007, Nucleic Acids Res..

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

Inna Dubchak, Axel Visel, Len A. Pennacchio, 2006, Nucleic Acids Res..

Comparative genomics approaches to study organism similarities and differences

Inna Dubchak, John Park, John Shon, 2002, J. Biomed. Informatics.

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

Inna Dubchak, Ilya B. Muchnik, Sung-Hou Kim, 1997, ISMB.

MicrobesOnline: an integrated portal for comparative and functional genomics

Inna Dubchak, Adam P. Arkin, Katherine H. Huang, 2009, Nucleic Acids Res..

VISTA Region Viewer (RViewer) - a computational system for prioritizing genomic intervals for biomedical studies

Inna Dubchak, Song Yang, Alex R. Paciorkowski, 2011, Bioinform..

The Genome Portal of the Department of Energy Joint Genome Institute

Inna Dubchak, Henrik Nordberg, Tatyana Smirnova, 2011, Nucleic Acids Res..

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

Chris H. Q. Ding, Inna Dubchak, C. Ding, 2001, Bioinform..

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

Inna Dubchak, Stephen R. Holbrook, Sung-Hou Kim, 1993, ISMB.

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

Inna Dubchak, Ilya B. Muchnik, Eddy Mayoraz, 1995, ISMB.

An experimental metagenome data management and analysis system

Inna Dubchak, Natalia Ivanova, Victor M. Markowitz, 2006, ISMB.

ASDB: database of alternatively spliced genes

Inna Dubchak, Mikhail S. Gelfand, Michael Brudno, 2000, Nucleic Acids Res..

VISTA: computational tools for comparative genomics

Lior Pachter, Inna Dubchak, Kelly A. Frazer, 2004, Nucleic Acids Res..

VISTA family of computational tools for comparative analysis of DNA sequences and whole genomes.

Inna Dubchak, Dmitriy V Ryaboy, I. Dubchak, 2006, Methods in molecular biology.

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments

Bernd Hamann, Inna Dubchak, Michael Brudno, 2004, Bioinform..

The VISTA Synteny Viewer: Navigating Whole Genome Alignments at Multiple Levels of Resolution

Inna Dubchak, Simon Minovitsky, Igor Ratnere, 2009 .

Comparisons of Long Genomic Sequences: Algorithms and Applications

Inna Dubchak, Michael Brudno, M. Brudno, 2005 .

The DOE Systems Biology Knowledgebase (KBase)

Fangfang Xia, Rick Stevens, Mark Gerstein, 2016, bioRxiv.

Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data

Inna Dubchak, Matthew Munoz, Alexander C. Zambon, 2013, Bioinform..

High-throughput translational medicine: challenges and solutions.

Inna Dubchak, Bhadrachalam Chitturi, Bo Feng, 2014, Advances in experimental medicine and biology.

ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

Inna Dubchak, Eugene V. Koonin, Yuri I. Wolf, 2008, Nucleic Acids Res..

ASDB: database of alternatively spliced genes

Inna Dubchak, Mikhail S. Gelfand, Manfred Zorn, 1999, Nucleic Acids Res..

The analysis and expansion of regulatory binding site data in a wide range of bacteria using a semi-automatic system - RegTransBase

Inna Dubchak, Mikhail S. Gelfand, Adam P. Arkin, 2008 .

TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities

Bernd Hamann, Gunther H. Weber, Inna Dubchak, 2007, Bioinform..

Rice SNP-seek database update: new SNPs, indels, and queries

Inna Dubchak, Kenneth L. McNally, Ruaraidh Sackville Hamilton, 2016, Nucleic Acids Res..

Phylo-VISTA: An Interactive Visualization Tool for Multiple DNA Sequence Alignments

Bernd Hamann, Inna Dubchak, Michael Brudno, 2003 .

Conservation patterns in different functional sequence categories of divergent Drosophila species.

Inna Dubchak, Dmitri Papatsenko, Michael Levine, 2005, Genomics.

Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus

Inna Dubchak, Ross Overbeek, Andrei L Osterman, 2011, BMC Genomics.

RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes

Inna Dubchak, Adam P Arkin, Dmitry A Rodionov, 2013, BMC Genomics.

Comparative Genomics of Regulation of Fatty Acid and Branched-Chain Amino Acid Utilization in Proteobacteria

Inna Dubchak, Mikhail S. Gelfand, Dmitry A. Rodionov, 2008, Journal of bacteriology.

Short sequence motifs, overrepresented in mammalian conserved non-coding sequences

Inna Dubchak, Philip Stegmaier, Simon Minovitsky, 2007, BMC Genomics.

comparative sequence-based discovery of functional transcription factor binding sites

Lior Pachter, Inna Dubchak, Ivan Ovcharenko, 2002 .

GENOME-WIDE ANALYSIS AND COMPARATIVE GENOMICS

Lior Pachter, Inna Dubchak, Liping Wei, 2001 .

Multiple whole-genome alignments without a reference organism.

Inna Dubchak, Michael Brudno, Andrey Kislyuk, 2009, Genome research.

SNP-Seek II: A resource for allele mining and analysis of big genomic data in Oryza sativa

Inna Dubchak, Kenneth L. McNally, Ruaraidh Sackville Hamilton, 2016 .

Reconstruction Of Regulatory And Metabolic Pathways In Metal-Reducing delta-Proteobacteria

Inna Dubchak, Mikhail S. Gelfand, Adam P. Arkin, 2004 .

Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria

Inna Dubchak, Adam Arkin, Dmitry A Rodionov, 2004, Genome Biology.

Multi-species sequence comparison: the next frontier in genome annotation

Inna Dubchak, Kelly Frazer, K. Frazer, 2003, Genome Biology.

The DNA sequence and biology of human chromosome 19

Terrence S. Furey, Inna Dubchak, Matt Nolan, 2004, Nature.

Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes

Inna Dubchak, Eugene V. Koonin, Yuri I. Wolf, 2008, Journal of bacteriology.

Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.

Inna Dubchak, Paul Havlak, Madeline A Crosby, 2005, Genome research.

Alignathon: a competitive assessment of whole-genome alignment methods

David Haussler, Inna Dubchak, Ngan Nguyen, 2014, bioRxiv.

Automated whole-genome multiple alignment of rat, mouse, and human.

Inna Dubchak, Michael Brudno, Serafim Batzoglou, 2004, Genome research.

An Integrative Computational Approach for Prioritization of Genomic Variants

Inna Dubchak, Jianzhu Ma, Jinbo Xu, 2014, PloS one.