Victor Olman

Victor Olman

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Victor Olman

Victor Olman

Publications by authors named "Victor Olman"

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Comprehensive characterization of the genomic alterations in human gastric cancer.

Int J Cancer 2015 Jul 3;137(1):86-95. Epub 2014 Dec 3.

Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE; Department of Biochemistry and Molecular Biology, Computational Systems Biology Laboratory, Institute of Bioinformatics, University of Georgia, Athens, GA.

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http://dx.doi.org/10.1002/ijc.29352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776643PMC
July 2015

Functional understanding of the diverse exon-intron structures of human GPCR genes.

J Bioinform Comput Biol 2014 Feb 11;12(1):1350019. Epub 2013 Dec 11.

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

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http://www.worldscientific.com/doi/abs/10.1142/S021972001350
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http://dx.doi.org/10.1142/S0219720013500194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905620PMC
February 2014

Barcode server: a visualization-based genome analysis system.

PLoS One 2013 15;8(2):e56726. Epub 2013 Feb 15.

Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0056726PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574017PMC
August 2013

Genomic arrangement of regulons in bacterial genomes.

PLoS One 2012 3;7(1):e29496. Epub 2012 Jan 3.

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0029496PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3250446PMC
May 2012

Optimal mutation sites for PRE data collection and membrane protein structure prediction.

Structure 2011 Apr;19(4):484-95

Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602-4712, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S096921261100070
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http://dx.doi.org/10.1016/j.str.2011.02.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3099474PMC
April 2011

Computational prediction and experimental validation of novel markers for detection of STEC O157:H7.

World J Gastroenterol 2011 Apr;17(14):1910-4

Department of Pathogenobiology, Norman Bethune Medical College of Jilin University, Changchun 130000, Jilin Province, China.

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http://dx.doi.org/10.3748/wjg.v17.i14.1910DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080728PMC
April 2011

A comparative analysis of gene-expression data of multiple cancer types.

PLoS One 2010 Oct 27;5(10):e13696. Epub 2010 Oct 27.

Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0013696PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965162PMC
October 2010

Computational prediction of the osmoregulation network in Synechococcus sp. WH8102.

BMC Genomics 2010 May 10;11:291. Epub 2010 May 10.

Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1186/1471-2164-11-291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874817PMC
May 2010

Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome.

Proc Natl Acad Sci U S A 2010 Apr 22;107(14):6310-5. Epub 2010 Mar 22.

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30605, USA.

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http://dx.doi.org/10.1073/pnas.0911237107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851940PMC
April 2010

Prediction of pathogenicity islands in enterohemorrhagic Escherichia coli O157:H7 using genomic barcodes.

FEBS Lett 2010 Jan;584(1):194-8

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 7229, USA.

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http://doi.wiley.com/10.1016/j.febslet.2009.11.067
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http://dx.doi.org/10.1016/j.febslet.2009.11.067DOI Listing
January 2010

Large-scale analyses of glycosylation in cellulases.

Genomics Proteomics Bioinformatics 2009 Dec;7(4):194-9

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology/Institute of Bioinformatics, University of Georgia, Athens, GA 30602-7229, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S167202290860049
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http://dx.doi.org/10.1016/S1672-0229(08)60049-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054413PMC
December 2009

Parallel clustering algorithm for large data sets with applications in bioinformatics.

IEEE/ACM Trans Comput Biol Bioinform 2009 Apr-Jun;6(2):344-52

Department of Biochemistry and Molecular Biology, Computational System Biology Laboratory, Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA.

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http://dx.doi.org/10.1109/TCBB.2007.70272DOI Listing
August 2009

DOOR: a database for prokaryotic operons.

Nucleic Acids Res 2009 Jan 6;37(Database issue):D459-63. Epub 2008 Nov 6.

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1093/nar/gkn757DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686520PMC
January 2009

Barcodes for genomes and applications.

BMC Bioinformatics 2008 Dec 17;9:546. Epub 2008 Dec 17.

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-9-546DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2621371PMC
December 2008

On application of directons to functional classification of genes in prokaryotes.

Comput Biol Chem 2008 Jun 2;32(3):176-84. Epub 2008 Mar 2.

School of Electrical and Computer Engineering, Georgia Institute of Technology, Savannah, GA 31407, USA.

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http://dx.doi.org/10.1016/j.compbiolchem.2008.02.007DOI Listing
June 2008

Improving the performance of protein threading using insertion/deletion frequency arrays.

J Bioinform Comput Biol 2008 Jun;6(3):585-602

Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1142/s0219720008003552DOI Listing
June 2008

Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea.

BMC Genomics 2008 Jan 24;9:36. Epub 2008 Jan 24.

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-9-36DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246112PMC
January 2008

Improvement in protein sequence-structure alignment using insertion/deletion frequency arrays.

Comput Syst Bioinformatics Conf 2007 ;6:335-42

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, The University of Georgia, Athens, Georgia 30602, USA.

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December 2007

Prediction of cis-regulatory elements: from high-information content analysis to motif identification.

J Bioinform Comput Biol 2007 Aug;5(4):817-38

School of Mathematics and System Sciences, Shandong University, Jinan 250100, China.

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http://dx.doi.org/10.1142/s021972000700293xDOI Listing
August 2007

Hierarchical classification of functionally equivalent genes in prokaryotes.

Nucleic Acids Res 2007 11;35(7):2125-40. Epub 2007 Mar 11.

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1093/nar/gkl1114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1874638PMC
June 2007

A generalized threading model using integer programming that allows for secondary structure element deletion.

Genome Inform 2006 ;17(2):248-58

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30622, USA.

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June 2007

Computational prediction of Pho regulons in cyanobacteria.

BMC Genomics 2007 Jun 8;8:156. Epub 2007 Jun 8.

Bioinformatics Research Center and Department of Computer Science, the University of North Carolina at Charlotte, Charlotte, NC 28233, USA.

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http://dx.doi.org/10.1186/1471-2164-8-156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1906773PMC
June 2007

Accurate prediction of orthologous gene groups in microbes.

Proc IEEE Comput Syst Bioinform Conf 2005 :73-9

Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30622, USA.

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http://dx.doi.org/10.1109/csb.2005.10DOI Listing
May 2007

Operon prediction using both genome-specific and general genomic information.

Nucleic Acids Res 2007 14;35(1):288-98. Epub 2006 Dec 14.

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkl1018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1802555PMC
February 2007

A point-process model for rapid identification of post-translational modifications.

Pac Symp Biocomput 2006 :327-38

Department of Biochemical and Molecular Biology, University of Georgia, GA, USA.

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January 2007

Gene expression data analysis in subtypes of ovarian cancer using covariance analysis.

J Bioinform Comput Biol 2006 Oct;4(5):999-1014

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1142/s0219720006002296DOI Listing
October 2006

Prediction of functional modules based on gene distributions in microbial genomes.

Genome Inform 2005 ;16(2):247-59

Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, USA.

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September 2006

Separation of ion types in tandem mass spectrometry data interpretation -- a graph-theoretic approach.

Proc IEEE Comput Syst Bioinform Conf 2004 :236-44

Department of Biochemical and Molecular Biology, University of Georgia, USA.

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http://dx.doi.org/10.1109/csb.2004.1332437DOI Listing
July 2006

Mapping of microbial pathways through constrained mapping of orthologous genes.

Proc IEEE Comput Syst Bioinform Conf 2004 :363-70

Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, USA.

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http://dx.doi.org/10.1109/csb.2004.1332449DOI Listing
July 2006

Mapping of orthologous genes in the context of biological pathways: An application of integer programming.

Proc Natl Acad Sci U S A 2006 Jan 22;103(1):129-34. Epub 2005 Dec 22.

Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602, USA.

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http://dx.doi.org/10.1073/pnas.0509737102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1325003PMC
January 2006

Comparative genomics analysis of NtcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis.

Nucleic Acids Res 2005 12;33(16):5156-71. Epub 2005 Sep 12.

Bioinformatics Institute and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gki817DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1214546PMC
September 2005

Prediction of functional modules based on comparative genome analysis and Gene Ontology application.

Nucleic Acids Res 2005 18;33(9):2822-37. Epub 2005 May 18.

Department of Biochemistry and Molecular Biology, University of Georgia 120 Green Street, Athens, GA 30602-7229, USA.

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http://dx.doi.org/10.1093/nar/gki573DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1130488PMC
June 2005

A graph-theoretic approach for the separation of b and y ions in tandem mass spectra.

Bioinformatics 2005 Mar 28;21(5):563-74. Epub 2004 Sep 28.

Computational Systems Biology Laboratory, Department of Biochemical and Molecular Biology, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti044DOI Listing
March 2005

Computational inference of regulatory pathways in microbes: an application to phosphorus assimilation pathways in Synechococcus sp. WH8102.

Genome Inform 2003 ;14:3-13

Department of Biochemistry and Molecular Biology, University of Georgia at Athens, and Computational Biology Institute, Oak Ridge National Laboratory.

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March 2005

Protein structure prediction using sparse dipolar coupling data.

Nucleic Acids Res 2004 26;32(2):551-61. Epub 2004 Jan 26.

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkh204DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373331PMC
April 2004

EXCAVATOR: a computer program for efficiently mining gene expression data.

Nucleic Acids Res 2003 Oct;31(19):5582-9

Protein Informatics Group, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6480, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC206478PMC
http://dx.doi.org/10.1093/nar/gkg783DOI Listing
October 2003

Identification of regulatory binding sites using minimum spanning trees.

Pac Symp Biocomput 2003 :327-38

Protein Informatics Group, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6480, USA.

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August 2003

CUBIC: identification of regulatory binding sites through data clustering.

J Bioinform Comput Biol 2003 Apr;1(1):21-40

Protein Informatics Group, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6480, USA.

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http://dx.doi.org/10.1142/s0219720003000162DOI Listing
April 2003

Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees.

Bioinformatics 2002 Apr;18(4):536-45

Protein Informatics Group, Life Sciences Division, Oak Ridge National Laboratory, MS 6480, Oak Ridge, TN 27831-6480, USA.

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http://dx.doi.org/10.1093/bioinformatics/18.4.536DOI Listing
April 2002