Victor Olman

Summary

Affiliation: University of Georgia
Country: USA

Publications

  1. pmc Computational prediction of Pho regulons in cyanobacteria
    Zhengchang Su
    Bioinformatics Research Center and Department of Computer Science, The University of North Carolina at Charlotte, Charlotte, NC 28233, USA
    BMC Genomics 8:156. 2007
  2. doi request reprint Parallel clustering algorithm for large data sets with applications in bioinformatics
    Victor Olman
    Department of Biochemistry and Molecular Biology, Computational System Biology Laboratory, Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA
    IEEE/ACM Trans Comput Biol Bioinform 6:344-52. 2009
  3. pmc Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102
    Zhengchang Su
    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
    Nucleic Acids Res 34:1050-65. 2006
  4. ncbi request reprint Improving the performance of protein threading using insertion/deletion frequency arrays
    Kyle Ellrott
    Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA 30602, USA
    J Bioinform Comput Biol 6:585-602. 2008
  5. pmc Barcode server: a visualization-based genome analysis system
    Fenglou Mao
    Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
    PLoS ONE 8:e56726. 2013
  6. pmc Genomic arrangement of regulons in bacterial genomes
    Han Zhang
    Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
    PLoS ONE 7:e29496. 2012
  7. pmc DOOR: a database for prokaryotic operons
    Fenglou Mao
    Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
    Nucleic Acids Res 37:D459-63. 2009
  8. ncbi request reprint Prediction of functional modules based on gene distributions in microbial genomes
    Hongwei Wu
    Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, USA
    Genome Inform 16:247-59. 2005
  9. pmc Hierarchical classification of functionally equivalent genes in prokaryotes
    Hongwei Wu
    Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
    Nucleic Acids Res 35:2125-40. 2007
  10. ncbi request reprint Improvement in protein sequence-structure alignment using insertion/deletion frequency arrays
    Kyle Ellrott
    Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, The University of Georgia, Athens, Georgia 30602, USA
    Comput Syst Bioinformatics Conf 6:335-42. 2007

Collaborators

Detail Information

Publications29

  1. pmc Computational prediction of Pho regulons in cyanobacteria
    Zhengchang Su
    Bioinformatics Research Center and Department of Computer Science, The University of North Carolina at Charlotte, Charlotte, NC 28233, USA
    BMC Genomics 8:156. 2007
    ..However, a systematic study of the Pho regulon, the core of the phosphorus assimilation pathway in a cyanobacterium, is hitherto lacking...
  2. doi request reprint Parallel clustering algorithm for large data sets with applications in bioinformatics
    Victor Olman
    Department of Biochemistry and Molecular Biology, Computational System Biology Laboratory, Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA
    IEEE/ACM Trans Comput Biol Bioinform 6:344-52. 2009
    ..We have implemented the clustering algorithm as the software CLUMP...
  3. pmc Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102
    Zhengchang Su
    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
    Nucleic Acids Res 34:1050-65. 2006
    ..Moreover, for some of these genes, this coordination is probably mediated by NtcA through the canonical NtcA promoters in their regulatory regions...
  4. ncbi request reprint Improving the performance of protein threading using insertion/deletion frequency arrays
    Kyle Ellrott
    Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA 30602, USA
    J Bioinform Comput Biol 6:585-602. 2008
    ..We have also demonstrated that the application of this information can lead to an improvement in fold recognition...
  5. pmc Barcode server: a visualization-based genome analysis system
    Fenglou Mao
    Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
    PLoS ONE 8:e56726. 2013
    ..The barcode server provides a job management capability, allowing processing of a large number of analysis jobs for barcode-based comparative genome analyses. The barcode server is accessible at http://csbl1.bmb.uga.edu/Barcode...
  6. pmc Genomic arrangement of regulons in bacterial genomes
    Han Zhang
    Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
    PLoS ONE 7:e29496. 2012
    ....
  7. pmc DOOR: a database for prokaryotic operons
    Fenglou Mao
    Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
    Nucleic Acids Res 37:D459-63. 2009
    ..We believe that DOOR provides a useful resource to many biologists working on bacteria and archaea, which can be accessed at http://csbl1.bmb.uga.edu/OperonDB...
  8. ncbi request reprint Prediction of functional modules based on gene distributions in microbial genomes
    Hongwei Wu
    Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, USA
    Genome Inform 16:247-59. 2005
    ..We have also examined the predicted functional modules that are common to both Escherichia coli K12 and Bacillus subtilis subsp. subtilis str. 168, and provide explanations for some functional modules...
  9. pmc Hierarchical classification of functionally equivalent genes in prokaryotes
    Hongwei Wu
    Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
    Nucleic Acids Res 35:2125-40. 2007
    ....
  10. ncbi request reprint Improvement in protein sequence-structure alignment using insertion/deletion frequency arrays
    Kyle Ellrott
    Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, The University of Georgia, Athens, Georgia 30602, USA
    Comput Syst Bioinformatics Conf 6:335-42. 2007
    ..We define these patterns as Insertion/Deletion (Indel) Frequency Arrays (IFA). By applying IFA to the protein threading problem, we have been able to improve the alignment accuracy, especially for proteins with low sequence identity...
  11. pmc Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea
    Fengfeng Zhou
    Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
    BMC Genomics 9:36. 2008
    ..Mobile genetic elements (MGEs) play an essential role in genome rearrangement and evolution, and are widely used as an important genetic tool...
  12. ncbi request reprint A generalized threading model using integer programming that allows for secondary structure element deletion
    Kyle Ellrott
    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30622, USA
    Genome Inform 17:248-58. 2006
    ..We have developed and implemented an expanded model of integer programming that has the capability to model secondary structure element deletion, which was not possible in previous version of integer programming based optimization...
  13. pmc Operon prediction using both genome-specific and general genomic information
    Phuongan Dam
    Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
    Nucleic Acids Res 35:288-98. 2007
    ..When no such information is available, our (linear) logistic function-based classifier can reach the prediction accuracy at 84.6 and 83.3% for E.coli and B.subtilis, respectively...
  14. pmc Mapping of orthologous genes in the context of biological pathways: An application of integer programming
    Fenglou Mao
    Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 103:129-34. 2006
    ..We conclude that using genomic structure information as constraints could greatly improve the pathway-mapping accuracy over methods that use sequence-similarity information alone...
  15. pmc Barcodes for genomes and applications
    Fengfeng Zhou
    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
    BMC Bioinformatics 9:546. 2008
    ..The collection of these k-mer frequency distributions is unique to each genome and termed the genome's barcode...
  16. pmc Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome
    Yanbin Yin
    Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30605, USA
    Proc Natl Acad Sci U S A 107:6310-5. 2010
    ..We found that the current arrangements of operons in most of the bacterial genomes we studied tend to minimize the overall distance between consecutive operons of a same pathway across all pathways encoded in the genome...
  17. pmc Comparative genomics analysis of NtcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis
    Zhengchang Su
    Bioinformatics Institute and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
    Nucleic Acids Res 33:5156-71. 2005
    ..We postulate for the fist time that these genes serve as the regulatory points to orchestrate these two important processes in a cyanobacterial cell...
  18. pmc Computational prediction of the osmoregulation network in Synechococcus sp. WH8102
    Xizeng Mao
    Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
    BMC Genomics 11:291. 2010
    ..Very little is known about the detailed response mechanism to osmotic stress in marine Synechococcus, one of the major oxygenic phototrophic cyanobacterial genera that contribute greatly to the global CO2 fixation...
  19. doi request reprint Prediction of pathogenicity islands in enterohemorrhagic Escherichia coli O157:H7 using genomic barcodes
    Guoqing Wang
    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 7229, USA
    FEBS Lett 584:194-8. 2010
    ..We have applied a novel method of genomic barcodes to identify PAIs. Using this technique, we have successfully identified both known and novel PAIs in the genomes of three strains of EHEC O157:H7...
  20. pmc Prediction of functional modules based on comparative genome analysis and Gene Ontology application
    Hongwei Wu
    Department of Biochemistry and Molecular Biology, University of Georgia 120 Green Street, Athens, GA 30602 7229, USA
    Nucleic Acids Res 33:2822-37. 2005
    ..coli. The application results have demonstrated that our approach is highly promising for the prediction of functional modules encoded in a microbial genome...
  21. ncbi request reprint Prediction of cis-regulatory elements: from high-information content analysis to motif identification
    Guojun Li
    School of Mathematics and System Sciences, Shandong University, Jinan 250100, China
    J Bioinform Comput Biol 5:817-38. 2007
    ..A limitation of the algorithm is that it does not work well when the size of the set of provided promoter sequences is too small or when desired motifs appear in only small portion of the given sequences...
  22. ncbi request reprint Computational inference of regulatory pathways in microbes: an application to phosphorus assimilation pathways in Synechococcus sp. WH8102
    Zhengchang Su
    Department of Biochemistry and Molecular Biology, University of Georgia at Athens, and Computational Biology Institute, Oak Ridge National Laboratory
    Genome Inform 14:3-13. 2003
    ..To demonstrate the effectiveness of this procedure, we have applied it to the construction of the phosphorus assimilation pathways in cyanobacterium sp. WH8102. We present, in this paper, a model of the core components of this pathway...
  23. doi request reprint Large-scale analyses of glycosylation in cellulases
    Fengfeng Zhou
    Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology Institute of Bioinformatics, University of Georgia, Athens, GA 30602 7229, USA
    Genomics Proteomics Bioinformatics 7:194-9. 2009
    ..Our analysis indicates that the O-linked glycosylated residues are significantly enriched in the linker regions between the carbohydrate binding module (CBM) domains and GH domains of cellulases. Possible mechanisms are discussed...
  24. ncbi request reprint Gene expression data analysis in subtypes of ovarian cancer using covariance analysis
    Victor Olman
    Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
    J Bioinform Comput Biol 4:999-1014. 2006
    ....
  25. pmc A comparative analysis of gene-expression data of multiple cancer types
    Kun Xu
    Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
    PLoS ONE 5:e13696. 2010
    ..The novel findings of this study offer considerable insight into these seven cancer types and have the potential to provide exciting new directions for diagnostic and therapeutic development...
  26. pmc Optimal mutation sites for PRE data collection and membrane protein structure prediction
    Huiling Chen
    Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602 4712, USA
    Structure 19:484-95. 2011
    ..The results show promise in facilitating experimentally constrained structure prediction of membrane proteins...
  27. pmc An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer
    Juan Cui
    Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
    Nucleic Acids Res 39:1197-207. 2011
    ..Overall, the novel information obtained in this study has led to identification of promising diagnostic markers for gastric cancer and can benefit further analyses of the key (early) abnormalities during its development...
  28. pmc Protein structure prediction using sparse dipolar coupling data
    Youxing Qu
    Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
    Nucleic Acids Res 32:551-61. 2004
    ..The program correctly identified structural folds for 83.7% of the target proteins, and achieved an average alignment accuracy of 98.1% residues within a four-residue shift...
  29. pmc Functional understanding of the diverse exon-intron structures of human GPCR genes
    Dorothy A Hammond
    Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
    J Bioinform Comput Biol 12:1350019. 2014
    ..Our interpretation of this observation is that the exon boundaries of the GPCR genes are not randomly determined; instead they may be selected to facilitate specific alternative splicing for functional purposes. ..