Research Topics
| Victor OlmanSummaryAffiliation: University of Georgia Country: USA Publications
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Detail Information
Publications
Computational prediction of Pho regulons in cyanobacteriaZhengchang 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...
Parallel clustering algorithm for large data sets with applications in bioinformaticsVictor 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...- Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102Zhengchang 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... 
Improving the performance of protein threading using insertion/deletion frequency arraysKyle 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...- Genomic arrangement of regulons in bacterial genomesHan 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.... - DOOR: a database for prokaryotic operonsFenglou 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... - Prediction of functional modules based on gene distributions in microbial genomesHongwei 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... - Hierarchical classification of functionally equivalent genes in prokaryotesHongwei 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.... - Improvement in protein sequence-structure alignment using insertion/deletion frequency arraysKyle 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... - Insertion Sequences show diverse recent activities in Cyanobacteria and ArchaeaFengfeng 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... - Operon prediction using both genome-specific and general genomic informationPhuongan 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... - Mapping of orthologous genes in the context of biological pathways: An application of integer programmingFenglou 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... - A generalized threading model using integer programming that allows for secondary structure element deletionKyle 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... - Barcodes for genomes and applicationsFengfeng 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... - Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genomeYanbin 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... - Comparative genomics analysis of NtcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesisZhengchang 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... - Computational prediction of the osmoregulation network in Synechococcus sp. WH8102Xizeng 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... - Prediction of functional modules based on comparative genome analysis and Gene Ontology applicationHongwei 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... - Prediction of pathogenicity islands in enterohemorrhagic Escherichia coli O157:H7 using genomic barcodesGuoqing 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... - Computational inference of regulatory pathways in microbes: an application to phosphorus assimilation pathways in Synechococcus sp. WH8102Zhengchang 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... - Prediction of cis-regulatory elements: from high-information content analysis to motif identificationGuojun 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... - Large-scale analyses of glycosylation in cellulasesFengfeng 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... - Gene expression data analysis in subtypes of ovarian cancer using covariance analysisVictor 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.... - A comparative analysis of gene-expression data of multiple cancer typesKun 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... - Optimal mutation sites for PRE data collection and membrane protein structure predictionHuiling 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... - An integrated transcriptomic and computational analysis for biomarker identification in gastric cancerJuan 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... - Protein structure prediction using sparse dipolar coupling dataYouxing 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...