Jan Mrazek

Summary

Affiliation: University of Georgia
Country: USA

Publications

  1. pmc Investigating the interplay between nucleoid-associated proteins, DNA curvature, and CRISPR elements using comparative genomics
    Hao Tong
    Department of Statistics, University of Georgia, Athens, Georgia, United States of America
    PLoS ONE 9:e90940. 2014
  2. pmc PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences
    Jan Mrazek
    Department of Microbiology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602 2605, USA
    Microb Inform Exp 1:13. 2011
  3. pmc Comparative analysis of sequence periodicity among prokaryotic genomes points to differences in nucleoid structure and a relationship to gene expression
    Jan Mrazek
    Department of Microbiology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602 2605, USA
    J Bacteriol 192:3763-72. 2010
  4. doi request reprint Finding sequence motifs in prokaryotic genomes--a brief practical guide for a microbiologist
    Jan Mrazek
    Department of Microbiology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602 2605, USA
    Brief Bioinform 10:525-36. 2009
  5. doi request reprint Phylogenetic signals in DNA composition: limitations and prospects
    Jan Mrazek
    Department of Microbiology and Institute of Bioinformatics, University of Georgia, USA
    Mol Biol Evol 26:1163-9. 2009
  6. doi request reprint AIMIE: a web-based environment for detection and interpretation of significant sequence motifs in prokaryotic genomes
    Jan Mrazek
    Department of Microbiology, University of Georgia, Athens, GA 30602 2605, USA
    Bioinformatics 24:1041-8. 2008
  7. ncbi request reprint Analysis of distribution indicates diverse functions of simple sequence repeats in Mycoplasma genomes
    Jan Mrazek
    Department of Microbiology and Institute of Bioinformatics, University of Georgia, USA
    Mol Biol Evol 23:1370-85. 2006
  8. ncbi request reprint Pattern locator: a new tool for finding local sequence patterns in genomic DNA sequences
    Jan Mrazek
    Department of Microbiology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
    Bioinformatics 22:3099-100. 2006
  9. pmc Simple sequence repeats in prokaryotic genomes
    Jan Mrazek
    Department of Microbiology, University of Georgia, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 104:8472-7. 2007
  10. doi request reprint Long simple sequence repeats in host-adapted pathogens localize near genes encoding antigens, housekeeping genes, and pseudogenes
    Xiangxue Guo
    Department of Microbiology, University of Georgia, Athens, GA 30602 2605, USA
    J Mol Evol 67:497-509. 2008

Detail Information

Publications17

  1. pmc Investigating the interplay between nucleoid-associated proteins, DNA curvature, and CRISPR elements using comparative genomics
    Hao Tong
    Department of Statistics, University of Georgia, Athens, Georgia, United States of America
    PLoS ONE 9:e90940. 2014
    ..This result is consistent with our earlier hypothesis that extensive A-tract periodicity could help protect the chromosome against integration of prophages, possibly due to its role in compaction of the nucleoid. ..
  2. pmc PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences
    Jan Mrazek
    Department of Microbiology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602 2605, USA
    Microb Inform Exp 1:13. 2011
    ..abstract:..
  3. pmc Comparative analysis of sequence periodicity among prokaryotic genomes points to differences in nucleoid structure and a relationship to gene expression
    Jan Mrazek
    Department of Microbiology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602 2605, USA
    J Bacteriol 192:3763-72. 2010
    ....
  4. doi request reprint Finding sequence motifs in prokaryotic genomes--a brief practical guide for a microbiologist
    Jan Mrazek
    Department of Microbiology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602 2605, USA
    Brief Bioinform 10:525-36. 2009
    ..This article provides a conceptual overview for each type of task, a brief description of basic algorithms used in their solution, and a review of selected relevant software available online...
  5. doi request reprint Phylogenetic signals in DNA composition: limitations and prospects
    Jan Mrazek
    Department of Microbiology and Institute of Bioinformatics, University of Georgia, USA
    Mol Biol Evol 26:1163-9. 2009
    ..Our results have practical implications for development and application of genome signature-based methods for analysis and classification of DNA sequences...
  6. doi request reprint AIMIE: a web-based environment for detection and interpretation of significant sequence motifs in prokaryotic genomes
    Jan Mrazek
    Department of Microbiology, University of Georgia, Athens, GA 30602 2605, USA
    Bioinformatics 24:1041-8. 2008
    ....
  7. ncbi request reprint Analysis of distribution indicates diverse functions of simple sequence repeats in Mycoplasma genomes
    Jan Mrazek
    Department of Microbiology and Institute of Bioinformatics, University of Georgia, USA
    Mol Biol Evol 23:1370-85. 2006
    ....
  8. ncbi request reprint Pattern locator: a new tool for finding local sequence patterns in genomic DNA sequences
    Jan Mrazek
    Department of Microbiology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
    Bioinformatics 22:3099-100. 2006
    ....
  9. pmc Simple sequence repeats in prokaryotic genomes
    Jan Mrazek
    Department of Microbiology, University of Georgia, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 104:8472-7. 2007
    ..Differences among genomes in terms of SSR representations and their possible interpretations are discussed...
  10. doi request reprint Long simple sequence repeats in host-adapted pathogens localize near genes encoding antigens, housekeeping genes, and pseudogenes
    Xiangxue Guo
    Department of Microbiology, University of Georgia, Athens, GA 30602 2605, USA
    J Mol Evol 67:497-509. 2008
    ..We speculate that LSSRs may have played a similar role in genome reduction of other host-adapted pathogens...
  11. pmc Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content
    Jacob Abel
    Department of Microbiology, University of Georgia, Athens, GA 30602, USA
    BMC Genomics 13:188. 2012
    ..In eukaryotes, the DNA bending is related to chromatin structure and nucleosome positioning. However, the physiological role of strong sequence periodicity detected in many prokaryotic genomes is not clear...
  12. pmc Mutational patterns in RNA secondary structure evolution examined in three RNA families
    Anuj Srivastava
    Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
    PLoS ONE 6:e20484. 2011
    ..Our findings will facilitate design of improved mutational models for RNA structure evolution...
  13. pmc Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis
    Felipe Sarmiento
    Department of Microbiology, University of Georgia, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 110:4726-31. 2013
    ..Similarly, 121 hypothetical ORFs were classified as possibly essential and likely play fundamental roles in methanococcal information processing or metabolism that are not established outside this group of prokaryotes...
  14. pmc Salmonella utilizes D-glucosaminate via a mannose family phosphotransferase system permease and associated enzymes
    Katherine A Miller
    Department of Microbiology, University of Georgia, Athens, GA, USA
    J Bacteriol 195:4057-66. 2013
    ..Examination of the Integrated Microbial Genomes database revealed that orthologs of the dga genes are largely restricted to certain enteric bacteria and a few species in the phylum Firmicutes. ..
  15. pmc Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ⁵⁴ (RpoN) regulon of Salmonella Typhimurium LT2
    David J Samuels
    Department of Microbiology, University of Georgia, 30602, Athens, GA, USA
    BMC Genomics 14:602. 2013
    ....
  16. pmc Distinctive features of large complex virus genomes and proteomes
    Jan Mrazek
    Department of Microbiology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 104:5127-32. 2007
    ..iii) Frequent oligonucleotides and peptides are characterized in the large viral genomes. The frequent words may provide structural flexibility to interact with host proteins...
  17. ncbi request reprint Type VI secretion is a major virulence determinant in Burkholderia mallei
    Mark A Schell
    Department of Microbiology, University of Georgia, Athens, GA 30602, USA
    Mol Microbiol 64:1466-85. 2007
    ..Purified His-tagged BMAA0742 was recognized by glanders antiserum from a horse, a human and mice, indicating that this Hcp-family protein is produced in vivo during infection...