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Welcome to Peter Hallin's homepage at CBS

Curriculum Vitae


Below you will find my CV, containing my most recent publications
Curriculum Vitae - Peter Fischer Hallin

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Genealogy

I currently maintain the familly genealogy Hallin descendants - other relatives are encourted to join the Hallin genealogy

Previous bioinformatics related study projects


January 2002, Trainee at SSI, 8.83Mb
Typning af Campylobacter ved RAPD-PCR

May 2002, Introduction to bioinformatics CBS/DTU, 1.82Mb
Pathogenic investigation of Staphylococcus aureus and Staphylococcus epidermis

September 2002, Special course at CBS/DTU 0.53Mb
Expression studies in Escherichia coli

July 2003, B.sc. thesis 4.3Mb
Oligo design for campylobacter jejuni - an approach using multiple genome aignment

December 2003, Report for CBS course in Comparative Microbial Genomics 5.0Mb
DNA uptake and plasmid homology in bacterial genomes

January 2004, Report for CBS source 27012 DNA Microarrays 3.7Mb
Gene expression analysis in Campylobacter jejuni using spotted microarrays - investigation of regulation during non-growth conditions

February 2005, Report for CBS 10p special on rRNA prediction 3.5Mb
RNAmmer: Fast two-level HMM prediction of rRNA in prokaryotic genome sequences

January 2006, Master thesis 16.0Mb
Design and application of high density microarray for Expression Analysis in Campylobacter jejuni

September 2009, Ph.D. thesis 34Mb
Computational tools and Interoperability in Comparative Genomics

Other Links


Supplemental information for Master's thesis

Publications



      2008
    1. Hallin PF, Binnewies TT, Ussery DW
      The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology.Mol Biosyst 4:363-71 (2008) PubMed | PDF
    2. Reva ON, Hallin PF, Willenbrock H, Sicheritz-Ponten T, Tummler B, Ussery DW
      Global features of the Alcanivorax borkumensis SK2 genome.Environ Microbiol 10:614-25 (2008) PubMed | PDF

    3. 2007
    4. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW
      RNAmmer: consistent and rapid annotation of ribosomal RNA genes.Nucleic Acids Res 35:3100-8 (2007) PubMed | PDF
    5. Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW
      Characterization of probiotic Escherichia coli isolates with a novelpan-genome microarray.Genome Biol 8:R267 (2007) PubMed | PDF
    6. Miller WG, Parker CT, Rubenfield M, Mendz GL, Wosten MM, Ussery DW, Stolz JF, Binnewies TT, Hallin PF, Wang G, Malek JA, Rogosin A, Stanker LH, Mandrell RE
      The complete genome sequence and analysis of the epsilonproteobacteriumArcobacter butzleri.PLoS One 2:e1358 (2007) PubMed | PDF

    7. 2006
    8. Binnewies TT, Motro Y, Hallin PF, Lund O, Dunn D, La T, Hampson DJ, Bellgard M, Wassenaar TM, Ussery DW
      Ten years of bacterial genome sequencing: comparative-genomics-baseddiscoveries.Funct Integr Genomics 6:165-85 (2006) PubMed | PDF
    9. Worning P, Jensen LJ, Hallin PF, Staerfeldt HH, Ussery DW
      Origin of replication in circular prokaryotic chromosomes.Environ Microbiol 8:353-61 (2006) PubMed | PDF

    10. 2005
    11. Kill K, Binnewies TT, Sicheritz-Ponten T, Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW
      Genome update: sigma factors in 240 bacterial genomes.Microbiology 151:3147-50 (2005) PubMed | PDF
    12. Bendtsen JD, Binnewies TT, Hallin PF, Ussery DW
      Genome update: prediction of membrane proteins in prokaryotic genomes.Microbiology 151:2119-21 (2005) PubMed | PDF
    13. Bendtsen JD, Binnewies TT, Hallin PF, Sicheritz-Ponten T, Ussery DW
      Genome update: prediction of secreted proteins in 225 bacterial proteomes.Microbiology 151:1725-7 (2005) PubMed | PDF
    14. Binnewies TT, Bendtsen JD, Hallin PF, Nielsen N, Wassenaar TM, Pedersen MB, Klemm P, Ussery DW
      Genome Update: Protein secretion systems in 225 bacterial genomes.Microbiology 151:1013-6 (2005) PubMed | PDF
    15. Hallin PF, Nielsen N, Devine KM, Binnewies TT, Willenbrock H, Ussery DW
      Genome update: base skews in 200+ bacterial chromosomes.Microbiology 151:633-7 (2005) PubMed | PDF
    16. Willenbrock H, Binnewies TT, Hallin PF, Ussery DW
      Genome update: 2D clustering of bacterial genomes.Microbiology 151:333-6 (2005) PubMed | PDF
    17. Binnewies TT, Hallin PF, Staerfeldt HH, Ussery DW
      Genome Update: proteome comparisons.Microbiology 151:1-4 (2005) PubMed | PDF

    18. 2004
    19. Hallin PF, Ussery DW
      CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data.Bioinformatics 20:3682-6 (2004) PubMed
    20. Hallin PF, Coenye T, Binnewies TT, Jarmer H, Saerfeldt HH, Ussery DW
      Genome update: correlation of bacterial genomic properties.Microbiology 150:3899-903 (2004) PubMed | PDF
    21. Ussery DW, Binnewies TT, Gouveia-Oliveira R, Jarmer H, Hallin PF
      Genome update: DNA repeats in bacterial genomes.Microbiology 150:3519-21 (2004) PubMed | PDF
    22. Hallin PF, Binnewies TT, Ussery DW
      Genome update: chromosome atlases.Microbiology 150:3091-3 (2004) PubMed | PDF
    23. Ussery DW, Tindbaek N, Hallin PF
      Genome update: promoter profiles.Microbiology 150:2791-3 (2004) PubMed | PDF
    24. Ussery DW, Jensen MS, Poulsen TR, Hallin PF
      Genome update: alignment of bacterial chromosomes.Microbiology 150:2491-3 (2004) PubMed | PDF
    25. Ussery DW, Hallin PF
      Genome Update: annotation quality in sequenced microbial genomes.Microbiology 150:2015-7 (2004) PubMed | PDF
    26. Ussery DW, Hallin PF, Lagesen K, Wassenaar TM
      Genome update: tRNAs in sequenced microbial genomes.Microbiology 150:1603-6 (2004) PubMed | PDF
    27. Ussery DW, Hallin PF, Lagesen K, Coenye T
      Genome update: rRNAs in sequenced microbial genomes.Microbiology 150:1113-5 (2004) PubMed | PDF
    28. Ussery DW, Hallin PF
      Genome Update: AT content in sequenced prokaryotic genomes.Microbiology 150:749-52 (2004) PubMed | PDF
    29. Ussery DW, Hallin PF
      Genome update: Length distributions of sequenced prokaryotic genomes.Microbiology 150:513-6 (2004) PubMed | PDF

Posters and presentations


Poster presentations

  1. TIGR Genomes 2004 April 2004, Hinxton United Kingdom
    Peter F. Hallin and David W. Ussery Global and Local analysis of AT content in 164 sequenced bacterial chromosomes

  2. Bioinformatics 2004 June 2004, Linkoping Sweden
    Peter F. Hallin, Nikolaj Tindbaek, Tianshun Ye, Haakan Ohlsson, and David W. Ussery Promoter binding profiles for microbial genomes

  3. Rocky04 December 2004, Aspen, Colorado U.S.A.
    Peter F. Hallin, Tim T. Binnewies, and David W. Ussery Comparing Microbial Genome Properties in Phylogenetic context

  4. CHRO 2005 September 2005, Gold Coast Australia
    Peter F. Hallin, Tim T. Binnewies, Anne-Lise Gravesen, Susanne Knoechel, and David W. Ussery Novel Design of a High Density Microarray for Campylobacter jejuni

  5. ASM Biodefense 2007 February 2007, Washington U.S.A.
    Tim T. Binnewies, Peter Fischer Hallin, Nadia Sellami, David W. Ussery Prediction of Pathogenicity Networks in Bacterial Genomes

  6. Metagenomics 2007 July 2007, San Diego U.S.A.
    Peter Fischer Hallin and Tim T. Binnewies Gene organization of RNA genes and secretion system components of the Sargasso Sea environmental samples

As Co-author - not attended

  1. Etox 2005 June 2005, Canterbury United Kingdom
    Tim T. Binnewies, Peter F. Hallin, Jannick D. Bendtsen, David W. Ussery Prediction of Pathogenicity Networks in Bacterial Genomes

Presentations, lectures and courses

  1. Exercises August 2006, Petropolis Brazil
    Peter F. Hallin, David Ussery Workshop on Comparative Microbial Genomics and Taxonomy

  2. EMBRACE Workshop on Bioinformatics of Immunology January 2007, DTU, Lyngby Denmark
    Peter F. Hallin Accessing SOAP based Web Services using Perl:

  3. Modern computer tools for the biosciences March 2007, Uppsala Sweden
    Peter F. Hallin Implementation of Web Services for bioinformatics

  4. EMBRACE 3rd Anual General Meeting 2007 April 2007, Lyon France
    Peter Fischer Hallin Implementation of web services

  5. EMBRACE: Client Side Scripting for Web Services February 2008, Lyngby Denmark
    Peter F. Hallin Interoperability of Web Services: granularity and data types

  6. Organizing workshop: Comparative Microbial Genomics Workshop June 2008, Bangkok Thailand
    Peter F. Hallin and Dave W. Ussery Organizing workshop: Comparative Microbial Genomics Workshop

Genomes