Curriculum vitae: Peter Fischer Hallin

Date of birth:August 16th 1977, Odense, Denmark
Nationality:Danish
Marital status:Married, 2 children
Address:Tunet 7,
3450 Allerød,
Denmark.
Email:peter.fischer [at] hallin.eu
LinkedIn:View Peter Fischer Hallin's profile on LinkedIn


Studies

1997:

Upper secondary school ('Matematisk Studentereksamen') from Odense Katedralskole.

2003:

Bachelor of Engineering in biochemistry from the Technical University of Denmark (DTU, 2003). David W. Ussery and Vivian Fussing (State Serum Institute) as supervisors. Bachelor thesis: Oligo design for Campylobacter jejuni - an approach using multiple genome alignment

2006:

Master of Science in Engineering (biotechnology), Technical University of Denmark (Center for Biological Sequence Analysis). Master thesis: Design and application of high density microarray for Expression Analysis in Campylobacter jejuni

2009:

PhD project in Comparative Genomics and Bioinformatics, CBS, Technical University of Denmark (Supervisor: Davis Ussery)

Employment

2003 - 2006:Research assistant in the Comparative Microbial Genomics group at Center for Biological Sequence Analysis (CBS) at Technical University of Denmark.
Fall 2007Visiting researcher at Professor Craig J. Benham's group at UC Davis Genome Center. Work on stress-induced DNA destabilization
2009 - 13

Research Scientist in Bioinformatics / Novozymes A/S

2013 -

Senior Scientist in Bioinformatics / Novozymes A/S

Language skills

My native tongue is Danish and I am fluent in English both written and spoken.

Courses

  • Patent course (Novozymes)
  • Novozymes ProMan I, basic project management course
  • Novozymes ProMan II, project management course
  • Novozymes Beyond project leadership (summer 2014)

Publications


    2013
  1. Hauptmann AL, Glaring MA, Hallin PF, Prieme A, Stougaard P
    Draft Genome Sequence of the Psychrophilic and Alkaliphilic Rhodonellum psychrophilum Strain GCM71T Genome Announc. 1:e01014-13 (2013) PubMed

  2. 2012
  3. Jensen DB, Vesth TC, Hallin PF, Pedersen AG, Ussery DW.
    Bayesian prediction of bacterial growth temperature range based on genome sequences BMC Genomics 13: (2012) PubMed

  4. 2010
  5. Crozat E, Winkworth C, Gaffé J, Hallin PF, Riley MA, Lenski RE, Schneider D.
    Parallel genetic and phenotypic evolution of DNA superhelicity in experimental populations of Escherichia coli. Mol Biol Evol. 5:2113-28 (2010) PubMed
  6. Friis C, Wassenaar TM, Javed MA, Snipen L, Lagesen K, Hallin PF, Newell DG, Toszeghy M, Ridley A, Manning G, Ussery DW.
    Genomic characterization of Campylobacter jejuni strain M1 PLoS One 5:e12253 (2010) PubMed
  7. Vesth T, Wassenaar TM, Hallin PF, Snipen L, Lagesen K, Ussery DW.
    On the origins of a Vibrio species. Microb Ecol 59:1-13 (2010) PubMed

  8. 2008
  9. 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
  10. 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

  11. 2007
  12. 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
  13. 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
  14. 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

  15. 2006
  16. 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
  17. 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

  18. 2005
  19. 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
  20. Bendtsen JD, Binnewies TT, Hallin PF, Ussery DW
    Genome update: prediction of membrane proteins in prokaryotic genomes. Microbiology 151:2119-21 (2005) PubMed | PDF
  21. 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
  22. 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
  23. 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
  24. Willenbrock H, Binnewies TT, Hallin PF, Ussery DW
    Genome update: 2D clustering of bacterial genomes. Microbiology 151:333-6 (2005) PubMed | PDF
  25. Binnewies TT, Hallin PF, Staerfeldt HH, Ussery DW
    Genome Update: proteome comparisons. Microbiology 151:1-4 (2005) PubMed | PDF

  26. 2004
  27. Hallin PF, Ussery DW
    CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics 20:3682-6 (2004) PubMed
  28. 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
  29. 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
  30. Hallin PF, Binnewies TT, Ussery DW
    Genome update: chromosome atlases. Microbiology 150:3091-3 (2004) PubMed | PDF
  31. Ussery DW, Tindbaek N, Hallin PF
    Genome update: promoter profiles. Microbiology 150:2791-3 (2004) PubMed | PDF
  32. Ussery DW, Jensen MS, Poulsen TR, Hallin PF
    Genome update: alignment of bacterial chromosomes. Microbiology 150:2491-3 (2004) PubMed | PDF
  33. Ussery DW, Hallin PF
    Genome Update: annotation quality in sequenced microbial genomes. Microbiology 150:2015-7 (2004) PubMed | PDF
  34. Ussery DW, Hallin PF, Lagesen K, Wassenaar TM
    Genome update: tRNAs in sequenced microbial genomes. Microbiology 150:1603-6 (2004) PubMed | PDF
  35. Ussery DW, Hallin PF, Lagesen K, Coenye T
    Genome update: rRNAs in sequenced microbial genomes. Microbiology 150:1113-5 (2004) PubMed | PDF
  36. Ussery DW, Hallin PF
    Genome Update: AT content in sequenced prokaryotic genomes. Microbiology 150:749-52 (2004) PubMed | PDF
  37. Ussery DW, Hallin PF
    Genome update: Length distributions of sequenced prokaryotic genomes. Microbiology 150:513-6 (2004) PubMed | PDF

Posters and 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

Other presentations

  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

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

  7. Computer exercises: DTU framework course in Biotechnology and Food Sciences September 2008, Lyngby Denmark
    Peter F. Hallin and Dave W. Ussery computer exercises: DTU framework course in Biotechnology and Food Sciences