Curriculum vitae: Peter Fischer Hallin

Date of birth:August 16th 1977, Odense, Denmark
Nationality:Danish
Address:Holtegårdsvej 100,
2840 Holte,
Denmark.
Phone:(+45) 4580 5444
Family:Married to Susanne Piilgaard Hallin. We have two children, Oliver (2006) and Victor (2009)
Email:pfh@cbs.dtu.dk
LinkedIn:View Peter Fischer Hallin's profile on LinkedIn
Online CV:http://www.cbs.dtu.dk/~pfh/cv.php


Studies

1997:

Danish 'Matematisk Studentereksamen' (Upper secondary school) from Odense Katedralskole. Mathematical profile with Mathematics, Physics and Chemistry on A level.

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

2006-2009:

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

Employment

2000 to 2006:Student jobs: Owner of private IT company (iCOM Hardware I/S, CVR 25303709) and technical assistent at NESA (now DONG energy)
2003 to 2006:Research assistant in the Comparative Microbial Genomics group at Center for Biological Sequence Analysis (CBS) at Technical University of Denmark.
Fall 2007At Professor Craig J. Benham's group at University of California Davis Genome Center to incorporate a mathematical model for stress-induced DNA destabilization into CBS' current visualization methods. (see CBS SIDDBase).
2009- Research scientist at Novozymes A/S

During my work in the field of bioinformatics I have gained experience in teaching graduate level students and presenting my work at various international conferences and talks. I have organized several workshops, including one on web services workshop at CBS (Feb 2008), one on comparative microbial genomics i Bangkok, Thailand (June 2008), and another in comparative microbial genomics and taxonomy in Rio de Janeiro, Brazil (August 2006). My scientific work is for a large part focussed on comparative analysis of prokaryotic genomes and computer models for predicting bacterial transcription activation. Also, I have been working on various methods for visualizing whole-genome homology across multiple species.

I master Perl, PHP/HTML/JavaScript/MySQL plus some R and have good experience in solving larger computational problems at the CBS super computer facility, which consist of several global shared memory servers (SGI Origin and Altix)

I have been involved with various software design projects like the Genome Atlas Database. I have authored CBS' SOAP Web Services server and implemented a number of CBS' applications in SOAP, to provide programmatic access to these tools. This was done in connection to deliverables for EMBRACE, which is a european project that aims to enhance interoperability throughout european bioinformatic institutions. I have lead the development of a protein analysis pipeline for the ENCODE project, called EPipe, which allows users to examine functional differences between splice variants, SNP variants or disease related genes. Also, the latest initiative I am involved in, is the GeneWiz browser, which in a Google Earth-like fashion allows users to zoom from a global genomic scale of a microbial genome into the single nucleotide. The service is called gwBrowser and it should the manuscript is submitted and close to publications as of September 2009.

Language skills

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

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
  3. 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
  4. 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
  5. 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

    6. 2006
  6. 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
  7. 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

    8. 2005
  8. 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
  9. Bendtsen JD, Binnewies TT, Hallin PF, Ussery DW
    Genome update: prediction of membrane proteins in prokaryotic genomes. Microbiology 151:2119-21 (2005) PubMed | PDF
  10. 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
  11. 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
  12. 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
  13. Willenbrock H, Binnewies TT, Hallin PF, Ussery DW
    Genome update: 2D clustering of bacterial genomes. Microbiology 151:333-6 (2005) PubMed | PDF
  14. Binnewies TT, Hallin PF, Staerfeldt HH, Ussery DW
    Genome Update: proteome comparisons. Microbiology 151:1-4 (2005) PubMed | PDF

    15. 2004
  15. Hallin PF, Ussery DW
    CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics 20:3682-6 (2004) PubMed
  16. 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
  17. 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
  18. Hallin PF, Binnewies TT, Ussery DW
    Genome update: chromosome atlases. Microbiology 150:3091-3 (2004) PubMed | PDF
  19. Ussery DW, Tindbaek N, Hallin PF
    Genome update: promoter profiles. Microbiology 150:2791-3 (2004) PubMed | PDF
  20. Ussery DW, Jensen MS, Poulsen TR, Hallin PF
    Genome update: alignment of bacterial chromosomes. Microbiology 150:2491-3 (2004) PubMed | PDF
  21. Ussery DW, Hallin PF
    Genome Update: annotation quality in sequenced microbial genomes. Microbiology 150:2015-7 (2004) PubMed | PDF
  22. Ussery DW, Hallin PF, Lagesen K, Wassenaar TM
    Genome update: tRNAs in sequenced microbial genomes. Microbiology 150:1603-6 (2004) PubMed | PDF
  23. Ussery DW, Hallin PF, Lagesen K, Coenye T
    Genome update: rRNAs in sequenced microbial genomes. Microbiology 150:1113-5 (2004) PubMed | PDF
  24. Ussery DW, Hallin PF
    Genome Update: AT content in sequenced prokaryotic genomes. Microbiology 150:749-52 (2004) PubMed | PDF
  25. 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