Karsten Hokamp's C.V.

Last update: January 28th, 2005
This is only a short version. The full C.V. is available upon request.


Surname: Hokamp
First Name: Karsten
Address: Smurfit Institute of Genetics
College Green
Trinity College Dublin
Dublin, Ireland
Telephone: ++353-1-896-2719 (work)

Educational History:

Oct 1998 - Oct 2001 Dept. of Genetics,
Trinity College, Dublin
Ph.D. in Bioinformatics and Molecular Evolution under supervision of Professor Kenneth H. Wolfe: A Bioinformatic Approach to (Intra-)Genome Comparison
Oct 1999 - Jun 2000 Statistics Dept.
Trinity College, Dublin
Postgraduate Diploma in Statistics
Jun 1999 Summer School,
Lipari, Italy
International School on Computational Biology for Computer Science Researchers in Lipari, Italy
Oct 1998 Maths Dept.,
Trinity College, Dublin
Course in High Performance Computing
Feb 1997 - Jan 1998 Bielefeld University,
Dept. of Computer Science
and Genetics
German 'Diplom' in Bioinformatics (grade 1) (M.Sc. level)
Oct 1991 - Jan 1997 Bielefeld University,
Faculty of Technology
Studies in Scientific Computer Science
Oct 1994 - Jun 1995 Dublin City University ERASMUS programme, studied at 4th year level in Computer Applications 


  • Next-generation sequence data analysis (RNA-seq, ChIP-seq, WGS)
  • Promoter analysis
  • Network analysis
  • ChIP-chip analysis
  • Microarray data analysis
  • Comparative genomics
  • Data integration
  • Database/tool development
  • Mac OS X and Linux system administration
  • Perl, C, Javascript, HTML
  • R/Bioconductor
  • MySQL administration and programming
  • CGI-programming
  • High Performance Computing
  • English (fluent)
  • German (mother tongue)
  • French (conversational)

Work Experience:

since Oct 2005 Bioinformatics Research Officer, providing bioinformatics support for SFI-funded biotechnology projects in Trinity College, Dublin
Oct 2002-Sep 2005 Research associate in Fiona Brinkman's lab, leading microarray analysis of cross-species platforms
Jul 2002-Aug 2002 Bioinformatics consultancy for IdentiGEN.
Nov 2001-Jun 2002 Post-doctoral position with Prof. Ken Wolfe.
Jun 2001-Sep 2001 Provision of bioinformatics support for a primer design study carried out by IdentiGEN.
Oct 1999-Feb 2001 Assisted in bioinformatics courses given by the Department of Genetics and INCBI (Irish National Centre for BioInformatics).
Nov 1999-Jan 2001 Setup of a Beowulf-type PC cluster (running Linux) for high performance computing; consisting of a 4-way server and 20 disk-less clients, connected via FastEthernet.
since Nov 1998 Development and administration of PubCrawler - an update alerting service for PubMed and GenBank, online databases for sequences and scientific journals.
This project has been started by Ken Wolfe, my PhD supervisor. I further developed his program and set up a Web service, which is used by more than 24,000 people all over the world.
Jul-Oct 1998 Employed by the Department of Genetics, Trinity College, Dublin, as a research assistant.
Apr-Jun 1998 Two months contract as a research assistant in the Department of Genetics, Bielefeld University, Germany.
Mar-Nov 1997 Scientific assistant in the Department of Genetics, Bielefeld University, Germany.
Responsible for maintenance of biological software, in particular the GDE-package (Genetic Data Environment).
Oct-Dec 1996 Programming experience in the Department of Genome Analysis at the Institute of Molecular Biotechnology (IMB), Jena, Germany.
Apr-Jun 1996 Involved in the sequencing project of Corynebacterium glutamicum at the Department of Genetics, Bielefeld University, Germany.

Teaching Experience:

Lecture: Computer programming for Biologists (since 2006). GE3M25, Genetics Department, TCD, Ireland.
Lecture: Microarrays: Introduction and Quality Assessment (2004). Canadian Bioinformatics Workshops: Genomics, August 16-21, 2004, Vancouver, B.C., Canada.
Lecture: Microarray Data Processing and Analysis (2004). University of British Columbia, Vancouver, B.C., Canada.
Problem Based Learning modules: Bioinformatics graduate programme (2003 - 2005), Simon Fraser University, Burnaby, B.C., Canada.

Publications: → see PubMed or Google Scholar

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