Contact:
|
| 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 |
|
Skills:
|
| Bioinformatics: |
- 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
|
| Computers: |
- Mac OS X and Linux system administration
- Perl, Python, C, Javascript, HTML
- R/Bioconductor
- MySQL administration and programming
- CGI-programming
- High Performance Computing
|
| Languages: |
- 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). 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.
|
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Publications: → see PubMed or Google Scholar
|