Curriculum Vitae


A full C.V. including references is available on request; a printer-friendly version of the resume shown here can be downloaded as PDF file (a PDF Reader required).
See also my Community of Science profile.

Personal record


Name : Riethoven, Jean-Jack Marco
Nationality : Netherlands (Dutch)
Address : Lincoln, Nebraska, USA
E-mail : riethoven bioinformatics

Summary of skills

Education


1985 - 1991 University of Leiden, Leiden, the Netherlands.
Drs. degree (equivalent M.Sc. + 2 years research) in Biology. Majored in bioinformatics/bio-computing science. Research topic: "STAR*PC, Structure Analysis of RNA" (Developing, programming. porting and documenting a research software-package that computes the secondary structure of RNA on the basis of its nucleotide sequence). Course highlights: Plant Ecology, Ethology, Numerical Analysis, Bioinformatics, Algorithms, Database Technology, Functional Modelling, and Mathematical Biology.

1979-1985 Philips van Horne S.G, Weert, the Netherlands.
Equivalent to grammar school (high school)

Employment


Mar 2006 - present University of Nebraska-Lincoln (E115 Beadle Center, University of Nebraska-Lincoln, 1901 Vine St., Lincoln, NE 68588-0665, USA.)
Manager of the Bioinformatics Core Research Facility/Research assistant professor.

One of my tentative research topics: regulatory control of chromatine structure (keywords: ChIP-chip, transcription factors, histone (modification), new computational approaches to tackle experiment data).
Teaching responsibilities: undergraduate/graduate course on "Perl Programming for Biological Applications", starting this Fall (2006) semester.

Jul 1996 - Jun 2005 EMBL-EBI (EMBL - Outstation Hinxton, the European Bioinformatics Institute), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
Bioinformatics staff scientist in the BioStandards Project, part of EBI's Industry Support Programme. The European Bioinformatics Institute is an academic research and service organisation, building and making available databases of information relevant to biological research and carrying out research in computational molecular biology. The Industry Support Programme has the overall aim of helping industry to adapt quickly to, and maximise the benefits from, developments in the fast-growing fields of bioinformatics and computational biology. Duties:
  1. communication services (until 2001). Besides strong scientific and technical information dissemination to pharmaceutical companies, academia, and the general public, this included: maintenance of both EBI's main web server and the industry secure web server, web site design and content master for various projects, and technical co-ordinator of EBI's team-based web authoring system. Furthermore, I was the editor of the EBI's newsletter on bioinformatics, called 'The BioInformer', which was published on the web (http://bioinformer.ebi.ac.uk) and in paper copy.
  2. bioinformatics tool development (until 2001). Interaction with EBI's bioinformatics databases via stand-alone software or services on the web that can be utilised by molecular biologists to further their research. One of these developed services is XEMBL, which outputs EMBL/Genbank data in XML format (BSML) and is being used as tie-in by commercial packages to extract up-to-date gene information. XEMBL was the first publicly available bioinformatics related (SOAP) WebService in the world.
  3. lead developer for Alternative Splicing Database (2001-Jun 2005). Duties involve design, development, maintenance, and regular runs of the massive parallel compute pipeline of the ASD project. Design and implementation of analysis tools with respect to alternative splicing and offering these in a workbench on the web. Development and implementation of Oracle databases for alternative splicing data; development and maintenance of submission/curation and query systems to said databases. Technical guidance/supervision of other team members.
Contributed to various workshops and conferences organised by the Industry Programme; visited a number of Bioinformatics groups at pharmaceutical companies (members of the Industry Programme). Co-organised the session "Sequencing, folding, and molecular structure" at the conference for Theory and Mathematics in Biology and Medicine, held in Amsterdam, The Netherlands from June 29 to July 3, 1999. Co-organised the conference "Datamining in Bioinformatics - towards in silico Biology", held at the Wellcome Trust Genome Campus, Hinxton, United Kingdom from 10th to 12th November 1999. Co-organised the conference "Genome Based Gene Structure Determination", held at the Wellcome Trust Genome Campus, Hinxton, United Kingdom from 1st to 2nd June 2000.

Oct 1992 - Jan 1996 AB-DLO (former name), (Research Institute for Agrobiology & Soil Fertility), (now: Plant Research International B.V), Wageningen, the Netherlands.
Bioinformatics support staff for the SARP-project (Simulation and System Analysis for Rice Production). The SARP-project was an international co-operation project of AB-DLO, Wageningen University and the International Rice Research Institute, aimed at building research capacity in the field of crop simulation and system analysis in the Asian rice research centres.
Duties: developing, programming and documenting a user-friendly and open structured simulation environment for crop growth models. Developing, programming and documenting a user-friendly system that is capable of maximising rice yield by optimising fertiliser applications. Co-developing crop growth models; co-developing new tools and procedures for simulation software. Providing general computer support to end-users.
Worked three months in the Philippines (IRRI, Los Baños) during this project and participated in three workshops: 'International Workshop on Agro-Ecological Zonation of Rice' (Zejiang Agricultural University, Hangzhou, P.R. of China, 14-17 April 1993), 'International Workshop on Nitrogen Management and Modelling in Irrigated Rice' (Crop Experiment Station, Rural Development Administration, Suweon, Korea, 1-10 November 1993), the 'SARP Applications Workshop' (IRRI, Los Baños, Philippines, 18 April - 6 May 1994), and the combined SARP and SAAD2 (System Analysis in Agricultural Development) symposium (IRRI, Los Baños, Philippines, 4 - 8 December 1995). Organised the Software Tools Bazaar that was part of the SAAD2 symposium.

1991-1992 NIOO-CEMO, Netherlands Institute for Ecological Research - Centre for Estuarine and Marine Ecology, Yerseke, the Netherlands.
Contract research as a bio-mathematician. Duties: analysing (calibration, validation, uncertainty analysis) a large estuarine ecosystems model and researching new techniques how to do so.

Sep 1991 University of Leiden, Institute for Theoretical Biology, Leiden, the Netherlands.
Assistant Researcher in the BioInformatics II course. Duties: teaching a group of 60 biology students the basics of programming in APL and Pascal.

Jan 1990 University of Leiden, Institute for Theoretical Biology, Leiden, the Netherlands.
Research Assistant in the BioInformatics Io course. Duties: teaching a group of 30 biology students the rudiments of programming in APL and basic knowledge of the most commonly used software packages.

Jan 1989 University of Leiden, Institute for Theoretical Biology, Leiden, the Netherlands.
Research Assistant in the BioInformatics Io course. Duties: teaching a group of 30 biology students the rudiments of programming in APL and basic knowledge of the most commonly used software packages.

1987 - 1991 University of Leiden, Laboratory for Physiology and Physiological Physics, Leiden, the Netherlands.
Research Assistant in the IT-group. Duties: data-analysis for physiological research, PC system administrator for 100+ PC's. Developed, programmed, maintained and ported software with focus on both research and education.

Human Languages

Computer Skills

Extra-curricular activities

Professional memberships

References

Available upon request.