Dr. Jean-Jack M. Riethoven

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University of Nebraska-Lincoln
Beadle Center for Biotechnology
Bioinformatics Core Facility
ManagerAppointed: 2006

Mailing Address

E115 Beadle Center
University of Nebraska-Lincoln
1901 Vine Street
Lincoln, Nebraska 68588-0665
United States

Contact Information

Phone: (402) 472-7949
Fax: (402) 472-3139
jriethoven@unl.edu
http://www.riethoven.org/

Qualifications

Drs., Leiden University, Biology (Bioinformatics), 1991.

Expertise and Research Interests

General areas of expertise are: bioinformatics, computational biology, alternative splicing, genomics, system analysis, software development, databases.

Specifically, more than 15 years experience in a range of biology topics, with a focus on the 'informatics' and the storage/processing/analysis of data. At the European Bioinformatics Institute, I have been the lead developer in creating a massively parallel pipeline for the purpose of generating a database of transcript confirmed alternative spliced genes, events, and alternative polyA sites. Included in this pipeline and database are further annotation and cross-linking to other databases and information sources, mapping of SNP's to splice events, and conservation of splice events across species.

Currently, at the Beadle Center for Biotechnology (Univ. of Nebraska-Lincoln) I am managing the Bioinformatics Core Research Facility.

Other Expertise

Alternative splicing
Sequence analysis
Microarray analysis
Web Services (SOAP, UDDI)
Fast prototyping (i.e. proof of concept)
Unix sysadmin (incl. security, dns, web servers, mail servers)
Various programming languages (Perl, C, Java, Fortran, APL)

Future Research

Regulatory control of chromatin

Keywords

COS Keywords:

Bioinformatics, Computational Biology, Genomics, Proteomics.

Additional Terms:

APL, Alternative PolyA, Alternative Splicing, Computational Biology, Genomic, Microarray Analysis, Perl, Proteomics, Regulatory Motifs.

Languages

(Reading, Writing, Speaking)

Dutch: (Fluent, Fluent, Fluent)
English: (Fluent, Fluent, Fluent)
German: (Fluent, Functional, Functional)
French: (Basic, None, None)

Memberships

International Society for Computational Biology
Netherlands Institute for Biologists
The Netherlands Society of Theoretical Biologists (NVTB)

Previous Positions

1996-2005, Staff Scientist, European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Industry Programme / Sequence Database Group
1992-1996, Bioinformatics Support Staff, Institute for Agrobiology and Soil Fertility
1991-1992, Researcher (Bio-mathematician), Netherlands Institute for Ecological Research, Center for Estuarine and Marine Research, Mathematics and Simulation
1991-1991, Assistant Researcher, Leiden University, Faculty of Mathematics and Natural Sciences, Institute for Theoretical Biology
1990-1990, Research Assistant, Leiden University, Faculty of Mathematics and Natural Sciences, Institute for Theoretical Biology
1989-1989, Research Assistant, Leiden University, Faculty of Mathematics and Natural Sciences, Institute for Theoretical Biology
1987-1991, Research Assistant, Leiden University, Faculty of Mathematics and Natural Sciences, Laboratory for Physiology and Physiological Physics, IT

Funding Received

  • Nebraska Research Initiative: Proposal for the Enhancement of the UNL Bioinformatics Core Research Facility (BCRF), $136,000, 2007 to 2008.

Publications

  • Gautier Koscielny, Vincent Le Texier, Chellappa Gopalakrishnan, Vasudev Kumanduri, Jean-Jack M. Riethoven, Francesco Nardone, Eleanor Whitfield, Christine Fallsehr, Oliver Hofmann, Meelis Knull, Eoghan Harrington, Stephanie Boue, Eduardo Eyras, Mireya Plass, Fabrice Lopez, William Ritchie, Virginie Moucadel, Takeshi Ara, Heike Pospisil, Alexander Herrmann, Jens G. Reich, Roderic Guigo, Peer Bork, Magnus von Knebel Doeberitz, Jaak Vilo, Winston Hide, Rolf Apweiler, Thangavel Alphonse Thanaraj, Daniel Gautheret (2008) ASTD: the Alternative Splicing and Transcript Diversity Database, Nucleic Acids Research, Submitted
  • Chris LaRosa, Jean-Jack M. Riethoven, Han Chen, Yuannan Xia, You Zhou, Mei Chen, Jess Miner, Michael E. Fromm (2007) Trans-10, Cis-12 Conjugated Linoleic Acid Activates the Integrated Stress Response Pathway in Adipocytes, Physiological Genomics, 31 (544), 553
  • V. Le Texier, J.J.M. Riethoven, V. Kumanduri, C. Gopalakhrishnan, F. Lopez, D. Gautheret, T.A. Thanaraj (2006) AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation, BMC Bioinformatics, 7 (169)
  • S. Stamm, J.J.M. Riethoven, V. Le Texier, C. Gopalakhrishnan, V. Kumanduri, Y. Tang, N.L. Barbosa-Morais, T.A. Thanaraj (2006) ASD: A Bioinformatics Resource on Alternative Splicing, Nucleic Acids Research, 34 (Database issue), D46-D55
  • V. Kumanduri, V. Le Texier, J.J.M. Riethoven, C. Gopalakhrishnan, T.A. Thanaraj (2005) Human-Mouse comparisons of splice structures in the AltSplice database, 4th European Conference on Computational Biology
  • J.J.M. Riethoven, V. Le Texier, C. Gopoalakrishnan, V. Kumanduri, S. Stamm, T.A. Thanaraj (2005) ASD: a Bioinformatics Resource for Alternative Splicing, ISMB 2005
  • T.A. Thanaraj, S. Stamm, F. Clark, J.J.M. Riethoven, V. Le Texier, J. Muilu (2004) ASD: the Alternative Splicing Database, ISMB/ECCB 2004
  • Thanaraj TA, Stamm S, Clark F, Riethoven JJ, Le Texier V, Muilu J (Jan 2004) ASD: the Alternative Splicing Database., Nucleic Acids Research, 32 Database issue, D64-9 Abstract
  • Wang L, Riethoven JJ, Robinson A (Aug 2002) XEMBL: distributing EMBL data in XML format., Bioinformatics (oxford, England), 18 (8), 1147-8 Abstract
  • L. Wang, J.J.M. Riethoven, P. Lijnzaad, N. Redaschi, A.J. Robinson (2001) Exploiting XML with CORBA to Improve Distributing EMBL data (best paper award), World Multiconference on Systemics, Cybernetics and Informatics (SCI 2001)
  • T. Wang, J.J.M. Riethoven, L. Wang (2001) Urban Environment Modelling Based on Data Fusion, World Multiconference on Systemics, Cybernetics and Informatics (SCI 2001)
  • Thanaraj TA, Robinson A, Muilu J, Riethoven JJ (Nov 2000) Paradigm shifts in the approaches for gene annotation., Briefings in Bioinformatics, 1 (4), 324-9 Abstract
  • H.F.M. ten Berge, J.J.M. Riethoven (1997) Applications of a simple rice-nitrogen model, Plant nutrition for sustainable food production and environment, Dordrecht, the Netherlands, Kluwer Acad. Publ, 793-798 pages (bookchapter)
  • H.F.M. ten Berge, Q. Shi, Z. Zheng, K.S. Rao, J.J.M. Riethoven, X. Zhong (1997) Numerical optimization of nitrogen application to rice. Part II. Field evaluations, Field Crops Research, 51, 43-54
  • J.J.M. Riethoven, H.F.M. ten Berge, H. Drenth (1995) Software developments in the SARP project - a guide to applications and tools, SARP Research Proceedings, Wageningen, the Netherlands/Los Baños, the Philippines, AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños, 301 pages, ISBN=90-73384-37-0
  • J.J.M. Riethoven (1995) Introduction to FSU, Software developments in the SARP project - a guide to applications and tools, Wageningen, the Netherlands/Los Baños, the Philippines, AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños, 1-11 pages, ISBN=90-73384-37-0 (bookchapter)
  • J.J.M. Riethoven (1995) Examples of FSU use, Software developments in the SARP project - a guide to applications and tools, Wageningen, the Netherlands/Los Baños, the Philippines, AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños, 13-30 pages, ISBN=90-73384-37-0 (bookchapter)
  • J.J.M. Riethoven (1995) FSU reference guide, Software developments in the SARP project - a guide to applications and tools, Wageningen, the Netherlands/Los Baños, the Philippines, AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños, 31-71 pages, ISBN=90-73384-37-0 (bookchapter)
  • H.F.M. ten Berge, J.J.M. Riethoven, H. Drenth (1995) The theory of optimising the N application pattern by MANAGE-N, Software developments in the SARP project - a guide to applications and tools, Wageningen, the Netherlands/Los Baños, the Philippines, AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños, 87-98 pages, ISBN=90-73384-37-0 (bookchapter)
  • J.J.M. Riethoven, H.F.M. ten Berge, H. Drenth (1995) Optimising the N application patterns by MANAGE-N, an example, Software developments in the SARP project - a guide to applications and tools, Wageningen, the Netherlands/Los Baños, the Philippines, AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños, 99-115 pages, ISBN=90-73384-37-0 (bookchapter)
  • J.J.M. Riethoven (1995) MANAGE-N reference guide, Software developments in the SARP project - a guide to applications and tools, Wageningen, the Netherlands/Los Baños, the Philippines, AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños, 117-142 pages, ISBN=90-73384-37-0 (bookchapter)
  • J.J.M. Riethoven (1995) FSU: a generic user interface for crop growth simulation models, SARP/SAAD2 symposium held at IRRI, Los Baños, Philippines from 4 - 8 December 1995, AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños, 110 pages
  • J.J.M. Riethoven, H.F.M. ten Berge (1995) MANAGE-N: The user friendly package for nitrogen management in rice, SARP/SAAD2 symposium held at IRRI, Los Baños, Philippines from 4 - 8 December 1995, AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños, 111 pages
  • B.A.M. Bouman, F.W.T. Penning de Vries, J.J.M. Riethoven, M.J. Kropff, M.C.S. Wopereis (1995) Application of simulation and system analysis in rice-cropping optimization, Red and Lateritic Soils. Volume I: Managing Red and Lateritic Soils for Sustainable Agriculture, Delhi, India, Oxford & IBH Publishing, 163-176 pages, ISBN=90-541-0271-3 (bookchapter)
  • J.J.M. Riethoven, H.F.M. ten Berge, H. Drenth (1995) Introduction to MANAGE-N, Software developments in the SARP project - a guide to applications and tools, Wageningen, the Netherlands/Los Baños, the Philippines, AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños, 75-86 pages, ISBN=90-73384-37-0 (bookchapter)
  • J.J.M. Riethoven, A.J. Robinson (1995) The Industry Programme at the European Bioinformatics Institute: assisting European pharmaceutical companies with bioinformatics, "BioInfomatics: from data to knowledge", held at Purmerend, The Netherlands
  • H.F.M. ten Berge, M.C.S. Wopereis, J.J.M. Riethoven, T.M. Thiyagarajan, R. Sivasamy (1994) The ORYZA_0 model applied to optimize nitrogen use in rice, International Workshop on Nitrogen Management and Modelling in Irrigated Rice, Wageningen, the Netherlands/Los Baños, the Philippines, AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños, 235-253 pages
  • B.A.M. Bouman, M.C.S. Wopereis, J.J.M. Riethoven, The use of crop growth models in agro-ecological zonation of rice, Wageningen, the Netherlands/Los Baños, the Philippines, AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños, 134, 13 Nov 1994
  • H. Drenth, H.F.M. ten Berge, J.J.M. Riethoven (1994) ORYZA simulation modules for potential and nitrogen limited rice production, SARP Research Proceedings, Wageningen, the Netherlands/Los Baños, the Philippines, AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños, 223 pages, ISBN=90-73384-28-1
  • H.F.M. ten Berge, M.C.S. Wopereis, H. Drenth, J.J.M. Riethoven (1994) Description of the ORYZA_0 modules (version 2.0), ORYZA simulation modules for potential and nitrogen limited rice production, Wageningen, the Netherlands/Los Baños, the Philippines, AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños, 43-55 pages, ISBN=90-73384-28-1 (bookchapter)
  • H. Drenth, H.F.M. ten Berge, J.J.M. Riethoven (1994) Description of the ORYZA_N modules (version 2.0), ORYZA simulation modules for potential and nitrogen limited rice production, Wageningen, the Netherlands/Los Baños, the Philippines, AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños, 7-42 pages, ISBN=90-73384-28-1 (bookchapter)
  • B.A.M. Bouman, F.W.T. Penning de Vries, J.J.M. Riethoven, M.J. Kropff, M.C.S. Wopereis (1993) Application of simulation and systems analysis in rice-cropping optimization, International Workshop on Agro-ecological zonation of rice, Wageningen, the Netherlands/Los Baños, the Philippines, CABO-DLO/Wageningen and IRRI/Los Baños, 1-15 pages
  • Bobbert AC, Duindam H, Riethoven JJ (Aug 1992) Pinealectomy decelerates the circadian food intake rhythm of cervically sympathectomized rabbits., Chronobiology International, 9 (4), 297-309 Abstract
  • Bobbert AC, Riethoven JJ (Fall 1991) Feedback in the rabbit's central circadian system, revealed by the changes in its free-running food intake pattern induced by blinding, cervical sympathectomy, pinealectomy, and melatonin administration., Journal of Biological Rhythms, 6 (3), 263-78 Abstract
  • A.C. Bobbert, J.J.M. Riethoven (1991) Entrainment of the rabbit's food intake rhythm to complete 24hr LD-regimes and to their separate light on- and off-transitions, 7th meeting ESC, J.Interdisc.Cycle Res., Vol. 22, 93-94 pages
  • A.C. Bobbert, A.W. van Rooy, J.J.M. Riethoven (1991) Circadian changes of the ERG can be imitated by electrical stimulation of the suprachiasmatic nucleus in rabbits with intact sympathetic innervation of the eyes, J.Interdisc.Cycle Res, 22 (1), 57-70
  • B. van den Bergh, J.J.M. Riethoven, K. Kortmulder (1989) Two approaches to territoriality in Barbus (Pisces, Cyprinidae) species, 21th International Ethological Congres
  • A.C. Bobbert, J.J.M. Riethoven, G.A. Kerkhof (1989) Threefold feedback in the rabbits's circadian system, mediated by sympathetic fibres influencing retinal outflow, melatonin secretion and the hypothalamus itself, 5th meeting ESC, J.Interdisc.Cycle Res., Vol. 20, 173 pages
  • A.C. Bobbert, J.J.M. Riethoven, H.A.M. Middelkoop (1989) Differential entrainment to the ON- and OFF-transients of the 24h LD-regimes, displayed by the components of the two-oscillator central circadian system of rabbits, 5th meeting ESC, J.Interdisc.Cycle Res., Vol. 20, 174 pages

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Last Updated: 3/20/2008

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