Dr. Jean-Jack M. Riethoven

(Reading, Writing, Speaking)

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

• Yong Ding, Hanna Lapko, Ivan Ndamukong, Yuannan Xia, Ayed Al-Abdallat, Sreedevi Lalithambika, Monther Sadder, Abdelaty Saleh, Michael Fromm, Jean-Jack Riethoven, Guoqing Lu, Zoya Avramova (2009) The Arabidopsis Chromatin Modifier ATX1, the Myotubularin-like AtMTM, and the Response to Drought; a view from the other end of the pathway, Plant Signaling & Behavior, 4 (11), In Press
• Jiang S, Wang Z, Riethoven JJ, Xia Y, Miner J, Fromm M (Oct 2009) Conjugated Linoleic Acid Activates AMP-Activated Protein Kinase and Reduces Adiposity More Effectively When Used with Metformin in Mice., The Journal of nutrition
• Galeota JA, Napier JE, Armstrong DL, Riethoven JJ, Rogers DG (Jul 2009) Herpesvirus infections in rock hyraxes (Procavia capensis)., Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc, 21 (4), 531-5
• Koscielny G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M, Harrington E, Boué S, Eyras E, Plass M, Lopez F, Ritchie W, Moucadel V, Ara T, Pospisil H, Herrmann A, G Reich J, Guigó R, Bork P, Doeberitz MK, Vilo J, Hide W, Apweiler R, Thanaraj TA, Gautheret D (Mar 2009) ASTD: The Alternative Splicing and Transcript Diversity database., Genomics, 93 (3), 213-20
• Chenhong Li, Jean-Jack M. Riethoven (2009) Exon-primed intron-crossing (EPIC) markers for non-model teleost fishes, Molecular Ecology, 20, 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
• Wang L, Riethoven JJ, Robinson A (Aug 2002) XEMBL: distributing EMBL data in XML format., Bioinformatics (oxford, England), 18 (8), 1147-8
• 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)
• 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)
• 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
• 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) 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, 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)
• 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 (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)
• 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) 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) 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. 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)
• 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)
• 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
• 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
• 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
• Thulsasingam S., Massilamany C., Yarbeva S., Subramaniam S., Riethoven J., Eudy J., Lou M., Reddy J., MiR-27b*, an oxidative stress-responsive microRNA modulates nuclear factor-kB pathway in RAW 264.7 cells, Biochemical and Biophysical Research Communications, Submitted
• J.J.M. Riethoven, Regulatory Regions in DNA: Promoters, Enhancers, Silencers, and Insulators, , Computational Biology of Transcription Factor Binding, in prep, Unpublished (bookchapter)