Publications

Books, Book Chapters, Peer-reviewed Publications, and Reports

Bobbert A.C. & J.J.M. Riethoven (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. Journ.Biol.Rhythms, Vol.6, No.3, p. 263-278.

Bobbert A.C., 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., Vol. 22, No. 1, p. 57-70.

Bobbert A.C., H. Duindam & J.J.M. Riethoven (1991). Pinealectomy decelerates the circadian food intake rhythm of cervically sympathectomized rabbits. Chronobiology International, Vol. 9, p. 297-309.

Batenburg van. F.H.D., V.W.A. Bos, J.J.M. Riethoven, J.P. Abrahams, M. van den Berg & C.W.A. Pleij (1991). Structure Analysis of RNA - reference guide STAR. Reference manual. ITB-RUL/Leiden: 151 pp.

Batenburg van F.H.D., V. Bos, J.J.M. Riethoven, J.P. Abrahams & C. Pley (1992). Porting and optimising STAR: a case study of suffering and surfacing. APL-Quote-Quad, Conf.proc.SIGAPL 1992, p. 265-274.

Riethoven J.J.M. & P.M.J. Herman (1992). PROEST*1, calibration and analysis of a complex estuarine ecosystemmodel. Internal report Tidal Waters Division of the Ministry of Transport and Public Works (DGW) in co-operation with the Centre of Estuarine and Marine Ecology (NIOO-CEMO). Dutch titel: PROEST*, calibratie en analyse van een complex estuarien ecosysteemmodel. 362 pp.

Bouman, B.A.M., 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. In: Agro-ecology of rice-based cropping systems: proceedings of the 'International Workshop on Agro-ecological zonation of rice', held at the Zhejiang Agricultural University, Hangzhou, P.R. of China, 15-17 April 1993. Bouman, B.A.M., H.H. van Laar & Wang Zhaoqian (Eds). SARP Research Proceedings. CABO-DLO/Wageningen: 1-15.

Berge, H.F.M. ten, 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. In: Nitrogen economy of irrigated rice: field and simulation studies: proceedings of the 'International Workshop on Nitrogen Management and Modelling in Irrigated Rice', held at the Crop Experiment Station, Rural Development Administration, Suweon, Korea, 1-10 November 1993. H.F.M. ten Berge, M.C.S. Wopereis & J.C. Shin (Eds). SARP Research Proceedings. AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños: 235-253.

Berge, H.F.M. ten, J.J.M. Riethoven & M.C.S. Wopereis (1994). Numerical optimization of nitrogen fertilizer use in irrigated rice, a user's manual for the ORYZA_0 model and optimization programs. SARP internal report. AB-DLO/Wageningen and IRRI/Los Baños, 59 pp + app.

Bouman, B.A.M., M.C.S. Wopereis & J.J.M. Riethoven (Eds) (1994). The use of crop growth models in agro-ecological zonation of rice. SARP Research Proceedings. AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños: 134 pp + app.

Berge, H.F.M. ten, H. Drenth & J.J.M. Riethoven (1994). Introduction. In: ORYZA simulation modules for potential and nitrogen limited rice production. Drenth, H., H.F.M. ten Berge & J.J.M. Riethoven (Eds). SARP Research Proceeedings. AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños: 1 - 5.

Berge, H.F.M. ten, M.C.S. Wopereis, J.J.M. Riethoven & H. Drenth (1994). Description of the ORYZA_0 modules (version 2.0). In: ORYZA simulation modules for potential and nitrogen limited rice production. Drenth, H., H.F.M. ten Berge & J.J.M. Riethoven (Eds). SARP Research Proceeedings. AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños: 43 - 55.

Drenth, H., H.F.M. ten Berge & J.J.M. Riethoven (1994). Description of the ORYZA_N modules (version 2.0). In: ORYZA simulation modules for potential and nitrogen limited rice production. Drenth, H., H.F.M. ten Berge & J.J.M. Riethoven (Eds). SARP Research Proceeedings. AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños: 7 - 42.

Drenth, H., H.F.M. ten Berge & J.J.M. Riethoven (Eds) (1994). ORYZA simulation modules for potential and nitrogen limited rice production. SARP Research Proceedings. AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños: 223 pp. ISBN 90-73384-28-1

Riethoven, J.J.M. (1994). The SARP-shell, a crop growth simulation environment. Simulation and Systems Analysis for Rice Production (SARP), revision 2, version 1.0. AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños: 114 pp.

Riethoven, J.J.M. (1995). Introduction to FSU. In: Software developments in the SARP-project, a guide to applications and tools. Riethoven, J.J.M., H.F.M. ten Berge & H. Drenth (Eds). SARP Research Proceedings. AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños: 1 - 11.

Riethoven, J.J.M. (1995). Examples of FSU use. In: Software developments in the SARP-project, a guide to applications and tools. Riethoven, J.J.M., H.F.M. ten Berge & H. Drenth (Eds). SARP Research Proceedings. AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños: 13 - 30.

Riethoven, J.J.M. (1995). FSU reference guide. In: Software developments in the SARP-project, a guide to applications and tools. Riethoven, J.J.M., H.F.M. ten Berge & H. Drenth (Eds). SARP Research Proceedings. AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños: 31 - 71.

Riethoven, J.J.M., H.F.M. ten Berge & H. Drenth (1995). Introduction to MANAGE-N. In: Software developments in the SARP-project, a guide to applications and tools. Riethoven, J.J.M., H.F.M. ten Berge & H. Drenth (Eds). SARP Research Proceedings. AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños: 75 - 86.

ten Berge, H.F.M., J.J.M. Riethoven & H. Drenth (1995). The theory of optimising the N application pattern by MANAGE-N. In: Software developments in the SARP-project, a guide to applications and tools. Riethoven, J.J.M., H.F.M. ten Berge & H. Drenth (Eds). SARP Research Proceedings. AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños: 87 - 98.

Riethoven, J.J.M., H.F.M. ten Berge & H. Drenth (1995). Optimising the N application patterns by MANAGE-N, an example. In: Software developments in the SARP-project, a guide to applications and tools. Riethoven, J.J.M., H.F.M. ten Berge & H. Drenth (Eds). SARP Research Proceedings. AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños: 99 - 115.

Riethoven, J.J.M (1995). MANAGE-N reference guide. In: Software developments in the SARP-project, a guide to applications and tools. Riethoven, J.J.M., H.F.M. ten Berge & H. Drenth (Eds). SARP Research Proceedings. AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños: 117 - 142.

Riethoven, J.J.M., H.F.M. ten Berge & H. Drenth (Eds) (1995). Software developments in the SARP-project, a guide to applications and tools. SARP Research Proceedings. AB-DLO/Wageningen, WAU-TPE/Wageningen, IRRI/Los Baños: 301 pp. ISBN 90-73384-37-0

Berge, H.F.M. ten, Qinghua Shi, Zhiming Zheng, K.S. Rao, J.J.M. Riethoven & Xuhua Zhong (1997). Numerical optimization of nitrogen application to rice. Part II. Field evaluations. Field Crops Research 51:43-54.

Berge, H.F.M. ten & J.J.M. Riethoven (1997). Applications of a simple rice-nitrogen model. In T. Ando et al (Eds) Plant nutrition for sustainable food production and environment 793-798. Kluwer Acad. Publ.

Bouman, B.A.M., F.W.T. Penning de Vries, J.J.M. Riethoven, M.J. Kropff & M.C.S. Wopereis (1998). Application of simulation and system analysis in rice-cropping optimization. In: J. Sehgal et al (Eds) Red and Lateritic Soils. Volume 1. Managing Red and Lateritic Soils for Sustainable Agriculture. Oxford & IBH Publishing, New Delhi, pp. 163-176.

Thanaraj, T.A., A.J. Robinson, J. Muilu & J.J.M. Riethoven (2000). Paradigm Shifts in the Approaches for Gene Annotation. Briefings in Bioinformatics, 1:4, 0-0

Wang, L., J.J.M. Riethoven & A.J. Robinson (2002). XEMBL - distributing EMBL data in XML format. Bioinformatics 18(8): pp1147-1148.

Thanaraj, T.A., S. Stamm, F. Clark, J.J. Riethoven, V. Le Texier & J. Muilu (2004). ASD: the Alternative Splicing Database. Nucleic Acids Research 32: D64-D69 (2004).

Stamm, S., J.J.M. Riethoven, V. Le Texier, C. Gopalakhrishnan, V. Kumanduri, Y. Tang, N.L. Barbosa-Morais, and T.A. Thanaraj (2006). ASD: A Bioinformatics Resource on Alternative Splicing. Nucleic Acids Research 34: D46-D55 (Database issue) (2006). [PDF]

Le Texier, V., J.J.M. Riethoven, V. Kumanduri, C. Gopalakhrishnan, F. Lopez, D. Gautheret, and T.A. Thanaraj (2006). AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation. BMC Bioinformatics 7:169 (2006). [PDF]

LaRosa, P. Christopher; J.J.M. Riethoven, H. Chen, Y. Xia, Y. Zhou, M. Chen, J. Miner, and M. Fromm (2007). Trans-10, Cis-12 Conjugated Linoleic Acid Activates the Integrated Stress Response Pathway in Adipocytes. Physiological Genomics PG-00156-2007.R1 (in press)

Invited talks, Conference Papers, and Poster Abstracts

Bobbert A.C., 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, abstract published in J.Interdisc.Cycle Res., Vol. 20, p. 173.

Bobbert A.C., 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, abstract published in J.Interdisc.Cycle Res., Vol. 20, p. 174.

Bergh van de B., J.J.M. Riethoven & K. Kortmulder (1989). Two approaches to territoriality in Barbus (Pisces, Cyprinidae) species. In: Proceedings of the 21th International Ethological Congres.

Bobbert A.C. & 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, abstract published in J.Interdisc.Cycle Res., Vol. 22, p. 93-94.

Riethoven, J.J.M. & H.F.M. ten Berge (1995). MANAGE-N: The user friendly package for nitrogen management in rice. Abstract in SARP/SAAD2 book of abstracts. van Laar, H.H., P.S. Teng & M.J. Kropff (Eds). SARP/SAAD2 symposium held at IRRI, Los Baños, Philippines from 4 - 8 December 1995: p. 111.

Riethoven, J.J.M. (1995). FSU: a generic user interface for crop growth simulation models. Abstract in SARP/SAAD2 book of abstracts. van Laar, H.H., P.S. Teng & M.J. Kropff (Eds). SARP/SAAD2 symposium held at IRRI, Los Baños, Philippines from 4 - 8 December 1995: p. 110.

Riethoven, J.J.M. & A.J. Robinson. The Industry Programme at the European Bioinformatics Institute: assisting European pharmaceutical companies with bioinformatics. In: Abstract book of the workshop on "BioInfomatics: from data to knowledge", held at Purmerend, The Netherlands from 8 - 9 April 1999.

L. Wang, J.J.M. Riethoven, P. Lijnzaad, N. Redaschi, and A.J. Robinson, Exploiting XML with CORBA to Improve Distributing EMBL data (2001). In: The Proceedings of World Multiconference on Systemics, Cybernetics and Informatics (SCI 2001), Orlando, USA, July 22-25, 2001 ("The Best Paper" winner).

T. Wang, J.J.M. Riethoven, and L. Wang (2001). Urban Environment Modelling Based on Data Fusion. The Proceedings of World Multiconference on Systemics, Cybernetics and Informatics (SCI 2001), Orlando, USA, July 22-25, 2001.

Thanaraj, T.A., Stamm, S., Clark, F., Riethoven, J.J.M., Le Texier, V. & J. Muilu. ASD: the Alternative Splicing Database. Abstract in the ISMB/ECCB 2004 book of abstracts of the 12th International Conference on Intelligent Systems for Molecular Biology / 3rd European Conference on Computational Biology, held in Glasgow, United Kingdom from 31 July - 4 August 2004.

Riethoven, J.J.M., Le Texier, V., Gopoalakrishnan, C., Kumanduri, V., Stamm, S. & Thanaraj, T.A. ASD: a Bioinformatics Resource for Alternative Splicing. Abstract in the ISMB 2005 book of abstracts of the 13th International Conference on Intelligent Systems for Molecular Biology, held in Detroit (MI), USA from 25 June - 29 June 2005.

Kumanduri, V., V. Le Texier, J.J.M. Riethoven, C. Gopalakrishnan, and T.A. Thanaraj. Human-Mouse comparisons of splice structures in the AltSplice database. ECCB 2005 book of abstracts of the fourth European Conference on Computational Biology, held in Madrid, Spain from 21 September - 1 October 2005.

Short Articles

Riethoven, J.J.M. (1997). Interview with dr. Richard Durbin, Head of Informatics, Sanger Centre. BioInformer, issue nr. 1, web version (ISSN 1462-1363) and paper copy (ISSN 1462-1355). http://www.riethoven.org/BioInformer/newsletter/archives/1/interview.html

Riethoven, J.J.M. (1997). Need for standards is key dilemma for software-sharing proposals. BioInform (ISSN 1094-205X), Bioinformatics Publishing LLC, New York: vol 1, nr. 2: 2 pp.

Riethoven, J.J.M. (1997). Objects in Bioinformatics'97: the report on the conference and an interview with the organiser. BioInformer, issue nr. 2, web version (ISSN 1462-1363) and paper copy (ISSN 1462-1355). http://www.riethoven.org/BioInformer/newsletter/archives/2/lead_article.html

Riethoven, J.J.M. (1997). New Bioinformatics Facility, Home for EBI, Officially Opened by HRH Princess Anne. BioInform (ISSN 1094-205X), Bioinformatics Publishing LLC, New York: vol 1, nr. 9: 2 pp.

Riethoven, J.J.M. (1998). EBI Conference Shows How Visualization Technology Can Assist Bioinformatics. BioInform (ISSN 1094-205X), Bioinformatics Publishing LLC, New York: vol 2, nr. 1: 2 pp.

Riethoven, J.J.M. (1998). Frontiers in Visualisation and Human-Computer Interaction´97 Conference. BioInformer, issue nr. 3, web version (ISSN 1462-1363) and paper copy (ISSN 1462-1355). http://www.riethoven.org/BioInformer/newsletter/archives/3/fiv97.html

Riethoven, J.J.M. (1998). Wellcome Trust Genome Campus officially opened by HRH Princess Anne. BioInformer, issue nr. 3, web version (ISSN 1462-1363) and paper copy (ISSN 1462-1355). http://www.riethoven.org/BioInformer/newsletter/archives/3/opening.html

Riethoven, J.J.M. (1998). Wellcome Trust Genome Campus Inaugural Symposium. BioInformer, issue nr. 4, web version (ISSN 1462-1363). http://www.riethoven.org/BioInformer/newsletter/archives/4/inaugural.html

Riethoven, J.J.M. (1998). CORBA Coming Quickly into Use in Bioinformatics, OIB Conference Proves. BioInform (ISSN 1094-205X), Bioinformatics Publishing LLC, New York: vol 2, nr. 17: 2 pp

Riethoven, J.J.M. (1998). Steady progress in bioinformatics software component technology, OiB'98 concludes. BioInformer, issue nr. 4, web version (ISSN 1462-1363) and paper copy (ISSN 1462-1355). http://www.riethoven.org/BioInformer/newsletter/archives/4/oib98.html

Riethoven, J.J.M. (1999). Data mining meeting highlights need for data comparability and novel algorithms. BioInform (ISSN 1094-205X), Bioinformatics Publishing LLC, New York: vol 3, nr. 23: 2 pp.

Riethoven, J.J.M. (2000). Wellcome Trust Symposium Shows How Data Compels Genome-Based Gene Prediction. BioInform (ISSN 1094-205X), Bioinformatics Publishing LLC, New York: vol 4, nr. 13: 2 pp., and in Agricultural Genomics, Bioinformatics Publishing LLC, New York: vol 3, nr. 13: 2 pp.

Riethoven, J.J.M. (2000). Novel algorithms and the need to resolve data comparability issue concludes data mining conference. BioInformer, issue nr. 6, web version (ISSN 1462-1363) and paper copy (ISSN 1462-1355). http://www.riethoven.org/BioInformer/newsletter/archives/6/datamining99.html

Riethoven, J.J.M. (2000). Paradigm shift in gene prediction as more completed genomes arrive. BioInformer, issue nr. 6, web version (ISSN 1462-1363) and paper copy (ISSN 1462-1355). http://www.riethoven.org/BioInformer/newsletter/archives/6/lead_article.html