Scientific Publications

• Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human.
  Clark, F. and T.A. Thanaraj. Human
  Molecular Genetics, 11:451-464 (2002).
• Prediction and statistical analysis of alternatively spliced exons.
  Thanaraj, T.A. & Stefan Stamm.
  Progress in Molecular and Subcellular Biology: invited review article (in press, 2002).
• GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions.
  Thanaraj, T.A., and F. Clark.
  Nucleic Acids Research, 29:2581-2593 (2001).
• GBuilder - An Application for the Visualization and Integration of EST
  Cluster Data.
  Muilu, J., P. Rodriguez-Tome, and A. Robinson.
  Genome Res. 11: 179-184. (2001)
• Links between kinetic data and sequences in the alpha/beta-hydrolases fold database.
  Chatonnet, A., X. Cousin, and A.J. Robinson.
  Briefings in Bioinformatics 2:30-37 (2001)
• One-stop shop for microarray data.
  Brazma, A., A. Robinson, G. Cameron, and M. Ashburner. Commentary.
  Nature 403:699-700 (2000).
• Synergy between combinatorial chemistry and de novo design.
  Leach A.R., R.A. Bryce, and A.J. Robinson.
  J Mol Graph Model. 2000 Aug-Oct;18(4-5):358-67, 526. PMID: 11143555; UI: 21005367 (2000)
• Positional Characterisation of False Positives from Computational Predictions of Human Splice Sites.
  Thanaraj, T.A.
  Nucleic Acids Research, 28(3):744-754 (2000).
  (Reproduced with permission from NAR online http://www.oup.co.uk/nar/)
• Prediction of Exact Boundaries of Exons.
  Thanaraj, T.A., and A.J. Robinson.
  Briefings in Bioinformatics, 1:4, 343-356 (2000).
• Paradigm Shifts in the Approaches for Gene Annotation.
  Thanaraj, T.A., A.J. Robinson, J. Muilu and J.J.M. Riethoven.
  Briefings in Bioinformatics, 1:4, 324-329 (2000).
• Accessing and distributing EMBL data using CORBA (common object request broker architecture).
  Wang, L., P. Rodriguez-Tomé, N. Redaschi, P. McNeil, A.J. Robinson, and P. Lijnzaad.
  Genome Biology 1(5): research0010.1-0010.10 (2000).
• A Clean Data Set of EST-confirmed Splice Sites From Homo Sapiens and Standards for Clean-up Procedures.
  Thanaraj, T.A.
  Nucleic Acids Research 27(13):2627-2637 (1999).
  [reproduced with permission from NAR Online http://www.oup.co.uk/nar/]
• Predicting Gene Regulatory Elements in Silico on a Genomic Scale.
  Brazma, A., I. Jonassen, J. Vilo, and E. Ukkonen.
  Genome Research Vol 8, 11:1202-1215 (1998).
• Approaches to Automatic Discovery of Patterns in Biosequences.
  Brazma, A., I. Jonassen, I. Eidhammer, and D. Gilbert.
  Journal of Computational Biology 5:277-303 (1998).
• Pattern Discovery in Biosequences.
  Brazma, A., I. Jonassen, J. Vilo, and E. Ukkonen.
  Lecture Notes in Artificial Intelligence, Vol. 1433, Springer, pp. 255-270 (1998).
• Functional Conformational Changes of Endo-1,4-xylanase II From Trichoderma reesei: A Molecular Dynamics Study.
  Muilu, J., A. To"rro"nen, M. Pera"kyla", and J. Rouvinen.
  Proteins: Structure, Function, and Genetics 31:434-444 (1998)
• Application of simulation and system analysis in rice-cropping optimization.
  Bouman, B.A.M., F.W.T. Penning de Vries, J.J.M. Riethoven, M.J. Kropff, and M.C.S. Wopereis.
  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 (1998)
• IARC Database of p53 Gene Mutations in Human Tumors and Cell Lines: Updated Compilation, Revised Formats and New Visualisation Tools.
  Hainuat, P., T. Hernandez, A.J. Robinson, P. Rodriguez-Tome, T. Flores, M. Hollstein, C.C. Harris, and R. Montesano.
  Nucleic Acids Research 26:205-213 (1998).
• Future Directions for Providing Public Access to Molecular Biology Databases and Services.
  Robinson, A.J.
  European BioPharmaceutical Review (June) pp. 68-76 (1998).
• W2H: WWW Interface to the GCG Sequence Analysis Package.
  Senger, M., T. Flores, K.H. Glatting, P. Ernst, A. Hotz-Wagenblatt, and S. Suhai.
  Bioinformatics 14(5):452-457 (1998).
• Assessment of Smith-Waterman Sequence Search Tools Implemented in Bioccelerator, FDF and MasPar.
  Thanaraj, T.A., and T. Flores.
  EMBL (1997).
• Data Mining for Regulatory Elements in Yeast Genome.
  Brazma, A., J. Vilo, E. Ukkonen, and K. Valtonen.
  In 'Proceedings of the Fifth International Conference Intelligent Systems for Molecular Biology', AAAI Press, pp. 65-74 (1997).
• Numerical optimization of nitrogen application to rice. Part II. Field evaluations.
  Berge, H.F.M. ten, T.M. Thiyagarajan, Zhiming Zheng, K.S. Rao, J.J.M. Riethoven, and Xuhua Zhong.
  Field Crops Research 51:43-54 (1997)
• Applications of a simple rice-nitrogen model.
  Berge, H.F.M. ten, and J.J.M. Riethoven.
  In: T. Ando et al (Eds) Plant Nutrition for sustainable food production and environment 793-798. Kluwer Acad. Publ. (1997)
• Novel Techniques for Visualising Biological Information.
  Robinson, A.J., and T. Flores.
  In 'Proceedings of the Fifth International Conference on Intelligent Systems in Molecular Biology', AAAI Press, pp. 241-249 (1997).