My bioinformatics journal watch - year 1999 [ this week | 2004 Jul-Dec |  2004 Jan-Jun | 2003 Jul-Dec | 2003 Jan-Jun | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 | 1996 & before]

General Applications Data mining Network/pathway reconstruction and analysis* Languages and Algorithms Databases Conference proceedings *Network/pathway studies using microarray technology are put under the microarray section of My functional genomics journal watch; the articles in this page are primarily theoretical.

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General

1. Butler D. IBM promises scientists 500-fold leap in supercomputing power...and a chance to tackle protein structure. Nature. 1999 Dec 16;402(6763):705-6. [PubMed]
2. Bortoluzzi S, Danieli GA.Towards an in silico analysis of transcription patterns. Trends Genet. 1999 Mar;15(3):118-9. [PubMed]

1. Walker MG, Volkmuth W, Sprinzak E, Hodgson D, Klingler T. Prediction of gene function by genome-scale expression analysis: prostate cancer-associated genes.  Genome Res. 1999 Dec;9(12):1198-203. [PubMed]
2. Wagner A. Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. Bioinformatics. 1999 Oct;15(10):776-84. [PubMed]
3. Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science. 1999 Jul 30;285(5428):751-3. [PubMed]
4. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A. 1999 Apr 13;96(8):4285-8. [PubMed][pdf]
5. Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N. The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2896-901. [PubMed][pdf]

1. Walker MG, Volkmuth W, Sprinzak E, Hodgson D, Klingler T. Prediction of gene function by genome-scale expression analysis: prostate cancer-associated genes.  Genome Res. 1999 Dec;9(12):1198-203. [PubMed]
2. Wagner A. Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. Bioinformatics. 1999 Oct;15(10):776-84. [PubMed]
3. Claverie JM. Computational methods for the identification of differential and coordinated gene expression. Hum Mol Genet. 1999;8(10):1821-32. [PubMed]
4. Chen T, Filkov V, Skiena SS. Identifying gene regulatory networks from experimental data. Third annual international conference on Computational molecular biology (RECOMB '99) [abstract][ps][pdf][pdf(2nd location)]

Network/pathway reconstruction and analysis

1. Bowden AC. Metabolic control analysis in biotechnology and medicine. Nat Biotechnol. 1999 Jul;17(7):641-3. [PubMed]
2. Schuster S, Dandekar T, Fell DA. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol. 1999 Feb;17(2):53-60. [PubMed]

1. Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. A combined algorithm for genome-wide prediction of protein function. Nature. 1999 Nov 4;402(6757):83-6. [PubMed]
2. Eric Mjolsness. Trainable Gene Regulation Networks with Applications to Drosophila Pattern Formation. To appear in: Computational Methods for Molecular and Cellular Biology, eds. J. M. Bower and H. Bolouri, MIT Press. [you can find full text pdf from their web]
3. E. Mjolsness, R. Castaño, A. Gray. Multi-Parent Clustering Algorithms for Large-Scale Gene Expression Analysis. Technical Report JPL-ICTR-99-5. [you can find full text pdf from their web]
4. E. Mjolsness, T. Mann, R. Castaño, B. Wold. From Coexpression to Coregulation: An Approach to Inferring Transcriptional Regulation among Gene Classes from Large-Scale Expression Data. In: Neural Information Processing Systems (NIPS) 1999. Also avail. as Technical Report JPL-ICTR-99-4. [you can find full text pdf from their web]
5. Karp RM, Stoughton R, Yeung KY. Algorithms for choosing differential gene expression experiments. Third annual international conference on Computational molecular biology (RECOMB '99) [pdf]

1. Fleischmann W, Moller S, Gateau A, Apweiler R. A novel method for automatic functional annotation of proteins. Bioinformatics. 1999 Mar;15(3):228-33. [PubMed]

Pacific Symposium of Biocomputing 1999
The International Conference on Computational Molecular Biology 1999