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• Bio::Blogs #20

Forum

• Requestion for Guide and Research publication ( )

• Upcoming Deadlines: ISCB Student Council Symposium and DREAM Team ( )

Members'
publications

• Saha S, Bridges S, Magbanua Z, Peterson D. Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences Tropical Plant Biol. 1 (1) , 85 - 96 (2008) (Epub 08 Feb 2008) doi: 10.1007/s12042-007-9007-5

• Saha S, Bridges S, Magbanua Z, Peterson D. Empirical comparison of ab initio repeat finding programs Nucleic Acids Research 36 (7) , 2284 - 2294 (2008) (Epub 16 Feb 2008) doi: 10.1093/nar/gkn064

• Basu M, Carmel L, Rogozin I, Koonin E. Evolution of protein domain promiscuity in eukaryotes. Genome research 18 (3) , 449-61 (2008) (Epub 29 Jan 2008) PubMed ID:(18230802)

• Markowetz F, Troyanskaya O. Computational identification of cellular networks and pathways. Molecular bioSystems 3 (7) , 478-82 (2007) (Epub 14 May 2007) PubMed ID:(17579773)

• Markowetz F, Spang R. Inferring cellular networks--a review. BMC bioinformatics 8 Suppl 6 , S5 (2007) (Epub 27 Sep 2007) PubMed ID:(17903286)

• Markowetz F, Kostka D, Troyanskaya O, Spang R. Nested effects models for high-dimensional phenotyping screens. Bioinformatics (Oxford, England) 23 (13) , i305-12 (2007) PubMed ID:(17646311)

• Tresch A, Markowetz F. Structure learning in Nested Effects Models. Statistical applications in genetics and molecular biology 7 , Article9 (2008) (Epub 01 Mar 2008) PubMed ID:(18312214 )

• Kuenne C, Grosse I, Matthies I, Scholz U, Sretenovic-Rajicic T, Stein N, Stephanik A, Steuernagel B, Weise, S. Using Data Warehouse Technology in Crop Plant Bioinformatics Journal of Integrative Bioinformatics 4 , e88 (2007)

• Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker B, Schreiber F. MetaCrop: a detailed database of crop plant metabolism. Nucleic acids research 36 (Database issue) , D954-8 (2008) (Epub 11 Oct 2007) PubMed ID:(17933764)

• Veerla S, Lindgren D, Kvist A, Frigyesi A, Staaf J, Persson H, Liedberg F, Chebil G, Gudjonsson S, Borg Å, Månsson W, Rovira C, Höglund M. Patterns of microRNA expression in urothelial carcinoma; identification of potential prognostic markers. (2008)

• Sinha AU, Kaimal V, Chen J, Jegga AG. Dissecting microregulation of a master regulatory network BMC Genomics 9 , 88 (2008)

• Heidenblad M, Lindgren D, Jonson T, Liedberg F, Veerla S, Chebil G, Gudjonsson S, Borg A, Månsson W, Höglund M. Tiling resolution array CGH and high density expression profiling of urothelial carcinomas delineate genomic amplicons and candidate target genes specific for advanced tumors. BMC medical genomics 1 , 3 (2008) (Epub 31 Jan 2008) PubMed ID:(18237450)

• Promoter analysis of epigenetically controlled genes in bladder cancer. (2008) (Epub 14 Jan 2008) PubMed ID:(18196590)

• Improved human disease candidate gene prioritization using mouse phenotype. 8 (1) , 392 (2007) (Epub 16 Oct 2007) PubMed ID:(17939863)

• In silico Modeling of a1A-Adrenoceptor: Interaction of its Normal and Mutated Active Sites with Noradrenaline as well as its Agonist and Antagonist American Journal of Biochemistry and Biotechnology 3 , 216-224 (2007 )

• Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors J Comput Aided Mol Des , DOI: 10.1007/s10822-007-9130-2 (2007)

• Independent component analysis for the extraction of reliable protein signal profiles from MALDI-TOF mass spectra. (2007) (Epub 14 Nov 2007) PubMed ID:(18003646)

• Reid A, Yeats C, Orengo C. Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone. Bioinformatics (Oxford, England) 23 (18) , 2353-60 (2007) (Epub 20 Aug 2007) PubMed ID:(17709341)

• Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. 8 (1) , 372 (2007) (Epub 04 Oct 2007) PubMed ID:(17916244)

• Mitchell A. METIS: multiple extraction techniques for informative sentences Bioinformatics 21 (22) , 4196 - 419 (Epub 06 Sep 2005) doi: 10.1093/bioinformatics/bti675

• Kim J, Mitchell A, Attwood T, Hilario M. Learning to extract relations for protein annotation Bioinformatics 23 (13) , i256 - i26 (Epub 26 Apr 2007) doi: 10.1093/bioinformatics/btm168

• Nebel J, Herzyk P, Gilbert D. Automatic generation of 3D motifs for classification of protein binding sites BMC Bioinformatics 8 (1) doi: 10.1186/1471-2105-8-321

• Veerla S, Höglund M. Analysis of promoter regions of co-expressed genes identified by microarray analysis. BMC bioinformatics 7 , 384 (Epub 17 Aug 2006) PubMed ID:(16916454 )

• Frigyesi A, Veerla S, Lindgren D, Höglund M. Independent component analysis reveals new and biologically significant structures in micro array data. BMC bioinformatics 7 , 290 (Epub 08 Jun 2006) PubMed ID:(16762055 )

• Veerla S. Bioinformatics-based exploration of regulatory regions in human genome LU TP 2 , 03-22 (2003)

• Macas J, Neumann P. Ogre elements--a distinct group of plant Ty3/gypsy-like retrotransposons. Gene 390 (1-2) , 108-16 (Epub 23 Aug 2006) PubMed ID:(17052864)

• Macas J, Mészáros T, Nouzová M. PlantSat: a specialized database for plant satellite repeats. Bioinformatics (Oxford, England) 18 (1) , 28-35 PubMed ID:(11836208)

• Autin L, Tufféry P. PMG: online generation of high-quality molecular pictures and storyboarded animations. Nucleic acids research 35 (Web Server issue) , W483-8 (Epub 03 May 2007) PubMed ID:(17478496 )

• Mantini D, Petrucci F, Pieragostino D, Del Boccio P, Di Nicola M, Di Ilio C, Federici G, Sacchetta P, Comani S, Urbani A. LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise. BMC bioinformatics 8 , 101 (Epub 26 Mar 2007) PubMed ID:(17386085)

• Donald J, Chen W, Shakhnovich E. Energetics of protein-DNA interactions Nucleic Acids Research 35 (4) , 1039 - 104 (Epub 30 Jan 2007) doi: 10.1093/nar/gkl1103

• Larsabal E, Danchin A. Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns". BMC bioinformatics 6 , 206 (Epub 24 Aug 2005) PubMed ID:(16120222)

• Zhou F, Xue Y, Yao X, Xu Y. A general user interface for prediction servers of proteins' post-translational modification sites. Nature protocols 1 (3) , 1318-21 PubMed ID:(17406417)

• Zhou F, Xue Y, Lu H, Chen G, Yao X. A genome-wide analysis of sumoylation-related biological processes and functions in human nucleus. FEBS letters 579 (16) , 3369-75 PubMed ID:(15922331)

• Zhou F, Xue Y, Chen G, Yao X. GPS: a novel group-based phosphorylation predicting and scoring method. Biochemical and biophysical research communications 325 (4) , 1443-8 PubMed ID:(15555589)

• Kofler R, Schlötterer C, Lelley T. SciRoKo: a new tool for whole genome microsatellite search and investigation. Bioinformatics (Oxford, England) 23 (13) , 1683-5 (Epub 26 Apr 2007) PubMed ID:(17463017)

• Weise S, Grosse I, Klukas C, Koschützki D, Scholz U, Schreiber F, Junker B. Meta-All: a system for managing metabolic pathway information. BMC bioinformatics 7 , 465 (Epub 23 Oct 2006) PubMed ID:(17059592)

• Valentini G. Clusterv: a tool for assessing the reliability of clusters discovered in DNA microarray data. Bioinformatics (Oxford, England) 22 (3) , 369-70 (Epub 06 Dec 2005) PubMed ID:(16332708)

• Bertoni A, Valentini G. Randomized maps for assessing the reliability of patients clusters in DNA microarray data analyses. Artificial intelligence in medicine 37 (2) , 85-109 (Epub 23 May 2006) PubMed ID:(16720093)

• Valentini G. Mosclust: a software library for discovering significant structures in bio-molecular data. Bioinformatics (Oxford, England) 23 (3) , 387-9 (Epub 24 Nov 2006) PubMed ID:(17127677)

• Bertoni A, Valentini G. Model order selection for bio-molecular data clustering. BMC bioinformatics 8 Suppl 2 , S7 (Epub 03 May 2007) PubMed ID:(17493256)

• Larionov A, Krause A, Miller W. A standard curve based method for relative real time PCR data processing. BMC bioinformatics 6 , 62 (Epub 21 Mar 2005) PubMed ID:(15780134 )

• Kaplan N, Morpurgo N, Linial M. Novel families of toxin-like peptides in insects and mammals: a computational approach. Journal of molecular biology 369 (2) , 553-66 (Epub 15 Mar 2007) PubMed ID:(17433819)

• Ringnér M, Veerla S, Andersson S, Staaf J, Häkkinen J. ACID: a database for microarray clone information. Bioinformatics (Oxford, England) 20 (14) , 2305-6 (Epub 12 Feb 2004) PubMed ID:(14962935)

• Kim H, Park H. Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis. Bioinformatics (Oxford, England) 23 (12) , 1495-502 (Epub 05 May 2007) PubMed ID:(17483501)

• Ning K, Leong H. Towards a better solution to the shortest common supersequence problem: the deposition and reduction algorithm. BMC bioinformatics 7 Suppl 4 , S12 (Epub 12 Dec 2006) PubMed ID:(17217504)

• Chong K, Ning K, Leong H, Pevzner P. Modeling and characterization of multi-charge mass spectra for peptide sequencing. Journal of bioinformatics and computational biology 4 (6) , 1329-52 PubMed ID:(17245817)

• Ning K, Choi K, Leong H, Zhang L. A post-processing method for optimizing synthesis strategy for oligonucleotide microarrays. Nucleic acids research 33 (17) , e144 (Epub 28 Sep 2005) PubMed ID:(16192568)

• Li F, Li M, Xiao Z, Zhang P, Li J, Chen Z. Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice. BMC bioinformatics 7 , 13 (Epub 11 Jan 2006) PubMed ID:(16403238)

• Good B, Wilkinson M. The Life Sciences Semantic Web is full of creeps! Briefings in bioinformatics 7 (3) , 275-86 (Epub 09 Aug 2006) PubMed ID:(16899496)

• Good B, Tranfield E, Tan P, Shehata M, Singhera G, Gosselink J, Okon E, Wilkinson M. Fast, cheap and out of control: a zero curation model for ontology development. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing , 128-39 PubMed ID:(17094234)

• Good B, Kawas E, Kuo B, Wilkinson M. iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website. BMC bioinformatics 7 , 534 (Epub 15 Dec 2006) PubMed ID:(17173692)

• Zhang S. A comprehensive evaluation of SAM, the SAM R-package and a simple modification to improve its performance BMC Bioinformatics 8 (1) doi: 10.1186/1471-2105-8-230

• A Samal, S Singh, V Giri, S Krishna, N Raghuram, S Jain. Low degree metabolites explain essential reactions and enhance modularity in biological networks BMC Bioinformatics 7 , 118 (2006)

• Rätsch G, Sonnenburg S, Srinivasan J, Witte H, Müller K, Sommer R, Schölkopf B. Improving the Caenorhabditis elegans genome annotation using machine learning. PLoS computational biology 3 (2) , e20 (Epub 21 Dec 2006) PubMed ID:(17319737)

• Diaz-Uriarte R, Alibes A, Morrissey E, Canada A, Rueda O, Neves M. Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite Nucleic Acids Research (Epub 08 May 2007) doi: 10.1093/nar/gkm229

• Alibés A, Morrissey ER, Cañada A, Rueda OM, Casado D, Yankilevich P, Díaz-Uriarte R. Asterias: A Parallelized Web-based Suite for the Analysis of Expression and aCGH Data Cancer Informatics 2 , 1-9 (2007)

• Alibés A, Yankilevich P, Cañada A, Díaz-Uriarte R. IDconverter and IDClight: conversion and annotation of gene and protein IDs. BMC bioinformatics 8 , 9 (Epub 10 Jan 2007) PubMed ID:(17214880)

• I-superfamily conotoxins: sequence and structure analysis Insilico Biology 5 , 0050 (2005) PubMed ID:(16268797)

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