Sat, 19 Jul 2008 00:41:14 BST CiteULike: neils's Aerts http://www.citeulike.org/user/neils/author/Aerts CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/neils/article/2843033 <i>Nucl. Acids Res. (28 May 2008), gkn325.</i><br /><br />ENDEAVOUR (http://www.esat.kuleuven.be/endeavourweb; this web site is free and open to all users and there is no login requirement) is a web resource for the prioritization of candidate genes. Using a training set of genes known to be involved in a biological process of interest, our approach consists of (i) inferring several models (based on various genomic data sources), (ii) applying each model to the candidate genes to rank those candidates against the profile of the known genes and (iii) merging the several rankings into a global ranking of the candidate genes. In the present article, we describe the latest developments of ENDEAVOUR. First, we provide a web-based user interface, besides our Java client, to make ENDEAVOUR more universally accessible. Second, we support multiple species: in addition to Homo sapiens, we now provide gene prioritization for three major model organisms: Mus musculus, Rattus norvegicus and Caenorhabditis elegans. Third, ENDEAVOUR makes use of additional data sources and is now including numerous databases: ontologies and annotations, protein-protein interactions, cis-regulatory information, gene expression data sets, sequence information and text-mining data. We tested the novel version of ENDEAVOUR on 32 recent disease gene associations from the literature. Additionally, we describe a number of recent independent studies that made use of ENDEAVOUR to prioritize candidate genes for obesity and Type II diabetes, cleft lip and cleft palate, and pulmonary fibrosis. 10.1093/nar/gkn325 ENDEAVOUR update: a web resource for gene prioritization in multiple species Leon-Charles Tranchevent Roland Barriot Shi Yu Steven Vooren Peter Loo Bert Coessens Bart Moor Stein Aerts Yves Moreau doi:10.1093/nar/gkn325 Nucl. Acids Res. (28 May 2008), gkn325. 2008-05-29T01:57:07-00:00 2008 Nucl. Acids Res. gkn325 bioinformatics candidate function gene selection webserver http://www.citeulike.org/user/neils/article/1090867 <i>Genome Res, Vol. 13, No. 7. (July 2003), pp. 1580-1588.</i><br /><br />We generated draft genome sequences for two cold-adapted Archaea, Methanogenium frigidum and Methanococcoides burtonii, to identify genotypic characteristics that distinguish them from Archaea with a higher optimal growth temperature (OGT). Comparative genomics revealed trends in amino acid and tRNA composition, and structural features of proteins. Proteins from the cold-adapted Archaea are characterized by a higher content of noncharged polar amino acids, particularly Gln and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15 degrees -98 degrees C) were used to generate 1111 modeled protein structures. Analysis of the models from the cold-adapted Archaea showed a strong tendency in the solvent-accessible area for more Gln, Thr, and hydrophobic residues and fewer charged residues. A cold shock domain (CSD) protein (CspA homolog) was identified in M. frigidum, two hypothetical proteins with CSD-folds in M. burtonii, and a unique winged helix DNA-binding domain protein in M. burtonii. This suggests that these types of nucleic acid binding proteins have a critical role in cold-adapted Archaea. Structural analysis of tRNA sequences from the Archaea indicated that GC content is the major factor influencing tRNA stability in hyperthermophiles, but not in the psychrophiles, mesophiles or moderate thermophiles. Below an OGT of 60 degrees C, the GC content in tRNA was largely unchanged, indicating that any requirement for flexibility of tRNA in psychrophiles is mediated by other means. This is the first time that comparisons have been performed with genome data from Archaea spanning the growth temperature extremes from psychrophiles to hyperthermophiles. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. NF Saunders T Thomas PM Curmi JS Mattick E Kuczek R Slade J Davis PD Franzmann D Boone K Rusterholtz R Feldman C Gates S Bench K Sowers K Kadner A Aerts P Dehal C Detter T Glavina S Lucas P Richardson F Larimer L Hauser M Land R Cavicchioli doi:10.1101/gr.1180903 Genome Res, Vol. 13, No. 7. (July 2003), pp. 1580-1588. 2007-02-06T16:51:44-00:00 2003 Genome Res 1088-9051 13 7 1580 1588 antarctic bioinformatics genomics methanococcoides methanogenium psychrophily http://www.citeulike.org/user/neils/article/2475666 <i>Nature, Vol. 452, No. 7183. (6 March 2008), pp. 88-92.</i> The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis F Martin A Aerts D Ahren A Brun EGJ Danchin F Duchaussoy J Gibon A Kohler E Lindquist V Pereda A Salamov HJ Shapiro J Wuyts D Blaudez M Buee P Brokstein B Canback D Cohen PE Courty PM Coutinho C Delaruelle JC Detter A Deveau S Difazio S Duplessis L Fraissinet-Tachet E Lucic P Frey-Klett C Fourrey I Feussner G Gay J Grimwood PJ Hoegger P Jain S Kilaru J Labbe YC Lin V Legue F Le Tacon R Marmeisse D Melayah B Montanini M Muratet U Nehls H Niculita-Hirzel Oudot-Le Secq M Peter H Quesneville B Rajashekar M Reich N Rouhier J Schmutz T Yin M Chalot B Henrissat U Kues S Lucas Y Van de Peer GK Podila A Polle PJ Pukkila PM Richardson P Rouze IR Sanders JE Stajich A Tunlid G Tuskan IV Grigoriev doi:10.1038/nature06556 Nature, Vol. 452, No. 7183. (6 March 2008), pp. 88-92. 2008-03-05T22:42:12-00:00 2008 Nature 452 7183 88 92 Nature Publishing Group bioinformatics genome laccaria mycorrhizae sequence symbiosis