Thu, 21 Aug 2008 17:18:47 BST CiteULike: neils Baenziger http://www.citeulike.org/user/neils/author/Baenziger CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/neils/article/3106934 <i>Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i241-247.</i><br /><br />Motivation: Coding-region mutations in human genes are responsible for a diverse spectrum of diseases and phenotypes. Among lesions that have been studied extensively, there are insights into several of the biochemical functions disrupted by disease-causing mutations. Currently, there are more than 60 000 coding-region mutations associated with inherited disease catalogued in the Human Gene Mutation Database (HGMD, August 2007) and more than 70 000 polymorphic amino acid substitutions recorded in dbSNP (dbSNP, build 127). Understanding the mechanism and contribution these variants make to a clinical phenotype is a formidable problem. Results: In this study, we investigate the role of phosphorylation in somatic cancer mutations and inherited diseases. Somatic cancer mutation datasets were shown to have a signi.cant enrichment for mutations that cause gain or loss of phosphorylation when compared to our control datasets (putatively neutral nsSNPs and random amino acid substitutions). Of the somatic cancer mutations, those in kinase genes represent the most enriched set of mutations that disrupt phosphorylation sites, suggesting phosphorylation target site mutation is an active cause of phosphorylation deregulation. Overall, this evidence suggests both gain and loss of a phosphorylation site in a target protein may be important features for predicting cancercausing mutations and may represent a molecular cause of disease for a number of inherited and somatic mutations. Contact: sdmooney@iupui.edu 10.1093/bioinformatics/btn267 Gain and loss of phosphorylation sites in human cancer Predrag Radivojac Peter Baenziger Maricel Kann Matthew Mort Matthew Hahn Sean Mooney doi:10.1093/bioinformatics/btn267 Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i241-247. 2008-08-10T23:37:41-00:00 2008 Bioinformatics 24 16 i241 247 cancer human mutation phosphorylation substrate http://www.citeulike.org/user/neils/article/2416352 <i>Brief Bioinform, Vol. 9, No. 1. (1 January 2008), pp. 69-74.</i><br /><br />A common challenge for bioinformaticians, in either academic or industry laboratory environments, is providing informatic solutions via the Internet or through a web browser. Recently, the open source community began developing tools for building and maintaining web applications for many disciplines. These content management systems (CMS) provide many of the basic needs of an informatics group, whether in a small company, a group within a larger organisation or an academic laboratory. These tools aid in managing software development, website development, document development, course development, datasets, collaborations and customers. Since many of these tools are extensible, they can be developed to support other research-specific activities, such as handling large biomedical datasets or deploying bioanalytic tools. In this review of open source website management tools, the basic features of content management systems are discussed along with commonly used open source software. Additionally, some examples of their use in biomedical research are given. 10.1093/bib/bbm057 Extensible open source content management systems and frameworks: a solution for many needs of a bioinformatics group Sean Mooney Peter Baenziger doi:10.1093/bib/bbm057 Brief Bioinform, Vol. 9, No. 1. (1 January 2008), pp. 69-74. 2008-02-23T01:31:26-00:00 2008 Brief Bioinform 9 1 69 74 bioinformatics cms lims opensource review