Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Brian E. Saunders 4043 Porte De Palmas, #96 San Diego, CA 92122 858-245-4294 [email protected] Overview Over 15 years experience in bioinformatic algorithms and algorithm development, data mining, sequence analysis, annotation of genes, database design and management. Professional Experience Bioinformatics Analyst (August 1999 - current) University of California, San Diego (UCSD) - San Diego Supercomputer Center Professor Shankar Subramaniam Group Project manager for the UCSD Signaling Gateway Molecule Pages (http://www.signaling-gateway.org). The Molecule Pages system contains essential information on over 4000 mammalian proteins involved in cellular signaling, with regularly updated annotation based on sequence analysis and biological database information. Nearly 700 Molecule Pages have expert authored annotation (as review articles and highly structured data), put through a peer and editorial review process. Manage a team of programmers and editors, and work closely with the Principle Investigator to determine project goals and timelines for meeting them. Develop, maintain, and operate sequence analysis and bioinformatic annotation pipelines for the Signaling Gateway. The automatic pipelines integrate results from computational methods (alignment and profile tools) with relational database searches of public databases. The pipelines have been applied to other projects as well, for example the LIPID MAPS consortium (http://www.lipidmaps.org/). Design, maintain, and manage a series of relational databases derived from public data sources (e.g. UniProt, Entrez Gene, Genbank). The public data is in a variety of textbased formats, or in some cases XML or raw web pages, and is parsed mostly by Perl scripts. The parsed data is stored in an Oracle system with large amount of optimization via indexing, query directives, and built in Oracle optimization mechanisms. Provided sequence and database bioinformatics support to the Alliance for Cellular Signaling (a consortium of scientists funded by a NIH glue grant). Used local and global alignment and profile tools and data mining of public bioinformatic databases for annotation of custom cDNA and oligonucleotide microarray chips (produced by Agilent and Operon), yeast 2-hybrid experiments, primer and plasmid design. Directed development and maintenance of the Biology Workbench (http://workbench.sdsc.edu), an integrated web-based tool for biologists. Required programming in various languages, an intimate familiarity with sequence analysis software and sequence databases, management of account system of over 100,000 users, and supervision of other programmers working on the project. Skills o Computer Languages: Perl, HTML, SQL, XML, C o Operating systems: UNIX, Windows, Linux, Mac o Other technologies: Perl DBI , CGI/Perl, CVS, TOAD, Oracle9i, Apache o Bioinformatics tools: BLAST, ClustalW, MAFFT, MUSCLE, HMMPFAM, FingerPRINTScan, PRIMER3, InterProScan etc. o Bioinformatics Resources: Genbank, Entrez Gene, UniProt, UniGene, Homologene, GO, ENSEMBL, PFAM, InterPro, PRINTS, BIND, IntACT, NCI Pathway Interaction Database Education University of Wisconsin-Madison: Ph.D. Chemical Engineering, Dec. 1996 (Minor: Computer Science) Purdue University: B.S. Chemical Engineering, 1990 (Honors Program and COOP Program, GPA 3.9/4.0) Publications Dinasarapu AR, Saunders B, Ozerlat I, Azam K, Subramaniam S. Signaling gateway molecule pages--a data model perspective. Bioinformatics. 2011 Jun 15;27(12):1736-8. Saunders B, Lyon S, Day M, Riley B, Chenette E, Subramaniam S, Vadivelu I. The Molecule Pages database. Nucleic Acids Res. 2008 Jan;36(Database issue):D700-6. Zavzavadjian JR et al. The alliance for cellular signaling plasmid collection: a flexible resource for protein localization studies and signaling pathway analysis. Mol Cell Proteomics. 2007 Mar;6(3):413-24. Lee JA et al. Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. BMC Bioinformatics. 2006 May 2; 7:237. Cotter D, Maer A, Guda C, Saunders B, Subramaniam S. LMPD: LIPID MAPS proteome database. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D507-10. Maer A, Saunders B, Unwin R, Subramaniam S. Chapter 9: Biology Workbenches in Databasing the Brain: From Data to Knowledge (Neuroinformatics) (eds Koslow S & Subramaniam S) 153-165 (Wiley, Hobken, NJ, 2005). Zhu X et al. Analysis of the major patterns of B cell gene expression changes in response to short-term stimulation with 33 single ligands. J Immunol. 2004 Dec 15;173(12):7141-9. Li J, Ning Y, Hedley W, Saunders B, Chen Y, Tindill N, Hannay T, Subramaniam S. The Molecule Pages Database. Nature. 2002 Dec 12;420(6916):716-7.