Download Brian E - San Diego Supercomputer Center

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.