Philip Cayting	
88 Bush St. #3211
San Jose, CA 95126
www.pcayting.com
pcayting@acm.org
(510) 517-3288

Education
University of California, Berkeley                                                   
B.A. Applied Mathematics, Minor in Computer Science

Computer Languages and Tools:  
Python, Java, C, C++, Perl, SQL, Scheme, LISP, HTML, XML, CVS/SVN, Google Data API, Django Web Framework

Experience
Stanford University, Stanford CA
January 2010 - Current
Dept. of Genetics - Snyder Lab
Software Developer, Research
Developed a pipeline for scoring chromatin IP genomic sequencing results
Interfaced with laboratory information management system through API and direct SQL queries to generate complex reports and supplement supplied user interface
Built genomic sequencing data submissions

Yale University, New Haven CT
Nov 2005 - December 2009
Dept. of Molecular Biophysics & Biochemistry - Gerstein Lab
Programmer Analyst
Expanded and maintained web-accessible pseudogene database application
Analyzed and mined genomic pseudogene data and genomic structural variations
Extended web-based laboratory management system
Modified existing database to accommodate changes in data schema
Integrated large amounts of data into system while maintaining data quality
Maintained large code-base
Distributed data across institutions and within the lab

Wheelchairs of Berkeley, Berkeley CA
Aug 2002 - Aug 2005
Network Administrator / Office Lead

Selected Projects
Table Element Display:  A database application developed to store and display biological data produced by the lab.  System designed to incorporate all kinds of data and used meta-information to apply templates for an intelligent display of the data.  (Python, MySQL)
DAS Server:  Implemented the Distributed Annotation System protocol to facilitate sharing of genomic data across various institutions and laboratories.  Connected DAS Server to existing data sources to simplify data sharing.  (Python, MySQL)
BreakDB:  A system to store, display and annotate genomic structural variations.  Records were versioned, so users could see the annotation modifications.  A new coordinate system was designed and implemented to account for the recursive nature of structural variations. (Python, MySQL)
Tracker:  Rule-based, event-driven system notifies responsible staff (and supervisors if necessary) when tasks fall out of timeliness using rules set by administrator.  Allows for per-order modifications and documentation.  (Java, Java Swing, MySQL)

Publications
"Segmental duplications in the human genome reveal details of pseudogene formation."  E Khurana, HY Lam, C Cheng, N Carriero, P Cayting, MB Gerstein (2010) Nucleic Acids Research 38:6997-7007.
"Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library." HY Lam, XJ Mu, AM Stütz, A Tanzer, P Cayting, M Snyder, PM Kim, JO Korbel, MB Gerstein (2010) Nat Biotechnol 28:47-55.
"PEMer:  a computational framework with simulator-based error models for inferring genomic structural variants from massive paired-end sequencing data"  J Korbel, A Abyzov, X Mu, N Carriero, P Cayting, Z Zhang, M Synder, MB Gerstein (2009) Genome Biology.
"Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes" S Balasubramanian, D Zheng, YJ Liu, G Fang, A Frankish, N Carriero, R Robilotto, P Cayting, MB Gerstein (2009) Genome Biology 10:R2.
"Pseudofam:  the pseudogene families database" HY Lam, E Khurana, G Fang, P Cayting, KH Cheung, MB Gerstein (2008) Nucleic Acids Research 37:D738-43.
"Uncovering trends in gene naming" M Seringhaus, P Cayting, MB Gerstein (2008) Genome Biology 9:401.
"Analysis of Nuclear Receptor Pseudogenes in Vertebrates:  How the Silent Tell Their Stories" ZD Zhang, P Cayting, G Weinstock, MB Gerstein (2007) Molecular Biology and Evolution 25:131-43.
"Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation" J Karro, Y Yan, D Zheng, Z Zhang, N Carriero, P Cayting, P Harrison, MB Gerstein Nucleic Acids Research (2006) 35: D55-60.

Volunteering
San Francisco Museum of Modern Art, March 2011 -- Current

Interests
Strategy board games, photography, politics, traveling