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| Summary |
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Research scientist in computational biology, particularly regarding metagenomics and machine learning. Expert in large-scale data management, database design, and cluster computing. Experienced in project management and system administration. Proficient with a wide variety of computing technologies and platforms. Effective team player; also able independently to complete entire projects from conception through launch. |
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Computing Skills
Advanced
Java
- Spring
- Hibernate
- Maven2
- TestNG
- JDBC
- Servlets
- Swing
- IntelliJ IDEA
XML
XSLT
Apache
Resin
MySQL
Postgres
Sysadmin
- Linux
- Solaris
- Mac OS X
Subversion, CVS
Intermediate
Perl
C/C++
Cold Fusion
Mathematica
Matlab
Oracle
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| Objective |
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Finish graduate school. Then (circa 2009), positions involving computational biology and machine learning in a dynamic and creative research environment. |
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| Education |
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University of California, Berkeley (2003-present) Berkeley, CA 94720
Stanford University (1995 - 1998) Stanford, CA 94305
California Institute of Technology (1993 - 1995) Pasadena, CA 91125
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| Publications |
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Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, et al. (2007). The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families. PLoS Biol 5: e16.
Lareau LF, Brooks AN, Soergel DAW, Meng Q, Brenner SE. (2007). The coupling of alternative splicing and nonsense-mediated mRNA decay. In Blencowe B and Graveley B, ed., Alternative splicing in the post-genomic era, Landes Bioscience.
Soergel DAW, Lareau LF, Brenner SE. (2006). Regulation of gene expression by the coupling of alternative splicing and nonsense-mediated mRNA decay. In Maquat L, ed., Nonsense-mediated mRNA decay, Landes Bioscience.
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| Academic Honors |
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Chang-Lin Tien Scholar in Environmental Sciences and Biodiversity, UC Berkeley, 2008-2009.
Predoctoral Fellow, Howard Hughes Medical Institute, 2003-2008.
National Defense Science and Engineering Graduate Fellowship (declined), 2003.
Summer Undergraduate Research Fellowships. Caltech: 1994, 1995. Stanford: 1997.
Caltech Merit Award, 1995.
Caltech Merit Award, 1994.
Robert Andrews Millikan Scholar, Caltech, 1993. |
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| Communication |
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Effective communicator in spoken and written English. Skilled at discussing technology projects with non-technical clients. Fluent in German. |
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| Work Experience |
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| October 2001 - August 2003 |
Lead Bioinformatics Developer, The Molecular Sciences Institute |
I built databases and software in support of basic research in biology, specifically regarding the modelling, simulation, and visualization of G-protein-initiated signal transduction pathways in yeast.
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| November 1999 - August 2003 |
Founder and Principal, Asha Technologies |
Ashatech was a consulting firm focussing on database-driven web applications for socially beneficial purposes. Clients included The Volunteer Center of San Mateo County and the Institute for Policy Studies.
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| May 2000 - February 2001 |
Co-founder and Director of Research and Development, Little Engine, Inc. |
Little Engine aimed to significantly improve the quality of early childhood education in preschools nationwide, through the judicious application of information technology for teachers and parents. Unfortunately, the scarcity of funds in the preschool and venture capital markets prevented us from continuing this important work.
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January 1999 -
May 2000 |
Research Associate, Department of Genetics, Stanford University School of Medicine |
Working with Prof. L. L. Cavalli-Sforza, I wrote programs for analyzing the geographic distribution of human genes and for studying correlations between genes and culture. In particular, I was responsible for the Human Genome Diversity Database.
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| November 1998 - November 1999 |
Vice President for Technology, Padra.org |
Padra.org was a volunteer-staffed effort to create a comprehensive nonprofit-oriented web portal. Partly because Padra was itself a 501c3 nonprofit organization, it ultimately failed for lack of funding— but not before we had built several strong business relationships and functional prototypes.
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April 1997 -
March 1999 |
Software Developer, Science and Technology in the Making, Stanford University Libraries |
I wrote code and provided technical support for a richly structured multimedia database for encoding humanities information, in this case concerning topics in the history of technology. The system had a complex web interface written in WebObjects.
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| Summer 1996 |
Research Assistant, Institute for Scientific Computing Research, Lawrence Livermore National Laboratory |
I worked on software and hardware related to computer vision. Among other projects, I constructed a robotic motion-tracking device and helped write and debug drivers for it.
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| Summer 1994 |
Samuel P. And Frances Krown Summer Undergraduate Research Fellow, San Onofre/Palo Verde Neutrino-Oscillation Experiment, Caltech |
I designed a large portion of the data-acquisition electronics for a neutrino detector designed to seek evidence for neutrino oscillations and hence for neutrino mass.
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| Summer 1992 |
Summer Intern, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany |
| I was involved in the data acquisition group of the ZEUS detector in the newly operating Hadron-Electron Ring Accelerator (HERA). I programmed a simulation of the data acquisition system; the results of the simulation suggested optimizations which doubled the system's data throughput.
I also worked at HASYLAB, the Hamburg Synchrotron Radiation Laboratory, building instrumentation for measuring the ultraviolet absorption spectrum of barium. |
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