Brandon Barker

Division of Nutritional Sciences

Cornell University
317 Savage Hall
Garden Ave.
Ithaca, NY 14853
(607) 262-6009
brandon.barker@gmail.com

Education ⋄ Cornell University, Ithaca, NY.

Ph.D. in Computational Biology and Medicine, expected June 2013.
Thesis Advisor: Zhenglong Gu.
⋄ University of Kentucky, Lexington, KY.
B.S. in Computer Science and Mathematics, Aug 2006.

Research ⋄ Yeast Metabolism, Biological Robustness, Flux Balance Analysis,

Mathematical Programming, Image Analysis, Sequence Alignment.
⋄ Publications:
· Zanders, S., Ma, X., RoyChoudhury, A., Hernandez, R., Demogines, A., Barker, B.,
Indap, A., Gu, Z., Bustamante, C., & Alani, E. Identification of a mutational hotspot
in yeast and humans by whole-genome sequencing. In revision, PLoS Biology.

Work ⋄ Bioinformatics IT Specialist (Aug 2006 – June 2008) Assist in Bioinformatics Research,
Experience develop and administer a microarray database, Department of Biology,
University of Kentucky, Lexington, KY.
⋄ Cluster Administrator (May 2006 – Aug 2006)
Department of Biology, University of Kentucky, Lexington, KY.
⋄ Grader (2004) Graded papers and projects for a Compilers class,
Department of Computer Science, University of Kentucky, Lexington, KY.
⋄ Research Summer Internship (Summer 2003)
Department of Computer Science, University of Kentucky, Lexington, KY.
– Supported by the Kentucky Biomedical Research Infrastructure Network.

Honors and ⋄ NIH Training Grant GM083937-01A1, 2009-2010.

Awards ⋄ Tri-Institutional Fellowship 2008-2013.
⋄ Senior Design project: Robot design, won 2nd place out of 7 at UK ECE competition, 2005,
project page located at URL:=http://sweb.uky.edu/∼bebark2/IEEERobot2005/.
⋄ University of Kentucky IEEE ECC Officer 2005.
⋄ University of Kentucky Microsoft Student Ambassador 2004-2005.
⋄ KEES Scholarship 2002-2006.
⋄ Henry Mason Lutes Scholarship.
⋄ Thurston Strunk Scholarship.
⋄ University of Kentucky Academic Scholarship.
Software ⋄ Extensions to the COBRA Flux Balance Analysis package (with Ben Heavner and
Kieran Smallbone), to be released.
⋄ Cell Phase Feature Analyzer (CPFA), URL:=http://code.google.com/p/cpfa/.
⋄ Polyalign (with Peter Huggins), parametric and inverse parametric
global and local alignment software, in development: URL:=http://polyalign.org/.
⋄ MADUK Customization (with Jim Lund and SMD Staff), A microarray database installation
based on the Stanford Micorarray Database, available at URL:=http://www.maduk.uky.edu/.
⋄ UK IEEE 2005 Robot, software and information regarding my senior design project,
available at URL:=http://sweb.uky.edu/∼bebark2/IEEERobot2005/.

Computing ⋄ Operating Systems

Skills · Unix (Linux, Solaris, *BSD, OS X), Plan 9 Distributed Operating System,
and Windows platforms.
⋄ Programming Languages
· C/C++, Perl, SQL, CGI, Python, SAGE, M2, Matlab and various CAS, Java,
functional languages, LATEX, C#/.NET.
⋄ Biological Applications
· FBA (COBRA), EMBOSS, FASTA, BLAST, Stanford Microarray Database, Biop-
erl/Biopython.

Selected ⋄ Lead discussion on Regulatory Flux Balanance Analysis and its peferomance in modeling
Talks Yeast, February 9th, 2010.
⋄ Designing Modern Alignment Software, University of Kentucky, Lexington, KY,
September 14th, 2007.
⋄ The Microsoft .NET CLR. University of Kentucky, Lexington, KY, 2005.
⋄ Mass Spectrometer Data Unification, Argonne National Laboratory, Chicago, IL, 2004.

Conferen- ⋄ 102nd Statistical Mechanics Conference 2009, Rutgers University, Piscataway, NJ.
ces ⋄ Northeast Regional Yeast Meeting 2009, Cornell University, Ithaca, NY.
⋄ SMBE annual meeting 2009, University of Iowa, Iowa City, IA.
⋄ SAMSI Program on Algebraic Methods in Systems Biology and Statistics 2008, RTP, NC.
⋄ UT-ORNL-KBRIN Bioinformatics Summit 2008, Cadiz KY. Poster presentation entitled
Promoter Complexity in C.elegans and C.briggsae.
⋄ UT-ORNL-KBRIN Bioinformatics Summit 2007, Cadiz, KY. Poster presentation entitled
Promoter Complexity in C.elegans and C.briggsae.
⋄ IMA Workshop: Applications in Biology, Dynamics, and Statistics 2007, University of Min-
nesota, Minneapolis-Saint Paul MN.
⋄ Tri-State Worm Meeting 2006, Purdue University, West Lafayette, IN.
⋄ Argonne National Labs Undergraduate Research conference 2004, Argonne, IL. Presentation
on mass spectrometer data unification.
⋄ NexTech (Student technology conference) 2001, Austin, TX.