Jeffrey G. Reid, Ph.D.
Research Assistant Professor
Human Genome Sequencing Center
Department of Molecular and Human Genetics
Baylor College of Medicine
One Baylor Plaza, Houston, TX 77030
(713) 798-7842 | jgreid@bcm.edu
Education
University of Washington
Seattle, WA
Doctor of Philosophy, Department of Physics, Center for Experimental Nuclear Physics and
Astrophysics. December 2002. Thesis: Event-by-event Analysis Methods and Applications
to Relativistic Heavy-ion Collision Data (http://arxiv.org/nucl-ex/0302001).
University of Washington
Seattle, WA
Master of Science, Department of Physics, CENPA. September 1997.
Research
Experience
Harvey Mudd College
Bachelor of Science, Physics, Minor in Film Studies. June 1993.
Claremont, CA
Human Genome Sequencing Center at BCM
May 2007 – present.
Houston, TX
Currently working on computational tools for sequence analysis using rapidly changing
next-generation sequencing technologies, and microRNA precursor resequencing to look
for variants associated with bipolar disorder and/or schizophrenia.
University of Houston Department of Chemistry
January 2006 – May 2007.
Houston, TX
Advisor: Monte Pettitt
Developed analysis tools to characterize and identify non-coding RNAs using structural
signals. Implemented a comprehensive short RNA structure database which finds and
catalogs all short RNA hairpins in a genome; this database lays the groundwork for a large
spectrum of future structural analysis. Designed, implemented, applied, and refined an
analysis chain for finding and characterizing microRNAs in deep-sequenced short RNA
data sets (short RNAomes).
BCM Department of Biochemistry and Molecular Biology
September 2003 – January 2006.
Houston, TX
Advisor: Jonathan Miller
Created new computational approaches to the characterization of functional noncoding RNAs and their targets. Identified novel candidate microRNAs in a variety of
animals using evolutionary conservation of sequence and structural elements. This
work may also yield new classes of functional non-coding RNAs for further
investigation. Characterized the position dependence of the microRNA targeting
mechanism using a statistical comparison of experimentally confirmed plant microRNAs
to a simulated miRNA population. This analysis also provided the first evidence for the
existence of microRNA anti-targets in the mRNA population of A. thaliana.
UW Department of Physics, CENPA
June 1994 - June 2003.
Seattle, WA
Advisor: Thomas Trainor
Developed model-independent correlation analysis tools for computational
investigation of the QCD phase diagram in the context of large international nuclear
physics collaborations. Designed and implemented a novel information-theoretic
analysis using entropy as a function of correlation scale. Consistent with other
experimental results in that energy regime, this analysis found no significant phase
transition at CERN SPS energies. Designed and implemented a statistical fluctuation
analysis of transverse momentum spectra. At RHIC energies, this analysis found
significant non-statistical fluctuations that remain uncharacterized, but are consistent
with some phase transition models.
Selected
Presentations
“microRNAs and Deep Sequencing of the short RNA-ome.” J.G. Reid. The 2008 Advances in
Genome Biology and Technology Conference in Marco Island, FL. February 2008.
“Snakes in a Genome: A Comprehensive RNA Structure Database on the Genomic Scale.”
J.G. Reid. W.M. Keck Center Seminar at Rice University in Houston, TX. February 2007.
“Simulation of miRNAs: shoot blind then draw a bull’s-eye where you hit.” J.G. Reid.
W.M. Keck Center Seminar at Rice University in Houston, TX. March 2005.
"Where Will They Strike Next? microRNA targeting tactics in the war on gene expression."
J.G. Reid. University of Texas Biophysics Seminar in Austin, TX. September 2004.
"Event-by-event Fluctuation Analysis in STAR: Methods and Results." J.G. Reid. CERN
Heavy Ion Forum in Geneva, Switzerland. April 2001.
"STAR Event-by-event Fluctuations." J.G. Reid for the STAR Collaboration. Fifteenth
International Conference on Ultra-Relativistic Nucleus-Nucleus Collisions in Stonybrook,
NY. January 2001.
"Event-by-event Physics in NA49." J.G. Reid for the NA49 Collaboration. Fourteenth
International Conference on Ultra-Relativistic Nucleus-Nucleus Collisions in Torino, Italy.
May 1999.
Selected
Publications
J.G. Reid, et al., “Mouse let-7 miRNA Populations Exhibit RNA Editing that is Constrained
in the 5’-seed/cleavage/anchor Regions and Stabilize Predicted mmu-let-7a:mRNA
Duplexes”, Genome Research, July 9 2008, ePublication ahead of print.
P. Gu, et al., “Novel microRNA Candidates and miRNA-mRNA pairs in embryonic stem
(ES) cells”, PLoS ONE, 3(7) (2008) e2548.
D.B. Weaver, et al., “Computational and transcriptional evidence for microRNAs in the
honey bee genome”, Genome Biology, 8(6) (2007) R97.
C. Putonti, B.M. Pettitt, J.G. Reid, Y. Fofanov, “PIDA: A new algorithm for pattern
identification”, Online Journal of Bioinformatics, 8 (2007) 30-40.
J. Adams, et al., "Event-wise mean pt fluctuations in Au-Au collisions at sqrt(sNN)=130 GeV",
Physical Review C, 71 (2005) 064906.
J.G. Reid for the STAR Collaboration, "STAR Event-by-event Fluctuations", Nuclear Physics
A, 698 (2002) 611c.
J.G. Reid and T.A. Trainor, "Statistical Fluctuations and Pair Mixing in Two-Point
Correlation Analysis", Nuclear Instruments and Methods in Physics Research A, 457 (2001)
378.
J.G. Reid for the NA49 Collaboration, "Event-by-Event Physics in NA49", Nuclear Physics
A, 661 (1999) 407c.