Rachel Patton McCord
G5; Harvard Biophysics Program
Laboratory of Dr. Martha Bulyk
Harvard Medical School New Research Building Room 466
77
Ave Louis Pasteur
Boston,
MA 02115
(617)-525-4754
rpmccord@fas.harvard.edu
Education
Ph.D.
candidate Biophysics Program Entered program Fall 2004
Harvard
University Cambridge, MA degree
expected March 2010
Relevant coursework: Computational Systems Biology, Systems Cell
Biology, Systems Analysis with Physiological Applications, Structural Biology from
Molecules to Cells, Frontiers in Biophysics: single molecule experimental
approaches, Computational Neuroscience, Cellular Basis of Neuronal Function
B.S.
summa cum laude Biophysics 2004
Davidson
College Davidson, NC
Relevant coursework: Genomics Proteomics and Bioinformatics,
Computational Biology, Programming and Problem Solving: Java, Cell Biology,
Molecular Biology, Differential Equations, Linear Algebra, Statistical and
Thermal Physics, Electricity and Magnetism, Electronics and Instrumentation,
Intermediate Mechanics, Modern Physics, Physical Chemistry, Organic Chemistry,
Inorganic/Analytical Chemistry
Research Experience
Graduate Thesis Research: Nov
2005 - present
Transcription factor mediated gene
regulation from yeast to humans
Genetics Division, Brigham and Women’s
Hospital, Harvard Medical School
Advisor: Dr. Martha
Bulyk
Research Focus: Computational and
experimental analysis of the mechanisms of condition- and cell type- specific control
of gene expression through sequence-specific transcription factor binding to
DNA in yeast and human. In yeast, I have developed computational methods to
integrate high-resolution TF DNA specificity data from protein binding
microarrays with genome wide expression data, in vivo TF binding data and other information to predict
condition-specific TF functions and to explore the biophysical details of TF
regulatory mechanisms, from the relationship between TF structure and
biological function to the biophysical characteristics of specific binding
sites used by TFs in vivo. In human
muscle, I have evaluated computational predictions of cis regulatory modules
that may control gene expression changes during differentiation by assessing
muscle TF binding to these regions using chromatin immunoprecipitation
techniques. I have further explored the
interactions between distal bound regulatory regions and target gene promoters
with variations on Chromosome Conformation Capture technology.
Graduate
Research Rotation: June
– Sept 2005
Reticulon proteins and ER network
formation
Department of Cell
Biology, Harvard Medical School
Advisor: Dr. Tom
Rapoport
Research Focus: Mechanisms of the formation
and maintenance of endoplasmic reticulum (ER) tubular network structure. Live cell imaging of GFP constructs of
membrane proteins Sec61 and reticulon to analyze ER dynamics and fluorescence
recovery after photobleaching (FRAP) to study protein mobility and potential
complex formation in the membrane.
Graduate Research
Rotation: Oct 2004 - Jan 2005
Mechanical properties of the hair cells of
the inner ear
Neuroscience
Program, Harvard Medical School
Advisor: Dr. David
Corey
Research Focus: Analyzing the mechanical
properties and responses of inner ear hair cells of the inner ear using optical
tweezers to deflect the hair bundles from a bullfrog saccule. Investigating questions of the mechanisms of
frequency selectivity and adaptation in hearing.
Independent
Undergraduate Thesis Research: 2003-2004
Measuring biological forces with optical
tweezers
Physics, Biology Departments, Center for
Interdisciplinary Studies, Davidson College
Advisors:
Dr. Karen Bernd and Dr. John Yukich
Research Focus: Design, construction, and
calibration of an optical tweezers laser trap apparatus and the use of this
trap to measure the swimming force exerted by the unicellular flagellated algae
Chlamydomonas reinhardtii. The
swimming force was used to study the function of dynein proteins in flagellar
force exertion and the dynamics of flagellar assembly.
Visiting Research Student July
2003
Design and optimization of a laser trap (optical tweezers) Atomic
Physics Division, National Institute of Standards and Technology (NIST)
Advisor: Dr. Kris
Helmerson
Research Focus:
Aligning two traps in a dual-laser optical tweezers apparatus and
achieving high quality
trapping of polystyrene microspheres.
University of
Tennessee Science Alliance Program
June-August 2002
Microcantilever-based calorimetric
spectroscopy with biological applications
Engineering Science and Technology Division,
Oak Ridge National Laboratory (ORNL)
Advisor: Dr.
Panos Datskos
Research Focus: Calorimetric spectroscopy: a
mechanical method for obtaining the infrared spectra of molecules using
microcantilevers, and its applications in identifying very small quantities of
different species of bacteria and distinguishing between DNA from different
sources. This method has potential uses
in small and highly sensitive biological detectors.
Higher Education Research Experience June-August 2001
Genetic characterization of woody plants
for use as bioenergy crops
Environmental Sciences Division, ORNL
Advisors:
Lee Gunter and Dr. Gerry Tuskan
Research Focus: Bulked segregant analysis
with random primer PCR to search for regions in the willow genome (Salix eriocephala and Salix matsudana)
that segregate with the phenotypes of gender or stem shape using random primer
PCR. The research confirmed a candidate
gene for gender determination and identified a region potentially involved in
corkscrew vs. straight stem determination.
Teaching/Mentoring
Experience
Teaching Fellow for Physical Sciences 2 Fall
2008
** Received a Harvard
University Certificate of Distinction in Teaching for work with this course
Responsibilities: Teaching two hour-long sections per week of
15 undergraduate students each in a course covering traditional introductory
classical mechanics concepts with a focus on biological examples. Section meetings involved review of material
presented in lecture and problem solving practice. I was responsible for grading homework
assignments and exams, organizing individual meetings with students as needed,
and staffing a course homework help room each week to provide advice on problem
sets.
Teaching Fellow for Biophysics 205:
Computational and Functional Genomics Spring
2006
** Received a Harvard
University Certificate of Distinction in Teaching for work with this course
Responsibilities: Administration of graduate level seminar course
in genomics and computational biology.
Development of course website, organization and assignment of student
paper presentation dates, assistance in planning course and selecting papers
for discussion, advising students on paper presentations and final projects,
and evaluation of student paper presentations and final projects.
Supervision of Undergraduate Research
Opportunity Students Summer
2007 and 2008
Responsibilities: Primary supervisor of one undergraduate
student each summer working on research projects in the Bulyk lab.
Publications and Presentations
Publications:
Zhu C*, Byers K*, McCord
RP*, Shi Z, Berger M, Newburger D, Saulrieta K, Smith Z, Shah M,
Radhakrishnan M, Philippakis A, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy T,
Labaer J, Bulyk ML. (2009) High-resolution DNA binding specificity analysis of
yeast transcription factors.
Genome Res. Jan 21. [Epub ahead of print] doi: 10.1101/gr.090233.108
* These authors contributed equally to this work
McCord RP, Bulyk ML. (2008) Functional trends in structural
classes of the DNA binding domains of regulatory transcription factors. Pacific
Symposium on Biocomputing. 441-52.
Lin J, Gunter LE,
Harding SA, Kopp RF, McCord RP, Tsai CJ, Tuskan GA, Smart LB. (2007)
Development of AFLP
and RAPD markers linked to a locus associated with twisted growth in corkscrew
willow (Salix matsudana 'Tortuosa'). Tree Physiology. 27: 1575-83.
McCord RP, Berger, MF,
Philippakis AA, Bulyk ML. (2007) Inferring condition-specific transcription
factor function from DNA binding and gene expression data. Molecular Systems
Biology 3:100.
McCord RP, Yukich JN, Bernd
KK. (2005) Analysis of Force Generation
during Flagellar Assembly through Optical Trapping of Free Swimming Chlamydomonas. Cell Motility and the Cytoskeleton 61:
137-144.
Gunter LE, Kopp RF, McCord RP, Tuskan
GA. (2003). Analysis of Sex-Linked, Sequence- Characterized Amplified Region
Markers in Salix eriocephala.
Canadian Journal of Forest Research 33: 1785-1790.
Presentations:
March 1, 2009: “Linking Detailed Yeast
Transcription Factor Binding Preferences with in vivo DNA Binding and
Regulatory Function” Poster presented at the at the Annual Meeting of the
Biophysical Society. Boston, MA.
March 20, 2008: “Translating the Cell’s ‘Instruction
Manual’: A Biophysicist’s Approach to Understanding Gene Regulation” Invited seminar
sponsored by the Davidson College Physics and Biology Departments. Davidson, NC.
January 7, 2008: “Functional Trends in
Structural Classes of Transcription Factor
DNA Binding Domains” Oral presentation at the Pacific Symposium on
Biocomputing. Kohala Coast, HI.
December 1, 2006: “Inferring
condition-specific transcription factor function from DNA binding sites and
gene expression” Oral presentation at the RECOMB Satellite Conference on Systems
Biology. San Diego, CA.
March 24, 2006: “Predicting Yeast
Transcription Factor Function from DNA Binding Specificities and Expression
Data” Poster presented at the Cold
Spring Harbor Laboratory Meeting on Systems Biology: Global Regulation of Gene
Expression. Cold Spring Harbor, NY
April 29, 2004: “The Swimming force of Chlamydomonas
reinhardtii: measurement with optical tweezers.” Oral presentation at the North Carolina
Academy of Science Annual Meeting.
February 15, 2004: “Optical Tweezers and
Biological Forces: Using a Laser Trap to Measure the Swimming Force Exerted by
the Flagella of Chlamydomonas reinhardtii.” Poster presented at the
Annual Meeting of the Biophysical Society at both the Undergraduate Symposium
and an appropriate poster session.
Baltimore, MD
November 6, 2003: “The Design and
Construction of an Optical Tweezers Laser Apparatus to Measure Piconewton
Scale Biological Forces.” Poster presented
at the Society of Physics Students Poster Session at the Southeastern Section
of the American Physical Society (SESAPS) meeting. Wilmington, NC.
Honors and Awards
Certificate
of Distinction in Teaching (Harvard University) 2008
Pacific
Symposium on Biocomputing Travel Grant 2008
NSF
Graduate Research Fellowship 2004-2007
Certificate
of Distinction in Teaching (Harvard University) 2006
Sigma
Xi (scientific research honor society) 2004
North
Carolina Academy of Science Derieux Award for excellence 2004
in
undergraduate research
Phi
Beta Kappa (Davidson College) 2004
Frontis
W. Johnston Thesis Award (Davidson College) 2004
Physics
Award (Davidson College) 2004
First
honors (valedictorian) (Davidson
College) 2004
2nd
place Marsh White Award for an Undergraduate Poster Presentation 2003
at SESAPS (Southeastern Section of the
American Physical Society)
Sigma
Pi Sigma (physics honor society) 2002