1. Jacob Clifford
Contact
Information
Email jacobc@msu.edu
Education Michigan State University, East Lansing, MI
Doctoral Advisor: Dr. Christoph Adami
Doctoral Advisor: Dr. David Arnosti
Ph.D. Physics, September 2015 Analysis of Cooperative Transcription Factor Binding at the Se-
quence Level
Physics; B.S. 2006 Physics; M.S. 2009
Experience Michigan State University, East Lansing, MI
Graduate Research
Adami Laboratory, Jun. 2012 – 2015
Arnosti Laboratory, Jun. 2008 – 2012
Undergraduate Research
Feig Laboratory, Jun. 2005 – Aug 2006
Lynch Laboratory, Jun. 2005 – Aug 2006
Graduate Teaching Assistant:
ISP 209L Mysteries of the Physical Universe, Fall 2006 - summer 2009 (13 sections)
PHY 251 Introduction To Physics (Mechanics), Summer 2007 (1 section)
PHY 252 Introduction To Physics (Electricity and Magnetism), Summer 2008 (1 section)
PHY 440 Electronics, Fall 2011 (2 sections)
PHY 486 Advanced Laboratory, Fall 2012 (1 section)
Courses Gene Regulatory Networks, Woods Hole Marine Biology Laboratory, summer 2009, directed
by Eric Davidson and Mike Levine
Honors & Awards Lawrence W. Hantel Endowed Fellowship (for physics bachelors) 2005
Quantitative Biology Graduate Fellowship Aug. 2009 -Jun 2010
Publications J. Clifford, C. Adami (2015): Discovery and information-theoretic characterization of tran-
scription factor binding sites that act cooperatively. Physical Biology pdf.

2. S. Tanizaki, J. Clifford, Brian D. Connelly, Michael Feig: Conformational Sampling of Peptides
in Cellular Environments. Biophysical Journal pdf (2008). 94, 747-759
M.S. Wallace, M.A. Famiano,b, M.-J. van Goethem, A.M. Rogers, W.G. Lynch, J. Clifford, F.
Delaunay, J. Lee, S. Labostov, M. Mocko, L. Morris, A. Moronie, B.E. Nett, D.J. Oostdyk,
R. Krishnasamy, M.B. Tsang, R.T. de Souzac, S. Hudanc, L.G. Sobotkad, R.J. Charityd, J.
Elsond, G.L. Engelf The high resolution array (HiRA) for rare isotope beam experiments pdf
Nuclear Instruments and Methods in Physics Research A 583 (2007) 302-312 experiments
Presentations “Dorsal Binding Sites Conditioned on Evolved Spacer Elements.”
BEACON Congress, poster, Aug. 2013. East Lansing, MI.
“ Discovery of cis-Context-Dependent Selection of DNA Binding Sites Using a Statistical Theory.”
ASBMB symposium Evolution and Ecology, poster, July 25-27 2013.
“Dorsal Binding Sites Conditioned on Genomic Spacer Elements.”
BEACON Congress, poster, Aug. 2012. East Lansing, MI.
“Context-dependent selection of binding sites on DNA by cooperating proteins using a statistical
theory.”
BEACON Congress, talk, Aug. 2014. East Lansing, MI.
Volunteer
Experience
Referee /Reviewer July 2012
PLoS Computational Biology.
Referee /Reviewer Feb. 2013
BEACON Grant Review, Thrust Group 1, Genome, Networks, and Evolvability.
Referee /Reviewer Feb. 2015
BEACON Grant Review, Thrust Group 1, Genome, Networks, and Evolvability.
Volunteer April 2012
2012 Michigan Science Olympiad State Tournament, helped in coordinating the thermody-
namics competition.
Volunteer Aug. 2012
Quantitative Biology, poster. East Lansing, MI.
“Dorsal Binding Sites Conditioned on Genomic Spacer Elements.”
Volunteer Aug. 2013
Quantitative Biology, poster. East Lansing, MI.
“Dorsal Binding Sites Conditioned on Evolved Spacer Elements.”
cowritten
grant and proposal
NSF BEACON Feb. 2013 “Evolution of the Dorsal-Ventral gene regulatory network in Drosophila
species”
Skills & Expertise Code Repository https://github.com/jacobclifford/
Computer Languages C/C++, fortran*, python, perl*, bash shell( with awk, sed*), R*, mat-
lab, SAS*, Mathematica, PHP* mySQL*, Open Office Calculate, Excel, latex, version control
(git). (* not frequently used language.)
Molecular Dynamics Tools & Platforms MMTSB (CHARMM force field), LAMMPS (LJ
pairwise potentials)