My palindromic moment of Zen:
Wolf's pal spots laminate wet animal, stops, laps flow.
Interests: Machine learning and
bioinspired computing, computational biology, modeling and prediction
in complex systems, algorithms, how computing helps us to understand
1989 B.A. in physics with Honors from the University of Chicago
Thesis Advisor: Professor Thomas Rosenbaum
1995 Ph.D. in physics from the
University of California at Santa Barbara
Thesis Advisor: Professor Jean Carlson
Computational Research Scientist, Lyrid LLC, 2012-present
• Research consulting and software development
Computational Research Scientist, California Institute of Technology, 2006-2012
data integration: Applied self-organizing maps to analysis of
genome-wide ChIP-seq chromatin mark data related to transcriptional
networks. (Wold lab/ENCODE).
• Models of Calcium signal
transduction in neurons: Derived coarse-grained mathematical
approximation to a complex reaction network in the post-synaptic
density, implemented multiple level-of-detail ODE models of the
reaction network and analyzed the results (Kennedy lab).
Developed stochastic simulations to analyze spatiotemporal dynamics of
• Graphic interface development
for simulation software: Designed and developed MDLWiz, a GUI front end
to MCell3. Screenshot.(Kennedy lab).
• Bioinformatics for Chip-seq data
for the fruit fly genome: Computed measures of sequence
conservation and motif density. Developed heuristics to improve binding
site inference based upon ChIP-seq data (Stathopoulos lab).
• Instruction: Lectured on
Mathematica for science applications for a joint biology/astronomy
Physics and Computational Biology Research
Genome Atlantic Postdoctoral Fellow, Dalhousie University, Halifax, NS, 2003-2006.
phylogenetic inference: Examined the likelihood surface for
phylogenetic problems and the utility of confidence set search
heuristics in improving robustness of inference. Explored the use of
site pattern conflicts to identify poorly modeled sites.
• Protein structure energies in
phylogenetics: Analyzed site-specific substitution rates based
upon structural information.
• Recombination: Devised
algorithms for detection of recombination in amino acid sequences based
upon site pattern information.
Postdoctoral Fellow, Computational Biology, Berlex Biosciences, Richmond, CA, 2001-2003.
• Genome-wide computation and analysis of
human DNA subsequence frequencies and biological function: Architected
software to compute whole genome sequence statistics and applied
exploratory data analysis to resulting annotation.
Postdoctoral Fellow, Sloan Center for Theoretical Neurobiology, University of California, San Francisco, 1995-1996.
• A numerical model of
reinforcement learning and action choice in honeybee foraging:
Simulated a model bee using reinforcement feedback to adjust the
weights of a predictive neural model for the amount of nectar it will
receive over some time period, given its current location and health,
the perceived flower distribution, and recent past experience. Invented
animated graphic display system with GUI for setting simulation
• Visuomotor system
smooth pursuit in primates: Modeled coordination of motor behavior and
visual input mathematically.
Algorithms and Software Engineering
Computer Scientist, Autonomy and
Robotics Area, Caelum Research and QSS Group, NASA Ames Research
Center, Moffett Field, CA, 1999-2001.
Livingstone2, a model-based temporal inference system for diagnosis of
engineered systems: Extended a conflict-directed best-first search
algorithm for simultaneous tracking of multiple system trajectories.
Ported a library (L2RTAPI) from Lisp to C++ for autonomous realtime
diagnosis in a multithreaded environment.
• Stratospheric Observatory for
Infrared Astronomy (SOFIA): Modeled flight scheduling constraints
as latitude/longitude interval pruning computations using positional
astronomy techniques. http://www.nasa.gov/mission_pages/SOFIA/.
• Sensorimotor integration and
biomorph control: Innovated the use of pulse-coupled neural oscillator
networks to map sensory input to adaptive output motor behaviors in
Software Engineer, GIS Division, Autodesk, San Rafael, CA, 1998-1999.
Physics Software Engineer, Radical Entertainment, San Francisco, CA, 1997-1998.
Software Engineer, The Learning Company, Fremont, CA, 1996-1997.
Graduate Research Assistant, Dept. of Physics, University of California, Santa Barbara, 1992-1995.
Teaching Assistant, Dept. of Physics, University of California, Santa Barbara, 1989-1990 ,1991-1992.
1. “Integrating and mining the chromatin landscape of cell type specificity using self-organizing maps,” A. Mortazavi, S. Pepke, C. Jansen, G. Marinov,
J. Ernst, M. Kellis, R. Hardison, R. M. Myers, and B. Wold. To appear in Genome Research.
2. “An integrated encyclopedia of DNA elements in the human genome,” The ENCODE Consortium. Nature, vol. 488 (7414), (2012).
3. “A user’s guide to the encyclopedia of DNA elements
(ENCODE),” The ENCODE Consortium. PLoS Biol. Epub Apr 19 (2011).
4. “High resolution mapping of Twist to DNA in
Drosophila embryos: Efficient functional analysis and evolutionary
conservation,” A. Ozdemir, K. Fisher, S. Pepke, M. Samanta, L.
Dunipace, K. McCue, L. Zeng, N. Ogawa, B. Wold, and A. Stathopolous.
Genome Research 21(4):566-77 (2011).
5. “A Dynamic model of interactions of Ca2+,
calmodulin, and catalytic subunits of Ca2+/calmodulin-dependent protein
kinase II,” S. Pepke, T Kinze.r-Ursem, S. Mihalas, and M. B. Kennedy,
PLoS Computational Biology, vol. 6(2), e1000675 (2010).
6. “Computation for ChIP-seq and RNA-seq studies,”
Shirley Pepke, Barbara Wold, and Ali Mortazavi. Nature Methods Nov;
6(11 Suppl):S22-32, (2009).
7. “Using Confidence Set Heuristics During Topology
Search Improves the Robustness of Phylogenetic Inference,” Shirley
Pepke, Davin Butt, Isabelle Nadeau, Andrew J. Roger, and Christian
Blouin. Journal of Molecular Evolution, vol. 64(1), p. 80 (2007).
8. "Dynamic Models of Earthquake Faults and
Forecasting in Complex Systems," S. L. Pepke, in the 1993 Lectures in
Complex Systems, eds. L. Nadel and D. L. Stein, Addison-Wesley:
Reading, MA (1995).
9. "Prediction Studies of Earthquake Fault Models and
Applications to Seismic Catalogs," J. M. Carlson, S. L. Pepke, and V.
Kossobokov, in Reduction and Predictability of Natural Disasters, eds.
J. Rundle, W. Klein, and D. Turcotte, Addison-Wesley: Reading, MA
10. "Predictability of Self-organizing Systems," S. L.
Pepke and J. M. Carlson, Physical Review E, vol. 50, p. 236 (1994).
"Prediction of Large Events on a Dynamical Model of a Fault," S. L.
Pepke, J. M. Carlson, and B. E. Shaw, Journal of Geophysical Research -
Solid Earth, vol. 99, p. 6769 (1994).
12. "Electronic States in a Disordered Metal -
Magnetotransport in Doped Germanium," T. F. Rosenbaum, S. Pepke, R. N.
Bhatt, and T. V. Ramakrishnan, Physical Review B, vol. 42, p. 11214
1. “Livingstone2,” automated spacecraft
diagnostic software, NASA opensource, 2002.
2. Autodesk World Release 2.1 (1999)
3. Mission Think (1996)
Selected Research Presentations
"Clustering of genome-wide chromatin mark data using Self-Organizing
Maps", Shirley Pepke, Ali Mortazavi, and Barbara Wold, Genome
Informatics, Cold Spring Harbor, NY, 2011.
"Visualization and Data Mining of Integrated Whole Genome Data Using Self-Organizing Maps", (poster) Shirley Pepke, Ali Mortazavi, Georgi Marinov, and Barbara Wold, ENCODE/modENCODE Consortium Conference, March 2010.
Kinetic models of interactions among Ca(2+), calmodulin, and CaMKII: molecular components of learning and memory,
(poster) Shirley Pepke, Tamara Kinzer-Ursem, Stefan Mihalas, and Mary
B. Kennedy, International Conference on Systems Biology, Stanford
Phylogenies by Confidence Set Optimization," (poster) Shirley Pepke,
Davin Butt, Isabelle Nadeau, Andrew Roger, and Christian
Blouin, Workshop and Mathematics of Evolution and Phylogenetics,
Paris, France, June 2005.
Short Sequence Repetition Statistics of Human DNA," (poster) Shirley
Pepke, Peter Bickel, and Hugh Salamon, 68th Annual Symposium on
Quantitative Biology, Cold Spring
Harbor, NY, May 2003.
Analysis of DNA Subsequence Frequencies,” UC Santa Cruz Bioinformatics
Seminar, March 18, 2003.
Integration and Biomorph Control," Bioinspired Engineering of
Exploration Systems, Jet Propulsion Laboratory, Pasadena, CA, December
in Space and Time of Model Earthquake Faults and Earth’s Seismicity,"
Brookhaven National Laboratory Condensed Matter Theory Seminar, NY,
April 3, 1995.
of Model Earthquake Faults and Earth’s Seismicity," Center for
Nonlinear Studies Colloquium, Los Alamos, NM, November 1994.
"Predictability of Self¬organizing Earthquake Fault Models," Dynamics
Days '94 ¬ 13th Annual Conference on Chaos and Nonlinear Dynamics, Duke
University, Durham, NC, January 1994.
1993 Complex Systems Summer School sponsored by the Santa Fe Institute, Saint John's College, Santa Fe, NM