C
V
Devin P. Sullivan
Ph.D. Student in Computational Biology
Carnegie Mellon University
5000 Forbes Avenue
Pittsburgh, Pennsylvania 15213
E DUCATION
Telephone: (315)730-7737
Email: devins@cmu.edu
Vanderbilt University, Nashville, TN, B.E., 2010, Chemical and Biomolecular Engineering
Carnegie Mellon University, Pittsburgh, PA, Ph.D., anticipated May 2015, Computational
Biology (Advisor: Dr. Robert F. Murphy; Committee: Dr. Murphy, Dr. James Faeder, Dr.
Gustavo Rhode, Dr. Ivo Sbalzarini)
P ROFESSIONAL E XPERIENCE
Ph.D. Student in Computational Biology, Carnegie Mellon University-University of Pittsburgh
Joint Ph.D. Program in Computational Biology, 2010-
H
ONORS
Trainee, NIH T32 Training Grant, 2010-2012
Invited Scholar, Max-Planck Institute of Molecular Cell Biology, MOSAIC Group, June 2013
Selected attendee, Woods Hole MBL Course on Computational Image Analysis, October 2013
P
ROFESSIONAL
S
ERVICE
Committee and Society Positions
Departmental Representative, Graduate Student Association, Carnegie Mellon University 2011-
2013
Founder and Inaugural President, Carnegie Mellon University-University of Pittsburgh Joint
PhD program in Computational Biology Graduate Student Association 2013-2014
Courses and Tutorials
Teaching Assistant, Quantitative Cell and Molecular Biology Lab, Fall 2011-Fall 2012
Teaching Assistant, Cellular Response To The Environment, Fall 2011-Fall 2012
Teaching Assistant, Lab Methods in Computational Biology, Spring 2012
Teaching Assistant, Quantitative Cell and Molecular Biology Lab, Fall 2011-Fall 2012
Teaching Assistant, Algorithms and Data Structures, Spring 2014
Course Organizer, Tutorial for Computational Methods for Spatially Realistic Microphysical
Simulations, Pittsburgh Pennsylvania, April 2014
Scientific Tutorial, “Cell Organizer: Building Models of Cell Structure from Microscope Images and Using them for High-Content Screening and Cell Simulations” CYTO Congress of the
International Society for Advancement of Cytometry, San Diego, CA 2013
P ROFESSIONAL S OCIETIES
International Society for Computational Biology (ISCB) 2011-

P
UBLICATIONS
1.
J. C. Schaff, L. Smith, D.P. Sullivan, A. Lakshminarayana, & Frank Bergmann (2015).
SBML Level 3 Package Specification – Spatial Processes. https://drive.google.com/file/d/0B71r5kLs3FliZUZFb2dmU3lCWUE/view.
2.
A.W. Naik, J.D. Kangas, D.P. Sullivan, C.J Langmead and R.F. Murphy (2015). Active
Learning of the Effects of Chemical Perturbagens on Protein Subcellular Location Patterns.
In Review.
3.
T. Buck, G. Johnson, D.P. Sullivan, and R.F. Murphy (2015). Shape-space models of cell and nuclear shape. In Review.
4.
R. M. Donovan, J.J. Tapia, D.P. Sullivan, J.R. Faeder, R.F. Murphy, M.T. Dittrich, D.M.
Zuckerman (2015). Rare Event Sampling and Time-scale Extrapolation in Spatial Stochastic
Systems Biology Models Using A Weighted Ensemble Of Trajectories. In Review.
5.
D.P. Sullivan, G. Johnson, and R.F. Murphy (2015). Dynamic model of cell shape changes.
In preparation.
6.
D.P. Sullivan, R. Elyanow, X. Jiang, A.W. Naik, and R.F. Murphy (2015). Generative
Models of Neurons. In preparation.
7.
D.P. Sullivan, J.J. Tapia, R. Arepally, J. Faeder, and R.F. Murphy (2015). High-throughput spatial modeling of cells reveals cell-shape and cell-organization dependent dynamics .
In preparation.
8.
R.F. Murphy, D.P. Sullivan, I. Cao-Berg, G. Johnson, T. Buck, J. Li, G.K. Rhode (2015).
Cellorganizer: Integrated tools for image-derived models. In preparation.
P
RESENTATIONS
Oral Presentation, Great Lakes Bioinformatics Conference, Ann Arbor, Michigan, May 15, 2012
Poster Presentation, National Institute of Biomedical Imaging and Bioengineering Training
Grantees Meeting, Bethesda, Maryland, June 27, 2012
Poster Presentation, Intelligent Systems for Molecular Biology, Long Beach, California, July 18,
2012
Oral Presentation, Highlight Talk on behalf of R.F. Murphy, International Society for
Computational Biology Conference, Long Beach, California, July 18, 2012
Oral Presentation, Spatial Rule-based Modeling of Cellular Biochemistry with MCell/
BioNetGen/CellBlender, Pittsburgh, Pennsylvania, May 14 2013
Oral Presentation, Great Lakes Bioinformatics Conference, Pittsburgh, Pennsylvania, May 15,
2013
Poster Presentation, CYTO Congress of the International Society for Advancement of
Cytometry, San Diego, California, May 21, 2013
Organizer and Oral Presentation, Computational Methods for Spatially Realistic Microphysical
Simulations, Pittsburgh, Pennsylvania, April 28, 2014
Poster Presentations (3), 18th Annual International Conference on Research in Computational
Molecular Biology, Pittsburgh, PA [two were my students, how to list this?]
Poster Presentation, Systems Developmental Biology Symposium, Pittsburgh Pennsylvania, July
26, 2014

S
TUDENT
M
ENTORING
Evan Cesank, Learning structure-localization relationships from imaging data, June 2012 –
August 2012
Xuexia Jiang, Generative models of Neurons, September 2012 – June 2013 ( Received the
Elizabeth W. Jones award for excellence in undergraduate research in Experimental or
Computational Biology)
Charlotte Darby, Generative models of Neurons, January 2013 – May 2013
Marc-Daniel Julien, CellOrganizer for Python, May 2013 – August 2013
Rohan Arepally, SBML-Spatial support in CellOrganizer, May 2013 – May 2014
Bilal Jaradat, Temporal changes in cellular organization, May 2014 – July 2014
Rebecca Elyanow, Generative models of Neurons, September 2013 –