Adam David Scott, Ph. D.
Adam David Scott, Ph. D.
1
McDonnell Genome Institute
Washington University School of Medicine
4444 Forest Park Ave
St. Louis, MO 63108
www.AdamScottPhD.com
adam@AdamScottPhD.com
(573)-745-0514
EDUCATION
Postdoctoral Training
McDonnell Genome Institute at Washington University School of Medicine – 2014-present
Ding Lab: Cancer Genomics/Bioinformatics
Ph.D. Physics – 2014
Dissertation: “Speciation Dynamics of an Agent-based Evolutionary Model in Phenotype Space”
University of Missouri at St. Louis, St. Louis, MO
Co-op through Missouri University of Science and Technology, Rolla, MO
Master of Science Physics – 2009
University of Missouri at St. Louis, St. Louis, MO
Bachelor of Arts Physics – 2007
Bachelor of Arts Mathematics – 2007
Minor Global Studies – 2007
Drury University, Springfield, MO
PUBLICATIONS
B. Niu*, A. D. Scott*, S. Sengupta*, M. H. Bailey, P. Batra, M. D. McClellan, M. Wyczalkowski, P. Tripathi, K.
Ye, R. J. Mashl, Q. Zhang, J. Wallis, M. C. Wendl, F. Chen, and L. Ding. “HotSpot3D: Inferring Functional and
Druggable Mutations from Protein Structure Spatial Analysis”. In preparation. (* = co-first)
A. D. Scott, D. M. King, and S. Bahar. “Directed Percolation in a Neutral Phenotype Evolution Mode”. In
preparation
D. M. King, A. D. Scott, N. Marić, S. Bahar. “Random Death Drives Neutral Phenotype Evolution Model Phase
Transition”. In preparation.
A. D. Scott, D. M. King, N. Marić, and S. Bahar. “Clustering and Phase Transitions on a Neutral Landscape”.
Europhysics Letters 102 68003. 2013. doi:10.1209/0295-5075/102/68003
Adam David Scott, Ph. D.
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RESEARCH EXPERIENCE
References available upon request
McDonnell Genome Institute at Washington University, 2014-present
Mutation Clustering and Software Development with Protein Structure Analysis
Added a mutation clustering module (Perl) for the HotSpot3D software that helps identify functional and
druggable genomic mutations through spatial protein structure analysis. (with a team under Dr. Li Ding,
2014-2015)
Software Development of Proteome Analysis
Developed a pipeline wrapper (Bash) for the PepScan software that finds genomic support from iTRAQ
mass spec proteome data. Also trained a graduate student on the software. (with Dr. Song Cao, 2014)
Software Development for Genomic Indels
Added a file conversion tool (C++) for the Pindel software that detects genomic insertions and deletions
(indels). The tool converts Pindel data into SAM/BAM files, aiding in the analysis of indel detection.
(with Dr. Kai Ye, 2014)
University of Missouri at St. Louis, 2008-2014
Computational Phase Transitions and Clustering of Evolving Populations
Designed and programmed new variations of an evolution model and focused on studying agent level
and cluster level interactions (dissertation research, adviser Dr. Sonya Bahar, 2008-present)
Computational Non-Linear Dynamics Modelling of Seizures
Introduced synaptic variability as a model for neurotransmitter fluctuation in a network of modified
Hodgkin-Huxley style neurons to model epileptic seizures in a mammalian neocortex (adviser Dr.
Sonya Bahar, 2008-2012)
Computational Synchronization of Neural Networks
Designed and programmed a clustering algorithm based on neuron synchronization (with Dr.
Kaushalya Premachandra and Dr. Sonya Bahar, 2012)
Experimental Neural Electrophysiology and Optical Imaging
Conducted surgeries and imaged (intrinsic optical imaging) in vivo drug-induced seizures in the
neocortex of rats as a model to study the dynamics of neurons during epileptic seizures (adviser Dr.
Sonya Bahar, 2008-2010)
Drury University & NASA Microgravity University, 2006-2007
Experimental Modelling of Human Arm Muscles
Helped design and construct a robotic arm to study microgravity effects on a muscle model in the
laboratory and on NASA’s Weightless Wonder aircraft (undergraduate physics major research, adviser
Dr. Greg Ojakangas)
Drury University, 2006-2007
Computational Signal Processing
Studied and designed guitar pedal effects (undergraduate mathematics major research, adviser Dr.
Scott Simmons)
University of Arkansas – Fayetteville, 2006
Computational Optical Properties of Quantum Dots
Data analysis of optical properties of quantum dots from first principles (research experience for
undergraduates, adviser Dr. Huaxiang Fu)
Adam David Scott, Ph. D.
TEACHING EXPERIENCE
University of Missouri at St. Louis
Graduate Teaching Assistant
Modern Physics, Fall 2012
Electricity & Magnetism review, Summer 2011
Introductory Electricity, Magnetism, and Optics lab for non-majors, Summer 2011
Introductory Electricity, Magnetism, and Optics lab for majors, Spring 2010
Introductory Electricity, Magnetism, and Optics discussion for majors, Spring 2010
2 courses: Introductory Electricity, Magnetism, and Optics lab for majors, Fall 2009
Introductory Mechanics and Heat lab for non-majors, Fall 2009
3 courses: Introductory Electricity, Magnetism, and Optics lab for non-majors, Summer 2009
2 courses: Introductory Electricity, Magnetism, and Optics lab for non-majors, Spring 2009
2 courses: Introductory Mechanics and Heat lab for non-majors, Fall 2008
3 courses: Introductory Electricity, Magnetism, and Optics lab for majors, Summer 2008
University of Arkansas – Fayetteville
Graduate Teaching Assistant
2 courses: Introductory Mechanics, Spring 2008
2 courses: Introductory Mechanics, Fall 2007
Drury University
Tutor
Physics Department, 2005-2007
Mathematics Department, 2004-2007
Self-Employed
Private Tutor
Physics & mathematics for high school students and undergraduates, 2003-present
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Adam David Scott, Ph. D.
WORKSHOPS & CONFERENCES
The American Physical Society March Meeting; Denver, CO, 2014
Talk: “Cluster-Level Dynamics in a Neutral Phenotype Evolution Model”
Evolution; Snowbird, UT, 2013
Talk: “Mutability Driven Phase Transitions in a Neutral Phenotype Evolution Model”
University of Missouri at St. Louis – Graduate Research Fair; St. Louis, MO, 2013
Poster: “Directed Percolation in a Neutral Phenotype Evolution Model”
The American Physical Society March Meeting; Baltimore, MD, 2013
Talk: “Characterization of Phase Transitions in a Model of Evolutionary Dynamics”
Evolution; Ottawa, Canada, 2012
Poster: “Clustering and Phase Transitions on a Neutral Landscape”
University of Missouri at St. Louis – Graduate Research Fair; St. Louis, MO, 2012
Poster: “Clustering and Phase Transitions on a Neutral Landscape”
The American Physical Society March Meeting; Boston, MA, 2012
Talk: “Clustering and Phase Transitions on a Neutral Landscape”
University of Missouri at St. Louis – Graduate Research Fair; St. Louis, MO, 2011
Poster: “Computational Evolution Modeling and Neutral Theory”
Evolution; Portland, OR, 2010
Poster: “Adaptation of Mutation in a Computational Evolutionary Model”
NEURON; San Diego, CA, 2010
Workshop: Learned to model neurons and networks of neurons with the software, Neuron and programming
in Python
Dynamics of Bursting Activity of Neurons; Atlanta, GA, 2010
Workshop: Attended talks focused on current research of neural bursting dynamics in model systems
Kappa Mu Epsilon National Convention; 2004, 2005, 2006
Attended the mathematics honor society’s national conventions
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Adam David Scott, Ph. D.
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SOCIETIES & INVOLVEMENT
American Physical Society Local Links – St. Louis, 2015Planning committee member – postdoc representative
Society for the Study of Evolution, 2013American Physical Society, 2011Division of Biological Physics
Division of Computational Physics
American Association of Physics Teachers, 2010-2011
Graduate Student Advisory Committee to the Dean
Representative for the Department of Physics and Astronomy, 2011-2012
Sigma Pi Sigma (Physics Honor Society), 2007
President, 2007
Helped to revive Drury’s chapter after 37 years of inactivity, 2007
Society of Physics Students, 2006-2007
President, 2006-2007
Helped to revive Drury’s chapter after 37 years of inactivity, 2006
Drury Physics Club, 2005-2007
President, 2006-2007
Kappa Mu Epsilon (Mathematics Honor Society), 2004-2007
President, 2006-2007
Vice President, 2005-2006
Drury Math and Computer Science Club, 2004-2007
President, 2006-2007
Vice President, 2005-2006
AWARDS
University of Missouri at St. Louis
Outstanding Poster
Department of Physics & Astronomy Graduate Research Fair, 2012
American Association of Physics Teachers: Outstanding Teaching Assistant of the Year
Department of Physics & Astronomy, 2010 (http://www.aapt.org/Programs/awards/otaawards2010.cfm)
Drury University
Outstanding Physics Student
Department of Physics, 2005-2006
Meritorious Winner
Mathematical Contest in Modeling, 2006
Honorary Mention
Mathematical Contest in Modeling, 2005