Adam Scott, Ph.D.
McDonnell Genome Institute
Washington University

I have made available some samples of my research publications, programming, presentations, and a list of current things I've been working on.


Niu, B., Scott A.D., Sengupta S., et al. "Protein-structure-guided discovery of functional mutations across 19 cancer types". Nature Genetics (2016).

Ye, K. et al. "Systematic discovery of complex insertions and deletions in human cancers". Nature Medicine (2015).

Scott, A.D., et al. "Clustering and Phase Transitions on a Neutral Landscape" Europhysics Letters (2013).

"Directed Percolation in a Neutral Phenotype Evolution Model" (under review)

"Cluster Lineage Branching-Fragmenting Characteristics" (in preparation)


For public programming contributions, please see my GitHub repositories.

HotSpot3D is a downloadable tool that determines mutation (drug) pairs and clusters by mapping mutations onto 3D protein structures.

Babies (also in parallel): Babies is the program that my entire dissertation is dependent upon. There is a README included in the zip file that downloads with the link to help describe its use. I use Windows 7 and Matlab 2013a, so I am unsure whether it will run on a Mac or with Linux. It uses the Statistics Toolbox, and parallel uses the Parallel Processing Toolbox.
If you'd like to use the program or make changes to it and do your own thing, then enjoy! I'm sure my advisor, Dr. Sonya Bahar would like to know what you do with it in case our lab has already given your idea a go. You can contact Sonya at her email or office phone listed on the Center for Neurodynamics website.

EvoSim: EvoSim is the C++ variant of Babies. I wanted Babies to be portable, so this is my contribution toward that goal. There are a few bugs left, so I apologize for that. It's been a year or two since I last worked on this heavily, but I'm still rather proud of where I got it. I've compiled it in Microsoft Visual Studio 2010, so I'm not sure how it will do in other compilers.

Wilson Neural Network: My implementation of a network of Wilson neurons (model of bursting and spiking mammalian neocortex neurons) includes my own model of variable glutamate for synaptic coupling. My synaptic model was derived by introducing an activity-dependent variable to influence the synaptic coupling between neurons. The link downloads a zip file that includes the necessary functions to run simulations in Matlab. The particular Wilson model I am referring to is described in "Simplified Dynamics of Human and Mammalian Neocortical Neurons", published in Journal of Theoretical Biology, 1999 by Hugh R. Wilson. I also reference model parameters used by a former colleague, Daisuke Takeshita. This is his article, "Transitions between multistable states as a model of epileptic seizure dynamics" , published in Physical Review E with co-authors Yasuomi D Sato and Sonya Bahar.

Hindmarsh Rose Project: For my final project in my graduate course in nonlinear dynamics, I explored the dynamics of the Hindmarsh-Rose model neuron. The link downloads a zip file containing my final paper as well as a folder with my Matlab scripts and functions. The main m-file to run is main_Hindmarsh_Rose.m. The paper details parameters I used along with the observed dynamics. There are many figures and measures from nonlinear dynamics included, such as bifurcation diagrams, cobweb diagrams, Lyapunov exponents, and Poincare sections.

Dissertation related works:

My dissertation defense:
"Speciation Dynamics of an Agent-based Evolution Model in Phenotype Space"

My dissertation feasibility study (proposal):
"Speciation Dynamics of an Agent-based Evolution Model in Phenotype Space"

My comprehensive exam presentation (more of an outline of the feasibility study):


"Cluster-Level Dynamics in a Neutral Phenotype Evolution Model"
APS March Meeting - Denver, CO - 2014 - Oral

"Mutability Driven Phase Transitions in a Neutral Phenotype Evolution Model"
Evolution - Snowbird, UT - 2013 - Oral

"Characterizing Phase Transitions in a Model of Neutral Evolutionary Dynamics"
APS March Meeting - Baltimore, MD - 2013 - Oral

"Clustering and Phase Transitions on a Neutral Landscape"
Evolution - Ottawa, Canada - 2012 - Poster

"Clustering and Phase Transitions on a Neutral Landscape"
APS March Meeting - Boston, MA - 2012 - Oral

"Computational Evolution Modeling and Neutral Theory"
UMSL Graduate Research Fair - 2011 - Poster

"Adaptation of Mutability in a Computational Evolutionary Model"
Evolution - Portland, OR - 2010 - Poster

Hobby programming:

I decided to program a simple game, Reversi (Othello according to some publishers). Here is the source code and application. It compiles in VS2010 and uses DirectX. DX9 should be sufficient, and if you compile, change the settings from Unicode to MultiByte. Also, don't forget to include the DX Include and Lib directories/library files. The controls are: arrow keys = move selected space (highlighted), right ctrl = plays piece, right shift = pass, backspace = reset.
Enjoy! (let me know if you find any bugs)

© 2016 Adam D. Scott, PhD