welcome.

I’m Sean (CV | LinkedIn), a senior research scientist in the Pollard Lab at the Gladstone Institutes, a non-profit affiliated with UC San Francisco. My research uses the intersection of machine learning, evolution, gene regulation, and functional genomics to study disease in brain and heart development. We develop and test our predictive models with our wet lab collaborators such as the Ahituv, Pollen, and Rubenstein labs at UCSF and the Srivastava lab at Gladstone.

I have a Ph.D. in cybersecurity from UC Davis (w/Matt Bishop & Jim Crutchfield) and was a postdoc at Lawrence Berkeley National Laboratory (I3P fellow) and Columbia University (w/Sal Stolfo) before switching to computational biology and doing a postdoc at Mount Sinai School of Medicine (w/Gaurav Pandey). I’m also interested in information visualization and virtual reality, having developed a network visualization tool with head tracking and gesture recognition for the KeckCAVES project.

My partner and frequent collaborator is Sophie Engle, an Associate Professor of Computer Science at the University of San Francisco.

publications.

The following papers, book chapters, and extended abstracts have all been peer reviewed. Computer science publishes much of its research via competitive peer-reviewed conference and workshop proceedings in addition to journals, whereas biology typically reserves peer review for journals.

Title	Publication	Year	Other
Three-dimensional genome re-wiring in loci with Human Accelerated Regions	Science	2023	nytimes
Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex	in review	2023
Machine learning dissection of Human Accelerated Regions in primate neurodevelopment	Neuron	2018/2023	press release scientific american
An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype	Genome Biology	2023
Single Cell Epigenetics Reveal Cell-Cell Communication Networks in Normal and Abnormal Cardiac Morphogenesis	in review	2022
Enhancer Function and Evolutionary Roles of Human Accelerated Regions	Annual Review of Genetics	2022
Navigating the pitfalls of applying machine learning in genomics	Nature Reviews Genetics	2021
Autism risk gene POGZ promotes chromatin accessibility and expression of clustered synaptic genes	Cell Reports	2021
A Chromatin Accessibility Atlas of the Developing Human Telencephalon	Cell	2020	press release
lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements	Nature Protocols	2020
AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design	Genome Biology	2019
The Glycan CA19-9 Promotes Pancreatitis and Pancreatic Cancer	Science	2019
Most chromatin interactions are not in linkage disequilibrium	Genome Research	2019
The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation	Journal of Virology	2018	spotlight
Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity	Cell Stem Cell	2017
Genomic analyses for age at menarche identify 389 independent signals and indicate BMI-independent effects of puberty timing on cancer susceptibility	Nature Genetics	2017
Enhancer-Promoter Interactions are Encoded by Complex Genomic Signatures on Looping Chromatin	Nature Genetics	2016	news & views research highlight press release
Unboxing Cluster Heatmaps	Proceedings of the 6th Symposium on Biological Data Visualization (held in conjunction with IEEE VIS)	2016
Prediction of Human Population Responses to Toxic Compounds by a Collaborative Competition	Nature Biotechnology	2015
Predicting Protein Function and Other Biomedical Characteristics with Heterogeneous Ensembles	Methods	2015
Model Aggregation for Distributed Content Anomaly Detection	Proceedings of the 7th ACM Workshop on Artificial Intelligence and Security (held in conjunction with the 21st ACM Conference on Computer and Communications Security)	2014	pdf
Enhancing the Functional Content of Eukaryotic Protein Interaction Networks	PLoS ONE	2014	bibtex
A Comparative Analysis of Ensemble Classifiers: Case Studies in Genomics	Proceedings of the 13th IEEE International Conference on Data Mining	2013	bibtex pdf
Multiclass Classification of Distributed Memory Parallel Computations	Pattern Recognition Letters	2013	bibtex pdf
Visualizing Distributed Memory Computations with Hive Plots	Proceedings of the 9th International Symposium on Visualization for Cyber Security (held in conjunction with the 14th Annual IEEE VIS Conference)	2012	bibtex
Structural Drift: The Population Dynamics of Sequential Learning	PLoS Computational Biology	2012	bibtex
Network-Theoretic Classification of Parallel Computation Patterns	International Journal of High Performance Computing Applications	2012	bibtex pdf
A Taxonomy of Buffer Overflow Characteristics	IEEE Transactions on Dependable and Secure Computing	2012	bibtex
This is the Remix: Structural Improvisation using Automated Pattern Discovery	Proceedings of the 4th International Workshop on Machine Learning and Music (held in conjunction with the 25th Annual Conference on Neural Information Processing Systems)	2011
Network-Theoretic Classification of Parallel Computation Patterns	Proceedings of the 1st International Workshop on Characterizing Applications for Heterogeneous Exascale Systems (held in conjunction with the 25th International Conference on Supercomputing)	2011	bibtex
Hidden Markov Models for Automated Protocol Learning	Proceedings of the 6th International ICST Conference on Security and Privacy in Communication Networks	2010	bibtex
A Risk Management Approach to the Insider Threat	Insider Threats in Cybersecurity — And Beyond, Springer Verlag	2010	bibtex
Case Studies of an Insider Framework	Proceedings of the 42nd Annual Hawaii International Conference on System Sciences	2009	bibtex
We Have Met the Enemy and He is Us	Proceedings of the 2008 New Security Paradigms Workshop	2008	bibtex

welcome.

publications.

tutorials.