node99.org | cv

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
Deep learning prediction of gene expression from personal genomes submitted 2024  
Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex Science 2024 press release
Three-dimensional genome re-wiring in loci with Human Accelerated Regions Science 2023 nytimes
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

tutorials.

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