I’m Sean (CV | LinkedIn), a research scientist in the Pollard Lab at the Gladstone Institutes, a non-profit affiliated with UC San Francisco. My research applies machine learning to diverse projects falling broadly under gene regulation and functional genomics, such as predicting regulatory elements and their targets. We validate these computational predictions with help from our wet lab collaborators, such as the Ahituv lab at UCSF.
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.
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.
|A Chromatin Accessibility Atlas of the Developing Human Telencephalon||Cell||2020||press release|
|An atlas of lamina-associated chromatin across thirteen human cell types reveals cell-type-specific and multiple subtypes of peripheral heterochromatin||in review||2020|
|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|
|Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors||in review||2018||scientific american|
|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|
|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|