Boston University

Wesleyan University

National Cancer Institute (NCI)

Staff scientist

Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch.

Performed data processing and analyses of high-throughput Illumina RNA-seq data, single-cell RNA-Seq data, Illumina MethylCap-seq data, and PacBio SMRT RNA-Seq data. Provided bioinformatic, computational, and statistical support for various projects. Designed and developed QoRTs, an RNA-Seq quality control, visualization, and data-processing toolkit. Designed and developed JunctionSeq, a novel method, implemented as a Bioconductor package, for identifying, assessing, and visualizing differential transcript usage in RNA-Seq data.

National Human Genome Research Institute (NHGRI) www.genome.gov

Postdoctoral Fellow

Developed and applied Bayesian methods to detect pleiotropic loci associated with multiple distinct traits in sickle cell disease patients. Designed and developed fast, flexible, computationally efficient genome wide association software utilities for identifying genetic associations with multiple traits, performing genetic risk prediction, and optimizing such prediction via cross-validation. Provided data management and data cleaning for high dimensional data. Maintained and modified a mySQL database with a php frontend, organizing phenotype and genotype data from a consortium of collaborating studies in The SickleGen Project. Developed various minor software tools for efficient automated analysis, error detection, and data manipulation of large-scale datasets. Developed an internal web-based application to collect and collate input from multiple research assistants performing data entry. Managed, upgraded, and maintained a linux server, and provided technical support.

Boston University School of Public Health

Research Assistant

Conducted a validation study on automated imaging tools intended to delineate the intracranial space on magnetic resonance images, measuring deviation from a manually delineated gold standard and testing for differential bias associated with subject characteristics. Assessed the usefulness of such tools for the purposes of large-scale epidemiological studies. Developed methods to overcome automated imaging problems associated with artifacts resulting from multichannel MRI acquisition.

USUHS

(Summers only) Provided data management support and developed tools for automated manipulation and analysis of three-dimensional medical images, related to a population-based study of hippocampal shape in Alzheimer’s disease. Provided data management, analysis, and technical support for various other projects.

Steve Hartley