Scientific Research- Established and managed a computational biology research group consisting of 3--10 postdoctoral scholars, graduate research assistants, and undergraduate students studying complex regulatory and developmental networks.- Authored 24 peer-reviewed publications with over 1100 citations.- Presented my work at 25+ national and international conferences.- Personally wrote hundreds-of-thousands of lines of code using both high- and low-level programming languages for computational biology investigations.Scientific Collaboration- Established collaborations with biology and biochemistry researchers wanting to use our analysis methods and expertise to further their research goals.- Developed joint project plans with collaborating investigators for executing the experiments, software development, and data analysis necessary for project success.- Communicated complex results to non-technical collaborators through visualization.Recent Computational Biology Projects- Analyzed next-gen sequencing data from RNA-Seq and Hi-C experiments to construct a Bayesian model of chromosome conformation dynamics.- Discovered and quantified new neuronal cell types in the retina using high-throughput cell identification and analysis in multi-TB tissue imaging data sets.- Wrote a deep learning pipeline for real-time control of microscopes performing live-cell imaging. Used our software to collect a data set of 1000+ cell growth movies.- Developed a convolutional neural network based on U-net to automate post-imaging data analysis and cell segmentation of time-lapse microscopy images.- Derived a novel stochastic model of liquid-liquid phase separation in cells. Created a Bayesian inference method to parameterize the model from single-molecule data.Group and Project Management- Trained and mentored junior group members in computational biology techniques.- Obtained federal funding for my research by writing competitive grant proposals.

- Built and analyzed novel stochastic models of cells.- Developed a Matlab pipleline for segmentation and quantification of gene expression in Methanosarcina cells following fluorescence microscopy. This was the first fluorescence imaging assay in methanogens.- Developed new algorithms for massive parallelization of reaction-diffusion codes on GPU clusters using CUDA.

- Created a pipeline for comparative structure and sequence analysis of genes from 1000+ bacterial and archaeal genomes. Used the pipeline to study the evolution of the ribosome and the origin of life with Carl Woese.- Developed the widely used and highly cited MultiSeq bioinformatics package for combined sequence and structure analysis of proteins and RNA.

- Lead a small team of software engineers developing a new business-to-business web application, which was widely credited with attracting an extensive new client base and dramatically reducing costs.

- Developed a new Java-based internet platform for business-to-business transactions.