Primary focus is the innovative implementation of bioinformatics resources for infectious disease surveillance. Specialize in the utilization of cloud computing resources for on demand, inexpensive, scalable bioinformatic solutions.

Designed and developed the CDPHE Advanced Molecular Detection (AMD) platform for outbreak surveillance and detection. Platform consists of pathogen characterization using next generation sequencing (NGS) and distributed cloud-based bioinformatics analysis. Sequencing and analysis occur in real-time for quick and effective public health response to pathogen outbreaks.Acquired funding to develop and direct the mountain region CDC AMD Bioinformatics Resource Support Site. One of only seven CDC funded bioinformatics resource support sites in the US. These sites were created to foster the development of bioinformatics capacity at the state and local level. Activities include assisting with bioinformatics development, training state and local public health laboratorians/epidemiologists, and performing ad-hoc bioinformatics analysis for outbreak detection and surveillance.Direct the Mountain Region CDC PulseNet Area Lab activities for CDPHE. The funding for the CDPHE area lab supports activities that overlap with the training goals of the Bioinformatics Resource Support Site and Workforce Development lead, but also support surge capacity for mountain region labs in the event of a regional or national outbreak.Co-founded the State Public Health Bioinformatics group (StaPH-B). StaPH-B is a consortium of public health scientists interested in addressing the common barriers impeding bioinformatics implementation in state public health laboratories.Chair of the CDC AMD Academy Steering Committee. The CDC's AMD Academy focuses on workforce development for both microbiologists and bioinformaticians as public health laboratories transition towards AMD focused workflows.Co-chair of the CDC Emerging Infections Program (EIP) AMD Workgroup and member of both the APHL Food Safety Committee and the APHL NGS Subcommittee.Direct the APHL/CDC Bioinformatics Host Lab at CDPHE. Mentor for an APHL/CDC Bioinformatics Fellow for 2017-2018.

Directed the Molecular and Microbiology Program responsible for developing novel microorganisms for the bioconversion of biomass derived sugars into valuable biochemicals traditionally produced by the petroleum industry. This program included genetic and metabolic engineering to develop microorganisms producing dicarboxylic acids, enzyme hydrolysis for the saccharification of pretreated biomass into monomeric sugars, and bioprospecting to isolate novel microorganisms with favorable characteristics for the bioconversion process.Designed, built, and developed our entire Advanced Molecular Detection Platform which includes nucleic acid extraction, PCR, qPCR, 16S community profiling and amplicon sequencing on an Illumina MiSeq, whole genome sequencing on an Illumina MiSeq, Linux server with computational capabilities for community profiling and whole genome assembly and analysis, and database storage (Tribal LIMS) of community sequencing and analysis to enable visualization of results using the Spotfire platform.Responsible for the active identification, establishment, and maintenance of research collaborations, both academic and industrial, aimed at accelerating Ciris Energy’s biomass conversion efforts.

Lead a multidisciplinary team of scientists improving the rate and yield of biogenic methane production from subsurface hydrocarbon deposits. Areas of responsibility include 1) understanding the nature and function of indigenous microbes in subsurface hydrocarbon deposits, 2) understanding the bioavailable hydrocarbon resource utilized by these microbes, 3) applying this knowledge to successfully achieve corporate objectives and execute commercialization strategies, and 4) active involvement in intellectual property management and strategy to protect our freedom to operate and first mover advantage.

A leader in the development and execution of our Intellectual Property Strategy aimed at protecting Luca’s proprietary technology both in the US and internationally.One of several team members directing the actions of a multidisciplinary team of microbiologists, molecular biologists, geologists, reservoir engineers, and field operators with regards to field project design, permitting, execution, and evaluation.Responsible for the active identification, establishment, and maintenance of research collaborations, both academic and industrial, aimed at accelerating Luca’s research efforts.Developed from the ground up a high throughput platform for microbial community profiling of subsurface, anaerobic microbial communities involved in hydrocarbon biodegradation. This platform has processes both field and laboratory samples to identify microbial community composition. Results from this platform add value to Luca through the identification of targets for 1) new amendment strategies, 2) monitoring field restoration progress, and 3) evaluating new assets for acquisition.

Created bioinformatics tools for whole genome searching using shotgun proteomic data for identification of novel open reading frames. Developed methods to apply this technology to microbial genome annotation using metagenomic sequences from mixed microbial communities. Tools also employed for the detection of novel SNPs in human clinical samples.Developed experimental design, along with experimental and analytical tools, for whole proteome profiling of dynamic protein turnover in microbial systems. Methods and tools used to examine protein turnover and metabolic regulation in Escherichia coli protease mutants and Pyrococcus furiosus.Lead scientist for project utilizing proteomics to classify the mechanism of action of natural product anti-cancer leads. Results will be used to design high-throughput assays to detect protein signatures of cancer cells in response to treatment with natural product compounds.Co-developed experimental design and data analysis methods for the proteomic analysis of the innate immune response in human subjects. Methods in use for $26 million contract examining biofluids in over 400 individuals immunized against typhoid and cholera. Methods include 2D gel (DIGE), LC-MS, and LC-MS/MS analysis of plasma, serum, and saliva.Created quantitative methods using peptide immobilized pH gradient isoelectric focusing and isotope labeling for shotgun proteomics. Methods solved previous pitfalls of trypsin catalyzed back-exchange of 18O during isoelectric focusing of peptides. Established methods for increased throughput using peptide immobilized pH gradient isoelectric focusing and shotgun proteomics. Improvements included parallel and robotic processing of samples for higher efficiency and reproducibility.

Integrated proteomic and genomic data sets to examine changes in mRNA and protein simultaneously during activation of the MAPK pathway during human megakaryocyte differentiation.Analyzed the transcriptional program of megakaryocyte differentiation in human peripheral blood CD34+ stem cells and K562 erythroleukemia cells using Affymetrix microarrays.Studied the role of the MAPK pathway in the regulation of human megakaryocyte differentiation.Discovered previously unknown role of the human transcription factor MafB in megakaryocyte differentiation.Demonstrated regulation of megakaryocyte differentiation through combinatorial activation of three separate transcription factors.

Integrated proteomic and genomic data sets to examine changes in mRNA and protein simultaneously during activation of the MAPK pathway during human megakaryocyte differentiation.Analyzed the transcriptional program of megakaryocyte differentiation in human peripheral blood CD34+ stem cells and K562 erythroleukemia cells using Affymetrix microarrays.Studied the role of the MAPK pathway in the regulation of human megakaryocyte differentiation.Discovered previously unknown role of the human transcription factor MafB in megakaryocyte differentiation.Demonstrated regulation of megakaryocyte differentiation through combinatorial activation of three separate transcription factors.

Discovered role of caveolae in regulating ligand-induced cell surface proteolysis of the tissue factor-dependent coagulation pathway.Research led to novel insights on how tissue factor, factor VII, factor X, and TFPI interact on the endothelial cell surface, sequester into caveolae, and regulate the tissue factor-dependent coagulation pathway.