We specialize in extracting useful information out of a sea of biological data, which includes next-generation sequencing (NGS) data encompassing genomic, epigenomic and transcriptomic profiling. We also have experience analyzing proteomics, metabolomics and single-cell data. Analysis tools utilized include: JMP Pro (SAS), Partek Genomics Suite (Partek Inc.), Ingenuity Pathway Analysis (Qiagen), DRAGEN Bio-IT, SPADES, MEGAHIT, Funannotate, NextFlow, Docker, DEseq2, antiSMASH , Rstudio, Phobius,… Show more We specialize in extracting useful information out of a sea of biological data, which includes next-generation sequencing (NGS) data encompassing genomic, epigenomic and transcriptomic profiling. We also have experience analyzing proteomics, metabolomics and single-cell data. Analysis tools utilized include: JMP Pro (SAS), Partek Genomics Suite (Partek Inc.), Ingenuity Pathway Analysis (Qiagen), DRAGEN Bio-IT, SPADES, MEGAHIT, Funannotate, NextFlow, Docker, DEseq2, antiSMASH , Rstudio, Phobius, SignalP and BaseSpace Suite/Illumina Connected Analytics/Correlation Engine (Illumina). Show less

I was originally hired as a bioinformatics consultant before coming on full-time as Director of Discovery and Data Science at Mycotechnology, managing up to eight R&D scientists at a time. Duties included project management, natural compound testing, regulatory compliance, strain development, database building, and data analytics. Extensive use of genomic and proteomic techniques to characterize natural compounds in filamentous fungal species. A list of some highlights during my employment are… Show more I was originally hired as a bioinformatics consultant before coming on full-time as Director of Discovery and Data Science at Mycotechnology, managing up to eight R&D scientists at a time. Duties included project management, natural compound testing, regulatory compliance, strain development, database building, and data analytics. Extensive use of genomic and proteomic techniques to characterize natural compounds in filamentous fungal species. A list of some highlights during my employment are given below:• Created and maintained bioinformatics pipelines for de novo genome assembly, RNAseq analysis, Secondary Metabolite Gene Cluster prediction, comparative genomics, variant analysis, gene prediction, functional annotation, global protein analytics and allergen/mycotoxin testing.• Identified gene that codes for sweet protein in the Hungarian honey truffle, the first sweet molecule found in the fungal kingdom. This work has resulted in two patents and is currently being developed for commercialization.• Created a platform for identifying and classifying bioactives in complex mixtures of natural compounds. This work has resulted in the filing of two provisional patents.• Worked closely with Regulatory and Compliance on Generally Recognized As Safe (GRAS) filings and de novo allergen and mycotoxin assessments for the FDA.Familiar with software platforms Illumina Connected Analytics, DRAGEN Bio-IT, SPADES, MEGAHIT, Funannotate, NextFlow, Docker, DEseq2, antiSMASH , Rstudio, Phobius and SignalP Show less

Position involved mentoring graduate students, post-docs, medical research fellows and junior faculty, as well as applying for and managing of federal funding. I was a member of many medical and academic associations, as well as serving as Bioinformatics Director for the UCCC Lung SPORE. I was fortunate enough to work on a wide variety of research projects during this time due to my specialization in bioinformatics:Disease States/Phenotypes Investigated• Lung ConditionsChronic… Show more Position involved mentoring graduate students, post-docs, medical research fellows and junior faculty, as well as applying for and managing of federal funding. I was a member of many medical and academic associations, as well as serving as Bioinformatics Director for the UCCC Lung SPORE. I was fortunate enough to work on a wide variety of research projects during this time due to my specialization in bioinformatics:Disease States/Phenotypes Investigated• Lung ConditionsChronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis, mechanical ventilation injury, hypoxia, non-small cell lung cancer, emphysema, pulmonary hypertension, acute respiratory distress syndrome, pre-malignant lung dysplasia and alcohol-related lung disease• Cancer typesPituitary gonadotrope, lung (NSCLC, SCLC, and pre-malignant lesions), bladder, skin and renal cancer• OtherSchizphprenia, schstosomiasis, atopic dermatitis, eczema, hepatitis C infection, skin development, non-alcoholic fatty acid liver disease, chronic spontaneous urticaria, HIV, obesity, and nerve repairTypes of Data Analyzed• Next-generation DNAseq/RNAseq, ChIPseq, single cell sequencing, miRNA and mRNA microarrays, single nucleotide polymorphisms, chromosomal aberrations, genome wide association studies, mass spectrometry, immunological-based protein arrays, metabolomics and qPCRBioinformatics Tools Utilized• DRAGEN Bio-IT, JMP/JMP Genomics, Partek Genomics Suite, Partek Flow, Cytoscape, BaseSpace Suite, Correlation Engine, Cohort Analyzer, STRING, Ingenuity Pathway Analysis, Pathway Studios, DAVID and GalaxyI was an author on 31 peer-reviewed science publications, as well as a co-author on many NIH/NCI/NHLBI Research Project Grants while assistant professor. I also served as Assistant Director, NHLBI Summer Course in Genomics and Proteomics of Heart, Lung, Blood and Sleep Disorders and Assistant Director of the Bioinformatics Section in the Division of Pulmonary and Critical Care Medicine. Show less

Director of the Bioinformatics Core for the Lung Specialized Program of Research Excellence (SPORE) at the University of Colorado Denver. Duties included experimental design of integrated research projects, analysis of high-throughput genomic and proteomic data, managing statisticians and programmers associated with the Core, and presenting research results and performance metrics at monthly updates and biannual reviews.

I provided bioinformatics support to a variety of lung focused projects, as well as conducting my own laboratory research on COPD. My salary and laboratory expenses were covered by a three year research fellowship from the Flight Attendants Medical Research Institute (FAMRI). I worked closely with the UC Denver Sequencing/Genomics Core, led by Dr. Befing Gao. Experience gained during this time was the exposure to many types of disease models and the opportunity to generatate experimentally the… Show more I provided bioinformatics support to a variety of lung focused projects, as well as conducting my own laboratory research on COPD. My salary and laboratory expenses were covered by a three year research fellowship from the Flight Attendants Medical Research Institute (FAMRI). I worked closely with the UC Denver Sequencing/Genomics Core, led by Dr. Befing Gao. Experience gained during this time was the exposure to many types of disease models and the opportunity to generatate experimentally the data I would eventually analyze. Show less

Fellowship in proteomics focused on identifying protein indicators of pathogen infection in blood samples. Techniques utilized included LC MS/MS, MALDI-TOF, SELDI, immuno-based protein arrays and extensive 2D gel differential analysis. Results from this work led to a patent on protein-based biomarkers used to classify infection by microscopic parasites (spread by certain ticks) in human blood samples.

My doctoral research focused on the effect of age, calorie restriction and oxidative stress on gene expression in muscle tissue. This work was done in the early days of gene expression array technology, and represents many 'firsts' in both arrayed biological conditions and new analytical techniques and findings. My initial publications were the first microarray studies to examine acute oxidative stress in vivo in the mammalian heart. I presented evidence for the first time of a delayed and… Show more My doctoral research focused on the effect of age, calorie restriction and oxidative stress on gene expression in muscle tissue. This work was done in the early days of gene expression array technology, and represents many 'firsts' in both arrayed biological conditions and new analytical techniques and findings. My initial publications were the first microarray studies to examine acute oxidative stress in vivo in the mammalian heart. I presented evidence for the first time of a delayed and reduced global gene expression response to acute oxidative injury with age, with specific impairment of early stress response genes and the GADD45 family of stress sensors. I also showed evidence for a p53-driven mechanism of aging in mammalian skeletal muscle, and how this effect is mitigated with the anti-aging regimen of caloric restriction. The increase in p53 activity with age was obtained indirectly by examining the change in expression of genes known to bind to, activate and inhibit p53 (a novel method at the time) and predates the “upstream regulator” analysis function on the popular bioinformatics software platform, Ingenuity Pathway Analysis, by at least five years. Show less