Experience

Variant Bio
• United States
• Biotechnology Research
• 1 - 100 Employee
• Computational Biologist

  • Jun 2022 - Present


Leidos Biomedical Research, Inc.

• United States
• Research Services
• 200 - 300 Employee

• • Feb 2022 - May 2022

  In addition to handling multiple analysis projects simultaneously, I particpate in manager meetings, helping to set policies and agendas for all groups within the Advanced Biomedical Computational Science (ABCS) section at Frederick National Lab for Cancer Research.-- multi-tasking a diverse set of analysis projects, along with supervisory duties-- Supervising three Ph.D.-level bioinformaticians, sharing both ideas and code with the team to standardize multi-omics analyses-- Administrative tasks for existing and new hires, performance reviews, project proposals Show less

• • Feb 2020 - Feb 2022

  Team leader at the CCR Collaborative Bioinformatics Resource (CCBR), providing bioinformatics support for investigators at the National Cancer Institute (NCI)-- Scalable pipeline development for use on local HPC systems and AWS-- Analyzed large exome, genome, and RNA datasets for human cohorts for publication in high-impact journals-- Supervised two embedded bioinformaticians dedicated to specific research programs at NCI

• • Apr 2018 - Feb 2020

  Providing bioinformatics support for the Center for Cancer Research (CCR) at the National Cancer Institute (NCI) through the CCR Collaborative Bioinformatics Resource.-- Experimental design and sequencing technology selection-- Raw data processing from short-read and long-read technologies-- Downstream analysis and publication-quality visualization for multi-omics data



The National Institutes of Health

• United States
• Biotechnology Research
• 700 & Above Employee

• Postdoctoral Fellow

  • Sep 2017 - Mar 2018

  -- Provide bioinformatics support and analysis for RNA and DNA sequencing using the Ion Torrent Proton Sequencer from Life Technologies -- Design NGS experiments to study disease variation and etiology using human clinical samples as well as animal models -- Bench-side sample preparation (RNA/DNA/protein isolations, library prep, quantitation and QC) to complement computational analyses -- Whole transcriptome analysis for differential expression, alternative splicing, functional/pathway enrichment, promoter analyses, etc. -- Metagenomics analyses using established tools (QIIME, mothur, LefSE) and custom analysis pipelines to study alterations in the microbiome in human disease and mouse models. Show less



Thomas Jefferson University

• United States
• Higher Education
• 700 & Above Employee

• Ph.D. Student

  • Sep 2011 - Aug 2017

  -- Set up an individual Graduate Partnership Program between Thomas Jefferson Unversity (TJU) and the National Institute for Dental and Craniofacial Research (NIDCR), which allows for the thesis research to be done at the NIH campus, while still being enrolled at TJU -- Established best practices for the bench work as well as the analysis to ensure optimal analysis for the sample types and sequencing platform being used -- Isolated histological features and study cell-type-specific aberrations in the transcriptome of minor salivary glands from Sjögren’s Syndrome (SS) patients using laser microdissection (LMD) -- Validated findings from RNA-Seq data with standard molecular biology techniques (qPCR, WB, IF) -- Used 3D cell culture model using human primary cells to study genes of interest from RNA-Seq data Show less



National Institute for Dental and Craniofacial Research (NIDCR) at NIH

• Post-Baccalaureate IRTA Fellow

  • Dec 2009 - Aug 2011

  -- Discovery of previously unidentified microRNAs in salivary gland samples using RNA sequencing -- Microarray and other custom bioinformatics analyses from clinical and laboratory studies -- Processed patient samples (blood, urine, saliva) for serum, PBMCs, exosomes, and RNA Publication: http://www.ncbi.nlm.nih.gov/pubmed/21895886 Sequences published on miRBase: http://mirbase.org/cgi-bin/reference.pl?medline=21895886 -- Discovery of previously unidentified microRNAs in salivary gland samples using RNA sequencing -- Microarray and other custom bioinformatics analyses from clinical and laboratory studies -- Processed patient samples (blood, urine, saliva) for serum, PBMCs, exosomes, and RNA Publication: http://www.ncbi.nlm.nih.gov/pubmed/21895886 Sequences published on miRBase: http://mirbase.org/cgi-bin/reference.pl?medline=21895886



Saucerman Lab at the University of Virginia

• Researcher

  • Sep 2008 - Dec 2009

  -- Created a mechanistic, computational model of myosin crossbridge cycling as part of a framework for studying the effects of Nitric Oxide on heart function using model simulations instead of expensive experiments. -- Combined modeling techniques with collected data to make a more accurate model -- Gained experience with systems modeling using Matlab and motility assays -- Created a mechanistic, computational model of myosin crossbridge cycling as part of a framework for studying the effects of Nitric Oxide on heart function using model simulations instead of expensive experiments. -- Combined modeling techniques with collected data to make a more accurate model -- Gained experience with systems modeling using Matlab and motility assays



Indoor Biotechnologies, Inc.

• Summer Intern

  • Jun 2008 - Aug 2008

  -- Optimized a new multiplex array technology (MARIA) for allergen detection -- Reduced data processing time from hours to seconds with a Graphical User Interface (GUI) based excel macro using Visual Basic to assist MARIA data analysis M. Tandon, M. Chapman, E. King (2009). “Optimization of a Multiplex Array for Indoor Allergens-Influence of Streptavidin-Phycoerythrin (SAPE) Lots on Assay Performance.” Journal of Allergy and Clinical Immunology, 123(2): S232. -- Optimized a new multiplex array technology (MARIA) for allergen detection -- Reduced data processing time from hours to seconds with a Graphical User Interface (GUI) based excel macro using Visual Basic to assist MARIA data analysis M. Tandon, M. Chapman, E. King (2009). “Optimization of a Multiplex Array for Indoor Allergens-Influence of Streptavidin-Phycoerythrin (SAPE) Lots on Assay Performance.” Journal of Allergy and Clinical Immunology, 123(2): S232.



Laurencin Lab at the University of Virginia

• Undergraduate Volunteer

  • Jan 2007 - Aug 2007

  -- Developed and characterized biocompatible heat-sensitive hydrogels for in vivo applications -- Contributed to publication: L. Nair, C. Laurencin, M. Tandon (2009) “Injectable Hydrogels as Biomaterials”. Advanced Materials. B Basu, D Katti, A Kumar (Eds). John Wiley & Sons. -- Developed and characterized biocompatible heat-sensitive hydrogels for in vivo applications -- Contributed to publication: L. Nair, C. Laurencin, M. Tandon (2009) “Injectable Hydrogels as Biomaterials”. Advanced Materials. B Basu, D Katti, A Kumar (Eds). John Wiley & Sons.