- Genomics, bioinformatics and biotechnology.
- Chip-seq, RNA-seq, DNA re-sequencing and de novo analysis.
- Analysis of Genotyping and Expression Microarrays.
- Strong programming experience with Perl, Bash, Java, R, and MySQL.
- Thorough knowledge of standard bioinformatics tools including UCSC and NCBI.
- High-performance computing including SGE clusters.
Expert Witness Experience
- Analyzed GenBank and PubMed to identify prior art for the BRCA1 patent litigation.
Independent Consultant, Present
- Develop techniques for variant calling from embryo biopsies for a fertility reference laboratory.
- Advised investment funds concerning genomics and biotechnology companies.
- Develop tools to analyze and synthesize 1000 Genomes data for variant annotation for a bioinformatics tool company.
- Served as an advisor and beta-tester for CNV calling methods and tools for sequencing data analysis
- Assisted a DNA forensics company in choosing a genotyping platform.
- Assisted a concierge physician in determining appropriate genetic tests for their patients.
Henry M. Jackson Foundation (for the Advancement of Military Medicine, Inc.), Co-Investigator
- Tuberculosis Drug Resistance Surveillance in Sub-Saharan Africa and Afghanistan using Acid-Fast Stained Smears .
Amazon AWS (Education Award ), Principal Investigator
- Development of a Browser for Bacterial Genomes
International 1000 Genomes Project, Co-Chair
- Complex Variant
- Data Analysis Group and the Functional Analysis
Association of Biomolecular Resource Facilities (ABRF)
- Next Generation Sequencing Study
- Genomics and Bioinformatics
Undisclosed University, 2012 - Present
Assistant Professor of Pathology, 2015
Assistant Professor of Medicine, 2012 - 2014
Scientific Programmer, 2011 - 2012
- Bioinformatics Lead for the implementation of a CLIA/CAP certified tumor sequencing panel.
- Development of a highly multiplexed sequencing assay for determining antibiotic resistance of Tuberculosis on a MiSeq.
- Key personnel and grant writer for an $1.7 million NIH S10 server grant
- Analytical analysis of the BRCA1 patent claims from a genomics perspective.
- Use of whole-genome-sequencing of families to investigate schizophrenia related mutations.
- Implementation of a Cystic Fibrosis carrier screen on an Ion Torrent.
- Co-investigator on numerous grants to support sequencing and computational analysis.
- Involvement in all aspects of sequencing related projects from experimental design through analysis and publication.
- Determination of the optimum length of sequencing reads for RNA-seq experiments
- Facilitator and Instructor for genomics courses and seminars
Reprogenetics, Livingston, NJ, Director of Bioinformatics and Genomics Research, 2015 - 2016
- Developed a technique for determining mitochondrial content of human embryos using Ion Torrent Sequencing
- Develop techniques to decrease the price of pre-implantation genetic screening of embryos.
- Investigated ways to sequence the whole exome of an embryo.
- Served as a bioinformatics lead and provided genomics insight for research projects.
American Museum of Natural History, New York, NY, Research Associate, 2011
- Primary investigator for the sequencing and annotation of the bedbug genome.
- De novo genome assembly and annotation.
- Supervisor of the sequencing of eukaryotic genomes from the museum collection including bedbugs, cockroaches and an Antarctic hydrothermal vent sea anemone.
- Whole Genome Phylogenetics and construction of a Tree of Life.
- Development of the Venninator pipeline for presence-absence phylogenetics.
- Investigation of the dynamics of e-value and tree morphology for presence-absence phylogenies.
- Development of a tool for the identification of ORFs in microbial genomes.
North Shore LIJ (Zucker Hillside Hospital), Long Island, NY, Research Scientist, 2009 - 2011
- Complex analysis of GWAS and exome sequencing data for schizophrenia.
- Investigation of the dynamics of Ashkenazi Jewish migrations from genetic data.
- Design of a framework the identification of multi-nucleotide polymorphisms in genomes.
- Supervisor of computational resources and developer of a high performance computing resource.
The Whitehead Institute, Cambridge, MA, 2000
- Scientific Programmer
Monell Chemical Senses Center, Philadelphia, PA, 1998 - 1999
- Research Apprentice
Hazeva Field School, HaMerkaz, Israel, 1998
- Field Researcher
Rutgers Business School, (UMDNJ/Rutgers Graduate School of Biological Sciences)
Advisor, Instructor and Lecturer
- Next Generation Sequencing and Data Analysis
- GSND 5001: Ethics in Science
- Special Topics in Microbiology
- BIO 5120 Introduction to Bioinformatics
Columbia University, Co Instructor
- EEEB 4030 Phylogenomics
American Museum of Natural History Richard Gilder Graduate School, Co-Instructor
- RGGS 664 Next Generation Sequencing Informatics
New York University, Teaching Assistant
- Introductory Biology
Honors & Publications
- Computer Science and Biological Basis of Behavior, (Minor) University of Pennsylvania
Academic and Professional Affiliations
- American Museum of Natural History, Research Associat
- Kean University, Assistant Professor
- Feinstein Institute for Medical Research, Institute Scientist
- American Museum of Natural History, Visiting Scientist
- Cold Spring Harbor Laboratory, Visiting Graduate Student
- Thesis Committee for MD with dissertation:
- Interviewer for doctoral applicants
- Recipient of a NARSAD $60,000 Young Investigator Grant.
- Intelligent Systems for Molecular Biology (ISMB)
- World Congress of Psychiatric Genetics, Early Career Investigator Program- Finalist
- Author and Co-Author of over 30 peer-reviewed publications.
- Author of Educational Text, Blogs, Conducts Conferences, Invited Speaker
- Ph.D. Biology, New York University and Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
- M.S. Biotechnology, (Concentration in Bioinformatics) University of Pennsylvania, Philadelphia, PA
- B.A. Biology, University of Pennsylvania, Philadelphia, PA