Ph.D. Genomics, Bioinformatics and Biotechnology Expert

Expertise

• 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.

Experience

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.

Projects

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

Accomplishments

• 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

Educator

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

Kean University

• 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