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Ph.D. Genomics, Bioinformatics and Biotechnology Expert

Technical Consultant #2290


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

Honors & Publications


Credentials

  • 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

Committees

  • Rutgers
  • Thesis Committee for MD with dissertation:
  • Interviewer for doctoral applicants

Awards

  • 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

Publications

  • Author and Co-Author of over 30 peer-reviewed publications.
  • Author of Educational Text, Blogs, Conducts Conferences, Invited Speaker

Education

  • 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
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