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Marc                           Halfon

Marc S. Halfon PhD

Department of Biochemistry

Associate Professor

Specialty/Research Focus

Bioinformatics; Cell growth, differentiation and development; Gene Expression; Genomics and proteomics; Molecular genetics; Signal Transduction

 
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Professional Summary:

Research in my laboratory investigates the genetic regulatory circuitry that controls how cell fates are determined during development. We focus on two key aspects, intercellular signaling and transcriptional regulation, using primarily the fruit fly Drosophila melanogaster due to its extremely well-annotated genome and amenability to experimental manipulation. All conclusions, however, are expected to relate directly to mammalian (including human) gene regulation. Recently, we have also started investigating the regulatory genomics of other insect species of both medical and agricultural importance, beginning with the development of methods for regulatory element discovery in species with fully sequenced genomes but little functional, experimental data.

A defining feature of my laboratory is that it takes both wet-lab and computational/bioinformatics approaches to studying the same set of problems about development and transcriptional regulation; hypotheses and ideas generated using one set of methods are tested and explored using the other. Current research in the laboratory falls into two main areas: 1) discovery and characterization of transcriptional cis-regulatory modules (CRMs), and 2) mechanisms of specificity for receptor tyrosine kinase (RTK) signaling. The combined results of these studies will provide insight into gene regulation, genome structure, intercellular signaling, and the regulatory networks that govern embryonic development.

My group is also heavily involved in biocuration through our development and maintenance of REDfly, an internationally-recognized curated database of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). Despite more than 25 years of experimental determination of these elements, the data have never been collected into a single searchable database. REDfly seeks to include all experimentally verified fly regulatory elements along with their DNA sequence, their associated genes, and the expression patterns they direct. REDfly is by far the most comprehensive database of regulatory elements for the higher eukaryotes and serves as an important resource for the fly and bioinformatics communities.

Education and Training:
  • Postdoctoral Fellow, Developmental Biology & Bioinformatics, Harvard Medical School/Brigham & Women‘s Hospital (2003)
  • MPhil, Biology, Yale University (1998)
  • PhD, Biology, Yale University (1998)
  • MS, Biology, Yale University (1993)
  • AB, Biochemical Sciences, Harvard University, magna cum laude (1991)
Employment:
  • Associate Professor, University at Buffalo-SUNY (2009-present)
  • Adjunct Faculty, Univeristy at Buffalo-SUNY, Dept. of Biological Sciences (2006-present)
  • Adjunct Faculty, Molecular and Cellular Biology, Roswell Park Cancer Institute (2006-present)
  • Assistant Professor, University at Buffalo-SUNY (2003–2009)
Awards and Honors:
  • Teaching Innovation Award (UB) (2011)

Research Expertise:
  • bioinformatics
  • model system genetics
  • regulatory genomics
  • transcriptional regulation
Research Centers:
  • Center of Excellence in Bioinformatics and Life Sciences
UB 2020 Strategic Strengths:
  • Molecular Recognition in Biological Systems and Bioinformatics
  • Information and Computing Technology
Grants and Sponsored Research:
  • March 2012–February 2017
    Regulatory element discovery in sequenced insect species
    USDA
    Role: Principal Investigator
    $462,000
  • July 2008–June 2013
    High Sensitivity Discovery of Cis-Regulatory Modules
    NIH/NIGMS
    Role: Co-Principal Investigator
    $1,700,000
  • January 2009–December 2012
    Mechanisms for Specificity in Receptor Tyrosine Kinase Signaling
    American Cancer Society
    Role: Principal Investigator
    $700,000
  • August 2009–July 2012
    The REDfly Database of Transcriptional Regulatory Elements
    National Science Foundation
    Role: Principal Investigator
    $524,049
  • December 2009–November 2010
    Integrated multi-dimensional genomic analysis of therapy related acute myeloid leukemia
    New York State Center of Excellence in Bioninformatics & Life Sciences
    Role: Co-Principal Investigator
    $60,000
  • December 2008–November 2009
    Computational Identification of Transcription Factor Binding Sites
    SUNY at Buffalo Interdisciplinary Research Development Fund
    Role: Co-Principal Investigator
    $27,000
  • July 2006–July 2009
    Nutrigenomics for the Study of Disease Prevention and Intervention
    USDA
    Role: Co-Investigator
    $36,500
  • March 2007–February 2009
    Empirical Assessment of Analysis Methods for DNA Microarrays
    NIH/NLM
    Role: Principal Investigator
    $79,250
  • February 2006–September 2008
    Genomic and Bioinformatic Approaches to Understanding Animal Development
    NASA
    Role: Consultant
    $125,000
  • July 2002–June 2008
    Computational and Functional Analysis of Gene Networks
    NIH/NHGRI
    Role: Principal Investigator
    $1,300,000
  • September 2005–July 2006
    Computational Approaches to Disease Causes and Treatment
    NIH/NIGMS
    Role: Co-Investigator
    $20,000
See All (11 Total) >

Journal Articles:
See All (31 Total) >

Professional Memberships:
  • International Society for Biocuration (2010)
  • International Society for Computational Biology (2005)
  • Society for Developmental Biology (1998)
  • Genetics Society of America (1995)
  • AAAS (1993)
  • Society for Neuroscience (1992–1997)
Presentations:
  • "Regulatory element discovery in sequenced insect genomes" Arthropod Genomics 2012 (2012)
  • "The REDfly database" Drosophila Research Conference, Genetics Society of America, Gene Expression (posters) (2012)
Service Activities:
  • Search committee, Bioinformatics; Committee Member (2011–2012)
  • Search committee, Biomedical Engineering; Committee Member (2011)
  • IGP admissions committee; Committee Member (2009)
  • Search committee, OBGYN chair; Committee Member (2009)
  • Health Science Library committee; Advisory Committee (2007)
  • Executive Committee, CCR; Advisory Committee (2005–2006)
  • Search committee, BIO; faculty hire in Cell Biology; Committee Member (2004–2005)

Clinical Specialties:
Clinical Offices:
Insurance Accepted:

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Contact Information

B3-307
COEBLS
701 Ellicott St.
Buffalo, NY 14203
Phone: (716) 829-3126
Fax: 716-849-6655
Email: mshalfon@buffalo.edu


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