Marc S. Halfon PhD

Marc Halfon

Marc S. Halfon


Department of Biochemistry

Jacobs School of Medicine & Biomedical Sciences

Specialty/Research Focus

Bioinformatics; Biomedical Informatics; Cell growth, differentiation and development; Computational Biology; Developmental Biology; Gene Expression; Genomics and proteomics; Molecular and Cellular Biology; Molecular genetics; Signal Transduction; Transcription - Gene; Transgenic organisms

Contact Information
955 Main Street
Room 5128
Buffalo, New York 14203
Phone: (716) 829-3126
Fax: 716-849-6655

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:

  • Fellowship, Developmental Biology & Bioinformatics, Harvard Medical School/Brigham & Women‘s Hospital (2003)
  • PhD, Biology, Yale University (1998)
  • MS, Biology, Yale University (1993)
  • Biochemical Sciences, Harvard University, Magna Cum Laude (1991)


  • Professor, Biochemistry, University at Buffalo-SUNY Jacobs School of Medicine & Biomedical Sciences (2016-present)
  • Adjunct Faculty, Molecular and Cellular Biology, Roswell Park Cancer Institute (2006-present)
  • Adjunct Faculty, Biological Sciences, University at Buffalo-SUNY, Dept. of Biological Sciences Faculty of Arts and Letters (2006-present)
  • Associate Professor, Biochemistry, University at Buffalo-SUNY Jacobs School of Medicine & Biomedical Sciences (2009–2015)
  • Assistant Professor, Biochemistry, University at Buffalo-SUNY Jacobs School of Medicine & Biomedical Sciences (2003–2009)

Awards and Honors:

  • Sustained Achievement Award- Exceptional Scholar Program (2020)
  • Editor's choice "Best in Trends" paper (2020)
  • Teaching Innovation Award (UB) (2011)
  • American Cancer Society Research Scholar (2009)

Research Expertise:

  • bioinformatics
  • model system genetics
  • regulatory genomics
  • transcriptional regulation

Research Centers:

  • Center of Excellence in Bioinformatics and Life Sciences

UB 2020 Strategic Strengths:

  • Information and Computing Technology
  • Molecular Recognition in Biological Systems and Bioinformatics

Grants and Sponsored Research:

  • September 2021–August 2024
    REDfly: The regulatory element database for Drosophila and other insects
    Role: Principal Investigator
  • September 2021–August 2023
    Measuring functional similarity between transcriptional enhancers using deep learning
    Role: Co-Investigator
  • September 2019–August 2023
    Mechanisms of Gene Regulatory Network Evolution
    Role: Principal Investigator
  • June 2019–May 2023
    Regulatory Element Discovery in Sequenced Insect Species
    Role: Principal Investigator
  • September 2018–August 2021
    ABI Sustaining: The REDfly database of transcriptional regulatory elements
    Role: Principal Investigator
  • January 2016–December 2019
    REDfly: The regulatory element database for Drosophila and other insects
    Role: Principal Investigator
  • June 2016–May 2018
    Regulatory element discovery in Anopheles gambiae
    Role: Principal Investigator
  • September 2014–August 2017
    ABI Sustaining: The REDfly database of transcriptional regulatory elements
    National Science Foundation
    Role: Principal Investigator
  • March 2012–February 2017
    Regulatory element discovery in sequenced insect species
    Role: Principal Investigator
  • July 2008–June 2013
    High Sensitivity Discovery of Cis-Regulatory Modules
    Role: Co-Principal Investigator
  • January 2009–December 2012
    Mechanisms for Specificity in Receptor Tyrosine Kinase Signaling
    American Cancer Society
    Role: Principal Investigator
  • August 2009–July 2012
    The REDfly Database of Transcriptional Regulatory Elements
    National Science Foundation
    Role: Principal Investigator
  • 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
  • December 2008–November 2009
    Computational Identification of Transcription Factor Binding Sites
    SUNY at Buffalo Interdisciplinary Research Development Fund
    Role: Co-Principal Investigator
  • July 2006–July 2009
    Nutrigenomics for the Study of Disease Prevention and Intervention
    Role: Co-Investigator
  • March 2007–February 2009
    Empirical Assessment of Analysis Methods for DNA Microarrays
    Role: Principal Investigator
  • February 2006–September 2008
    Genomic and Bioinformatic Approaches to Understanding Animal Development
    Role: Consultant
  • July 2002–June 2008
    Computational and Functional Analysis of Gene Networks
    Role: Principal Investigator
  • September 2005–July 2006
    Computational Approaches to Disease Causes and Treatment
    Role: Co-Investigator
See all (9 more)

Journal Articles:

See all (49 more)

Professional Memberships:

  • Pan-American Society for Evolutionary Developmental Biology (2017–present)
  • International Society for Biocuration (2010–present)
  • International Society for Computational Biology (2005–present)
  • Society for Developmental Biology (1998–present)
  • Genetics Society of America (1995–present)
  • AAAS (1993–present)
  • Society for Neuroscience (1992–1997)


  • "The regulatory genomes of class Insecta" Department seminar series, University of Dayton (2023)
  • "Convergence and Divergence of Enhancer Sequences" Genetics Society (UK) symposium “Functional Regulatory Genomics and Disease” (2022)

Service Activities:

  • ; Ad hoc reviewer for multiple (5-6) NIH, NSF panels (2023)
  • i5k consortium (insect genomics); executive committee member (2023–present)
  • ; ad hoc reviewer, multiple study sections (2022)
  • journals including (inter alia): Bioinformatics; BMC Bioinformatics; BMC Genomics; Cell Reports; Critical Reviews In Biochemistry & Molecular Biology; Current Bioinformatics; Development; Developmental Biology; eLife; Fly; G3; Gene; Genetics; Genome Biology; Genome Research; Genomics; JoVE; Molecular Systems Biology; Nature Chemical Biology; Nature Communications; Nature Genetics; Nature Methods; Nucleic Acids Research; PLoS Biology; PLoS Computational Biology; PLoS Genetics; PLoS One; PNAS; Science; review for multiple journals (2021–present)
  • NSF BIO/IOS; ad hoc reviewer (2021)
  • JSMBS Promotions and Tenure Committee (tenurial ranks); member (2020–2023)
  • JSMBS junior faculty mentoring committee; member (2019–present)
  • MSTP Admissions Committee; member (2018–2022)
  • Graduate Affairs Committee; member (2013–present)
  • NIH; GCAT;; Ad Hoc Reviewer (2012–present)
  • GCAT SEP; Special emphasis panel for GCAT;; Ad Hoc Reviewer (2011)
  • Search committee, Bioinformatics; Committee Member (2011–2012)
  • Search committee, Biomedical Engineering; Committee Member (2011)
  • PPBS admissions committee; Committee Member (2009–2015)
  • Search committee, OBGYN chair; Committee Member (2009–2010)
  • American Cancer Society; Development, Differentiation and Cancer;; Panel Member (2008–2012)
  • Health Science Library committee; Advisory Committee (2007–2014)
  • Executive Committee, CCR; Advisory Committee (2005–2006)
  • Search committee, BIO faculty hire in Cell Biology; Committee Member (2004–2005)
  • IFR committee; member (2003–present)
  • n/a; assorted external reviews for NSF;; External Reviewer (2003–present)

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Contact Information

955 Main Street
Room 5128
Buffalo, New York 14203
Phone: (716) 829-3126
Fax: 716-849-6655