Michael Hoffman PhD

Assistant Professor

Department of Medical Biophysics, University of Toronto

City
Toronto, Canada
Discipline
Biological Sciences
Interests
functional genomics, machine learning, chromatin
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About

I develop machine learning methods for functional genomics. I am responsible for Segway, a dynamic Bayesian network method for simultaneously segmenting and clustering multiple tracks of data from ChIP-seq or DNase-seq experiments.
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Publications

  • Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell type-specific expression

    Libbrecht M, Ay F, Hoffman M, Gilbert D, Bilmes J, Noble W

    Genome Research (2015)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Comparative analysis of metazoan chromatin organization

    Ho J, Jung Y, Liu T, Alver B, Lee S, Ikegami K et al.

    Nature (2014)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Integrative annotation of chromatin elements from ENCODE data.

    Hoffman M, Ernst J, Wilder S, Kundaje A, Harris R, Libbrecht M et al.

    Nucleic Acids Research (2013)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

    Landt S, Marinov G, Kundaje A, Kheradpour P, Pauli F, Batzoglou S et al.

    Genome Research (2012)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • An integrated encyclopedia of DNA elements in the human genome.

    Bernstein B, Birney E, Dunham I, Green E, Gunter C, Snyder M

    Nature (2012)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Unsupervised pattern discovery in human chromatin structure through genomic segmentation.

    Hoffman M, Buske O, Wang J, Weng Z, Bilmes J, Noble W

    Nature methods (2012)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • An effective model for natural selection in promoters.

    Hoffman M, Birney E

    Genome Research (2010)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

    International Chicken Genome Sequencing Consortium

    Nature (2004)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Estimating the neutral rate of nucleotide substitution using introns.

    Hoffman M, Birney E

    Molecular Biology and Evolution (2007)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • A user's guide to the encyclopedia of DNA elements (ENCODE).

    ENCODE Project Consortium

    PLoS Biology (2011)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • AANT: the Amino Acid-Nucleotide Interaction Database.

    Hoffman M, Khrapov M, Cox J, Yao J, Tong L, Ellington A

    Nucleic Acids Research (2004)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data.

    Chen X, Hoffman M, Bilmes J, Hesselberth J, Noble W

    Bioinformatics (2010)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • The Genomedata format for storing large-scale functional genomics data.

    Hoffman M, Buske O, Noble W

    Bioinformatics (2010)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.
  • Exploratory analysis of genomic segmentations with Segtools.

    Buske O, Hoffman M, Ponts N, Le Roch K, Noble W

    BMC Bioinformatics (2011)

    • -- Readers Readers not available. This publication is not currently accessible in the Mendeley catalog.

Professional experience

Assistant Professor

Department of Medical Biophysics, University of Toronto

April 2014 - Present

Scientist

Princess Margaret Cancer Centre

November 2013 - Present

Senior Fellow

Department of Genome Sciences, University of Washington

September 2008 - October 2013 (5 years 1 month)

Predoctoral Fellow

European Bioinformatics Institute

October 2003 - July 2008 (4 years 9 months)

Research Assistant

Department of Chemistry and Biochemistry, University of Texas at Austin

May 1999 - September 2003 (4 years 4 months)

Education history

Trinity College, University of Cambridge

Doctor of Philosophy

October 2003 - July 2008 (4 years 9 months)

The University of Texas at Austin

Bachelor of Science, Biochemistry; Bachelor of Arts, Plan II Honors Liberal Arts

August 1998 - May 2003 (4 years 9 months)