Michael Hoffman PhD

Assistant Professor

Department of Medical Biophysics, University of Toronto

Location
Toronto, Canada
Discipline
Biological Sciences
Interests
functional genomics, machine learning, chromatin
more... less...

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.
more... less...

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)