Michael Hoffman

  • PhD
  • Assistant Professor
  • University of Toronto Department of Medical Biophysics

Research 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.

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)

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Statistical Inference , Learning and Models in Big Data

Franke B, Plante J, Roscher R, Lee A, Smyth C, Hatefi A, Chen F, Gil E, Schwing A, Selvitella A, Hoffman M, Grosse R, Hendricks D, Reid N

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Comparative analysis of metazoan chromatin organization

Ho J, Jung Y, Liu T, Alver B, Lee S, Ikegami K, Sohn K, Minoda A, Tolstorukov M, Appert A, Parker S, Gu T, Kundaje A, Riddle N, Bishop E, Egelhofer T, Hu S, Alekseyenko A, Rechtsteiner A, Asker D, Belsky J, Bowman S, Chen Q, Chen R, Day D, Dong Y, Dose A, Duan X, Epstein C, Ercan S, Feingold E, Ferrari F, Garrigues J, Gehlenborg N, Good P, Haseley P, He D, Herrmann M, Hoffman M, Jeffers T, Kharchenko P, Kolasinska-Zwierz P, Kotwaliwale C, Kumar N, Langley S, Larschan E, Latorre I, Libbrecht M, Lin X, Park R, Pazin M, Pham H, Plachetka A, Qin B, Schwartz Y, Shoresh N, Stempor P, Vielle A, Wang C, Whittle C, Xue H, Kingston R, Kim J, Bernstein B, Dernburg A, Pirrotta V, Kuroda M, Noble W, Tullius T, Kellis M, MacAlpine D, Strome S, Elgin S, Liu X, Lieb J, Ahringer J, Karpen G, Park P

Nature (2014)

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Integrative annotation of chromatin elements from ENCODE data.

Hoffman M, Ernst J, Wilder S, Kundaje A, Harris R, Libbrecht M, Giardine B, Ellenbogen P, Bilmes J, Birney E, Hardison R, Dunham I, Kellis M, Noble W

Nucleic Acids Research (2013)

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An integrated encyclopedia of DNA elements in the human genome.

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

Nature (2012)

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ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt S, Marinov G, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein B, Bickel P, Brown J, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor K, Euskirchen G, Gerstein M, Gertz J, Hartemink A, Hoffman M, Iyer V, Jung Y, Karmakar S, Kellis M, Kharchenko P, Li Q, Liu T, Liu X, Ma L, Milosavljevic A, Myers R, Park P, Pazin M, Perry M, Raha D, Reddy T, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos J, Tolstorukov M, White K, Xi S, Farnham P, Lieb J, Wold B, Snyder M

Genome Research (2012)

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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)

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A user's guide to the encyclopedia of DNA elements (ENCODE).

ENCODE Project Consortium

PLoS Biology (2011)

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Exploratory analysis of genomic segmentations with Segtools.

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

BMC Bioinformatics (2011)

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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)

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An effective model for natural selection in promoters.

Hoffman M, Birney E

Genome Research (2010)

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The Genomedata format for storing large-scale functional genomics data.

Hoffman M, Buske O, Noble W

Bioinformatics (2010)

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Estimating the neutral rate of nucleotide substitution using introns.

Hoffman M, Birney E

Molecular Biology and Evolution (2007)

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AANT: the Amino Acid-Nucleotide Interaction Database.

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

Nucleic Acids Research (2004)

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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

International Chicken Genome Sequencing Consortium

Nature (2004)

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Professional experience

Assistant Professor

University of Toronto Department of Medical Biophysics

April 2014 - Present

Scientist

Princess Margaret Hospital Cancer Centre

November 2013 - Present

Senior Fellow

University of Washington Department of Genome Sciences

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

University of Cambridge Trinity College

Doctor of Philosophy

October 2003 - July 2008 (4 years 9 months)

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)