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Michael M. Hoffman, PhD

Affiliations: 
1998-2003 Chemistry and Biochemistry University of Texas at Austin, Austin, Texas, U.S.A. 
 1998-2003 Plan II Honors Liberal Arts University of Texas at Austin, Austin, Texas, U.S.A. 
 2003-2008 European Bioinformatics Institute University of Cambridge, Cambridge, England, United Kingdom 
 2008-2013 Genome Sciences University of Washington, Seattle, Seattle, WA 
 2014- Medical Biophysics University of Toronto, Toronto, ON, Canada 
 2014- Computer Science University of Toronto, Toronto, ON, Canada 
Area:
computational biology, epigenomics, machine learning
Website:
https://hoffmanlab.org/
Google:
"Michael M. Hoffman"
Bio:

Michael Hoffman creates predictive computational models to understand interactions between genome, epigenome, and phenotype in human cancers. He implemented the genome annotation method Segway, which simplifies interpretation of large multivariate genomic datasets, and was a linchpin of the NIH ENCODE Project analysis. He is a Senior Scientist at Princess Margaret Cancer Centre and Associate Professor in the Departments of Medical Biophysics and Computer Science, University of Toronto. He was named a CIHR New Investigator and has received several awards for his academic work, including the NIH K99/R00 Pathway to Independence Award, and the Ontario Early Researcher Award.

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Parents

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Ewan Birney grad student 2008 Cambridge
 (Quantifying evolution and natural selection in vertebrate noncoding sequence)
William Stafford Noble post-doc 2008-2013 University of Washington

Children

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Mehran Karimzadeh grad student 2016-2020 University of Toronto
Samantha L Wilson post-doc 2018- (Chemistry Tree)

Collaborators

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Publications

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Karimzadeh M, Arlidge C, Rostami A, et al. (2023) Human papillomavirus integration transforms chromatin to drive oncogenesis. Genome Biology. 24: 142
Wilson SL, Shen SY, Harmon L, et al. (2022) Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls. Cell Reports Methods. 2: 100294
Karimzadeh M, Hoffman MM. (2022) Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome. Genome Biology. 23: 126
Rehm HL, Page AJH, Smith L, et al. (2021) GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genomics. 1
Libbrecht MW, Chan RCW, Hoffman MM. (2021) Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns. Plos Computational Biology. 17: e1009423
Wilson SL, Way GP, Bittremieux W, et al. (2021) Sharing biological data: why, when, and how. Febs Letters. 595: 847-863
Ramilowski JA, Yip CW, Agrawal S, et al. (2020) Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Research
Libbrecht MW, Rodriguez OL, Weng Z, et al. (2019) A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types. Genome Biology. 20: 180
Sood AJ, Viner C, Hoffman MM. (2019) DNAmod: the DNA modification database. Journal of Cheminformatics. 11: 30
Zitnik M, Nguyen F, Wang B, et al. (2019) Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities. An International Journal On Information Fusion. 50: 71-91
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