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 learningWebsite:
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.
Parents
Sign in to add mentor| 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
Sign in to add trainee| Mehran Karimzadeh | grad student | 2016-2020 | University of Toronto |
| Mickaël Mendez | grad student | 2016-2023 | University of Toronto |
| Coby Viner | grad student | 2014-2024 | University of Toronto |
| Samantha L Wilson | post-doc | 2018- | (Chemistry Tree) |
Publications
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| Agrawal S, Buyan A, Severin J, et al. (2024) Annotation of nuclear lncRNAs based on chromatin interactions. Plos One. 19: e0295971 |
| Viner C, Ishak CA, Johnson J, et al. (2024) Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome Biology. 25: 11 |
| Karimzadeh M, Arlidge C, Rostami A, et al. (2023) Human papillomavirus integration transforms chromatin to drive oncogenesis. Genome Biology. 24: 142 |
| Denisko D, Viner C, Hoffman MM. (2023) Motif elucidation in ChIP-seq datasets with a knockout control. Bioinformatics Advances. 3: vbad031 |
| 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 |