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Author Details

Michael M Hoffman
University of Toronto
2004
36
22
PMIDPaper TitleJournal TitlePublished Year
37033469Motif elucidation in ChIP-seq datasets with a knockout control.Bioinform Adv2023
37738673Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma.Nucleic Acids Res2023
37033469Motif elucidation in ChIP-seq datasets with a knockout control.Bioinform Adv2023
37365652Human papillomavirus integration transforms chromatin to drive oncogenesis.Genome Biol2023
37738673Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma.Nucleic Acids Res2023
37365652Human papillomavirus integration transforms chromatin to drive oncogenesis.Genome Biol2023
36160046Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls.Cell Rep Methods2022
36160046Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls.Cell Rep Methods2022
35575355Assessing and assuring interoperability of a genomics file format.Bioinformatics2022
35681170Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome.Genome Biol2022
35575355Assessing and assuring interoperability of a genomics file format.Bioinformatics2022
35681170Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome.Genome Biol2022
34158359Tumor-Naïve Multimodal Profiling of Circulating Tumor DNA in Head and Neck Squamous Cell Carcinoma.Clin Cancer Res2021
33843054Sharing biological data: why, when, and how.FEBS Lett2021
34158359Tumor-Naïve Multimodal Profiling of Circulating Tumor DNA in Head and Neck Squamous Cell Carcinoma.Clin Cancer Res2021
34462593Reproducibility standards for machine learning in the life sciences.Nat Methods2021
34648491Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns.PLoS Comput Biol2021
35072136GA4GH: International policies and standards for data sharing across genomic research and healthcare.Cell Genom2021
33843054Sharing biological data: why, when, and how.FEBS Lett2021
35072136GA4GH: International policies and standards for data sharing across genomic research and healthcare.Cell Genom2021
34648491Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns.PLoS Comput Biol2021
34462593Reproducibility standards for machine learning in the life sciences.Nat Methods2021
33057217Transparency and reproducibility in artificial intelligence.Nature2020
33057217Transparency and reproducibility in artificial intelligence.Nature2020
30467459Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities.Inf Fusion2019
30467459Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities.Inf Fusion2019
31016417DNAmod: the DNA modification database.J Cheminform2019
31462275A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types.Genome Biol2019
31462275A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types.Genome Biol2019
31016417DNAmod: the DNA modification database.J Cheminform2019
29028889Segway 2.0: Gaussian mixture models and minibatch training.Bioinformatics2018
29028889Segway 2.0: Gaussian mixture models and minibatch training.Bioinformatics2018
30169659Umap and Bismap: quantifying genome and methylome mappability.Nucleic Acids Res2018
30429608Sensitive tumour detection and classification using plasma cell-free DNA methylomes.Nature2018
29618526Opportunities and obstacles for deep learning in biology and medicine.J R Soc Interface2018
29440440Classification and interaction in random forests.Proc Natl Acad Sci U S A2018
28088754Top considerations for creating bioinformatics software documentation.Brief Bioinform2018
30169659Umap and Bismap: quantifying genome and methylome mappability.Nucleic Acids Res2018
30429608Sensitive tumour detection and classification using plasma cell-free DNA methylomes.Nature2018
28088754Top considerations for creating bioinformatics software documentation.Brief Bioinform2018
29618526Opportunities and obstacles for deep learning in biology and medicine.J R Soc Interface2018
29440440Classification and interaction in random forests.Proc Natl Acad Sci U S A2018
28093077Genome Informatics 2016.Genome Biol2017
28093077Genome Informatics 2016.Genome Biol2017
27139377ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data.Genome Biol2016
27139377ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data.Genome Biol2016
25719827Determining the epigenome using DNA alone.Nat Methods2015
25651527Extending reference assembly models.Genome Biol2015
25677182Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression.Genome Res2015
25719827Determining the epigenome using DNA alone.Nat Methods2015
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Collaborators

William Stafford Noble
Co-authored papers 9
Jeff A Bilmes
Co-authored papers 6
Maxwell W Libbrecht
Co-authored papers 6
Anshul Kundaje
Stanford University.
Co-authored papers 6
Danielle Denisko
University of Toronto
Co-authored papers 4
Orion J Buske
The Hospital for Sick Children
Co-authored papers 4
Ewan Birney
European Bioinformatics Institute
Co-authored papers 4
Coby Viner
Princess Margaret Cancer Centre, University Health Network
Co-authored papers 4
Anna Goldenberg
SickKids Research Institute
Co-authored papers 3
Casey S Greene
Dartmouth College Geisel School of Medicine, Princeton University, University of Colorado Anschutz Medical Campus, University of Pennsylvania Perelman School of Medicine
Co-authored papers 3
Manolis Kellis
Massachusetts Institute of Technology
Co-authored papers 3
Zhiping Weng
University of Massachusetts Medical School
Co-authored papers 2
Barbara J Wold
Merkin Institute for Translational Research, California Institute of Technology
Co-authored papers 2
Charles B Epstein
Co-authored papers 2
Paul Flicek
European Bioinformatics Institute
Co-authored papers 2
Peter V Kharchenko
Co-authored papers 2
Xiaole Shirley Liu
Co-authored papers 2
Noam Shoresh
Co-authored papers 2
Melissa A Haendel
Co-authored papers 2
Peter J Park
Harvard Medical School
Co-authored papers 2
Casey S Greene
Co-authored papers 2
Bradley E Bernstein
Broad Institute of MIT and Harvard
Co-authored papers 2
Michael Y Tolstorukov
Dana-Farber Cancer Institute
Co-authored papers 2
Tao Liu
Co-authored papers 2
Jason D Lieb
The University of Chicago
Co-authored papers 2
Su-In Lee
University of Washington
Co-authored papers 2
Michael J Pazin
Co-authored papers 2
Youngsook L Jung
Co-authored papers 2
Melissa A Haendel
American Medical Informatics Association, Oregon Health and Science University, Oregon State University, University of Colorado Anschutz Medical Campus, University of North Carolina at Chapel Hill, University of Wisconsin-Madison
Co-authored papers 2
Gregory P Way
Broad Institute of MIT and Harvard
Co-authored papers 2
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