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Michael M. Hoffman, PhD - Publications

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/
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28 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Karimzadeh M, Arlidge C, Rostami A, Lupien M, Bratman SV, Hoffman MM. Human papillomavirus integration transforms chromatin to drive oncogenesis. Genome Biology. 24: 142. PMID 37365652 DOI: 10.1186/s13059-023-02926-9  0.684
2022 Wilson SL, Shen SY, Harmon L, Burgener JM, Triche T, Bratman SV, De Carvalho DD, Hoffman MM. Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls. Cell Reports Methods. 2: 100294. PMID 36160046 DOI: 10.1016/j.crmeth.2022.100294  0.611
2022 Karimzadeh M, Hoffman MM. Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome. Genome Biology. 23: 126. PMID 35681170 DOI: 10.1186/s13059-022-02690-2  0.713
2021 Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJS, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, ... ... Hoffman MM, et al. GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genomics. 1. PMID 35072136 DOI: 10.1016/j.xgen.2021.100029  0.648
2021 Libbrecht MW, Chan RCW, Hoffman MM. Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns. Plos Computational Biology. 17: e1009423. PMID 34648491 DOI: 10.1371/journal.pcbi.1009423  0.339
2021 Wilson SL, Way GP, Bittremieux W, Armache JP, Haendel MA, Hoffman MM. Sharing biological data: why, when, and how. Febs Letters. 595: 847-863. PMID 33843054 DOI: 10.1002/1873-3468.14067  0.586
2020 Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, ... ... Hoffman MM, et al. Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Research. PMID 32718982 DOI: 10.1101/Gr.254219.119  0.346
2019 Libbrecht MW, Rodriguez OL, Weng Z, Bilmes JA, Hoffman MM, Noble WS. A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types. Genome Biology. 20: 180. PMID 31462275 DOI: 10.1186/S13059-019-1784-2  0.612
2019 Sood AJ, Viner C, Hoffman MM. DNAmod: the DNA modification database. Journal of Cheminformatics. 11: 30. PMID 31016417 DOI: 10.1186/S13321-019-0349-4  0.348
2019 Zitnik M, Nguyen F, Wang B, Leskovec J, Goldenberg A, Hoffman MM. Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities. An International Journal On Information Fusion. 50: 71-91. PMID 30467459 DOI: 10.1016/J.Inffus.2018.09.012  0.373
2018 Karimzadeh M, Ernst C, Kundaje A, Hoffman MM. Umap and Bismap: quantifying genome and methylome mappability. Nucleic Acids Research. PMID 30169659 DOI: 10.1093/Nar/Gky677  0.734
2017 Chan RCW, Libbrecht MW, Roberts EG, Bilmes JA, Noble WS, Hoffman MM. Segway 2.0: Gaussian mixture models and minibatch training. Bioinformatics (Oxford, England). PMID 29028889 DOI: 10.1093/Bioinformatics/Btx603  0.537
2017 Chicco D, Hoffman MM. Genome Informatics 2016. Genome Biology. 18: 5. PMID 28093077 DOI: 10.1186/S13059-016-1135-5  0.414
2017 Karimzadeh M, Hoffman MM. Top considerations for creating bioinformatics software documentation. Briefings in Bioinformatics. PMID 28088754 DOI: 10.1093/Bib/Bbw134  0.685
2016 Lundberg SM, Tu WB, Raught B, Penn LZ, Hoffman MM, Lee SI. ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data. Genome Biology. 17: 82. PMID 27139377 DOI: 10.1186/S13059-016-0925-0  0.381
2015 Libbrecht MW, Ay F, Hoffman MM, Gilbert DM, Bilmes JA, Noble WS. Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression. Genome Research. 25: 544-57. PMID 25677182 DOI: 10.1101/Gr.184341.114  0.59
2015 Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, Chin CS, Kitts PA, Aken B, Marth GT, Hoffman MM, Herrero J, Mendoza ML, Durbin R, Flicek P. Extending reference assembly models. Genome Biology. 16: 13. PMID 25651527 DOI: 10.1186/S13059-015-0587-3  0.606
2014 Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, ... ... Hoffman MM, et al. Comparative analysis of metazoan chromatin organization. Nature. 512: 449-52. PMID 25164756 DOI: 10.1038/Nature13415  0.567
2014 Viner C, Johnson J, Grant CE, Bailey TL, Noble WS, Hoffman MM. Transcription factor motif discovery and prediction in an expanded epigenetic alphabet Genome. 57: 378-379. DOI: 10.1139/Gen-2014-0153  0.495
2013 Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Research. 41: 827-41. PMID 23221638 DOI: 10.1093/Nar/Gks1284  0.673
2013 Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. Unsupervised pattern discovery in human chromatin structure through genomic segmentation 2013 Acm Conference On Bioinformatics, Computational Biology and Biomedical Informatics, Acm-Bcb 2013. 813-814. DOI: 10.1145/2506583.2506701  0.599
2012 Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, ... ... Hoffman MM, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/Gr.136184.111  0.416
2012 Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nature Methods. 9: 473-6. PMID 22426492 DOI: 10.1038/nmeth.1937  0.556
2011 Buske OJ, Hoffman MM, Ponts N, Le Roch KG, Noble WS. Exploratory analysis of genomic segmentations with Segtools. Bmc Bioinformatics. 12: 415. PMID 22029426 DOI: 10.1186/1471-2105-12-415  0.616
2010 Chen X, Hoffman MM, Bilmes JA, Hesselberth JR, Noble WS. A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data. Bioinformatics (Oxford, England). 26: i334-42. PMID 20529925 DOI: 10.1093/Bioinformatics/Btq175  0.662
2010 Hoffman MM, Buske OJ, Noble WS. The Genomedata format for storing large-scale functional genomics data. Bioinformatics (Oxford, England). 26: 1458-9. PMID 20435580 DOI: 10.1093/Bioinformatics/Btq164  0.556
2010 Hoffman MM, Birney E. An effective model for natural selection in promoters. Genome Research. 20: 685-92. PMID 20194951 DOI: 10.1101/Gr.096719.109  0.548
2007 Hoffman MM, Birney E. Estimating the neutral rate of nucleotide substitution using introns. Molecular Biology and Evolution. 24: 522-31. PMID 17122369 DOI: 10.1093/Molbev/Msl179  0.49
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