Michael M. Hoffman, PhD - Publications

1998-2003 Chemistry and Biochemistry 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 
computational biology, epigenomics, machine learning

29 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
2020 Haibe-Kains B, Adam GA, Hosny A, Khodakarami F, Waldron L, Wang B, McIntosh C, Goldenberg A, Kundaje A, Greene CS, Broderick T, Hoffman MM, Leek JT, Korthauer K, et al. Transparency and reproducibility in artificial intelligence. Nature. 586: E14-E16. PMID 33057217 DOI: 10.1038/s41586-020-2766-y  1
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  1
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  1
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  0.01
2018 Shen SY, Singhania R, Fehringer G, Chakravarthy A, Roehrl MHA, Chadwick D, Zuzarte PC, Borgida A, Wang TT, Li T, Kis O, Zhao Z, Spreafico A, Medina TDS, Wang Y, ... ... Hoffman MM, et al. Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Nature. PMID 30429608 DOI: 10.1038/s41586-018-0703-0  1
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  1
2018 Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, et al. Opportunities and obstacles for deep learning in biology and medicine. Journal of the Royal Society, Interface. 15. PMID 29618526 DOI: 10.1098/rsif.2017.0387  1
2018 Denisko D, Hoffman MM. Classification and interaction in random forests. Proceedings of the National Academy of Sciences of the United States of America. 115: 1690-1692. PMID 29440440 DOI: 10.1073/pnas.1800256115  0.01
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  1
2017 Chicco D, Hoffman MM. Genome Informatics 2016. Genome Biology. 18: 5. PMID 28093077 DOI: 10.1186/s13059-016-1135-5  0.01
2017 Karimzadeh M, Hoffman MM. Top considerations for creating bioinformatics software documentation. Briefings in Bioinformatics. PMID 28088754 DOI: 10.1093/bib/bbw134  1
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  1
2015 Viner C, Hoffman MM. Determining the epigenome using DNA alone. Nature Methods. 12: 191-2. PMID 25719827 DOI: 10.1038/nmeth.3291  1
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  1
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  1
2015 Viner C, Hoffman MM. Determining the epigenome using DNA alone Nature Methods. 12: 191-192. DOI: 10.1038/nmeth.3291  1
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  0.56
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  1
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  1
2012 . An integrated encyclopedia of DNA elements in the human genome. Nature. 489: 57-74. PMID 22955616 DOI: 10.1038/nature11247  0.76
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  1
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  1
2011 . A user's guide to the encyclopedia of DNA elements (ENCODE). Plos Biology. 9: e1001046. PMID 21526222 DOI: 10.1371/journal.pbio.1001046  0.04
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  1
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  1
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  1
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  1
2004 . Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 432: 695-716. PMID 15592404 DOI: 10.1038/nature03154  0.01
2004 Hoffman MM, Khrapov MA, Cox JC, Yao J, Tong L, Ellington AD. AANT: the Amino Acid-Nucleotide Interaction Database. Nucleic Acids Research. 32: D174-81. PMID 14681388 DOI: 10.1093/nar/gkh128  1
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