Michael M. Hoffman

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William Stafford NobleProfessor of Genome Sciences, University of WashingtonVerified email at uw.edu
Jeffrey A. BilmesProfessor of Electrical Engineering and Computer Science, University of Washington SeattleVerified email at uw.edu
Maxwell W LibbrechtAssistant Professor, Computing Science, Simon Fraser UniversityVerified email at sfu.ca
Anshul KundajeAssistant Professor, Dept. of Genetics, Dept. of Computer Science, Stanford UniversityVerified email at stanford.edu
Orion BuskePhenoTipsVerified email at cs.toronto.edu
Ewan BirneyDirector, EMBL-EBIVerified email at ebi.ac.uk
Mehran KarimzadehVector Institute and UCSFVerified email at vectorinstitute.ai
Zhiping WengDirector, Professor of Program in Bioinformatics and Integrative Biology, University ofVerified email at umassmed.edu
Bo WangLead AI Scientist, PMCC UHN; CIFAR AI Chair, Vector Institute; Assistant Professor, U of TorontoVerified email at vectorinstitute.ai
Anna GoldenbergScientist, SickKids Research Institute; Assistant Professor Department of Computer Science, University of TorontoVerified email at utoronto.ca
Jie WangAssistant Professor of Oncology, Roswell Park Comprehensive Cancer CenterVerified email at roswellpark.org
Ross C. HardisonProfessor of Biochemistry and Molecular Biology, The Pennsylvania State UniversityVerified email at psu.edu
Manolis KellisProfessor of Computer Science, MIT and Broad InstituteVerified email at mit.edu
Jason ErnstAssociate Professor, University of California, Los AngelesVerified email at ucla.edu
Ian DunhamEMBL-EBIVerified email at ebi.ac.uk
Paul EllenbogenPrinceton UniversityVerified email at cs.princeton.edu
Belinda Giardinecomputer programmer, Penn State UniversityVerified email at bx.psu.edu
Robert S HarrisAssistant Research Professor, Pennsylvania State UniversityVerified email at bx.psu.edu
Coby VinerGraduate Student, Department of Computer Science, University of TorontoVerified email at cs.toronto.edu
Rachel C. W. ChanUniversity of TorontoVerified email at cs.toronto.edu

Michael M. Hoffman

Senior Scientist, University Health Network/Associate Professor, University of Toronto

Verified email at utoronto.ca - Homepage

Epigenomics Computational Genomics Machine Learning Computational Biology Bioinformatics


Title Sort by citations Sort by year Sort by title	Cited by Cited by	Year
An integrated Encyclopedia of DNA Elements in the human genome ENCODE Project Consortium Nature 489 (7414), 57-74, 2012	12528	2012
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution International Chicken Genome Sequencing Consortium Nature 432 (7018), 695-716, 2004	2504	2004
ChIP-seq guidelines and practices used by the ENCODE and modENCODE consortia SG Landt, GK Marinov, A Kundaje, P Kheradpour, F Pauli, S Batzoglou, ... Genome Research 22 (9), 1813-31, 2012	1713	2012
A user's guide to the encyclopedia of DNA elements (ENCODE) ENCODE Project Consortium PLoS biology 9 (4), e1001046, 2011	1265	2011
Opportunities and obstacles for deep learning in biology and medicine T Ching, DS Himmelstein, BK Beaulieu-Jones, AA Kalinin, BT Do, ... Journal of The Royal Society Interface 15 (141), 20170387, 2018	1001	2018
Unsupervised pattern discovery in human chromatin structure through genomic segmentation MM Hoffman, OJ Buske, J Wang, Z Weng, JA Bilmes, WS Noble Nature Methods 9 (5), 473, 2012	606	2012
Integrative annotation of chromatin elements from ENCODE data MM Hoffman, J Ernst, SP Wilder, A Kundaje, RS Harris, M Libbrecht, ... Nucleic Acids Res 41 (2), 827-841, 2013	527	2013
Sensitive tumour detection and classification using plasma cell-free DNA methylomes SY Shen, R Singhania, G Fehringer, A Chakravarthy, MHA Roehrl, ... Nature 563 (7732), 579-583, 2018	335	2018
Comparative analysis of metazoan chromatin organization JWK Ho, YL Jung, T Liu, BH Alver, S Lee, K Ikegami, KA Sohn, A Minoda, ... Nature 512 (7515), 449-452, 2014	331	2014
Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities M Zitnik, F Nguyen, B Wang, J Leskovec, A Goldenberg, MM Hoffman Information Fusion 50, 71-91, 2019	203	2019
Extending reference assembly models DM Church, VA Schneider, KM Steinberg, MC Schatz, AR Quinlan, ... Genome Biol 16, 13, 2015	148	2015
AANT: the Amino Acid–Nucleotide Interaction Database MM Hoffman, MA Khrapov, JC Cox, J Yao, L Tong, AD Ellington Nucleic Acids Research 32 (Database issue), D174-D181, 2004	137	2004
Classification and interaction in random forests D Denisko, MM Hoffman Proceedings of the National Academy of Sciences 115 (8), 1690-1692, 2018	95	2018
Umap and Bismap: quantifying genome and methylome mappability M Karimzadeh, C Ernst, A Kundaje, MM Hoffman Nucleic acids research 46 (20), e120-e120, 2018	80	2018
Transparency and reproducibility in artificial intelligence B Haibe-Kains, GA Adam, A Hosny, F Khodakarami, L Waldron, B Wang, ... Nature 586 (7829), E14-E16, 2020	72	2020
Statistical Inference, Learning and Models in Big Data B Franke, JF Plante, R Roscher, A Lee, C Smyth, A Hatefi, F Chen, E Gil, ... Int Stat Rev, in press, 2016	65	2016
Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell type-specific expression MW Libbrecht, F Ay, MM Hoffman, DM Gilbert, JA Bilmes, WS Noble Genome Res 25 (4), 544-557, 2015	64	2015
A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data X Chen, MM Hoffman, JA Bilmes, JR Hesselberth, WS Noble Bioinformatics 26 (12), i334-i342, 2010	51	2010
Functional annotation of human long noncoding RNAs via molecular phenotyping JA Ramilowski, CW Yip, S Agrawal, JC Chang, Y Ciani, IV Kulakovskiy, ... Genome research 30 (7), 1060-1072, 2020	49	2020
Estimating the neutral rate of nucleotide substitution using introns MM Hoffman, E Birney Molecular Biology and Evolution 24 (2), 522-531, 2007	44	2007

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