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M. M. Hoffman · SciRah

Researcher profile · Semantic Scholar

M. M. Hoffman

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M. M. Hoffman — researcher profile on SciRah

h-index: 30
Works: 71
Citations: 11K

Most-cited papers

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
L. Hillier, W. Miller, E. Birney, W. Warren +171 more
2004Nature2,815 citations Open access
Semantic Scholar
Opportunities and obstacles for deep learning in biology and medicine
T. Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A Kalinin +32 more
2017bioRxiv2,095 citations Open access
Semantic Scholar
Sensitive tumour detection and classification using plasma cell-free DNA methylomes
Shu Y. Shen, Rajat Singhania, G. Fehringer, A. Chakravarthy +34 more
2018Nature859 citations Open access
Semantic Scholar
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
M. M. Hoffman, Orion J. Buske, Jie Wang, Z. Weng +2 more
2012Nature Methods626 citations Open access
Semantic Scholar
Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities
M. Zitnik, F. Nguyen, Bo Wang, J. Leskovec +2 more
2018Information Fusion617 citations Open access
Semantic Scholar
Metrics Reloaded: Recommendations for image analysis validation
L. Maier-Hein, A. Reinke, Patrick Godau, M. Tizabi +69 more
2022Nature Methods598 citations Open access
Semantic Scholar
Integrative annotation of chromatin elements from ENCODE data
M. M. Hoffman, J. Ernst, S. Wilder, A. Kundaje +10 more
2012Nucleic Acids Research470 citations Open access
Semantic Scholar
Transparency and reproducibility in artificial intelligence
B. Haibe-Kains, George Alexandru Adam, A. Hosny, F. Khodakarami +27 more
2020Nature463 citations Open access
Semantic Scholar
GA4GH: International policies and standards for data sharing across genomic research and healthcare
H. Rehm, A. Page, Lindsay D. Smith, Jeremy B. Adams +198 more
2021Cell Genomics306 citations Open access
Semantic Scholar
Reproducibility standards for machine learning in the life sciences
Benjamin J. Heil, M. M. Hoffman, F. Markowetz, Su-In Lee +2 more
2021Nature Methods269 citations Open access
Semantic Scholar
Classification and interaction in random forests
Danielle Denisko, M. M. Hoffman
2018Proceedings of the National Academy of Sciences of the United States of America264 citations Open access
Semantic Scholar
Understanding metric-related pitfalls in image analysis validation
A. Reinke, M. Tizabi, M. Baumgartner, M. Eisenmann +66 more
2023Nature Methods245 citations Open access
Semantic Scholar
Umap and Bismap: quantifying genome and methylome mappability
Mehran Karimzadeh, Carl Ernst, A. Kundaje, M. M. Hoffman
2016bioRxiv173 citations Open access
Semantic Scholar
Digital Commons@Becker
D. Church, Valerie A. Schneider, K. Steinberg, M. Schatz +12 more
154 citations
Semantic Scholar
Metrics reloaded: Pitfalls and recommendations for image analysis validation
Lena Maier-Hein, A. Reinke, E. Christodoulou, Ben Glocker +63 more
2022arXiv.org117 citations Open access
Semantic Scholar
AANT: the Amino Aciduchleotide Interaction Database
M. M. Hoffman, M. Khrapov, J. Cox, Jian-Chao Yao +2 more
2004Nucleic Acids Res.94 citations Open access
Semantic Scholar
Tumor-Naïve Multimodal Profiling of Circulating Tumor DNA in Head and Neck Squamous Cell Carcinoma
J. Burgener, Jinfeng Zou, Zhen Zhao, Yang-Qiao Zheng +15 more
2021Clinical Cancer Research85 citations Open access
Semantic Scholar
DNAmod: the DNA modification database
Ankur Sood, Coby Viner, M. M. Hoffman
2016bioRxiv77 citations Open access
Semantic Scholar
Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression
M. Libbrecht, F. Ay, M. M. Hoffman, David M. Gilbert +2 more
2014bioRxiv75 citations Open access
Semantic Scholar
The MCC-F1 curve: a performance evaluation technique for binary classification
Chang Cao, D. Chicco, M. M. Hoffman
2020arXiv.org65 citations
Semantic Scholar
AANT: the Amino Acid-Nucleotide Interaction Database.
M. M. Hoffman, M. Khrapov, J. Cox, Jian-Chao Yao +2 more
2004Nucleic Acids Research62 citations
Semantic Scholar
Statistical Inference, Learning and Models in Big Data
Beate Franke, Jean-François Plante, R. Roscher, E. Lee +10 more
2015arXiv.org58 citations Open access
Semantic Scholar
Sharing biological data: why, when, and how
S. Wilson, G. Way, Wout Bittremieux, J. Armache +2 more
2021FEBS Letters56 citations Open access
Semantic Scholar
A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types
M. Libbrecht, Oscar L. Rodriguez, Z. Weng, Jeff A. Bilmes +2 more
2016Genome Biology56 citations Open access
Semantic Scholar
Top considerations for creating bioinformatics software documentation
Mehran Karimzadeh, M. M. Hoffman
2017Briefings Bioinform.46 citations Open access
Semantic Scholar
Supplementary material for “A dynamic Bayesian network for identifying protein binding footprints from single molecule based sequencing data”
Xiaoyu Chen, M. M. Hoffman, Jeff A. Bilmes, J. Hesselberth +1 more
201045 citations
Semantic Scholar
Estimating the neutral rate of nucleotide substitution using introns.
M. M. Hoffman, E. Birney
2006Molecular biology and evolution40 citations Open access
Semantic Scholar
Segway 2.0: Gaussian mixture models and minibatch training
Rachel C. W. Chan, M. Libbrecht, Eric G. Roberts, Jeff A. Bilmes +2 more
2017bioRxiv39 citations Open access
Semantic Scholar
Human papillomavirus integration transforms chromatin to drive oncogenesis
Mehran Karimzadeh, C. Arlidge, A. Rostami, M. Lupien +2 more
2020bioRxiv38 citations Open access
Semantic Scholar
Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome
Mehran Karimzadeh, M. M. Hoffman
2018Genome Biology33 citations Open access
Semantic Scholar
An effective model for natural selection in promoters.
M. M. Hoffman, E. Birney
2010Genome Research28 citations Open access
Semantic Scholar
Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns
M. Libbrecht, Rachel C W Chan, M. M. Hoffman
2021PLoS Comput. Biol.27 citations Open access
Semantic Scholar
Learning the human chromatin network from all ENCODE ChIP-seq data
Scott M. Lundberg, William B. Tu, B. Raught, L. Penn +2 more
2015bioRxiv26 citations Open access
Semantic Scholar
Exploratory analysis of genomic segmentations with Segtools
Orion J. Buske, M. M. Hoffman, N. Ponts, K. L. Le Roch +1 more
2011BMC Bioinformatics26 citations Open access
Semantic Scholar
The importance of transparency and reproducibility in artificial intelligence research
B. Haibe-Kains, George Adam, A. Hosny, F. Khodakarami +15 more
202025 citations
Semantic Scholar
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet
Coby Viner, Charles A. Ishak, James Johnson, Nicolas J. Walker +10 more
2016bioRxiv20 citations Open access
Semantic Scholar
The Genomedata format for storing large-scale functional genomics data
M. M. Hoffman, Orion J. Buske, William Stafford Noble
2010Bioinform.19 citations Open access
Semantic Scholar
Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma
Luis E. Abatti, Patricia Lado-Fernández, Linh Huynh, Manuel Collado +2 more
2023Nucleic Acids Research17 citations Open access
Semantic Scholar
Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls
S. Wilson, Shu Y. Shen, L. Harmon, J. Burgener +4 more
2021bioRxiv16 citations Open access
Semantic Scholar
Assessing and assuring interoperability of a genomics file format
Yi-Nian Niu, Eric G. Roberts, Danielle Denisko, M. M. Hoffman
2022bioRxiv12 citations Open access
Semantic Scholar
BEHST: genomic set enrichment analysis enhanced through integration of chromatin long-range interactions
D. Chicco, H. Bi, J. Reimand, M. M. Hoffman
2019bioRxiv10 citations Open access
Semantic Scholar
Systematic identification of cis-interacting lncRNAs and their targets
Saumya Agrawal, I. Kulakovskiy, Jessica Severin, M. Koido +25 more
2021bioRxiv9 citations Open access
Semantic Scholar
Entropic Graph-based Posterior Regularization
M. Libbrecht, M. M. Hoffman, Jeff A. Bilmes, William Stafford Noble
2015International Conference on Machine Learning8 citations
Semantic Scholar
Understanding metric-related pitfalls in image analysis validation
A. Reinke, M. Tizabi, M. Baumgartner, M. Eisenmann +74 more
2023arXiv.org7 citations Open access
Semantic Scholar
Unsupervised analysis of multi-experiment transcriptomic patterns with SegRNA identifies unannotated transcripts
Mickaël Mendez, Michelle S. Scott, M. M. Hoffman
2020bioRxiv5 citations Open access
Semantic Scholar
Semi-automated genome annotation using epigenomic data and Segway
Eric G. Roberts, Mickaël Mendez, Coby Viner, Mehran Karimzadeh +6 more
2016bioRxiv3 citations Open access
Semantic Scholar
Creating great documentation for bioinformatics software
Mehran Karimzadeh, M. M. Hoffman
20162 citations
Semantic Scholar
A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data
Xiaoyu Chen, M. M. Hoffman, Jeff A. Bilmes, J. Hesselberth +1 more
2010Bioinform.2 citations Open access
Semantic Scholar
Segway : simultaneous segmentation of multiple functional genomics data sets with heterogeneous patterns of missing data
M. M. Hoffman, Orion J. Buske, Jeff A. Bilmes, William Stafford Noble
20092 citations
Semantic Scholar
Software Reliability: Determination and Prediction.
L. Gephart, C. Greenwald, M. M. Hoffman, D. Osterfeld
19782 citations Open access
Semantic Scholar

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