AANT: the Amino Aciduchleotide Interaction Database. - Michael M. Hoffman; Maksim A. Khrapov; J. Colin Cox; Jianchao Yao; Lingnan Tong; Andrew D. Ellington (Nucleic Acids Res., 2004)

A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data. - Xiaoyu Chen; Michael M. Hoffman; Jeff A. Bilmes; Jay R. Hesselberth; William Stafford Noble (Bioinform., 2010)

The Genomedata format for storing large-scale functional genomics data. - Michael M. Hoffman; Orion J. Buske; William Stafford Noble (Bioinform., 2010)

Exploratory analysis of genomic segmentations with Segtools. - Orion J. Buske; Michael M. Hoffman; Nadia Ponts; Karine G. Le Roch; William Stafford Noble (BMC Bioinform., 2011)

Unsupervised pattern discovery in human chromatin structure through genomic segmentation. - Michael M. Hoffman; Orion J. Buske; Jie Wang; Zhiping Weng; Jeff A. Bilmes; William Stafford Noble (BCB, 2013)

Comparative analysis of metazoan chromatin organization Open. - Joshua Wing Kei Ho; Youngsook L. Jung; Tao Liu 022; Burak Han Alver; Soohyun Lee; Kohta Ikegami; Kyung-Ah Sohn; Aki Minoda; Michael Y. Tolstorukov; Alex Appert; Stephen C. J. Parker; Tingting Gu; et al. (Nat., 2014)

Entropic Graph-based Posterior Regularization. - Maxwell W. Libbrecht; Michael M. Hoffman; Jeff A. Bilmes; William Stafford Noble (ICML, 2015)

Statistical Inference, Learning and Models in Big Data. - Beate Franke; Jean-François Plante; Ribana Roscher; Annie Lee; Cathal Smyth; Armin Hatefi; Fuqi Chen; Einat Gil; Alexander G. Schwing; Alessandro Selvitella; Michael M. Hoffman; Roger B. Grosse; et al. (CoRR, 2015)

Segway 2.0 Application Note Datasets. - Rachel C. W. Chan; Maxwell W. Libbrecht; Eric G. Roberts; Jeffrey A. Bilmes; William Stafford Noble; Michael M. Hoffman (Zenodo, 2017)

Segway 2.0 Application Note Scripts. - Rachel C. W. Chan; Maxwell W. Libbrecht; Eric G. Roberts; Jeffrey A. Bilmes; William Stafford Noble; Michael M. Hoffman (Zenodo, 2017)

Top considerations for creating bioinformatics software documentation. - Mehran Karimzadeh; Michael M. Hoffman (Briefings Bioinform., 2018)

Segway 2.0: Gaussian mixture models and minibatch training. - Rachel C. W. Chan; Maxwell W. Libbrecht; Eric G. Roberts; Jeffrey A. Bilmes; William Stafford Noble; Michael M. Hoffman (Bioinform., 2018)

Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities. - Marinka Zitnik; Francis Nguyen; Bo Wang 044; Jure Leskovec; Anna Goldenberg; Michael M. Hoffman (Inf. Fusion, 2019)

DNAmod: the DNA modification database. - Ankur Jai Sood; Coby Viner; Michael M. Hoffman (J. Cheminformatics, 2019)

The MCC-F1 curve: a performance evaluation technique for binary classification. - Chang Cao; Davide Chicco; Michael M. Hoffman (CoRR, 2020)

Segmentation and genome annotation algorithms. - Maxwell W. Libbrecht; Rachel C. W. Chan; Michael M. Hoffman (CoRR, 2021)

Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns. - Maxwell W. Libbrecht; Rachel C. W. Chan; Michael M. Hoffman (PLoS Comput. Biol., 2021)

Assessing and assuring interoperability of a genomics file format. - Yi Nian Niu; Eric G. Roberts; Danielle Denisko; Michael M. Hoffman (Bioinform., 2022)

Metrics reloaded: Pitfalls and recommendations for image analysis validation. - Lena Maier-Hein; Annika Reinke; Evangelia Christodoulou; Ben Glocker; Patrick Godau; Fabian Isensee; Jens Kleesiek; Michal Kozubek 001; Mauricio Reyes 001; Michael A. Riegler; Manuel Wiesenfarth; Michael Baumgartner 001; et al. (CoRR, 2022)

Understanding metric-related pitfalls in image analysis validation. - Annika Reinke; Minu Tizabi; Michael Baumgartner 001; Matthias Eisenmann; Doreen Heckmann-Nötzel; A. Emre Kavur; Tim Rädsch; Carole H. Sudre; Laura Ación; Michela Antonelli; Tal Arbel; Spyridon Bakas; et al. (CoRR, 2023)