Clustering reveals ubiquitous heterogeneity and asymmetry of genomic signals at functional elements. - Anshul Kundaje; Sofia Kyriazopoulou-Panagiotopoulou; Max W. Libbrecht; Cheryl L. Smith; Debasish Raha; Elliott E. Winters; Steven M. Johnson; Michael P. Snyder; Serafim Batzoglou; Arend Sidow (Adv. Math. Commun., 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)

Understanding human genome regulation through entropic graph-based regularization and submodular optimization. - Maxwell W. Libbrecht (2016)

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)

Choosing Non-redundant Representative Subsets Of Protein Sequence Data Sets Using Submodular Optimization. - Maxwell W. Libbrecht; Jeffrey A. Bilmes; William Stafford Noble (BCB, 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)

An Interpretable Classification Method for Predicting Drug Resistance in M. Tuberculosis. - Hooman Zabeti; Nick C. Dexter; Amir Hosein Safari; Nafiseh Sedaghat; Maxwell W. Libbrecht; Leonid Chindelevitch (WABI, 2020)

Predicting drug resistance in M. tuberculosis using a long-term recurrent convolutional network. - Amir Hosein Safari; Nafiseh Sedaghat; Hooman Zabeti; Alpha Forna; Leonid Chindelevitch; Maxwell W. Libbrecht (BCB, 2021)

INGOT-DR: an interpretable classifier for predicting drug resistance in M. tuberculosis. - Hooman Zabeti; Nick C. Dexter; Amir Hosein Safari; Nafiseh Sedaghat; Maxwell W. Libbrecht; Leonid Chindelevitch (Algorithms Mol. Biol., 2021)

VSS: variance-stabilized signals for sequencing-based genomic signals. - Faezeh Bayat; Maxwell W. Libbrecht (Bioinform., 2021)

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

DEEMD: Drug Efficacy Estimation against SARS-CoV-2 based on cell Morphology with Deep multiple instance learning. - M. Sadegh Saberian; Kathleen P. Moriarty; Andrea D. Olmstead; Ivan Robert Nabi; François Jean; Maxwell W. Libbrecht; Ghassan Hamarneh (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)

Continuous chromatin state feature annotation of the human epigenome. - Habib Daneshpajouh; Bowen Chen; Neda Shokraneh; Shohre Masoumi; Kay C. Wiese; Maxwell W. Libbrecht (Bioinform., 2022)

SigTools: exploratory visualization for genomic signals. - Shohre Masoumi; Maxwell W. Libbrecht; Kay C. Wiese (Bioinform., 2022)

Latent Representation of the Human Pan-Celltype Epigenome Through a Deep Recurrent Neural Network. - Kevin B. Dsouza; Adam Y. Li; Vijay K. Bhargava; Maxwell W. Libbrecht (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

DEEMD: Drug Efficacy Estimation Against SARS-CoV-2 Based on Cell Morphology With Deep Multiple Instance Learning. - M. Sadegh Saberian; Kathleen P. Moriarty; Andrea D. Olmstead; Christian Hallgrimson; François Jean; Ivan Robert Nabi; Maxwell W. Libbrecht; Ghassan Hamarneh (IEEE Trans. Medical Imaging, 2022)

Model-based imputation enables improved resolution for identifying differential chromatin contacts in single-cell Hi-C data. - Neda Shokraneh Kenari; Megan Andrews; Max W. Libbrecht (MLCB, 2023)

Integrative chromatin domain annotation through graph embedding of Hi-C data. - Neda Shokraneh; Mariam Arab; Maxwell W. Libbrecht (Bioinform., 2023)

Generalized Attention Flow: Feature Attribution for Transformer Models via Maximum Flow. - Behrooz Azarkhalili; Maxwell W. Libbrecht (ACL (1), 2025)