Publications by authors named "Maxwell Libbrecht"

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Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway.
Marjan Farahbod, Aboud Diab, Paul Sud, Meenakshi S Kagda, Ian Whaling, Maxwell W Libbrecht

Genome Res· October 2025

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GAME: Genomic API for Model Evaluation.
Ishika Luthra, Satyam Priyadarshi, Rui Guo, Lukas Mahieu, Niklas Kempynck, Maxwell Libbrecht

bioRxiv· July 2025

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VSS-Hi-C: variance-stabilized signals for chromatin contacts.
Neda Shokraneh Kenari, Faezeh Bayat, Maxwell W Libbrecht

Bioinformatics· November 2024

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Robust chromatin state annotation.
Mehdi Foroozandeh Shahraki, Marjan Farahbod, Maxwell W Libbrecht

Genome Res· April 2024

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Obtaining genetics insights from deep learning via explainable artificial intelligence.
Gherman Novakovsky, Nick Dexter, Maxwell W Libbrecht, Wyeth W Wasserman, Sara Mostafavi

Nat Rev Genet· February 2023

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Integrative chromatin domain annotation through graph embedding of Hi-C data.
Neda Shokraneh, Mariam Arab, Maxwell Libbrecht

Bioinformatics· January 2023

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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, Francois Jean, Maxwell W Libbrecht

IEEE Trans Med Imaging· November 2022

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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· August 2022

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Learning representations of chromatin contacts using a recurrent neural network identifies genomic drivers of conformation.
Kevin B Dsouza, Alexandra Maslova, Ediem Al-Jibury, Matthias Merkenschlager, Vijay K Bhargava, Maxwell W Libbrecht

Nat Commun· June 2022

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

Bioinformatics· May 2022

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Automated identification of maximal differential cell populations in flow cytometry data.
Alice Yue, Cedric Chauve, Maxwell W Libbrecht, Ryan R Brinkman

Cytometry A· February 2022

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SigTools: exploratory visualization for genomic signals.
Shohre Masoumi, Maxwell W Libbrecht, Kay C Wiese

Bioinformatics· January 2022

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VSS: variance-stabilized signals for sequencing-based genomic signals.
Faezeh Bayat, Maxwell Libbrecht

Bioinformatics· December 2021

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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· October 2021

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INGOT-DR: an interpretable classifier for predicting drug resistance in M. tuberculosis.
Hooman Zabeti, Nick Dexter, Amir Hosein Safari, Nafiseh Sedaghat, Maxwell Libbrecht

Algorithms Mol Biol· August 2021

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SplitStrains, a tool to identify and separate mixed infections from WGS data.
Einar Gabbassov, Miguel Moreno-Molina, Iñaki Comas, Maxwell Libbrecht, Leonid Chindelevitch

Microb Genom· June 2021

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A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types.
Maxwell W Libbrecht, Oscar L Rodriguez, Zhiping Weng, Jeffrey A Bilmes, Michael M Hoffman

Genome Biol· August 2019

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Choosing non-redundant representative subsets of protein sequence data sets using submodular optimization.
Maxwell W Libbrecht, Jeffrey A Bilmes, William Stafford Noble

Proteins· April 2018

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PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition.
Timothy J Durham, Maxwell W Libbrecht, J Jeffry Howbert, Jeff Bilmes, William Stafford Noble

Nat Commun· April 2018

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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

Bioinformatics· February 2018

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Choosing panels of genomics assays using submodular optimization.
Kai Wei, Maxwell W Libbrecht, Jeffrey A Bilmes, William Stafford Noble

Genome Biol· November 2016

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Distinct epigenetic features of differentiation-regulated replication origins.
Owen K Smith, RyanGuk Kim, Haiqing Fu, Melvenia M Martin, Chii Mei Lin, Maxwell W Libbrecht

Epigenetics Chromatin· May 2016

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Entropic Graph-based Posterior Regularization.
Maxwell W Libbrecht, Michael M Hoffman, Jeffrey A Bilmes, William S Noble

JMLR Workshop Conf Proc· July 2015

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Machine learning applications in genetics and genomics.
Maxwell W Libbrecht, William Stafford Noble

Nat Rev Genet· June 2015

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Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression.
Maxwell W Libbrecht, Ferhat Ay, Michael M Hoffman, David M Gilbert, Jeffrey A Bilmes

Genome Res· April 2015

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