Publications

Publications (sorted by year):

Lab members are in bold.

Preprints

Mehdi Foroozandeh Shahraki, Abdul Rahman Diab, MW Libbrecht.

CANDI: self-supervised, confidence-aware denoising imputation of genomic data

bioRxiv, 2025

https://doi.org/10.1101/2025.01.23.634626

Marjan Farahbod, Abdul Rahman Diab, Paul Sud, Meenakshi Kagda, Ian Whaling, Mehdi Foroozandeh, Ishan Goel, Habib Daneshpajouh, Benjamin Hitz, J. Michael Cherry, Maxwell Libbrecht

Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway reveals disease drivers

bioRxiv, 2023

https://doi.org/10.1101/2023.10.26.564254

2024

Mehdi Foroozandeh Shahraki, Marjan Farahbod, Maxwell Libbrecht

Robust chromatin state annotation

Genome Research, 2024

https://doi.org/10.1101/gr.278343.123

Neda Shokraneh Kenari, Faezeh Bayat, Maxwell Libbrecht

VSS-Hi-C: Variance-stabilized signals for chromatin 3D contacts

Bioinformatics, 2024

https://doi.org/10.1093/bioinformatics/btae715

2023

Neda Shokraneh Kenari, Megan Andrews, Maxwell Libbrecht

Model-based imputation enables improved resolution for identifying differential chromatin contacts in single-cell Hi-C data

Proceedings of Machine Learning Research, Machine Learning in Computational Biology (MLCB) 2023

https://proceedings.mlr.press/v240/shokraneh-kenari24a.html

2022

Neda Shokraneh, Mariam Arab, Maxwell Libbrecht

Integrative chromatin domain annotation through graph embedding of Hi-C data

Bioinformatics, 2022

https://doi.org/10.1093/bioinformatics/btac813

Gherman Novakovsky*, Nick Dexter*, Maxwell W. Libbrecht**, Wyeth W. Wasserman** and Sara Mostafavi**

"Obtaining genetics insights from deep learning via explainable artificial intelligence"

Nature Reviews Genetics

https://www.nature.com/articles/s41576-022-00532-2

Full text: https://rdcu.be/cWO2R

Kevin B. Dsouza, Alexandra Maslova, Ediem Al-Jibury, Matthias Merkenschlager, Vijay K. Bhargava, Maxwell W. Libbrecht

"Hi-C-LSTM: Learning representations of chromatin contacts using a recurrent neural network identifies genomic drivers of conformation"

Nature Communications, 2022

https://doi.org/10.1038/s41467-022-31337-w

M.Sadegh Saberian, Kathleen P. Moriarty, Andrea D. Olmstead, Ivan R. Nabi, François Jean, Maxwell W. Libbrecht, Ghassan Hamarneh

"DEEMD: Drug Efficacy Estimation against SARS-CoV-2 based on cell Morphology with Deep multiple instance learning"

IEEE Transactions on Medical Imaging, 2022

https://doi.org/10.1109/tmi.2022.3178523

Habib Daneshpajouh, Bowen Chen, Neda Shokraneh, Shohre Masoumi, Kay C Wiese, Maxwell W Libbrecht

Continuous chromatin state feature annotation of the human epigenome

Bioinformatics, 2022

https://doi.org/10.1093/bioinformatics/btac283

2021

Alice Yue, Cedric Chauve, Maxwell W Libbrecht, Ryan R Brinkman

"Automated identification of maximal differential cell populations in flow cytometry data"

Cytometry A, 2021

Wiley #TopDownloadedArticle certificate 2021.

https://doi.org/10.1002/cyto.a.24503

Shohre Masoumi, Maxwell Libbrecht, Kay Weise

SigTools: Exploratory Visualization for Genomic Signals

Bioinformatics, 2021, In press

https://www.biorxiv.org/content/10.1101/2021.08.02.454408v1

Maxwell W Libbrecht, Rachel CW Chan, Michael M Hoffman

"Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns"

PLoS Computational Biology, 2021

https://doi.org/10.1371/journal.pcbi.1009423

Einar Gabbassov, Miguel Moreno-Molina, Iñaki Comas, Maxwell Libbrecht, Leonid Chindelevitch

SplitStrains, a tool to identify and separate mixed Mycobacterium tuberculosis infections from WGS data

MICROBIAL GENOMICS 2021

https://pubmed.ncbi.nlm.nih.gov/34165419

Faezeh Bayat, Maxwell W Libbrecht

Variance-stabilized units for sequencing-based genomic signals

Bioinformatics, 2021

https://doi.org/10.1093/bioinformatics/btab457

AH Safari, N Sedaghat, H Zabeti, A Forna, L Chindelevitch, M Libbrecht

Predicting drug resistance in M. tuberculosis using a long-term recurrent convolutional network architecture

Proceedings of ACM-BCB 2021

https://doi.org/10.1145/3459930.3469534

Kevin B. Dsouza, Adam Y. Li, Vijay K. Bhargava, Maxwell W. Libbrecht

"Latent representation of the human pan-celltype epigenome through a deep recurrent neural network"

IEEE/ACM Transactions on Computational Biology and Bioinformatics

https://ieeexplore.ieee.org/document/9442933

2020

H Zabeti, N Dexter, AH Safari, N Sedaghat, M Libbrecht, L Chindelevitch

"An interpretable classification method for predicting drug resistance in M. tuberculosis"

20th International Workshop on Algorithms in Bioinformatics (WABI 2020)

https://drops.dagstuhl.de/opus/frontdoor.php?source_opus=12791

The ENCODE Project Consortium, Michael P. Snyder, Thomas R. Gingeras, Jill E. Moore, Zhiping Weng, Mark B. Gerstein, Bing Ren, Ross C. Hardison, John A. Stamatoyannopoulos, Brenton R. Graveley, Elise A. Feingold, Michael J. Pazin, Michael Pagan, Daniel A. Gilchrist, Benjamin C. Hitz, J. Michael Cherry, Bradley E. Bernstein, Eric M. Mendenhall, Daniel R. Zerbino, Adam Frankish, Paul Flicek & Richard M. Myers

"Perspectives on ENCODE"

Nature 583, 693–698(2020)

https://www.nature.com/articles/s41586-020-2449-8

Rachel CW Chan, Matthew McNeil, Eric G Roberts, Mickaël Mendez, Maxwell W Libbrecht, Michael M Hoffman

"Semi-supervised segmentation and genome annotation"

bioRxiv, 2020

https://www.biorxiv.org/content/10.1101/2020.01.30.926923v1.abstract

Guo Liang Gan*, Matthew Nguyen*, Elijah Willie, Brian Lee, Cedric Chauve, Maxwell Libbrecht, Leonid Chindelevitch

"Geographic heterogeneity impacts drug resistance predictions in Mycobacterium tuberculosis"

bioRxiv, 2020

https://www.biorxiv.org/content/10.1101/2020.09.17.301226v1.abstract

2019

Maxwell W Libbrecht, Oscar L Rodriguez, Zhiping Weng, Jeffrey A Bilmes, Michael M Hoffman, William Stafford Noble

"A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types"

Genome Biology 20 (1), 180, 2019

https://link.springer.com/article/10.1186/s13059-019-1784-2

2018

Timothy J Durham, Maxwell W Libbrecht, J Jeffry Howbert, Jeff Bilmes, William Stafford Noble

"PREDICTD parallel epigenomics data imputation with cloud-based tensor decomposition"

Nature Communications 9 (1), 1-15, 2018

https://www.nature.com/articles/s41467-018-03635-9

Maxwell W Libbrecht, Jeffrey A Bilmes, William Stafford Noble

"Choosing non‐redundant representative subsets of protein sequence data sets using submodular optimization"

Proteins: Structure, Function, and Bioinformatics 86 (4), 454-466, 2018

https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.25461

Rachel CW Chan, Maxwell W Libbrecht, Eric G Roberts, Jeffrey A Bilmes, William Stafford Noble, Michael M Hoffman

"Segway 2.0: Gaussian mixture models and minibatch training"

Bioinformatics 34 (4), 669-671, 2018

https://academic.oup.com/bioinformatics/article-abstract/34/4/669/4209995

Jacob Schreiber, Maxwell Libbrecht, Jeffrey Bilmes, William Stafford Noble

"Nucleotide sequence and DNaseI sensitivity are predictive of 3D chromatin architecture"

bioRxiv, 103614, 2017

https://www.biorxiv.org/content/10.1101/103614v1.abstract

2016

Owen K Smith, RyanGuk Kim, Haiqing Fu, Melvenia M Martin, Chii Mei Lin, Koichi Utani, Ya Zhang, Anna B Marks, Marc Lalande, Stormy Chamberlain, Maxwell W Libbrecht, Eric E Bouhassira, Michael C Ryan, William S Noble, Mirit I Aladjem

"Distinct epigenetic features of differentiation-regulated replication origins"

Epigenetics & chromatin 9 (1), 18, 2016

https://link.springer.com/article/10.1186/s13072-016-0067-3

Kai Wei, Maxwell W Libbrecht, Jeffrey A Bilmes, William Stafford Noble

"Choosing panels of genomics assays using submodular optimization"

Genome biology 17 (1), 229, 2016

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1089-7?optIn=true

2015

Maxwell Libbrecht, Michael Hoffman, Jeff Bilmes, William Noble

"Entropic graph-based posterior regularization"

International Conference on Machine Learning, 1992-2001, 2015

http://proceedings.mlr.press/v37/libbrecht15.html

Maxwell Libbrecht, William Stafford Noble

"Machine learning applications in genetics and genomics"

Nature Reviews Genetics, 2015

https://www.nature.com/articles/nrg3920

Maxwell W. Libbrecht, Ferhat Ay, Michael M. Hoffman, David M. Gilbert, Jeffrey A. Bilmes, William Stafford Noble

"Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression"

Genome Research 25, 544-557, 2015

https://genome.cshlp.org/content/25/4/544.short

2014

Joshua WK Ho, Youngsook L Jung, Tao Liu, Burak H Alver, Soohyun Lee, Kohta Ikegami, Kyung-Ah Sohn, Aki Minoda, Michael Y Tolstorukov, Alex Appert, Stephen CJ Parker, Tingting Gu, Anshul Kundaje, Nicole C Riddle, Eric Bishop, Thea A Egelhofer, Artyom A Alekseyenko, Andreas Rechtsteiner, Dalal Asker, Jason A Belsky, Sarah K Bowman, Q Brent Chen, Ron A-J Chen, Daniel S Day, Yan Dong, Andrea C Dose, Xikun Duan, Charles B Epstein, Sevinc Ercan, Elise A Feingold, Francesco Ferrari, Jacob M Garrigues, Nils Gehlenborg, Peter J Good, Psalm Haseley, Daniel He, Moritz Herrmann, Michael M Hoffman, Tess E Jeffers, Peter V Kharchenko, Paulina Kolasinska-Zwierz, Chitra V Kotwaliwale, Nischay Kumar, Sasha A Langley, Erica N Larschan, Isabel Latorre, Maxwell W Libbrecht, Xueqiu Lin, Richard Park, Michael J Pazin, Hoang N Pham, Annette Plachetka, Bo Qin, Yuri B Schwartz, Noam Shoresh, Przemyslaw Stempor, Anne Vielle, Chengyang Wang, Christina M Whittle, Huiling Xue, Robert E Kingston, Ju Han Kim, Bradley E Bernstein, Abby F Dernburg, Vincenzo Pirrotta, Mitzi I Kuroda, William S Noble, Thomas D Tullius, Manolis Kellis, David M MacAlpine, Susan Strome, Sarah CR Elgin, Xiaole Shirley Liu, Jason D Lieb, Julie Ahringer, Gary H Karpen, Peter J Park

"Comparative analysis of metazoan chromatin organization"

Nature 512 (7515), 449-452, 2014

https://www.nature.com/articles/nature13415?report=reader

2013

Michael M Hoffman, Jason Ernst, Steven P Wilder, Anshul Kundaje, Robert S Harris, Maxwell Libbrecht, Belinda Giardine, Paul M Ellenbogen, Jeffrey A Bilmes, Ewan Birney, Ross C Hardison, Ian Dunham, Manolis Kellis, William Stafford Noble

"Integrative annotation of chromatin elements from ENCODE data"

Nucleic acids research 41 (2), 827-841, 2013

https://academic.oup.com/nar/article-abstract/41/2/827/1071531

2012

ENCODE Project Consortium

"An integrated encyclopedia of DNA elements in the human genome"

Nature 489 (7414), 57-74, 2012

https://www.nature.com/articles/nature11247

Anshul Kundaje, Sofia Kyriazopoulou-Panagiotopoulou, Maxwell Libbrecht, Cheryl L Smith, Debasish Raha, Elliott E Winters, Steven M Johnson, Michael Snyder, Serafim Batzoglou, Arend Sidow

"Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements"

Genome research 22 (9), 1735-1747, 2012

https://genome.cshlp.org/content/22/9/1735.short

2011