Publications
Publications (sorted by year):
Lab members are in bold.
Preprints
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
Mehdi Foroozandeh Shahraki, Marjan Farahbod, Maxwell Libbrecht
Robust chromatin state annotation
bioRxiv, 2023
Faezeh Bayat, Maxwell Libbrecht
VSS-Hi-C: Variance-stabilized signals for chromatin 3D contacts
bioRxiv, 2022
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
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
Jacob Schreiber, Maxwell Libbrecht, Jeffrey Bilmes, William Stafford Noble
"Nucleotide sequence and DNaseI sensitivity are predictive of 3D chromatin architecture"
bioRxiv, 103614, 2017
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
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
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"
PLoS Computational Biology, 2021, In press
https://arxiv.org/abs/2101.00688
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
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)
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
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
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
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
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
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
Maxwell Libbrecht, William Stafford Noble
"Machine learning applications in genetics and genomics"
Nature Reviews Genetics, 2015
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
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
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
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
2011
ENCODE Project Consortium
"A user’s guide to the encyclopedia of DNA elements (ENCODE)"
PLoS Biol 9 (4), e1001046, 2011
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001046