Patents
Predicting biological functions of proteins using dilated convolutional neural networks
US Patent 12,353,999 B2
Inventor: Drew H. Bryant
This patent covers novel deep learning architectures using dilated convolutions to predict protein function from amino acid sequences, enabling scalable annotation of millions of proteins. The approach combines insights from computational biology with modern ML techniques to solve a fundamental challenge in understanding the protein universe.
Research Publications
Deep diversification of an AAV capsid protein by machine learning
Nature Biotechnology (2021)
Drew H. Bryant*, Ali Bashir*, Sam Sinai*, Nina K. Jain, Pierce J. Ogden, Patrick F. Riley, George M. Church, Lucy J. Colwell, Eric D. Kelsic
Karyotype AI for Precision Oncology
arXiv
Zahra Shamsi*, Isaac Reid*, Drew H. Bryant*, Jacob Wilson*, Xiaoyu Qu, Avinava Dubey, Konik Kothari, Mostafa Dehghani, Mariya Chavarha, Valerii Likhosherstov, Brian Williams, Michael Frumkin, Anurag Arnab, Adrian Weller, Frederick Appelbaum MD, Krzysztof Choromanski**, Ali Bashir**, Min Fang MD**
Longitudinal fundus imaging and its genome-wide association analysis provide evidence for a human retinal aging clock
eLife (2023)
Sara Ahadi, Kenneth A Wilson, Boris Babenko, Cory Y McLean, Drew H. Bryant, Orion Pritchard, Ajay Kumar, Enrique M Carrera, Ricardo Lamy, Jay M Stewart, Avinash Varadarajan, Marc Berndl, Pankaj Kapahi**, Ali Bashir**
Using deep learning to annotate the protein universe
Nature Biotechnology (2022)
Maxwell L. Bileschi, David Belanger, Drew H. Bryant, Theo Sanderson, Brandon Carter, D. Sculley, Alex Bateman, Mark A. DePristo, Lucy J. Colwell
Critiquing Protein Family Classification Models Using Sufficient Input Subsets
Journal of Computational Biology
Brandon Carter, Maxwell Bileschi, Jamie Smith, Theo Sanderson, Drew H. Bryant, David Belanger, Lucy J Colwell
Machine Learning Optimization of Photosynthetic Microbe Cultivation and Recombinant Protein Production
bioRxiv
Caitlin Gamble, Drew H. Bryant, Damian Carrieri, Eli Bixby, Jason Dang, Jacob Marshall, David Doughty, Lucy Colwell, Marc Berndl, James Roberts, Michael Frumkin
Analyzing energy technologies and policies using DOSCOE
SSRN
John C. Platt, J. Orion Pritchard, Drew H. Bryant
The LabelHash Server and Tools for substructure-based functional annotation
Bioinformatics (2011)
Mark Moll, Drew H. Bryant, Lydia E. Kavraki
The LabelHash Algorithm for Substructure Matching
BMC Bioinformatics (2010)
Mark Moll, Drew H. Bryant, Lydia E. Kavraki
Combinatorial clustering of residue position subsets predicts inhibitor affinity across the human kinome
PLoS Computational Biology (2013)
Drew H. Bryant, Mark Moll, Paul W. Finn, Lydia E. Kavraki
Cavity Scaling: Automated Refinement of Cavity-Aware motifs in protein Function Prediction
Journal of Bioinformatics and Computational Biology (2007)
Brian Y. Chen, Drew H. Bryant, Viacheslav Fofanov, David M. Kristensen, Amanda E. Cruess, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs
Journal of Computational Biology (2007)
Brian Y. Chen, Viacheslav Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas Martin Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction
RECOMB (2006)
Brian Y. Chen, Viacheslav Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas Martin Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction
BMC Bioinformatics (2005)
Drew H. Bryant, Mark Moll, Brian Y. Chen, Viacheslav Y. Fofanov, Lydia E. Kavraki