Jared Adolf-bryfogle
Associate Director
Whitpain Township, Pennsylvania, United States
Summary
👤
Senior🎓
Top SchoolJared Adolf-bryfogle is an Associate Director and computational protein design leader with 13 years of experience applying bioinformatics, deep learning, and Rosetta-based methods to design enzymes, antibodies, and other therapeutic modalities. He has built and led cross-functional teams and infrastructure for at-scale model training and inference at Johnson & Johnson, and previously created integrated automated enzyme design platforms at Manus Bio and advanced de novo protein design at the Institute for Protein Innovation. A long-standing RosettaCommons contributor and PyRosetta notebook author, he blends hands-on tool development with strategic research to push both methodology and application. Jared’s work emphasizes proteins as dynamic systems—melding simulation, ML, and classical modeling—to create novel enzymes and pathways for sustainable manufacturing and ambitious future goals like bio-enabled BCI technologies.
13 years of coding experience
10 years of employment as a software developer
B.S. Cellular/Organismal Biology, B.S. Cellular/Organismal Biology at Commonwealth University-Lock HavenPhD. Molecular Cell Biology and Genetics, PhD. Molecular Cell Biology and Genetics at Drexel College of Medicine
python, c++, matlab, r, tk/tcl, perl
Stackoverflow
1reputation
0reached
0answers
0questions
Github Skills (2)
jupyter-notebook10
python10
Programming languages (3)
Github contributions (5)
RosettaCommons/PyRosetta.notebooks
Aug 2019 - Aug 2021
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
Role in this project:
Back-end Developer
Back-end DeveloperContributions:3 reviews, 84 commits, 27 PRs in 1 year 11 months
Contributions summary:Jared's commits primarily involve modifying and adding Jupyter Notebooks related to PyRosetta for biomolecular structure prediction and design. Their contributions include adding notebooks, introducing core concepts such as packing, design, refinement, and illustrating examples of point mutations within the antibody framework. They added code related to the use of different types of movers (like FastRelax) and the setup of a basic scorefunction.
rna-structure-predictionpredictiondnagoogle-colabjupyter-notebook
SchiefLab/Jade
Aug 2015 - Nov 2018
A repository for modules and applications to aid in the design and analysis of Biological molecules. Replaced by Jade2
Contributions:349 commits, 128 pushes in 3 years 3 months
aidbioinformaticsbiologicalmolecules
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