As non-“self” macromolecules, biotherapeutics can trigger an immune response that can reduce drug efficacy, require patients to be taken off…Journal of Chemical Information and Modeling
At the Systems Biology group, we are developing new methods to learn the networks that run life’s program.
Key aims include developing new methods to annotate genes (characterize the parts list for biology) and building new methods that learn biological networks, and eventually dynamic models (put the parts together). These network models will help us to predict the functional effect of genetic variation, design interventions and therapies, and understand how living systems respond to changes in their environment.
Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks
Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software…bioRxiv 2021.04.04.438423
Constrained non-negative matrix factorization enabling real-time insights of in situ and high-throughput experiments
Non-negative Matrix Factorization (NMF) methods offer an appealing unsupervised learning method for real-time analysis of streaming spectral data in time-sensitive…arXiv:2104.00864v1
Richard Bonneau joined the Simons Foundation in 2014 to develop next-generation computational biology methods for the Center for Computational Biology. He focuses on creating new methods for using protein structure modeling to interpret genetic variation and new methods for understanding biological networks.
Mariano Gabitto joined the Systems Biology group in October 2016 as research fellow in the Center for Computational Biology. Gabitto comes to the foundation from Columbia University where he earned his Ph.D. in computational neuroscience. He will be responsible for research on informatics tools and…
Julia Koehler Leman joined the Simons Foundation in 2016 as a member of Richard Bonneau’s lab. She was previously a postdoctoral fellow in the chemical and biomolecular engineering department at Johns Hopkins University. There, she developed applications in the Rosetta software suite for biomolecular modeling,…
Douglas Renfrew came to the Simons Foundation in 2014 to work on bioinformatics and protein structure determination with the Systems Biology group at the Center for Computational Biology. Before joining the foundation, Renfrew was a postdoctoral researcher at New York University, where he focused on…