Systems Biology

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.

Research Highlights

September 11, 2017

A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity

V Ruiz, T Battaglia, S Kurtz, L Bijnens, A Ou, I Engstrand, X Zheng, T Iizumi, B Mullins, C. Müller, K Cadwell, R. Bonneau, G Perez-Perez, M Blaser

Broad-spectrum antibiotics are frequently prescribed to children. Early childhood represents a dynamic period for the intestinal microbial ecosystem, which is…

Nature Communications

September 1, 2017

Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells

M Tang, R Bowcutt, J Leung, M Wolff, U Gundra, D Hudesman, L Malter, M Poles, L Chen, Z Pei, A Neto, W Abidi, T Ullman, L Mayer, R. Bonneau, P Loke

Background: Inflammatory bowel diseases (IBD) are believed to be driven by dysregulated interactions between the host and the gut microbiota.…

Inflammatory Bowel Diseases

August 14, 2017

Discovery of peptide ligands through docking and virtual screening at nicotinic acetylcholine receptor homology models

A Leffler, A Kuryatov, H Zebroski, S Powell, P Filipenko, A Hussein, J Gorson, A Heizmann, S Lyskov, R. W. Tsien, S Poget, A Nicke, J Lindstrom, B Rudy, R. Bonneau, M Holford

Venom peptide toxins such as conotoxins play a critical role in the characterization of nicotinic acetylcholine receptor (nAChR) structure and…

Proceedings of the National Academy of Sciences of the United States of America

News & Announcements

Deep Beneath Your Feet, They Live in the Octillions (New York Times)

Study Shows How the Body Prevents Potentially Useful Bacteria from Causing Disease (NYU Langone News)

Flatiron Scientists — With Help From the Public — Study Connection Between Body Bacteria and Autoimmune Disease

Group Members

Richard Bonneau, Ph.D.

Group Leader, Systems Biology

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, Ph.D.

Research Scientist, Systems Biology

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…

Vladimir Gligorijevic, Ph.D.

Flatiron Research Fellow, Systems Biology

Vladimir Gligorijevic joined the Simons Foundation in March 2017 as a member of Systems Biology group at the Center for Computational Biology.

Julia Koehler Leman, Ph.D.

Research Scientist, Systems Biology

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, Ph.D.

Research Scientist, Systems Biology

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…

Cara Magnabosco, Ph.D.

Flatiron Research Fellow, Systems Biology

Cara Magnabosco joined the Simons Foundation in 2016 as a member of the Systems Biology group at the Center for Computational Biology. Her research focuses on developing computational methods to better understand the evolution of microorganisms throughout Earth’s history and their interactions in the modern…

James (Jamie) Morton joined the foundation in 2019 as a member for the Center of Computational Biology.

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Open Positions

Research Position (Various Levels), Systems Biology