System Biology: Staff

Tarmo Äijö

Tarmo Äijö, Ph.D.

Research Scientist, Computational Biology

Tarmo Äijö joined the Simons Foundation in 2015 to work in the Systems Biology group at the Center for Computational Biology. Before joining the foundation, Äijö was a postdoctoral researcher at Aalto University School of Science in Finland, where he focused on the probabilistic modeling of 5-methylcytosine and its Tet-induced oxidation products. He works to build predictive probabilistic models of various biological processes, such as gut microbiota-host interactions and transcriptional regulation through epigenetic modifications, especially in the context of immune function. Äijö holds a B.Sc. and M.Sc. in signal processing and mathematics from Tampere University of Technology in Finland and a Ph.D. in bioinformatics and computer science from Aalto University School of Science.

Meet Barot

Meet Barot

Associate Software Engineer, Simons Center for Data Analysis

Meet Barot joined the foundation in 2016 as a part of the systems biology group in the Simons Center for Data Analysis to develop a protein function prediction system using machine learning techniques. Barot graduated with a bachelor’s degree in chemistry and computer science from New York University in 2016.

Richard Bonneau

Richard Bonneau, Ph.D.

Group Leader for Systems Biology, Center for Computational 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. Before coming to the foundation, Bonneau was a senior scientist at the Institute for Systems Biology in Seattle, Washington, and before that he was a senior scientist at Structural GenomiX in San Diego, California. Currently, he is associate professor of biology and computer science as well as co-director of the Social Media and Political Participation Lab at New York University. He holds a B.A. in biochemistry from Florida State University and a Ph.D. in biomolecular structure and design from the University of Washington.

Mariano Gabitto

Mariano Gabitto, Ph.D.

Flatiron Research Fellow, Center for Computational 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 biological networks as well as other potential data-intensive projects.

Julia Koehler Leman

Julia Koehler Leman, Ph.D.

Research Scientist, Center for Computational 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, docking and design. Leman has an M.S. in physics from Leipzig University in Germany and a Ph.D. in chemical and physical biology from Vanderbilt University.

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Cara Magnabosco, Ph.D.

Flatiron Research Fellow, Center for Computational 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 world. Before joining the foundation, Magnabosco was a graduate student at Princeton University, where she completed her Ph.D. in the Department of Geosciences. Magnabosco holds a B.S. in biochemistry from the University of Southern California.

Emily R. Miraldi

Emily Miraldi, Ph.D.

Research Scientist, Center for Computational Biology

Emily Miraldi joined the Simons Foundation in 2014 to work in the systems biology group at the Center for Computational Biology. Since 2012, Miraldi has been a postdoctoral researcher, co-advised by Rich Bonneau at New York University (NYU) and Dan Littman at NYU School of Medicine. She works to predictively, mathematically model the interactions among gut-resident microbiota and associated immune-cell types at the ecological and molecular levels. Before that, she worked in the laboratory of Forest White at the Massachusetts Institute of Technology, where she combined quantitative mass-spectrometry techniques and statistical modeling to describe physiological measurements as functions of underlying molecular measurements. She holds a B.A. in biochemistry with a minor in mathematics from Oberlin College in Ohio and a Ph.D. in computational and systems biology from the Massachusetts Institute of Technology.

Doug Renfrew

Douglas Renfrew, Ph.D.

Research Scientist, Center for Computational 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 adapting tools developed for protein design to work with several classes of protein-like molecules called foldamers. His work there provided additional information about protein structure that could improve the results of several bioinformatics protocols and pipelines. Renfrew holds a Ph.D. in biophysics from the University of North Carolina at Chapel Hill.