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

December 16, 2020

A New Era for Space Life Science: International Standards for Space Omics Processing

L. Rutter, R. Barker, D. Bezdan, H. Cope, S. Costes, L. Degoricija, K. Fisch, M. Gabitto, S. Gebre, S. Giacomello, S. Gilroy, S. Green, C. Mason, S. Reinsch, N. Szewczyk, D. Taylor, J. Galazka, R. Herranz, M. Muratani

With the rise of commercial spaceflight and prospective human missions to Mars, a wider health range of humans will enter…

Patterns

November 26, 2020

CHD8 haploinsufficiency alters the developmental trajectories of human excitatory and inhibitory neurons linking autism phenotypes with transient cellular defects

C. Villa, C. Cheroni, A. López-Tóbon, C. Dotter, B. Oliveira, R. Sacco, A. Yahya, J. Morandell, M. Gabriele, C. Sommer, M. Gabitto, G. Testa, G. Novarino

Chromodomain helicase DNA-binding 8 (CHD8) is one of the most frequently mutated genes causative of autism spectrum disorder (ASD). While…

bioRxiv 2020.11.26.399469

November 11, 2020

Lower airway dysbiosis affects lung cancer progression

J Tsay,, B Wu, I Sulaiman, K Gershner , R Schluger, Y Li, T Yie, P Meyn, E Olsen, L Perez, B Franca, J Carpenito, T Iizumi, M El-Ashmawy, M Badri, J. Morton, N Shen, L He, G Michaud, S Rafeq, J Bessich, R L Smith, H Sauthoff, K Felner, R Pillai, A-M Zavitsanou, S B Koralov, V Mezzano, C A Loomis, A L Moreira, W Moore, A Tsirigos, A Heguy, W N Rom, D H Sterman, H I Pass , J C Clemente, H Li, R. Bonneau, K-K Wong, T Papagiannakopoulos, L N Degal

In lung cancer, enrichment of the lower airway microbiota with oral commensals commonly occurs and ex vivo models support that…

Cancer Discovery

News & Announcements

July 30, 2020

A Software, a Community and a Different Way to Do Science By Susan Reslewic Keatley, Ph.D.

January 04, 2019

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

February 09, 2018

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

Upcoming Events

March 2021

01 Mon
- Meeting 10:00 - 11:00 AM
  Systems Biology Group Meeting
08 Mon
- Meeting 10:00 - 11:00 AM
  Systems Biology Group Meeting
15 Mon
- Meeting 10:00 - 11:00 AM
  Systems Biology Group Meeting
22 Mon
- Meeting 10:00 - 11:00 AM
  Systems Biology Group Meeting
29 Mon
- Meeting 10:00 - 11:00 AM
  Systems Biology Group Meeting

April 2021

05 Mon
- Meeting 10:00 - 11:00 AM
  Systems Biology Group Meeting
12 Mon
- Meeting 10:00 - 11:00 AM
  Systems Biology Group Meeting
19 Mon
- Meeting 10:00 - 11:00 AM
  Systems Biology Group Meeting
26 Mon
- Meeting 10:00 - 11:00 AM
  Systems Biology Group Meeting

May 2021

03 Mon
- Meeting 10:00 - 11:00 AM
  Systems Biology Group Meeting

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.

Aidan Daly, Ph.D.

Flatiron Research Fellow, Systems Biology

Aidan Daly joined the foundation in 2019 as a member of the Center for Computational Biology, and is jointly appointed to the New York Genome Center’s Center for Genomics of Neurodegenerative Disease.

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.

Research Scientist, 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,…

Danxun Li

Research Analyst, Systems Biology

Danxun Li joined the Center for Computational Biology at the Flatiron Institute in September, 2018.

James Morton, Ph.D.

Flatiron Research Fellow, Systems Biology

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

Vikram K. Mulligan, Ph.D.

Research Scientist, Systems Biology

Vikram K. Mulligan joined the Center for Computational Biology in September, 2018.

Anders Rasmussen

Associate Software Engineer, Systems Biology

Anders joined the Systems Biology group in 2017. He is responsible for research in statistical methods and the development of novel bioinformatics tools.

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…

Claudia Skok Gibbs

Research Analyst, Systems Biology

Claudia joined the Systems Biology group in 2018 to work on gene regulatory network inference. Claudia has a B.S. in Mathematics from the University of Miami.

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Open Positions

Research Position, Various Levels (rolling application)