CCB Team

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.

Xi Chen

Xi Chen, Ph.D.

Flatiron Research Fellow, Genomics

Xi Chen joined the Flatiron Institute’s Center for Computational Biology in 2016 in the genomics group. Chen’s research focuses on developing algorithms for processing and statistical analysis of heterogeneous genomics data. He has a Ph.D. in electrical engineering from Virginia Polytechnic Institute and State University, where he worked on developing Bayesian models of transcriptional networks using transcriptomics and genomics data collected from breast cancer cell lines or from patients. Chen holds a B.S. and an M.S. in electrical engineering from Harbin Institute of Technology in China.

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Dmitri ‘Mitya’ Chklovskii, Ph.D.

Group Leader for Neuroscience, Center for Computational Biology

Before coming to the Simons Foundation in 2014, Mitya Chklovskii was a group leader at the Howard Hughes Medical Institute’s (HHMI) Janelia Farm Research Campus in Ashburn, Virginia. Chklovskii also initiated and led a collaborative project at HHMI that assembled the largest-ever connectome, a comprehensive map of neural connections in the brain. Before that, he worked at Cold Spring Harbor Laboratory in New York, where he founded the first theoretical neuroscience group, having worked there as a first assistant, and later an associate professor.

As group leader for neuroscience, Chklovskii will lead an effort to understand how the brain analyzes complex datasets streamed by sensory organs, in an attempt to create artificial neural systems. He holds a Ph.D. in physics from the Massachusetts Institute of Technology.

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Salim Chowdhury, Ph.D.

Research Scientist, Center for Computational Biology

Before coming to the Center for Computational Biology’s genomics group in 2015, Salim Chowdhury earned his Ph.D. in Russell Schwartz’s lab at Carnegie Mellon University in Pittsburgh. There, he worked on developing evolutionary models of tumor progression using genomics data collected across diverse types of cancer patients. At the Simons Foundation, Chowdhury’s research will focus on building dynamics of protein functional networks and identifying how they are affected by genetic perturbations. Chowdhury holds an M.S. in computer science from Case Western Reserve University and a B.S. in computer science from Bangladesh University of Engineering and Technology.

Nick De Veaux

Nick De Veaux

Data Scientist, Center for Computational Biology

Nick De Veaux joined the Scientific Computing Core in 2016 as a data scientist. He was previously a bioinformatics engineer and later a team lead for bioinformatics at Recombine, a clinical genomics testing company. De Veaux, who holds a B.S. in computer science from Princeton, works in research and development on data-intensive computing projects in systems biology.

Sebastian Fürthauer

Sebastian Fürthauer, Ph.D.

Flatiron Research Fellow, Center for Computational Biology

Sebastian Fürthauer joined the Center for Computational Biology in June 2016. Fürthauer is interested in the physics of cellular scale processes, such as cell division and cell motility and their role in developmental biology. After earning his Ph.D. at the Max Planck Institute for Physics of Complex Systems and the Max Planck Institute for Cellular Biology and Genetics, in Dresden, Germany, he did research at the Tata Centre for Interdisciplinary Sciences in Hyderabad, India, the Courant Institute at New York University and Harvard University. His current work focuses on understanding the role of self-organized processes in the microtubule cytoskeleton of cells, which enable the segregation of chromosomes during cell division.

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.

Andrea Giovannucci

Andrea Giovannucci, Ph.D.

Data Scientist, Center for Computational Biology

Andrea Giovannucci joined the Center for Computational Biology as a data scientist in the neuroscience group in 2015. He is responsible for the development of calcium imaging software, general-purpose neural networks and other potential data-intensive computing projects. Prior to joining the foundation, Giovannucci was a post-doctoral fellow at the Neuroscience Institute at Princeton University. He has a Ph.D. in computer science from Universitat Autònoma de Barcelona in Spain and a B.S. in electronic engineering from Politecnico di Milano in Italy.

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Leslie Greengard, M.D., Ph.D.

Director, Center for Computational Biology

Leslie Greengard joined the Simons Foundation in 2013 as founding director of the Simons Center for Data Analysis, now called the Center for Computational Biology. Prior to that, Greengard served as director of the Courant Institute of Mathematical Sciences at New York University, where he has been a member of the faculty since 1989. Greengard holds an M.D. and Ph.D. in computer science from Yale University.

A member of the National Academy of Sciences and the National Academy of Engineering, Greengard has contributed to the fields of scientific computing, data analysis and integral equations. One of his most significant scientific achievements, together with Vladimir Rokhlin, was the development of the Fast Multipole Method (FMM), a mathematical technique with an enormous range of applications, from chip simulation to molecular modeling. In 2000, the Institute of Electrical and Electronics Engineers recognized the FMM as one of the top ten algorithms of the 20th century and in 2001, Greengard and Rokhlin received the Steele Prize for Seminal Contribution to Research from the American Mathematical Society for their work.

In addition to his research contributions, Greengard co-founded MadMax Optics, which developed advanced numerical algorithms to solve complex engineering problems in opto-electronics. At MadMax Optics, Greengard served as chief executive officer and chief technology officer from 2001 to 2004.

John Hayward

John Hayward, M.S.

Senior Software Engineer, Center for Computational Biology

John Hayward joined the Simons Foundation in 2016 as a senior software engineer in Center for Computational Biology’s genomics group. Before joining the foundation, Hayward worked as a research and development analyst for the Bloomberg Tokyo Marunouchi office, adapting East Asian market data feeds for the Bloomberg news and financial analysis services. Prior to this, he was an associate engineer with the Air Traffic Control Systems Group at the Massachusetts Institute of Technology Lincoln Laboratory, serving as a principal developer for the Route Availability Planning Tool, an automated decision system for air traffic congestion management currently in nationwide deployment. In graduate school, he was a researcher in the surgical oncology division of the University of Massachusetts Memorial Medical School, where he studied predictive modeling in the clinical performance of gastrointestinal cancer patients, focusing on pancreatic adenocarcinoma. He holds an M.S. in computer science from Worcester Polytechnic Institute and a B.S. in computer science from the University of Massachusetts Amherst.

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Marian Jakubiak, M.P.A.

Manager of Program Administration, Center for Computational Biology

Marian Jakubiak joined the Simons Foundation in 2014 to manage business operations and assist in long-term planning and strategy development at the Center for Computational Biology. Before coming to the foundation, Jakubiak was budget analyst and executive assistant in the office of the executive vice president at New York University, where she provided oversight of revenue, expenses and budgets. Before that, she worked at Columbia University as special assistant to the executive vice president and dean of the faculties of medicine. Jakubiak holds a B.A. in political science from Baruch College, City University of New York and an M.P.A. from New York University’s Wagner School of Public Service.

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.

Jeremy Magland

Jeremy Magland, Ph.D.

Senior Data Scientist, Center for Computational Biology

Jeremy Magland joined the Simons Foundation in 2015 to develop new computational techniques and algorithms to solve data analysis problems in neuroscience. Before joining the foundation, Magland was a research associate professor of radiology at the University of Pennsylvania. He has more than a decade of experience in magnetic resonance imaging research, including data acquisition, reconstruction and image processing. Magland has also created several reusable software frameworks for exploratory scientific research. He earned a B.S. and M.S. in mathematics from Brigham Young University and a Ph.D. in mathematics from the University of Pennsylvania.

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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.

Christian L. Müller

Christian L. Müller, M.S., M.S., Ph.D.

Research Scientist and Project Leader, Computational Center for Biology

Christian L. Müller joined the Simons Foundation in 2014 to work in the systems biology group, developing high-dimensional statistics methods and algorithms with applications to microbial and regulatory networks. Prior to joining the foundation, Müller was a postdoctoral researcher at the Courant Institute and the Center for Genomics and Systems Biology at New York University. Before that, he was a postdoctoral researcher at the Institute of Theoretical Computer Science at ETH Zurich in Switzerland. Müller holds an M.S. in computer science from Uppsala University in Sweden, an M.S. in bioinformatics and computer science, as well as a university certificate in literature and poetry, from the University of Tübingen in Germany, and a Ph.D. in computer science from ETH Zurich.

Ehssan Nazockdast

Ehssan Nazockdast, Ph.D.

Flatiron Research Fellow, Center for Computational Biology

Ehssan Nazockdast joined the foundation in 2016 as part of the biophysical modeling group, where he develops efficient simulation methodologies of the dynamics of microtubule and motor-protein assemblies in complex geometries. Nazockdast received both a B.S. and M.S. in polymer engineering from Amirkabir University of Technology in Tehran and a Ph.D. in chemical engineering from City College of New York. He then became a postdoctoral researcher at the Applied Mathematics Laboratory, which is part of the Courant Institute at New York University.

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Camille Norrell

Program Associate, Center for Computational Biology

Camille Norrell came to the Simons Foundation in 2014 after working as office manager and executive assistant to the president at Rialto Capital Management. Before that, she was an executive assistant at Intermediate Capital Group, Inc. where she managed office relocation and design, acted as liaison between Intermediate Capital Group’s worldwide subsidiaries, and supported accounting activities. Norrell supports day-to-day operations at the Center for Computational Biology.

Naomi Oppenheimer

Naomi Oppenheimer, Ph.D.

Flatiron Research Fellow, Center for Computational Biology

Naomi Oppenheimer joined the foundation in 2016 as a research fellow at the Center for Computational Biology in the biophysical modeling group. Her research interests are in fluid dynamics, elasticity and the interplay between them. Her work uses analytical and computational tools to solve biophysical problems related to membrane hydrodynamics, active particles, living cells and more. She did her Ph.D. at Tel-Aviv University under the supervision of Haim Diamant and went on to work as a postdoctoral researcher at the University of Chicago with Thomas Witten and then at Princeton with Howard Stone.

Cengiz Pehlevan

Cengiz Pehlevan, Ph.D.

Research Scientist, Center for Computational Biology

Cengiz Pehlevan joined Center for Computational Biology’s neuroscience group in 2015 to build theories of neural computation and to develop methods to analyze large neuroscience datasets in order to test such theories. Prior to joining the foundation, Pehlevan was a postdoctoral associate at the Janelia Research Campus of the Howard Hughes Medical Institute in Virginia. There, he focused on theoretical neuroscience, working to construct a matrix factorization model of neural computation. Before that, he was a Swartz Fellow at Harvard University, where he studied sensory selectivity in neural network models, neural mechanisms underlying modification of motor timing, and an integrated neuromechanical model of crawling. Pehlevan holds a B.Sc. in physics and in electrical and electronics engineering from Bogazici University in Istanbul, and an Sc.M. and Ph.D. in physics from Brown University in Providence, Rhode Island.

Eftychios Pnevmatikakis

Eftychios A. Pnevmatikakis, Ph.D.

Research Scientist, Center for Computational Biology

Eftychios Pnevmatikakis joined the Simons Foundation after working as a postdoctoral research scientist in the department of statistics and the Center for Theoretical Neuroscience at Columbia University. During his postdoctoral research, Pnevmatikakis created efficient machine-learning and optimization algorithms for statistical analysis of large-scale electrophysiology and optical-physiology data. As part of CCB’s neuroscience group, Pnevmatikakis develops methods and software for analysis of large sets of neuroscience data, as well as theories of neural computation. He holds a Ph.D. in electrical engineering from Columbia University.

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.

Alex Rives

Alexander Rives

Data Scientist, Center for Computational Biology

Alexander Rives joined the Simons Foundation in 2014 after working as a venture partner and entrepreneur at ARCH Venture Partners. He is a co-founder of Fate Therapeutics, the first company to develop a stem cell modulator that has advanced to clinical testing for regenerative medicine. As a member of the software development team at the Center for Computational Biology, Rives works on basic research related to biological circuits, machine learning, neural networks and visualization of large-scale datasets. He holds a Bachelor of Science in philosophy and biology from Yale University.

A. Mark Roberts

A. Mark Roberts, Ph.D.

Data Scientist, Scientific Computing Core

Mark Roberts joined the Scientific Computing Core in 2016 as a data scientist in the computing group. He develops robust and efficient systems for functional genomics in collaboration with the center’s genomics group and integrates them into a widely used open-source software platform for data analysis. Roberts worked as a consultant at the foundation starting in June 2015 before joining the staff full time. Previously, he was a quantitative analyst at Citigroup. He has a Ph.D. in electrical engineering from Princeton University, where his research focused on novel computer architectures for fast cryptography.

Rachel Sealfon

Rachel Sealfon, Ph.D.

Research Scientist, Center for Computational Biology

Rachel Sealfon joined the foundation in 2016 as a research scientist in the center’s genomics group. She is applying data integration methods and prediction approaches to study functional genomic data. Sealfon has a Ph.D. in computer science from the Massachusetts Institute of Technology, where she was advised by Pardis Sabeti and Manolis Kellis. She has an A.B. in computer science from Princeton University.

Mike Shelley

Michael Shelley, Ph.D.

Group Leader for Biophysical Modeling, Center for Computational Biology

Michael Shelley joined the Simons Foundation in 2016 to work on the modeling and simulation of complex systems arising in physics and biology. He is an applied mathematician who co-founded and co-directs the Courant Institute’s Applied Mathematics Laboratory at New York University. Shelley joined the Courant Institute in 1992 and is the Lilian and George Lyttle Professor of Applied Mathematics. He holds a B.A. in mathematics from the University of Colorado and a Ph.D. in applied mathematics from the University of Arizona. He was a postdoctoral researcher at Princeton University and a member of the mathematics faculty at the University of Chicago before joining NYU. Shelley has received the François Frenkiel Award from the American Physical Society and the Julian Cole Lectureship from the Society for Industrial and Applied Mathematics, and he is a fellow of both societies.

Marina Spivak

Marina Spivak, Ph.D.

Research Scientist, Center for Computational Biology

Marina Spivak joined the Scientific Computing Core in 2014 to work on new computational techniques and software for bioinformatics problems. Prior to joining the foundation, Spivak did postdoctoral work at the University of Washington, Seattle, in the genome sciences department. Before that, she worked at NEC Research Laboratories in Princeton, New Jersey, where she developed new machine learning techniques for analysis of shotgun proteomics data. Spivak holds a B.A. in molecular cell biology and computer science from the University of California, Berkeley, and a Ph.D. in computer science from New York University.

Nikos Trikoupis

Nikos Trikoupis, M.B.A.

System Architect, SCC

Nikos Trikoupis joined the foundation as a systems architect in the Scientific Computing Core in October 2016. Trikoupis comes to the foundation from the City University of New York where he was a high performance computing systems architect. He will participate in the design, planning, acquisition and operations of data processing resources for the foundation’s computational centers.

Olga Troyanskaya

Olga Troyanskaya, Ph.D.

Deputy Director for Genomics, Center for Computational Biology

Olga Troyanskaya became deputy director for genomics in 2014 after working with CCB as a consultant since 2013. Troyanskaya is also a professor at the Lewis-Sigler Institute for Integrative Genomics and at the department of computer science at Princeton University, where she has been on the faculty since 2003. At Princeton, she runs the Laboratory of Bioinformatics and Functional Genomics. She holds a Ph.D. in biomedical informatics from Stanford University, and is a recipient of the Sloan Research Fellowship, the National Science Foundation CAREER award, Overton award from International Society for Computational Biology and the Ira Herskowitz award from the Genetic Society of America. She was also a finalist for the Blavatnik Award. As deputy director for genomics, Troyanskaya is responsible for building and leading a group of junior and senior scientists working on genomics, bioinformatics and their associated applications.

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Benjamin VanderSluis, Ph.D.

Research Scientist, Center for Computational Biology

Benjamin VanderSluis joined the Center for Computational Biology’s genomics group in 2015 to research data integration methods and prediction approaches for functional genomic data, as well as to conduct research on other bioinformatics projects. Before coming to the foundation, VanderSluis was a postdoctoral associate in the functional genomics laboratory of Chad L. Myers, associate professor of computer science at the University of Minnesota, Twin Cities. His work there focused on mapping and interpreting the genetic interaction network in yeast, and on integrating diverse functional data to predict gene function. VanderSluis holds a B.S. and a Ph.D. in computer science, also from the University of Minnesota.

Aaron Watters

Aaron Watters, Ph.D.

Senior Software Engineer, Scientific Computing Core

Aaron Watters joined the Scientific Computing Core in 2015 to develop tools that will help biologists examine, manage and process data generated by gene expression and regulatory networks experiments. Previously, Watters worked at Enthought, Inc. as a scientific software engineer, where he consulted on projects related to chemical process control and credit risk assessment and helped design and develop Enthought Web services and applications. Before that, Watters worked at Audible, Inc. where he integrated Audible’s databases and services into Amazon’s standard infrastructure. Watters also has extensive experience creating and contributing to open source projects related to database development and implementation. He holds a Ph.D. in computer science from the University of Pennsylvania and a B.S. in mathematics from the University of California, Davis.

Aaron Wong

Aaron Wong, Ph.D.

Data Scientist and Project Leader, Center for Computational Biology

Aaron Wong joined the center’s Genomics Group in 2015 to develop algorithms and models for analyzing high-throughput biomedical data and to coordinate the development of a public database of human functional genomics. Prior to coming to the foundation, Wong completed his Ph.D. in computer science at Princeton University, where he worked on integrative analysis of functional genomic data, developing algorithms to predict tissue-specific signals in biological networks and advanced search algorithms for large biomedical data collections. Before that, he was a research programmer in bioinformatics at the University of California, Davis. In addition to his Ph.D., Wong holds a B.S. in computer science and engineering from the University of California, Davis.

Wen Yan

Wen Yan, Ph.D.

Research Fellow, Center for Computational Biology

Wen Yan joined the Simons Foundation in 2016 as part of CCB’s biophysical modeling group. His research focuses on the development and simulation of mathematical models pertaining to phenomena in biophysics and active materials and the development of simulations of suspensions of such active objects. Wen comes to the foundation from the California Institute of Technology where he earned his Ph.D. in mechanical engineering.