From my Research Statement:
My laboratory is focused on two areas in computational and systems biology: 1) Predicting and designing protein and peptidomimetic structure and 2) Learning dynamic network models automatically from functional genomics data using scalable methods.
In both research areas I have played key roles in achieving critical field-wide milestones. In the area of structure prediction I was one of the early authors on the Rosetta code, which was one of the first codes to demonstrate accurate and comprehensive ability to predict protein structure in the absence of detectable sequence homology to proteins with known structures. My lab continues to be a core contributor to the Rosetta research community, participating in the recent refactoring of the code and adding several new functionalities.
My lab has also made key contributions to the area of genomics data analysis in a systems-biology context. We focus on developing new methods for network inference that simultaneously learn dynamics and topology from data (the Inferelator), and methods that learn condition-dependent co-regulated gene groups from integrations of different genomics data- types (e.g. transcriptomic, proteomic, etc.) using approaches we have developed (cMonkey and multi-species-cMonkey integrative biclustering). In the DREAM3 and DREAM4 blind assessment of network inference methods we were top performers in the network inference category, and are currently contributing to a joint paper resulting from DREAM5 (the most current assessment of network inference methods).
Research and Software Engineering
Ashish's interests intersect programming language theory, functional programming, and biology. His long-term goal is to design a domain specific language for genomics entailing data management and analysis. He is currently working towards this goal by developing a software library for bioinformatics in the functional programming language OCaml. His more theoretical efforts regard a constructive foundation for optimization and statistics grounded in type theory. This has the promise of mechanizing much more of mathematics than is attained by existing mathematics software.
Research Scientist / Lab Shaman
Research interests: Rational design of peptidomimetics and proteins, functional genomics, energy function development.
Special power: Granting spirit animal imprimatur.
I am a Biology Postdoc with the Bonneau research group , at the Center for Genomics and Systems Biology (CGSB) at New York University. I moved to NYC ~3 years ago from Israel. I would like to consider myself as intelligent, spicy, someone who loves to travel and exploring new things. I love cooking (everything), movies, a good exercise, good conversations and interesting people.
Network Inference Postdoc
I am a postdoc on the network inference side of Rich Bonneau's Lab at NYU's Center for Genomics and Systems Biology and am co-advised by Dan Littman at the NYU Medical School's Skirball Institute. The goal of my postdoctoral research is to develop models of immune-cell and gut microbiome co-evolution that will further our understanding of the molecular network alterations and interactions underlying autoimmune disease. My background, developed as a Ph.D. student in Forest White's Lab at MIT, is in cellular signaling, quantitative mass-spectrometry-based analysis of protein post-translation modifications and metabolites, and machine learning.
I am a postdoc in Rich Bonneau's lab at the Courant Institute and NYU's Center for Genomics and Systems Biology. My research interests include (non-)convex continuous optimization and Markov Chain Monte Carlo methods. I'm currently concerned with the development and the successful application of such schemes to biological problems including parameter identification, network inference, and protein structure prediction.
Before joining NYU I did my PhD and postdoctoral research in Ivo Sbalzarini's MOSAIC group at ETH Zurich. I’m also a member of the consortium of the EU FP-7 project Computational Geometric Learning. Within this project I contribute to research on adaptive gradient-free optimization schemes and on Morse-Smale descriptions of high-dimensional sampled cost and energy landscapes.
P. Douglas Renfrew
I am a postdoc in the Bonneau lab studying the use of peptoids (oligo N-substituted glycines) and other peptidomimetics and their use in developing protine-like therapeutics and biological tools. I graduated from the University of Vermont (UVM) with a B.S. in 2003 with major in Molecular Genetics and a minors in Chemistry and Computer Science. While at UVM I preformed undergraduate research in the lab of Sylvie Doublie studying the structure of mammalian poly-A-poylmerase and fell in love with protein structures. I went on to study at the University of North Carolina at Chapel Hill where I joined the Molecular and Cellular Biophysics training program in the Department of Biochemistry and Biophysics. My thesis work was done in the laboratory of Brian Kuhlman Ph.D. and focused on using noncanonical amino acids in computational protein design. I started in the Bonneau lab in June of 2010.
Outside of lab I enjoy movies and making my own beer and mead.
I am a second year PhD student working on structural bioinformatics. I am interested in combining structural and evolutionary analyses of proteins to infer function and the effects of mutation. Sequences provide (lossy) structural information which can be used to guide structural simulations, although the specific information contained is still somewhat obscure. I am also interested in integrating/refining the "user interface" to biological analysis software (since tools, databases, servers, and algorithms are sparse and mostly isolated yet users require an integrated interface). During my undergrad, I studied chemical engineering and worked as a software developer for PyRosetta.
I enjoy watching movies and playing games (card, board, video, role-playing, etc.).
I am a PhD student in the Bonneau (NYU) and Kempa (BIMSB-MDC) lab and my thesis is about the integrative analysis of cell metabolism and proteome in fast versus slow growing cells. Currently I am working with primary cells and setting up a target proteomic approach for quantitative proteomics. Before joining the BIMSB-NYU PhD program in July 2010 I worked for a short time at the chemical and veterinary investigations office in Stuttgart. I received my diploma in technical biology from the University of Stuttgart. During my thesis I got in touch for the first time with flux modeling of eukaryotic cells with flux balance analysis. In my free time I'd like to do archery and sometimes basketball. I am also enjoying cooking and going out with friends.
Tim studies protein structure.
My research in the Bonneau Lab currently involves two topics: protein annotation and peptidomimetic design.
Many proteins have limited or no functional information known about them and this hinders analysis of many high throughput experimental techniques. I work on a computational annotation pipeline that de novo predicts the three dimensional structure of proteins using Rosetta molecular modeling software and uses the predicted structures to infer function. The computation of de novo folding is distributed on IBM's World CommunityGrid (over 1.5 million cpus) and allows us to annotate proteins in multiple genomes (>100) in a reasonable timescale.
My other research includes the design of a helical peptidomimetic, specifically oligooxopiperazines (OOPs) (collaboration with Arora Lab, NYU Chem). Helical peptides are often found at the interfaces of protein interactions and mimicking them with a more stable backbone such as an OOP would provide a valuable tool to disrupting those interactions. I use Rosetta's design protocol to sample different side chain combinations placed on the backbone attempting to create higher affinity and higher specificity binding for a protein target. I am currently working on disrupting the p53 MDM2 protein interaction.
Christoph is a bioinformagician.
I am a PhD student in the Bonneau lab working on optimizing protein-protein interfaces using non-canonical amino acids. I moved to New York from Orlando where I did my undergrad at The University of Central Florida in computer science and my masters in molecular biology at the Burnett School of Biomedical Sciences. I'm excited about the possibilities for engineering macromolecules and the methods for their in silico simulation. I like traveling to foreign lands, sailing boats, scuba diving, and hikes in the woods. I also dig indie films and science fiction.
I am a PhD student at NYU School of Medicine/Sackler Institute. I hail from Long Island, NY, where I got my BS in Biochemistry at Stony Brook University. After working throughout undergrad in an experimental microbiology lab and later in an immunology lab at Mount Sinai School of Medicine, I realized that computational approaches to data-intensive biology research is where it’s at. In the Bonneau lab, my goal is to study microbes from a systems levels and learn something about their evolution. When I’m not being a scientist you might find me brewing beer, playing the accordion or pondering human rationality and it’s applications to behavior, economics and artificial intelligence.
Abba Leffler is a neuroscience graduate student in the Sackler Institute of Graduate Biomedical Sciences at NYU Medical Center. As an undergraduate he attended Princeton University, where he majored in Chemistry with Certificates in Applied Mathematics and Engineering Biology. His senior thesis on Drosophila morphogen gradients won the Robert Thornton McKay Prize in Physical Chemistry, awarded to the senior whose research shows the most promise in the field of physical chemistry.
Abba also worked as a Junior Scientist at D. E. Shaw Research, an independent research lab based in New York City, where he was involved in simulating the complete gating mechanism of voltage gated potassium channels and developed novel computational methods for fragment based drug design. He is currently interested in computationally designing both ligand-gated ion channels and peptides to selectively manipulate neural circuits.
I work on algorithmic development for enzyme design, specifically using peptoids to mimic peptide active sites. I also do some work on using learning algorithms for protein function prediction using sequence and structural information. Coming from a background of physics, economics, as well as pure and computational math, I enjoy working on problems that cross-over traditional academic boundaries and require diverse approaches from different disciplines.
Research and Software
Structure Research and Software Engineering
At the moment, Duncan is too tired from filling out Bios to write his own bio. He designed this website, thinks science is awesome, and dictates all his code to a parrot he trained to type during his jungle adolescence (this last is not strictly true).
Interests: bioinformatics, self-organizing (multiagent, swarm, autonomic, self-adaptive) systems, cloud computing.
Riley W. Simmons-Edler
I'm an undergraduate working in Prof. Bonneau's lab whilst I survive my remaining years at NYU. When not having my wild-eyed optimism crushed or being "the undergrad", I work on protein design and structure prediction, though I also have a love of AI and machine learning that gets neglected. Currently I'm working on a project related to predicting temperature sensitive mutations.
High School Students
I am a highschool student working at the Bonneau lab and in collaboration with Jin Montclare at NYU Poly, working with a protein called Phosphotriesterase (pictured) related to degrading pesticides.
I am a high school student working at the Bonneau Lab, interested in structure prediction and modeling the effects of mutations on protein function, particularly in neurological disorders. Currently, I am working on a protocol using computational modeling to identify temperature sensitive mutants of membrane proteins.
I am a student at Commack High School and a researcher in the Bonneau Lab. I am interested in network inference and as of now, I hope my college education includes majoring in biology and computer science.
New Lab Members
Mario Luis Arrieta Ortizmao355[at]nyu.edu
Former Lab Members
Research and SE
Currently: Bioinformatics PhD at University of California, San Franciscokgm5[at]nyu.edu
MSc, Research, and Software Engineeringpatrick.winters[at]nyu.edu