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    Biological Transport and Networks Integrating computation, theory and experimental data to decipher the inner workings of living processes.

    Biomolecular Design Using exotic building blocks to design novel heteropolymers that fold into well-defined 3D structures.

    Biophysical Modeling Modeling and simulating the complex systems that arise in biology and soft condensed matter physics.

    CCBScope Observatory The Flatiron Institute's in-house, state-of-the-art imaging facility for live-cell confocal microscopy.

    CCBx Uniting theorists and experimentalists to develop and test theories of biological systems.

    COMPASS Connecting researchers working on molecular sampling, simulation and design.

    Developmental Dynamics Combining experiment, theory and computing to elucidate the inner workings of embryonic development.

    Genomics Working to unravel the complexity of the genome, its regulation and its phenotypic consequences.

    Statistical Biophysics Developing a nonequilibrium physics of living systems and learning machines.

    Structural and Molecular Biophysics Developing novel mathematical approaches to decipher the molecular mechanisms involved in key biological processes.

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Flatiron Institute Computational Biology

Computational Biology: Publications

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  1. OXOPIPERAZINE HELIX MIMETICS AS INHIBITORS OF THE p53-MDM2 INTERACTION

    Patent, April 15, 2015

    P.S. Arora, B.B. Lao, D. Guarracino, R. Bonneau, and K. Drew

  2. A Hebbian/Anti-Hebbian Neural Network for Linear Subspace Learning: A Derivation from Multidimensional Scaling of Streaming Data

    arXiv, March 2, 2015

    C. Pehlevan, T. Hu, and D. Chklovskii

  3. A Hebbian/Anti-Hebbian Network Derived from Online Non-Negative Matrix Factorization Can Cluster and Discover Sparse Features

    arXiv, March 2, 2015

    C. Pehlevan and D. Chklovskii

  4. Inter-species pathway perturbation prediction via data-driven detection of functional homology

    Bioinformatics, February 15, 2015

    C. Hafemeister, R. Romero, E. Bilal, P. Meyer, R. Norel, K. Rhrissorrakrai, et al.

  5. Political Expression and Action on Social Media: Exploring the Relationship Between Lower- and Higher-Threshold Political Activities Among Twitter Users in Italy

    Journal of Computer-Mediated Communication, January 12, 2015

    C. Vaccari, A, Valeriani, P. Barberá, R. Bonneau, J.T. Jost, J. Nagler, et al.

  6. Protest in the age of social media

    Medium, January 8, 2015

    J.A. Tucker, M. Metzger, D. Penfold-Brown, R. Bonneau, J. Jost, and J. Nagler

  7. A consistent muscle activation strategy underlies crawling and swimming in Caenorhabditis elegans

    Journal of The Royal Society Interface, November 26, 2014

    V. Butler, R. Branicky, E. Yemini, and R. Schafer

  8. Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks

    IEEE transactions on visualization and computer graphics, November 6, 2014

    B. Yu, H. Doraiswamy, X. Chen, E. Miraldi, C. Hafemeister, A. Madar, et al.

  9. A Hebbian/Anti-Hebbian Network for Online Sparse Dictionary Learning Derived from Symmetric Matrix Factorization

    2014 48th Asilomar Conference on Signals, Systems and Computers, arXiv:1503.00690, 2014

    T. Hu, C. Pehlevan, and D. Chklovskii

  10. Dynamics of influence in online protest networks: Evidence from the 2013 Turkish protests

    APSA Annual Meeting, October 7, 2014

    K. Munger

  11. Abinitio Relax

    RosettaCommons.org, October 1, 2014

    K. Simons, R. Bonneau, K. Misura, P. Bradley, O. Lange, M. Tyka, et al.

  12. Conformational preferences of peptide–peptoid hybrid oligomers

    Peptide Science, September 20, 2014

    G.L. Butterfoss, K. Drew, D. Renfrew, K. Kirshenbaum, and R. Bonneau

  13. Leaders or followers? Measuring political responsiveness in the US Congress using social media data

    110th American Political Science Association Annual Meeting, August 28, 2014

    P. Barberá, R. Bonneau, P. Egan, J.T. Jost, J. Nagler, and J. Tucker

  14. ICOS-based chimeric antigen receptors program bipolar TH17/TH1 cells

    Blood, August 14, 2014

    S. Guedan, X. Chen, A. Madar, C. Carpenito, S.E. McGettigan, M.J. Frigault, et al.

  15. One third of dynamic protein expression profiles can be predicted by a simple rate equation

    Molecular BioSystems, August 1, 2014

    K. Tchourine, C.S. Poultney, L. Wang, G.M. Silva, S. Manohar, C. Müller, et al.

  16. Improved Stability and Half-Life of Fluorinated Phosphotriesterase Using Rosetta

    ChemBioChem, July 25, 2014

    C.-Y. Yang, D. Renfrew, A.J. Olsen, M. Zhang, C. Yuvienco, R. Bonneau, et al.

  17. CX3CR1+ mononuclear phagocytes support colitis-associated innate lymphoid cell production of IL-22

    Journal of Experimental Medicine, July 14, 2014

    R.S. Longman, G.E. Diehl, D.A. Victorio, J.R. Huh, C. Galan, E. Miraldi, et al.

  18. Engineered coiled-coil protein microfibers

    Biomacromolecules, June 18, 2014

    J. Hume, J. Sun, R. Jacquet, D. Renfrew, J. Martin, R. Bonneau, et al.

  19. Negative Example Selection for Protein Function Prediction: The NoGO Database

    PLOS Computational Biology, June 12, 2014

    N. Youngs, D. Penfold-Brown, R. Bonneau, and D. Shasha

  20. Rational Design of Topographical Helix Mimics as Potent Inhibitors of Protein–Protein Interactions

    Journal of the American Chemical Society, May 23, 2014

    B.B. Lao, K. Drew, D.A. Guarracino, T.F. Brewer, D.W. Heindel, R. Bonneau, et al.

  21. Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota

    PLOS Neglected Tropical Diseases, May 22, 2014

    S.C. Lee, M.S. Tang, Y.A.L. Lim, S.H. Choy, Z.D. Kurtz, L.M. Cox, et al.

  22. Intrinsic bioconjugation for site-specific protein PEGylation at N-terminal serine

    Chemical Communications, May 19, 2014

    P.M. Levine, T.W. Craven, R. Bonneau, and K. Kirshenbaum

  23. A Rotamer Library to Enable Modeling and Design of Peptoid Foldamers

    Journal of the American Chemical Society, May 13, 2014

    D. Renfrew, T.W. Craven, G.L. Butterfoss, K. Kirshenbaum, and R. Bonneau

  24. Collier/OLF/EBF-Dependent Transcriptional Dynamics Control Pharyngeal Muscle Specification from Primed Cardiopharyngeal Progenitors

    Developmental Cell, May 12, 2014

    F. Razy-Krajka, K. Lam, W. Wang, A. Stolfi, M. Joly, R. Bonneau, et al.

  25. A Neuron as a Signal Processing Device

    arXiv, May 12, 2014

    T. Hu, Z. Towfic, C. Pehlevan, A. Genkin, and D. Chklovskii

  26. Bacillus subtilis systems biology

    Microbiology Spectrum, 2014

    A.R. Bate, R. Bonneau, and P. Eichenberger

  27. FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

    Nature Methods, March 23, 2014

    M. Murtha, Z. Tokcaer-Keskin, Z. Tang, F. Strino, X. Chen, Y. Wang, et al.

  28. Toward large-scale connectome reconstructions

    Current Opinion in Neurobiology, March 7, 2014

    S.M. Plaza, L.K. Scheffer, and D. Chklovskii

  29. Wiring economy can account for cell body placement across species and brain areas

    Current Biology, February 3, 2014

    M. Rivera-Alba, H. Peng, G. de Polavieja, and D. Chklovskii

  30. Semisynthesis of Peptoid–Protein Hybrids by Chemical Ligation at Serine

    Organic Letters, January 3, 2014

    P.M. Levine, T.W. Craven, R. Bonneau, and K. Kirshenbaum

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