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  1. An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network

    Molecular Systems Biology, November 17, 2015

    M.L. Arrieta‐Ortiz, C. Hafemeister, A.R. Bate, T. Chu, A. Greenfield, B. Shuster, et al.

  2. Positive-Unlabeled Learning in the Face of Labeling Bias

    2015 IEEE International Conference on Data Mining Workshop (ICDMW), November 14, 2015

    N. Youngs, D. Shasha, and Richard Bonneau

  3. Synaptic circuits and their variations within different columns in the visual system of Drosophila

    PNAS, November 3, 2015

    S. Takemura, C.S. Xu, Z. Lu, P.K. Rivlin, T. Parag, D.J. Olbris, et al.

  4. An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses

    Cell, October 8, 2015

    T. Sano, W. Huang, J.A. Hall, Yi Yang, A. Chen, S.J. Gavzy, et al.

  5. Cohesin loss alters adult hematopoietic stem cell homeostasis, leading to myeloproliferative neoplasms

    Journal of Experimental Medicine, October 5, 2015

    J. Mullenders, B. Aranda-Orgilles, P. Lhoumaud, M. Keller, J. Pae, K. Wang, et al.

  6. Optimization theory of Hebbian/anti-Hebbian networks for PCA and whitening

    2015 53rd Annual Allerton Conference on Communication, Control, and Computing (Allerton), 2015

    Cengiz Pehlevan and Dmitri B. Chklovskii

  7. Synaptic circuits and their variations within different columns in the visual system of Drosophila

    PNAS, 2015

    Dmitri B. Chklovskii, S. Takemura, C. Shan Xu, Z. Lu, P. K. Rivlina, T. Parag, et al.

  8. Tweeting From Left to Right

    Psychological Science, August 21, 2015

    P. Barberá, J.T. Jost, J. Nagler, J.A. Tucker, and Richard Bonneau

  9. Unimodal clustering using isotonic regression: ISO-SPLIT

    arXiv:1508.04841, August 20, 2015

    Jeremy Magland and Alex H. Barnett

  10. Automatic Adaptation to Fast Input Changes in a Time-Invariant Neural Circuit

    PLOS, 2015

    Dmitri B. Chklovskii and A. Bharioke

  11. Automatic adaptation to fast input changes in a time-invariant neural circuit

    PLOS Computational Biology, August 6, 2015

    A. Bharioke and Dmitri B. Chklovskii

  12. Primacy of Flexor Locomotor Pattern Revealed by Ancestral Reversion of Motor Neuron Identity

    Cell, July 16, 2015

    Timonty A Machado, Eftychios Pnevmatikakis, Liam Paninski, Thomas M Jessell, and Andrew Miri

  13. Simple and efficient representations for the fundamental solutions of Stokes flow in a half-space

    Journal of Fluid Mechanics, arxiv:1504.00102, July 2, 2015

    Zydrunas Gimbutas, Leslie Greengard, and Shravan Veerapaneni

  14. FNTM: A Server for Predicting Functional Networks of Tissues in Mouse

    Nucleic Acids Res, 2015

    J. Goya, A. Wong, V. Yao, A. Krishnan, M. Homilius, and Olga G. Troyanskaya

  15. Variable metric random pursuit

    Mathematical Programming, arXiv: 1210.5114, May 24, 2015

    Sebastian U Stich, Christian Müller, and Bernd Gärtner

  16. Oxopiperazine helix mimetics for control of hypoxia-inducible gene expression

    Patent, May 20, 2015

    P.S. Arora, B.B. Lao, Richard Bonneau, and K. Drew

  17. Sparse and Compositionally Robust Inference of Microbial Ecological Networks

    PLOS Computational Biology, May 7, 2015

    Z.D. Kurtz, Christian Müller, Emily R. Miraldi, D.R. Littman, M.J. Blaser, and Richard Bonneau

  18. Interpreting 4C-Seq data: how far can we go?

    Epigenomics, April 22, 2015

    R. Raviram, P.P. Rocha, Richard Bonneau, and J.A. Skok

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

    Patent, April 15, 2015

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

  20. 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 Dmitri B. Chklovskii

  21. 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 Dmitri B. Chklovskii

  22. 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.

  23. Inverse Obstacle Scattering in Two Dimensions with Multiple Frequency Data and Multiple Angles of Incidence

    SIAM Journal on Imaging Sciences, arxiv:1408.5436, January 27, 2015

    Carlos Borges and Leslie Greengard

  24. 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, Richard Bonneau, J.T. Jost, J. Nagler, et al.

  25. Protest in the age of social media

    Medium, January 8, 2015

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

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

    The Royal Society Publishing, 2015

    Dmitri B. Chklovskii, V. J. Butler, R. Branicky, E.Yemini, J. F. Liewald, A. Gottschalk, et al.

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

    MIT Press Direct, 2015

    Dmitri B. Chklovskii, C. Pehlevan, and T. Hu

  28. 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

  29. 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, Emily R. Miraldi, C. Hafemeister, A. Madar, et al.

  30. A Fast Direct Solver for High Frequency Scattering from a Large Cavity in Two Dimensions

    SIAM Journal on Scientific Computing, arxiv:1404.3451, November 4, 2014

    Jun Lai, Sivaram Ambikasaran, and Leslie Greengard

  31. 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, Cengiz Pehlevan, and Dmitri B. Chklovskii

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

    APSA Annual Meeting, October 7, 2014

    K. Munger

  33. Abinitio Relax

    RosettaCommons.org, October 1, 2014

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

  34. Conformational preferences of peptide–peptoid hybrid oligomers

    Peptide Science, September 20, 2014

    G.L. Butterfoss, K. Drew, P. Douglas Renfrew, K. Kirshenbaum, and Richard Bonneau

  35. 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, Richard Bonneau, P. Egan, J.T. Jost, J. Nagler, and J. Tucker

  36. 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.

  37. 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, Christian Müller, et al.

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

    ChemBioChem, July 25, 2014

    C.-Y. Yang, P. Douglas Renfrew, A.J. Olsen, M. Zhang, C. Yuvienco, Richard Bonneau, et al.

  39. 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, Emily R. Miraldi, et al.

  40. Engineered coiled-coil protein microfibers

    Biomacromolecules, June 18, 2014

    J. Hume, J. Sun, R. Jacquet, P. Douglas Renfrew, J. Martin, Richard Bonneau, et al.

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

    PLOS Computational Biology, June 12, 2014

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

  42. 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, Richard Bonneau, et al.

  43. 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.

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

    Chemical Communications, May 19, 2014

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

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

    Journal of the American Chemical Society, May 13, 2014

    P. Douglas Renfrew, T.W. Craven, G.L. Butterfoss, K. Kirshenbaum, and Richard Bonneau

  46. 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, Richard Bonneau, et al.

  47. A Neuron as a Signal Processing Device

    arXiv, May 12, 2014

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

  48. Bacillus subtilis systems biology

    Microbiology Spectrum, 2014

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

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