Publications

J. Sanfilippo, A. Lorestani, M. Koch, B. Bratton, A. Siryaporn, H. Stone and Z. Gita. Microfluidic-based transcriptomics reveal  force-independent bacterial rheosensing. Nature Microbiology. 2019. DOI: 10.1038/s41564-019-0455-0

Z. Sethna, Y. ElhanatiC. Callan Jr,  A. Walczak, and T. Mora. OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs. Bioinformatics, btz035, 2019. DOI: 10.1093/bioinformatics/btz035

S-W Wang, A-F Bitbol, N. Wingreen. Revealing evolutionary constraints on proteins through sequence analysis. PLoS Computational Biology 15(4): e1007010, 2019. DOI: 10.1371/journal.pcbi.1007010

A.Thawani, H. Stone, J. Shaevitz, S. Petry. Spatiotemporal organization of branched microtubule networks. eLife 8:e43890, 2019. DOI: 10.7554/eLife.43890

A. Mayera, V. Balasubramanian, AM Walczakb, and T. Mora. How a well-adapting immune system remembers. PNAS , 2019. DOI: 10.1073/pnas.1812810116

V. Singha, N. Murphy, V. Balasubramaniana, and J. Mainland. Competitive binding predicts nonlinear responses ofolfactory receptors to complex mixtures. PNAS, 116(19), 9598, 2019. DOI: 10.1073/pnas.1813230116

A. Mayera, Y. Zhangb, AS. Perelsonc, and NS. Wingreen. Regulation of T cell expansion by antigenpresentation dynamics. PNAS, 116 (13) 5914, 2019. DOI: 10.1073/pnas.1812800116

M. Petkova, G. Tkačik, W. Bialek, E. Wieschaus, T. Gregor. Optimal Decoding of Cellular Identities in a Genetic Network. Cell 176, 1. 2019. DOI: 10.1016/j.cell.2019.01.007

T. Pereira, D. Aldarondo, L. Willmore, M. Kislin, S. Wang, M. Murthy and J. Shaevitz. Fast animal pose estimation using deep neural networks. Nature Methods 16, 117, 2019. DOI: 10.1038/s41592-018-0234-5

T. Teşileanu, S.Cocco, R. Monasson, V. Balasubramanian. Adaptation of olfactory receptor abundances for efficient coding, eLife 8:e39279, 2019. DOI: 10.7554/eLife.39279

M. Jemielita, N. Wingreen, B. Bassler. Quorum sensing controls Vibrio cholerae multicellular aggregate formation. eLife, 7:e42057, 2018. DOI: 10.7554/eLife.42057

B. Bratton, J. Shaevitz, Z. Gitai and R. Morgenstein. MreB polymers and curvature localization are enhanced by RodZ and predict E. coli's cylindrical uniformity. Nature Communications 9: 2797, 2018. DOI: 10.1038/s41467-018-05186-5

B. Zoller, SC. Little, T. GregorDiverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting. Cell 175(3), 835, 2018. DOI: 10.1016/j.cell.2018.09.056

H. Chen, M. Levo, L. Barinov, M. Fujioka, JB. Jaynes, T. GregorDynamic interplay between enhancer-promoter topology and gene activity. Nature Genetics 50, 1296, 2018. DOI: 10.1038/s41588-018-0175-z

A. Keinath, R. Epstein, V. Balasubramanian. Environmental deformations dynamically shift the grid cell spatial metric. eLife, 7: e38169, 2018. DOI: 10.7554/eLife.38169

L. Kang, V. Balasubramanian. A geometric attractor mechanism for self-organization of entorhinal grid modules. bioRxiv: 338087, 2018. DOI: 10.1101/338087

M. Liu, A. Sharma, J. Shaevitz, A. Leifer. Temporal processing and context dependency in Caenorhabditis elegans response to mechanosensation. eLife, 7:e36419, 2018. DOI: 10.7554/eLife.36419

DJ. Strouse, M. Kleiman-Weiner, J. Tenenbaum, M. Botvinick, D. Schwab. Learning to Share and Hide Intentions usingInformation Regularization.  Advances in Neural Information Processing Systems 31 (NIPS 2018).