Publications

L. Meshulam, J. Gauthier, C. Brody, D. Tank, W. Bialek. Coarse–graining, fixed points, and scaling in a large population of neurons. Phys. Rev. Lett. 123(17), 178103. DOI:10.1103/PhysRevLett.123.178103

S. Robert Datta, D. J.Anderson, K. Branson, P. Perona, A. Leifer. Computational Neuroethology: A Call to Action. Neuron 104(1), 11, 2019. DOI: 10.1016/j.neuron.2019.09.038

G. Hall and W. Bialek. The statistical mechanics of Twitter communities. J. Stat. Mech, 093406, 2019

S. Rath, E. Prangley, J. Donovan, K. Demarest, N. Wingreen, Y. Meir, A. Korennykh. Concerted 2-5A-Mediated mRNA Decay and Transcription Reprogram Protein Synthesis in the dsRNA Response. Mol Cell 75(6), 1218, 2019. DOI: 10.1016/j.molcel.2019.07.027

B. Weiner, A. Posfai, N. Wingreen. Spatial Ecology of Territorial Populations.

C. Holmes and I. Nemenman. Estimation of mutual information for real-valued data with error bars and controlled bias. Phys. Rev. E 100(2), 022404, 2019. DOI: 10.1103/PhysRevE.100.022404

 L. Kang, V. Balasubramanian. A geometric attractor mechanism for self-organization of entorhinal grid modules. eLife 8: e46687, 2019. DOI: 10.7554/eLife.46687

N. Khanna, Y. Zhang, J. Lucas, O. Dudko, C. Murre. Chromosome dynamics near the sol-gel phase transition dictate the timing of remote genomic interactions. Nature Communications 10: 2771, 2019. DOI: 10.1038/s41467-019-10628

X. Chen, F. RandiA. Leifer, W. BialekSearching for collective behavior in a small brain. Phys Rev E99(5), 052418, 2019. DOI: 10.1103/PhysRevE.99.052418

G. Liu, A. Patch, F. Bahar, D. Yllanes, R. Welch, M. Marchetti, S. Thutupalli, J. Shaevitz. Self-driven phase transitions drive Myxococcus xanthus fruiting body formation. Phys Rev Lett 122(24), 248102, 2019. DOI: 10.1103/PhysRevLett.122.248102 

J. Zan, Z. Li, M. Diarey Tianero, J. Davis, R. Hill, M. Donia. A microbial factory for defensive kahalalides in a tripartitemarine symbiosis. Science 364(6445), eaaw6732. 2019. DOI: 10.1126/science.aaw6732

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 4,  1274. 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 N. 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), 844, 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

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).

Y. Elhanati, Z. SethnaC. Callan, T. Mora, AM Walczak. Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination. Immunological Reviews 284(1), 167, 2018. DOI: 10.1111/imr.12665

E. Westerman, N. VanKuren, D. Massardo, A. Tenger-Trolander, W. Zhang, R. Hill, M. Perry, E. Bayala, K. Barr, N. Chamberlain, T. Douglas, N. Buerkle, S. Palmer, M. Kronforst. Aristaless controls butterfly wing color variation used in mimicry and mate choice. Current Biology 28(21), 3469, 2018. DOI: 10.1016/j.cub.2018.08.051

M. Eickhoff, B. Bassler. SnapShot: Bacterial Quorum Sensing. Cell 174(5), 1328,  2018. DOI: 10.1016/j.cell.2018.08.003

S. Mukherjee, D. Moustafa, V. Stergioula, C. Smith, J. Goldberg, B. BasslerThe PqsE and RhlR proteins are an autoinducer synthase-receptor pair that control virulence and biofilm development in Pseudomonas aeruginosa. PNAS 115(40), E9411, 2018. DOI: 10.1073/pnas.1814023115

N. Hoyland-Kroghsbo, K. Muñoz, B. BasslerTemperature, by controlling growth rate, regulates CRISPR-Cas activity in Pseudomonas aeruginosa. mBio 9(6): e02184, 2018.  DOI: 10.1128/mBio.02184-18

J. Yan, A. Moreau, S. Khodaparast, A. Perazzo, J. Feng, C. Fei, S. Mao, S. Mukherjee, A. Košmrlj, N. Wingreen, B. Bassler, H. Stone.  Bacterial biofilm material properties enable removal and transfer by capillary peeling. Adv Mater 30(46): e1804153, 2018 DOI: 10.1002/adma.201804153

Q. Xie, A. Zhao, P. Jeffrey, M. Kim, B. Bassler, H. Stone, RP Novick, and TW Muir. 2019. Identification of a molecular latch that regulates Staphylococcal virulence. Cell Chem Biol. 26(4), 548, 2019. DOI: 10.1016/j.chembiol.2019.01.006 

J. Yan, C. Fei, S. Mao, A. Moreau, N. Wingreen, A. Košmrlj, H. Stone, B. Bassler. Mechanical instability and interfacial energy drive biofilm morphogenesis. eLife 8: e43920, 2019 DOI: 10.7554/eLife.43920

T. Phan, R. Morris, H. Lam, P. Hulamm, M. Black, J. Bos, R. Austin. Emergence of Escherichia coli critically buckled motile helices under stress. PNAS 115(51), 12979, 2018. DOI: 10.1073/pnas.1809374115

H. Garcia, T. GregorLive Imaging of mRNA Synthesis in Drosophila. Methods Mol. Biol. 1649, 349, 2018. DOI: 10.1007/978-1-4939-7213-5_23

S. LittleT. Gregor. Single mRNA Molecule Detection in Drosophila. Methods Mol. Biol. 1649, 127, 2018. DOI: 10.1007/978-1-4939-7213-5_8

S. Palmer and colleagues. Chicago motion database. https://cmd.rcc.uchicago.edu

J. SilpeB. BasslerA host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Cell, 176(1-2), 268, 2019. DOI: 10.1016/j.cell.2018.10.059

A. McCready, J. Paczkowski, B. Henke, B. Bassler. Structural determinants driving homoserine lactone ligand selection in the Pseudomonas aeruginosa LasR quorum-sensing receptor. PNAS 116(1), 245, 2018. DOI: 10.1073/pnas.1817239116

J. Paczkowski, A. McCready, J-P Cong, Z. Li, P. Jeffrey, C. Smith, B. Henke, F. Hughson, B. Bassler. An autoinducer analog reveals an alternative mode of ligand binding for the LasR quorum-sensing receptor. ACS Chem Biol 14(3), 378, 2019. DOI: 10.1021/acschembio.8b00971

J. Clemens, P. Coen, F. Roemschied, T. Pereira, D. Mazumder, D. Aldarondo, D. Pacheco, M. MurthyDiscovery of a new song mode in Drosophila reveals hidden structure in the sensory and neural drivers of behavior. Current Biology 28(15), 2400, 2018. DOI: 10.1016/j.cub.2018.06.011

J. Clemens, N. Ozeri-Engelhard, M. MurthyFast Intensity Adaptation Enhances the Encoding of Sound in Drosophila. Nature Communications 9 (1), 134, 2018. DOI: 10.1038/s41467-017-02453-9

S. Mukherjee, B. Bassler. Bacterial quorum sensing in complex and dynamically changing environments. Nat Rev Microbiol, 17(6), 371, 2019. DOI: 10.1038/s41579-019-0186-5 

J. Silpe, B. Bassler. Phage-encoded LuxR type receptors responsive to host- produced bacterial quorum-sensing autoinducers. mBio 10:e00638-19, 2019. DOI:10.1128/mBio.00638-19

A. McCready, J. Paczkowski, J-P Cong, B. Bassler. An autoinducer-independent RhlR quorum-sensing receptor enables analysis of RhlR regulation. PLOS Pathogens 15(6): e1007820, 2019. DOI: 10.1371/journal.ppat.1007820

J. Lombardo, M. Macellaio, B. Liu, L. Osborne, S. PalmerState Dependence of Stimulus-Induced Variability Tuning in Macaque MT. PLoS computational biology, 14(10): e1006527, 2018. DOI: 10.1371/journal.pcbi.1006527

D. Deutsch, J. Clemens, SY Thiberge, G. Guan, M. Murthy. Shared Song Object Detector Neurons in Drosophila Male and Female Brains Drive Divergent, Sex-Specific Behaviors. Curr. Biol.  2019. DOI: 10.1016/j.cub.2019.08.008

2018-2019 APS Abstracts

To learn more about current research at the Center, see the abstracts we have presented at the  March Meetings of the American Physical Society

Preprint: arXiv and bioRxiv

M. Wei, D. Schwab. How noise affects the Hessian spectrum in over-parameterized neural networks. 2019. arXiv:1910.00195

M. Junaid Amin, S. Petry, H. Yang, J. Shaevitz. Uniform intensity in multifocal microscopy using a spatial light modulator. 2019. arXiv:1907.12609

L. Meshulam, J. Gauthier, C. Brody, D. Tank, W. Bialek. Coarse–graining, fixed points, and scaling in a large population of neurons. 2018. arXiv:1809.08461

W. Zhong, Z. Lu, D. Schwab, A. Murugan. Non-equilibrium statistical mechanics of continuous attractors. 2018. arXiv:1809.11167

M. Wei, J. Stokes, D. SchwabMean-field analysis of batch normalization. 2019. arXiv:1903.02606

V. Ngampruetikorn, D. Schwab, G. Stephens. Nonequilibrium cooperative sensing. 2018. arXiv:1809.04095

W. Johnston, S. Palmer, D. Freedman. Nonlinear mixed selectivity supports reliable neural computation. 2019. bioRxiv 577288 DOI: 10.1101/577288

S. Sinha, W. Bialek, R. de Ruyter van Steveninck. Optimal local estimates of visual motion in a natural environment. 2018.  arXiv:1812.11878

B. Xu, G. He, P. Ronceray, Y. Meir, M. Jonikas, N. Wingreen. Magic numbers in polymer phase separation - the importance of being rigid. 2019
arXiv:1901.09352

G. Tavoni, V. Balasubramanian, JI Gold. The complexity dividend: when sophisticated inference matters. bioRxiv 563346, 2019. DOI: 10.1101/563346

S. Bradde, A. Nourmohammad, S. Goyal, V. Balasubramanian. The size of the immune repertoire of bacteria. bioRxiv 565366, 2019. DOI: 10.1101/565366

V. Singh, M. Tchernookov, V. Balasubramanian. What the odor is not: Estimation by elimination. bioRxiv 568626, 2019. DOI: 10.1101/568626

F. Rossine, R. Martinez-Garcia, A. Sgro, T. Gregor, CE Tarnita. Eco-evolutionary significance of loners. bioRxiv 508507, 2018. DOI: 10.1101/508507

E. Pollock, N. Desai, XX Wei, V. Balasubramanian. Dynamic self-organized error-correction of grid cells by border cells. bioRxiv 385229, 2018. DOI: 10.1101/385229

U. Klibaite, J. Shaevitz. Interacting fruit flies synchronize behavior. bioRxiv 545483, 2019. DOI: 10.1101/545483

Z. Li, B. Liu, SHJ Li, C. King, Z. Gitai, N. Wingreen. Modeling microbial diversity with metabolic trade-offs. bioRxiv 664698, 2019. DOI: 10.1101/664698

J. Taylor, B. Bratton, S. Sichel, K. Blair, H. Jacobs, K. DeMeester, E. Kuru, J. Gray, J. Biboy, M. VanNieuwenhze, W. Vollmer, C. Grimes, J. Shaevitz, N. Salama. Distinct cytoskeletal proteins define zones of enhanced cell wall synthesis in Helicobacter pylori. bioRxiv 545517. 

M. Scholz, A. Linder, F. Randi, A. Sharma, X. Yu, J. Shaevitz, A. Leifer. Predicting natural behavior from whole-brain neural dynamics. bioRxiv 445643. 2018. DOI: 10.1101/445643

R. Low, S. Lewallen, D. Aronov, R. Nevers, D. Tank. Probing variability in a cognitive map using manifold inference from neural dynamics. bioRxiv 418939, 2018. DOI: 10.1101/418939 

V. Antonetti, W. Bialek, T. Gregor, G. Muhaxheri, M. Petkova, M. Scheeler. Precise spatial scaling in the early fly embryo. arXiv:1812.11384