Publications


A. Keinath, R. Epstein, V. Balasubramanian. Environmental deformations dynamically shift human spatialmemory. Hippocampus, 2020. DOI: 10.1002/hipo.23265

U. Klibaite, JW. Shaevitz. Paired fruit flies synchronize behavior: Uncovering social interactions in Drosophila melanogaster
PLoS Comput Biol 16(10): e1008230, 2020. DOI: 10.1371/journal.pcbi.1008230

T. Teşileanu, M. Conte, J. Briguglio, A. Hermundstad, J. Victor, V. Balasubramanian. Sensitivity to grayscale textures is adapted to natural scene statistics. eLife 9:e54347, 2020. DOI: 10.7554/eLife.54347bioRxiv 872994 

A. Erez, J. Lopez, B. Weiner, Y. Meir, N. Wingreen. Nutrient levels and trade-offs control diversity in a model seasonal ecosystem. eLife 9:e57790, 2020. DOI: 10.7554/eLife.57790; arXiv:1902.09039 [physics.bio-ph] (2019)

Z. Li, B. Liu, SHJ Li, C. King, Z. Gitai, N. Wingreen. Modeling microbial diversity with metabolic trade-offs. PLoS Comput Biol 16(8): e1008156. 2020. DOI: 10.1371/journal.pcbi.1008156; bioRxiv 664698

A. Erez, TA. Byrd, M. Vennettilli, and A. Mugler. Cell-to-Cell Information at a Feedback-Induced Bifurcation Point. Phys. Rev. Lett. 125(4), 048103, 2020. DOI: 10.1103/PhysRevLett.125.048103arXiv:1910.13899 [physics.bio-ph] (2019)

DB. Brückner, P. Ronceray, and CP. Broedersz. Inferring the Dynamics of Underdamped Stochastic Systems. Phys. Rev. Lett. 125(5), 058103, 2020. DOI: 10.1103/PhysRevLett.125.058103arXiv:2002.06680 [physics.bio-ph] (2020)

A. Tareen, N. Wingreen, R. Mukhopadhyay. Asymmetry between Activators and Deactivators in Functional Protein Networks. Scientific Reports 10: 10131, 2020. DOI: 10.1038/s41598-020-66699-y; arXiv:1807.09431 [q-bio.MN] (2018)

D. Shams, X. Yang, P. Mehta, and D. Schwab. Spatial gradient sensing and chemotaxis via excitability in Dictyostelium discoideum. Physical Review E 101, 062410, 2020. DOI:10.1103/PhysRevE.101.062410

A. Thawani, M. Rale, N. Coudray, G. Bhabha, H. Stone, J. Shaevitz, S. Petry. The transition state and regulation of γ-TuRC-mediated microtubule nucleation revealed by single molecule microscopy. eLife 9: e54253, 2020. DOI: 10.7554/eLife.54253;

J. Martin, J. Sheehan, B. Bratton, G. Moore, A.  Mateus, S. Hsin-Jung Li, H. Kim, J. Rabinowitz, A. Typas, M.Savitski, M. Wilson, Z. Gitai. A Dual-Mechanism Antibiotic Kills Gram-Negative Bacteria and Avoids Drug Resistance. Cell. 2020. DOI: 10.1016/j.cell.2020.05.005bioRxiv 984229 [Microbiology] (2020)

C. Saad-Roy, N. Wingreen, S. Levin, and B. Grenfell. Dynamics in a simple evolutionary-epidemiological model for the evolution of an initial asymptomatic infection stage. PNAS, 2020. DOI: 10.1073/pnas.1920761117

B. Xu, G. He, BG. Weiner, P. Ronceray, Y. Meir, M. Jonikas, N. Wingreen. Magic numbers in polymer phase separation - the importance of being rigid. Nature Communications 11: 1561, 2020. DOI: 10.1038/s41467-020-15395-6; arXiv:1901.09352 [physics.bio-ph] (2019)

A. Frishman, P. Ronceray. Learning force fields from stochastic trajectories. Physical Review X10, 021009, 2020. DOI: 10.1103/PhysRevX.10.021009arXiv:1809.09650 [cond-mat.soft] (2018)

V. Ngampruetikorn, D. Schwab, G. Stephens. Energy consumption and cooperation for optimal sensing. Nature Communications 11: 975, 2020. DOI: 10.1038/s41467-020-14806-y; arXiv:1809.04095 [physics.bio-ph] (2018)

S. Bradde, A. Nourmohammad, S. Goyal, V. Balasubramanian. The size of the immune repertoire of bacteria. PNAS 117(10),  5144, 2020.
DOI:

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. eLife 9: e52482, 2020. DOI: 10.7554/eLife.52482;

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, 2019. DOI:10.1103/PhysRevLett.123.178103; arXiv:1812.11904  [q-bio.NC] (2018)

SR. Datta, DJ. 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

B. Bratton, B. Barton, R. Morgenstein. Three-dimensional Imaging of Bacterial Cells for Accurate Cellular Representations and Precise Protein Localization. J. Vis. Exp. 152, e60350, 2019. DOI: 10.3791/60350. URL: https://www.jove.com/video/60350

G. Hall and W. Bialek. The statistical mechanics of Twitter communities. Journal of Statistical Mechanics: Theory and Experiment, 093406, 2019. DOI: 0.1088/1742-5468/ab3af0; arXiv:1812.07029 [physics.soc-ph] (2018)

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; arXiv:1810.07623 [physics.bio-ph] (2018)

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; arXiv:1709.06012 [physics.bio-ph] (2017)

J. Zan, Z. Li, M. Diarey Tianero, J. Davis, R. Hill, M. Donia. A microbial factory for defensive kahalalides in a tripartite marine 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

SW Wang, AF Bitbol, N. Wingreen. Revealing evolutionary constraints on proteins through sequence analysis. PLoS Computational Biology 15(4), e1007010, 2019. DOI: 10.1371/journal.pcbi.1007010; arXiv:1808.07149 [q-bio.BM] (2018)

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

V. Singh, 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. Zhang, AS. Perelson, 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; arXiv:1612.08084 [q-bio.MN] (2016)

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 of the brain. 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; arXiv:1803.04085 [q-bio.NC] (2018)

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). arXiv:1808.02093 [cs.AI] (2018)

MJ. Amin, S. Petry, H. Yang, J. Shaevitz. Uniform intensity in multifocal microscopy using a spatial light modulator. PLOS ONE, 2020
DOI: 10.1371/journal.pone.0230217; arXiv:1907.12609 [physics.bio-ph] (2019)

WJ. Johnston, SE. Palmer, and DJ. Freedman. Nonlinear mixed selectivity supports reliable neural computation. PLoS Comput Biol. 16(2):e1007544. 2020. DOI: 10.1371/journal.pcbi.1007544.

F. Rossine, R. Martinez-Garcia, A. Sgro, T. Gregor, CE Tarnita. Eco-evolutionary significance of 'loners'. PLoS Biol 18(3): e3000642, 2020. DOI: 10.1371/journal.pbio.3000642

C. Fei, S. Mao, J. Yan, R. Alert, H. Stone, B. Bassler, N. Wingreen, A. Košmrlj. Nonuniform growth and surface friction determine bacterial biofilm morphology on soft substrates. PNAS 117(14), 7622, 2020. DOI: 10.1073/pnas.1919607117; arXiv:1910.14645 [physics.bio-ph] (2019)

M.A. Heinrich, R. Alert, J.M. LaChance, T.J. Zajdel, A. Košmrlj, and D.J. Cohen. Size-dependent patterns of cell proliferation and migration in freely-expanding epithelia. eLife 9:e58945, 2020. DOI: 10.7554/eLife.58945. bioRxiv 970418

X. Huang, O. Duddy, J. Silpe, J. Paczkowski, J. Cong, B. Henke, B. Bassler. Mechanism underlying autoinducer recognition in the Vibrio cholerae DPO-VqmA quorum-sensing pathway. J Biol Chem 6, 295(10), 2916, 2020. DOI: 10.1074/jbc.RA119.012104

Bonnie Bassler. From Biochemistry to Genetics in a Flash of Light. Genetics 215(2),  287.  2020. DOI: 10.1534/genetics.120.303285

B. Qin, C. Fei, A. Bridges, A. Mashruwala, H. Stone, N. Wingreen, and B. Bassler. Cell fates and collective fountain flow in bacterial biofilms revealed by light-sheet microscopy. Science :eabb8501. 2020. DOI: 10.1126/science.abb8501

A. Mashruwala, and B. Bassler. The Vibrio cholerae quorum-sensing protein VqmA integrates cell density, environmental, and host-derived cues into the control of virulence. mBio. 2020. In press

J. Valastyan, M. Tota, I. Taylor, V. Stergioula, G. Hone Chari, D. Smith, B. Henke,  K. Carson, B. Bassler. Discovery of PqsE Thioesterase Inhibitors for Pseudomonas aeruginosa Using DNA-Encoded Small Molecule Library Screening. ACS Chem. Biol. 15(2) 446, 2020.
DOI: 10.1021/acschembio.9b00905

J. Silpe, A. Bridges, X. Huang, D. Coronado, O. Duddy, B. Bassler. Separating Functions of the Phage-Encoded Quorum-Sensing-Activated Antirepressor Qtip. Cell Host Microbe 8 27(4), 629, 2020. DOI: 10.1016/j.chom.2020.01.024

R. Alert, J-F. Joanny, and J. Casademunt. Universal scaling of active nematic turbulence. Nature Physics 16,  2020.
DOI: 10.1038/s41567-020-0854-4

R. Alert and X. Trepat. Physical Models of Collective Cell Migration. Annual Review of Condensed Matter Physics 11, 77,  2020.
DOI: 10.1146/annurev-conmatphys-031218-013516

W. Zhong, Z. Lu, DJ Schwab, A. Murugan. Nonequilibrium statistical mechanics of continuous attractors. Neural Computation 32 (6), 1033, 2020
DOI: (2018) arXiv:1809.11167

Md-Z. Ali, K-C Huang, N. Wingreen, and R. Mukhopadhyay. Cell geometry and leaflet bilayer asymmetry regulate domain formation in plasma membranes. Phys Rev E 99(1-1): 012401, 2019. DOI: 10.1103/PhysRevE.99.012401

P. Mehta, M. Bukov, C-H. Wang, A.G.R. Day, C. Richardson, CK. Fisher, D. Schwab. A high-bias, low-variance introduction to machine learning for physicists. Physics Reports, 810,1, 2019. DOI: 10.1016/j.physrep.2019.03.001; arXiv:1803.08823 [physics.comp-ph] (2018)

DJ Strouse and David Schwab.The information bottleneck and geometric clustering. The MIT Press Journals. Neural Computation 31:3, 596, 2019. DOI: 10.1162/neco_a_01136; arXiv:1712.09657 [stat.ML] (2017)

AN. Simsek, A. Braeutigam, M. Koch, J. Shaevitz, Y. Huang, G. Gompper and B. Sabass. Substrate-rigidity dependent migration of an idealized twitching bacterium. Soft Matter 15(30), 6224, 2019. DOI: 10.1039/C9SM00541B;

L. Pinto, K Rajan, B DePasquale, SY Thiberge, DW Tank. Task-Dependent Changes in the Large-Scale Dynamics and Necessity of Cortical Regions. Neuron 104(4), 810, 2019.  DOI: 10.1016/j.neuron.2019.08.025

B. Deverett, M. Kislin, DW Tank, SSH Wang. Cerebellar disruption impairs working memory during evidence accumulation. Nature communications10: 3128, 2019. DOI: 10.1038/s41467-019-11050-x

B. Engelhard, J. Finkelstein, J. Cox, W. Fleming, HJ. Jang, S. Ornelas, SA Koay, SY Thiberge, ND Daw, DW. Tank, IB. Witten. Specialized coding of sensory, motor and cognitive variables in VTA dopamine neurons. Nature 570(7762), 509, 2019. DOI: 10.1038/s41586-019-1261-9

A. Giovannucci, J. Friedrich, P. Gunn, J. Kalfon, BL Brown, SA. Koay, J. Taxidis, F Najafi, JL Gauthier, P Zhou, BS Khakh, DW Tank. CaImAn an open source tool for scalable calcium imaging data analysis. eLife 8: e38173, 2019.  DOI: 10.7554/eLife.38173

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, 2019DOI: 10.7554/eLife.43920

J. Yan, B. Bassler. Surviving as a Community: Antibiotic Tolerance and Persistence in Bacterial Biofilms. Cell Host Microbe.10 26(1), 15, 2019. DOI: 10.1016/j.chom.2019.06.002.

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

K-C Lin, G. Torga, Y. Sun, K. Pienta, J. Sturm, R. Austin. Generation of Heterogeneous Drug Gradients Across Cancer Populations on a Microfluidic Evolution Accelerator for Real-Time Observation. J. Vis. Exp. 19(151), 2019. DOI: 10.3791/60185. URL: https://www.jove.com/video/60185

S. Amend, G. Torga, Ke‐C. Lin, L. Kostecka,|A. de Marzo, R. Austin, K. Pienta. Polyploid giant cancer cells: Unrecognized actuators of tumorigenesis, metastasis, and resistance. The Prostate 79(13), 1489, 2019. DOI: 10.1002/pros.23877

J. Pribis, L. García-Villada, Y. Zhai, O. Lewin-Epstein, AZ. Wang, J. Liu, J. Xia, Q. Mei, D. Fitzgerald, J. Bos, R. Austin, C. Herman, D. Bates, L. Hadany, PJ. Hastings, SM. Rosenberg. Gamblers: an antibiotic-induced evolvable cell subpopulation differentiated by reactive-oxygen-induced general stress response. Mol cell 74 (4), 785, 2019. DOI: 10.1016/j.molcel.2019.02.037

KC. Lin, G. Torga, Y. Sun, R. Axelrod, KJ. Pienta, JC. Sturm, R. Austin. The role of heterogeneous environment and docetaxel gradient in the emergence of polyploid, mesenchymal and resistant prostate cancer cells. Clinical & experimental metastasis 36(2), 97, 2019.
DOI: 10.1007/s10585-019-09958-1

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

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 

S. Mukherjee, M. Jemielita, V. Stergioula, M. Tikhonov, B. Bassler. Photosensing and quorum sensing are integrated to control Pseudomonas aeruginosa collective behaviors. PLoS Biol 17(12): e3000579. DOI: 10.1371/journal.pbio.3000579

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, B. Henke, B. Bassler. Structural determinants driving homoserine lactone ligand selection in the Pseudomonas aeruginosa LasR quorum-sensing receptor. PNAS 116(1), 245, 2019. DOI: 10.1073/pnas.1817239116

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. 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

A. Bridges, and B. Bassler. The intragenus and interspecies quorum-sensing autoinducers exert distinct control over Vibrio cholerae biofilm formation and dispersal. PLoS Biol 17(11): e3000429, 2019. DOI: 10.1371/journal.pbio.3000429

D. Deutsch, J. Clemens, SY Thiberge, G. Guan, M. MurthyShared Song Object Detector Neurons in Drosophila Male and Female Brains Drive Divergent, Sex-Specific Behaviors. Current Biology 29(19), 3200. 2019. DOI: 10.1016/j.cub.2019.08.008

A. Calhoun, J. Pillow, and M. Murthy. Unsupervised identification of the internal states that shape natural behavior. Nature Neuroscience 22, 2040, 2019. DOI: 10.1038/s41593-019-0533-x

O. Ahmed, and M. Murthy. Neuroscience: Tantalized Flies Are Primed for Satiety. Current Biology, 29(21), R1146-R1148, 2019.
DOI: 10.1016/j.cub.2019.09.029

C. Baker, J. Clemens, and M. Murthy. Acoustic Pattern Recognitionand Courtship Songs: Insights from Insects. Annual Review of Neuroscience 42, 129, 2019. DOI: 10.1146/annurev-neuro-080317-061839

G. Tavoni, V. Balasubramanian, J. Gold. What is optimal in optimal inference? Current Opinion in Behavioral Sciences, 29, 117, 2019.
DOI: 10.1016/j.cobeha.2019.07.008

M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora. Receptor crosstalk allows improved concentration sensing. Physical Review E 99(2), 022423, 2019. DOI: 10.1103/PhysRevE.99.022423

S. Mayer,  J. Chen, D. Velmeshev, A. Mayer, U. Eze, M. Paredes, B. Alvarado, S. Wang, CE. Cunha,  N. Lovegren, ML. Gonzales, L. Szpankowski, A. Leyrat, JAA. West, A. Alvarez-Buylla, TJ. Nowakowski, AA. Pollen, AR. Kriegstein.  Multimodal single-cell analysis reveals physiological maturation in the developing human neocortex. Neuron 102(1), 143, 2019. DOI: 10.1016/j.neuron.2019.01.027

M. Eickhoff, B. BasslerSnapShot: 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

Y. Shin, Y-C. Chang, D. Lee, J. Berry, D. Sanders, P. Ronceray, N. Wingreen, M. Haataja, C. Brangwynne. Liquid nuclear condensates mechanically sense and restructure the genome cell 175(6), 1481, 2018. DOI: 10.1016/j.cell.2018.10.057

 F. Beroz, J. Yan, Y. Meir, B. Sabass, HA. Stone, BL. Bassler & NS. Wingreen. Verticalization of BActerial biofilms. Nature Physics 14, 954, 2018. DOI: 10.1038/s41567-018-0170-4    arXiv:1801.03064 [physics.bio-ph] (2018)

S. Hsin-Jung Li, Z. Li, JO. Park, CG. King,  JD. Rabinowitz, NS. Wingreen, and Z. Gitai, Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions. Nature Microbiology  3, 939, 2018. DOI: 10.1038/s41564-018-0199-2;

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

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

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

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

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

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

2018-2020 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

TD. Pereira, N. Tabris, J. Li, S. Ravindranath, ES. Papadoyannis, ZY Wang, DM. Turner, G. McKenzie-Smith, SD. Kocher, AL. Falkner, JW. Shaevitz, M. Murthy. SLEAP: Multi-animal pose tracking. bioRxiv 276246, 2020. DOI: 10.1101/2020.08.31.276246

M. Junaid Amin, S. Petry, JW. Shaevitz, H. Yang. Localization precision in chromatic multifocal imaging. 2020. arXiv:2008.10488 [physics.optics]

W. Bialek, SE. Palmer, DJ. Schwab. What makes it possible to learn probability distributions in the natural world? 2020. arXiv:2008.12279 [cond-mat.stat-mech]

X. Chen, W. Bialek. Searching for long time scales without fine tuning. 2020.  arXiv:2008.11674 [physics.bio-ph]

William Bialek. What do we mean by the dimensionality of behavior? 2020.  arXiv:2008.09574 [q-bio.NC] 

Y. Zhang, B. Xu, BG. Weiner, Y. Meir, NS. Wingreen. Decoding the physical principles of two-component biomolecular phase separation. bioRxiv 264655, 2020. DOI: 10.1101/2020.08.24.264655

F Randi, AM Leifer. Nonequilibrium Green's functions for functional connectivity in the brain. 2020. arXiv:2008.06093 [q-bio.NC]

DB. Brückner, N. Arlt, A. Fink, P. Ronceray, JO. Rädler, CP. Broedersz. Learning the dynamics of cell-cell interactions in confined cell migration. 2020.  arXiv:2008.03978

J. Scheffler, Y. Sugimoto, BP. Bratton, C K. Ellison, MD. Koch, MS. Donia, Z. Gitai. Pseudomonas aeruginosa detachment from surfaces via a self-made small molecule. bioRxiv 203174, 2020. DOI:10.1101/2020.07.14.203174

T. Can, K. Krishnamurthy, DJ. SchwabTheory of gating in recurrent neural networks. 2020. arXiv preprint arXiv:2007.14823

J. Ding, A. Chen, J. Chung, H. Acaron Ledesma, DM. Berson, S. Palmer, W. Wei. Spatially displaced excitation contributes to the encoding of interrupted motion by the retinal direction-selective circuit. bioRxiv 124461, 2020. DOI: 10.1101/2020.05.29.124461

S. Wang, A. Borst, I. Segev, S. Palmer. Axonal gap junctions in the fly visual system enable fast prediction for evasive flight maneuvers. bioRxiv 814319, 2020. DOI: 10.1101/814319

J. Frankle, D J. Schwab, A. Morcos. The early phase of neural network training. 2020. arXiv:2002.10365

J. Frankle, D J. Schwab, A. Morcosar. Training batchNorm and only batchNorm: on the expressive power of random features in CNNs. 2020. arXiv:2003.00152

D. Lee, N. Wingreen, C. Brangwynne. Chromatin Mechanics DictatesSubdiffusion and Coarsening Dynamics of Embedded Condensates. bioRXiv 128561, 2020. DOI: 10.1101/2020.06.03.128561

M. Vennettilli, A.  Erez, and A. Mugler. Multicellular sensing at a feedback-induced critical point.  2020. arXiv:2005.07010

H Falahati, W Hur, S Di Tali, EF Wieschaus. Temperature-induced uncoupling of cell cycle regulators. bioRxiv 943266, 2020. DOI: 10.1101/2020.02.11.943266

D. Deutsch, D. Pacheco, L. Encarnacion-Rivera, T. Pereira, R. Fathy, A. Calhoun, E. Ireland, A. Burke, S. Dorkenwald,
C. McKellar, T. Macrina, R. Lu, K. Lee, N. Kemnitz, D. Ih, M. Castro, A. Halageri, C. Jordan, W. Silversmith, J. Wu, H. S Seung, and M. Murthy. The Neural Basis for a Persistent Internal State in Drosophila Females. bioRxiv 947952, 2020. DOI: 10.1101/2020.02.13.947952.

V. Sachdeva, T. Mora, A. Walczak, S. Palmer. Optimal prediction with resource constraints using the information bottleneck. bioRxiv 069179, 2020. DOI: 10.1101/2020.04.29.069179

M. Koch, C. Fei, N. Wingreen, J. Shaevitz, Z. Gitai. Competitive binding of independent extension and retraction motors explains the quantitative dynamics of type IV pili. , 2020. DOI:

T. Can, K. Krishnamurthy, D. Schwab. Gating creates slow modes and controls phase-space complexity in GRUs and LSTMs. 2020. arXiv:2002.00025

SU. Setru,1, B. Gouveia, R. Alfaro-Aco, J. Shaevitz, H. Stone, S. Petry. A hydrodynamic instability drives protein dropletformation on microtubules to nucleate branches. 2020. arXiv:2001.06389 [physics.bio-ph]

RM. Wagner, SU. Setru, B. Machta, N. Wingreen, D. Lopez. The Bacterial Cytoskeleton Spatially Confines Functional Membrane Microdomains. bioRxiv 060970. DOI: 10.1101/2020.04.25.060970

K. Copenhagen, R. Alert, N. Wingreen, and J. Shaevitz. Topological defects induce layer formation inMyxococcus xanthuscolonies. 2020.  arXiv:2001.03804 [physics.bio-ph]

DA. Pacheco, SY. Thiberge, E. Pnevmatikakis and M. Murthy. Auditory Activity is Diverse and Widespread Throughout the Central Brain of Drosophila. bioRxiv 709519, 2019. DOI: 10.1101/709519

W. Bialek, T. Gregor, G. Tkačik. Action at a distance in transcriptional regulation. 2019. arXiv:1912.08579

R. Rousseau, and W. Bialek. Information costs in the control of protein synthesis. 2019. arXiv:1912.13017

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

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

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

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

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

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

E Piasini, L Soltuzu, R Caramellin, V. Balasubramanian and D. Zoccolan. Intrinsic dynamics enhance temporal stability of stimulus representation along a visual cortical hierarchy. bioRxiv 822130, 2019. DOI:10.1101/822130

U. Klibaite, J. Shaevitz. Interacting fruit flies synchronize behavior. bioRxiv 545483, 2019. DOI: 10.1101/545483 [Animal Bihavior and Cognition]

NP Buerkle, SE Palmer. Ancestral neural computations constrain the evolution of novel computations in simulated color vision networks. bioRxiv , 2019. DOI: 10.1101/2019.12.30.891382

SA. Koay, SY. Thiberge, C Brody, DW Tank. Neural Correlates of Cognition in Primary Visual versus Neighboring Posterior Cortices during Visual Evidence-Accumulation-based Navigation. bioRxiv 568766, 2019. DOI: 10.1101/568766

AS. Charles, A. Song, JL. Gauthier, JW. Pillow, DW. Tank. Neural Anatomy and Optical Microscopy (NAOMi) Simulation for evaluating calcium imaging method. bioRxiv 726174, 2019. DOI: 10.1101/726174

H. Kim, J. Homann, DW. Tank, MJ. Berry II. A Long Timescale Stimulus History Effect in the Primary Visual Cortex. bioRxiv 585539, 2019. DOI: 10.1101/585539

SA. Koay, SY. Thiberge, CD. Brody, DW. Tank. Neural Correlates of Cognition in Primary Visual versus Neighboring Posterior Cortices during Visual Evidence-Accumulation-based Navigation. bioRxiv 568766, 2019. DOI: 10.1101/568766

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

R. Low, S. Lewallen, D. Aronov, R. Nevers, DW. 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 [q-bio.MN] (2018)

N. Khanna, Y. Zhang, JS. Lucas, OK. Dudko, C. Murre. Antigen receptor locus dynamics is orchestrated near the sol-gel phase transition to enforce stepwise VDJ gene rearrangement. bioRxiv 441444, 2018. DOI: 10.1101/441444