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Computer Simulation

  • 1.
    Valentino M, Ortega B, Ulrich B, Doyle D, Farnum E, Joiner D, Gavis E, Niepielko M. Computational modeling offers new insight into Drosophila germ granule development. Biophys J. 2022;121(8):1465–1482. PMCID: PMC9072583
    Reference Link
  • 1.
    Jaslove J, Goodwin K, Sundarakrishnan A, Spurlin J, Mao S, Košmrlj A, Nelson C. Transmural pressure signals through retinoic acid to regulate lung branching. Development. 2022;149(2). PMCID: PMC8917413
    Reference Link
  • 1.
    Wang M, Nicodemi M, Dekker N, Gregor T, Holcman D, van Oijen A, Manley S. Physics meets biology: The joining of two forces to further our understanding of cellular function. Mol Cell. 2021;81(15):3033–3037. PMID: 34358454
    Reference Link
  • 1.
    Qin B, Fei C, Wang B, Stone H, Wingreen N, Bassler B. Hierarchical transitions and fractal wrinkling drive bacterial pellicle morphogenesis. Proc Natl Acad Sci U S A. 2021;118(20). PMCID: PMC8157956
    Reference Link
  • 1.
    Narla A, Borenstein D, Wingreen N. A biophysical limit for quorum sensing in biofilms. Proc Natl Acad Sci U S A. 2021;118(21). PMCID: PMC8166027
    Reference Link
  • 1.
    Diegmiller R, Zhang L, Gameiro M, Barr J, Alsous J, Schedl P, Shvartsman S, Mischaikow K. Mapping parameter spaces of biological switches. PLoS Comput Biol. 2021;17(2):e1008711. PMCID: PMC7895388
    Reference Link
  • 1.
    Fiore V, Krajnc M, Quiroz F, Levorse J, Pasolli A, Shvartsman S, Fuchs E. Mechanics of a multilayer epithelium instruct tumour architecture and function. Nature. 2020;585(7825):433–439. PMCID: PMC7787055
    Reference Link
  • 1.
    Zhou J, Schor I, Yao V, Theesfeld C, Marco-Ferreres R, Tadych A, Furlong E, Troyanskaya O. Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development. PLoS Genet. 2019;15(9):e1008382. PMCID: PMC6779412
    Reference Link
  • 1.
    Simsek A, Braeutigam A, Koch M, Shaevitz J, Huang Y, Gompper G, Sabass B. Substrate-rigidity dependent migration of an idealized twitching bacterium. Soft Matter. 2019;15(30):6224–6236. PMID: 31334524
    Reference Link
  • 1.
    Dutta S, Djabrayan N, Torquato S, Shvartsman S, Krajnc M. Self-Similar Dynamics of Nuclear Packing in the Early Drosophila Embryo. Biophys J. 2019;117(4):743–750. PMCID: PMC6712419
    Reference Link
  • 1.
    Zhou J, Theesfeld C, Yao K, Chen K, Wong A, Troyanskaya O. Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk. Nat Genet. 2018;50(8):1171–1179. PMCID: PMC6094955
    Reference Link
  • 1.
    Dine E, Gil A, Uribe G, Brangwynne C, Toettcher J. Protein Phase Separation Provides Long-Term Memory of Transient Spatial Stimuli. Cell Syst. 2018;6(6):655–663.e5. PMCID: PMC6023754
    Reference Link
  • 1.
    Hristov B, Singh M. Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. Cell Syst. 2017;5(3):221–229.e4. PMCID: PMC5997485
    Reference Link
  • 1.
    Nofal M, Zhang K, Han S, Rabinowitz J. mTOR Inhibition Restores Amino Acid Balance in Cells Dependent on Catabolism of Extracellular Protein. Mol Cell. 2017;67(6):936–946.e5. PMCID: PMC5612669
    Reference Link
  • 1.
    Wilson M, Ravindran P, Lim W, Toettcher J. Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control. Mol Cell. 2017;67(5):757–769.e5. PMCID: PMC5591080
    Reference Link
  • 1.
    Tanaka H, Stone H, Nelson D. Spatial gene drives and pushed genetic waves. Proc Natl Acad Sci U S A. 2017;114(32):8452–8457. PMCID: PMC5559037
    Reference Link
  • 1.
    Piet A, Erlich J, Kopec C, Brody C. Rat Prefrontal Cortex Inactivations during Decision Making Are Explained by Bistable Attractor Dynamics. Neural Comput. 2017;29(11):2861–2886. PMCID: PMC6535097
    Reference Link
  • 1.
    Siedlik M, Manivannan S, Kevrekidis I, Nelson C. Cell Division Induces and Switches Coherent Angular Motion within Bounded Cellular Collectives. Biophys J. 2017;112(11):2419–2427. PMCID: PMC5474845
    Reference Link
  • 1.
    Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Error-Robust Modes of the Retinal Population Code. PLoS Comput Biol. 2016;12(11):e1005148. PMCID: PMC5113862
    Reference Link
  • 1.
    Nerger B, Siedlik M, Nelson C. Microfabricated tissues for investigating traction forces involved in cell migration and tissue morphogenesis. Cell Mol Life Sci. 2017;74(10):1819–1834. PMCID: PMC5391279
    Reference Link
  • 1.
    Schumer M, Cui R, Rosenthal G, Andolfatto P. simMSG: an experimental design tool for high-throughput genotyping of hybrids. Mol Ecol Resour. 2016;16(1):183–92. PMID: 26032857
    Reference Link
  • 1.
    He B, Martin A, Wieschaus E. Flow-dependent myosin recruitment during Drosophila cellularization requires zygotic dunk activity. Development. 2016;143(13):2417–30. PMCID: PMC4958320
    Reference Link
  • 1.
    Snir S, vonHoldt B, Pellegrini M. A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging. PLoS Comput Biol. 2016;12(11):e1005183. PMCID: PMC5106012
    Reference Link
  • 1.
    Varner V, Nelson C. Computational models of airway branching morphogenesis. Semin Cell Dev Biol. 2017;67:170–176. PMCID: PMC5136345
    Reference Link
  • 1.
    Murisic N, Hakim V, Kevrekidis I, Shvartsman S, Audoly B. From discrete to continuum models of three-dimensional deformations in epithelial sheets. Biophys J. 2015;109(1):154–63. PMCID: PMC4571022
    Reference Link
  • 1.
    Chung N, Storey J. Statistical significance of variables driving systematic variation in high-dimensional data. Bioinformatics. 2015;31(4):545–54. PMCID: PMC4325543
    Reference Link
  • 1.
    Song M, Hao W, Storey J. Testing for genetic associations in arbitrarily structured populations. Nat Genet. 2015;47(5):550–4. PMCID: PMC4464830
    Reference Link
  • 1.
    Berezhkovskii A, Shvartsman S. Dynamics of gradient formation by intracellular shuttling. J Chem Phys. 2015;143(7):074116. PMCID: PMC5562396
    Reference Link
  • 1.
    Robinson J, Brynildsen M. Discovery and dissection of metabolic oscillations in the microaerobic nitric oxide response network of Escherichia coli. Proc Natl Acad Sci U S A. 2016;113(12):E1757–66. PMCID: PMC4812703
    Reference Link
  • 1.
    Aronov D, Tank D. Engagement of neural circuits underlying 2D spatial navigation in a rodent virtual reality system. Neuron. 2014;84(2):442–56. PMCID: PMC4454359
    Reference Link
  • 1.
    Borenstein D, Ringel P, Basler M, Wingreen N. Established Microbial Colonies Can Survive Type VI Secretion Assault. PLoS Comput Biol. 2015;11(10):e1004520. PMCID: PMC4619000
    Reference Link
  • 1.
    Chen E, Chou J, Park J, Schwartz G, Berry M. The neural circuit mechanisms underlying the retinal response to motion reversal. J Neurosci. 2014;34(47):15557–75. PMCID: PMC4236393
    Reference Link
  • 1.
    Marre O, Botella-Soler V, Simmons K, Mora T, Tkačik G, Berry M. High Accuracy Decoding of Dynamical Motion from a Large Retinal Population. PLoS Comput Biol. 2015;11(7):e1004304. PMCID: PMC4489022
    Reference Link
  • 1.
    Brody C, Hopfield J. Simple networks for spike-timing-based computation, with application to olfactory processing. Neuron. 2003;37(5):843–52. PMID: 12628174
    Reference Link
  • 1.
    Machens C, Romo R, Brody C. Flexible control of mutual inhibition: a neural model of two-interval discrimination. Science. 2005;307(5712):1121–4. PMID: 15718474
    Reference Link

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