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2022
Valentino M, Ortega BM, Ulrich B, Doyle DA, Farnum ED, Joiner DA, et al. Computational modeling offers new insight into Drosophila germ granule development. Biophys J. 2022 ;121(8):1465-1482.
Jaslove JM, Goodwin K, Sundarakrishnan A, Spurlin JW, Mao S, Košmrlj A, et al.. Transmural pressure signals through retinoic acid to regulate lung branching. Development. 2022 ;149(2).
2021
Narla AV, Borenstein DBruce, Wingreen NS. A biophysical limit for quorum sensing in biofilms. Proc Natl Acad Sci U S A. 2021 ;118(21).
Qin B, Fei C, Wang B, Stone HA, Wingreen NS, Bassler BL. Hierarchical transitions and fractal wrinkling drive bacterial pellicle morphogenesis. Proc Natl Acad Sci U S A. 2021 ;118(20).
Diegmiller R, Zhang L, Gameiro M, Barr J, Alsous JImran, Schedl P, et al. Mapping parameter spaces of biological switches. PLoS Comput Biol. 2021 ;17(2):e1008711.
Wang MD, Nicodemi M, Dekker NH, Gregor T, Holcman D, van Oijen AM, et al. Physics meets biology: The joining of two forces to further our understanding of cellular function. Mol Cell. 2021 ;81(15):3033-3037.
2020
Fiore VF, Krajnc M, Quiroz FGarcia, Levorse J, H Pasolli A, Shvartsman SY, et al. Mechanics of a multilayer epithelium instruct tumour architecture and function. Nature. 2020 ;585(7825):433-439.
2019
Zhou J, Schor IE, Yao V, Theesfeld CL, Marco-Ferreres R, Tadych A, et al. Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development. PLoS Genet. 2019 ;15(9):e1008382.
Dutta S, Djabrayan NJ-V, Torquato S, Shvartsman SY, Krajnc M. Self-Similar Dynamics of Nuclear Packing in the Early Drosophila Embryo. Biophys J. 2019 ;117(4):743-750.
Simsek ANihat, Braeutigam A, Koch MD, Shaevitz JW, Huang Y, Gompper G, et al. Substrate-rigidity dependent migration of an idealized twitching bacterium. Soft Matter. 2019 ;15(30):6224-6236.
2018
Zhou J, Theesfeld CL, Yao K, Chen KM, Wong AK, Troyanskaya OG. Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk. Nat Genet. 2018 ;50(8):1171-1179.
Dine E, Gil AA, Uribe G, Brangwynne CP, Toettcher JE. Protein Phase Separation Provides Long-Term Memory of Transient Spatial Stimuli. Cell Syst. 2018 ;6(6):655-663.e5.
2017
Siedlik MJ, Manivannan S, Kevrekidis IG, Nelson CM. Cell Division Induces and Switches Coherent Angular Motion within Bounded Cellular Collectives. Biophys J. 2017 ;112(11):2419-2427.
Varner VD, Nelson CM. Computational models of airway branching morphogenesis. Semin Cell Dev Biol. 2017 ;67:170-176.
Nerger BA, Siedlik MJ, Nelson CM. Microfabricated tissues for investigating traction forces involved in cell migration and tissue morphogenesis. Cell Mol Life Sci. 2017 ;74(10):1819-1834.
Nofal M, Zhang K, Han S, Rabinowitz JD. mTOR Inhibition Restores Amino Acid Balance in Cells Dependent on Catabolism of Extracellular Protein. Mol Cell. 2017 ;67(6):936-946.e5.
Hristov BH, Singh M. Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. Cell Syst. 2017 ;5(3):221-229.e4.
Piet AT, Erlich JC, Kopec CD, Brody CD. Rat Prefrontal Cortex Inactivations during Decision Making Are Explained by Bistable Attractor Dynamics. Neural Comput. 2017 ;29(11):2861-2886.
Tanaka H, Stone HA, Nelson DR. Spatial gene drives and pushed genetic waves. Proc Natl Acad Sci U S A. 2017 ;114(32):8452-8457.
Wilson MZ, Ravindran PT, Lim WA, Toettcher JE. Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control. Mol Cell. 2017 ;67(5):757-769.e5.
2016
Robinson JL, Brynildsen MP. 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.
Prentice JS, Marre O, Ioffe ML, Loback AR, Tkačik G, Berry MJ. Error-Robust Modes of the Retinal Population Code. PLoS Comput Biol. 2016 ;12(11):e1005148.
He B, Martin A, Wieschaus E. Flow-dependent myosin recruitment during Drosophila cellularization requires zygotic dunk activity. Development. 2016 ;143(13):2417-30.
Schumer M, Cui R, Rosenthal GG, Andolfatto P. simMSG: an experimental design tool for high-throughput genotyping of hybrids. Mol Ecol Resour. 2016 ;16(1):183-92.
Snir S, vonHoldt BM, Pellegrini M. A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging. PLoS Comput Biol. 2016 ;12(11):e1005183.