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Items: 48

1.

Self-organized shape dynamics of active surfaces.

Mietke A, Jülicher F, Sbalzarini IF.

Proc Natl Acad Sci U S A. 2019 Jan 2;116(1):29-34. doi: 10.1073/pnas.1810896115. Epub 2018 Dec 19.

2.

Adaptive particle representation of fluorescence microscopy images.

Cheeseman BL, Günther U, Gonciarz K, Susik M, Sbalzarini IF.

Nat Commun. 2018 Dec 4;9(1):5160. doi: 10.1038/s41467-018-07390-9.

3.

How Computational Models Enable Mechanistic Insights into Virus Infection.

Sbalzarini IF, Greber UF.

Methods Mol Biol. 2018;1836:609-631. doi: 10.1007/978-1-4939-8678-1_30. Review.

PMID:
30151595
4.

pSSAlib: The partial-propensity stochastic chemical network simulator.

Ostrenko O, Incardona P, Ramaswamy R, Brusch L, Sbalzarini IF.

PLoS Comput Biol. 2017 Dec 4;13(12):e1005865. doi: 10.1371/journal.pcbi.1005865. eCollection 2017 Dec.

5.

L p -Adaptation: Simultaneous Design Centering and Robustness Estimation of Electronic and Biological Systems.

Asmus J, Müller CL, Sbalzarini IF.

Sci Rep. 2017 Jul 27;7(1):6660. doi: 10.1038/s41598-017-03556-5.

6.

A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule.

Meyer K, Ostrenko O, Bourantas G, Morales-Navarrete H, Porat-Shliom N, Segovia-Miranda F, Nonaka H, Ghaemi A, Verbavatz JM, Brusch L, Sbalzarini I, Kalaidzidis Y, Weigert R, Zerial M.

Cell Syst. 2017 Mar 22;4(3):277-290.e9. doi: 10.1016/j.cels.2017.02.008. Epub 2017 Mar 18.

7.

Curvature Filters Efficiently Reduce Certain Variational Energies.

Gong Y, Sbalzarini IF.

IEEE Trans Image Process. 2017 Apr;26(4):1786-1798. doi: 10.1109/TIP.2017.2658954. Epub 2017 Jan 26.

PMID:
28141519
8.

Infectio: a Generic Framework for Computational Simulation of Virus Transmission between Cells.

Yakimovich A, Yakimovich Y, Schmid M, Mercer J, Sbalzarini IF, Greber UF.

mSphere. 2016 Feb 10;1(1). pii: e00078-15. doi: 10.1128/mSphere.00078-15. eCollection 2016 Jan-Feb.

9.

Seeing Is Believing: Quantifying Is Convincing: Computational Image Analysis in Biology.

Sbalzarini IF.

Adv Anat Embryol Cell Biol. 2016;219:1-39. doi: 10.1007/978-3-319-28549-8_1. Review.

PMID:
27207361
10.

Automatic optimal filament segmentation with sub-pixel accuracy using generalized linear models and B-spline level-sets.

Xiao X, Geyer VF, Bowne-Anderson H, Howard J, Sbalzarini IF.

Med Image Anal. 2016 Aug;32:157-72. doi: 10.1016/j.media.2016.03.007. Epub 2016 Apr 4.

11.

A Parallel Distributed-Memory Particle Method Enables Acquisition-Rate Segmentation of Large Fluorescence Microscopy Images.

Afshar Y, Sbalzarini IF.

PLoS One. 2016 Apr 5;11(4):e0152528. doi: 10.1371/journal.pone.0152528. eCollection 2016.

12.

ClearVolume: open-source live 3D visualization for light-sheet microscopy.

Royer LA, Weigert M, Günther U, Maghelli N, Jug F, Sbalzarini IF, Myers EW.

Nat Methods. 2015 Jun;12(6):480-1. doi: 10.1038/nmeth.3372. No abstract available.

PMID:
26020498
13.

A method for modeling growth of organs and transplants based on the general growth law: application to the liver in dogs and humans.

Shestopaloff YK, Sbalzarini IF.

PLoS One. 2014 Jun 9;9(6):e99275. doi: 10.1371/journal.pone.0099275. eCollection 2014. Erratum in: PLoS One. 2014;9(8):e105483.

14.

Contact angle at the leading edge controls cell protrusion rate.

Gabella C, Bertseva E, Bottier C, Piacentini N, Bornert A, Jeney S, Forró L, Sbalzarini IF, Meister JJ, Verkhovsky AB.

Curr Biol. 2014 May 19;24(10):1126-32. doi: 10.1016/j.cub.2014.03.050. Epub 2014 May 1.

15.

Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh.

Rizk A, Paul G, Incardona P, Bugarski M, Mansouri M, Niemann A, Ziegler U, Berger P, Sbalzarini IF.

Nat Protoc. 2014 Mar;9(3):586-96. doi: 10.1038/nprot.2014.037. Epub 2014 Feb 13.

PMID:
24525752
16.

Directing traffic into the future.

Antonny B, Audhya J, l Bagnat M, von Blume J, Briggs JA, Giraudo C, Kaeser PS, Miller E, Reinisch K, Sbalzarini IF, Schuldiner M, Shen J, Takamori S, Verstreken P, Walther T.

Dev Cell. 2013 Dec 9;27(5):480-4. No abstract available.

17.

Objective comparison of particle tracking methods.

Chenouard N, Smal I, de Chaumont F, Maška M, Sbalzarini IF, Gong Y, Cardinale J, Carthel C, Coraluppi S, Winter M, Cohen AR, Godinez WJ, Rohr K, Kalaidzidis Y, Liang L, Duncan J, Shen H, Xu Y, Magnusson KE, Jaldén J, Blau HM, Paul-Gilloteaux P, Roudot P, Kervrann C, Waharte F, Tinevez JY, Shorte SL, Willemse J, Celler K, van Wezel GP, Dan HW, Tsai YS, Ortiz de Solórzano C, Olivo-Marin JC, Meijering E.

Nat Methods. 2014 Mar;11(3):281-9. doi: 10.1038/nmeth.2808. Epub 2014 Jan 19.

18.

MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis.

Shivanandan A, Radenovic A, Sbalzarini IF.

BMC Bioinformatics. 2013 Dec 3;14:349. doi: 10.1186/1471-2105-14-349.

19.

Receptor concentration and diffusivity control multivalent binding of Sv40 to membrane bilayers.

Szklarczyk OM, González-Segredo N, Kukura P, Oppenheim A, Choquet D, Sandoghdar V, Helenius A, Sbalzarini IF, Ewers H.

PLoS Comput Biol. 2013;9(11):e1003310. doi: 10.1371/journal.pcbi.1003310. Epub 2013 Nov 14.

20.

Modeling and simulation of biological systems from image data.

Sbalzarini IF.

Bioessays. 2013 May;35(5):482-90. doi: 10.1002/bies.201200051. Epub 2013 Mar 27.

21.

Cell-free transmission of human adenovirus by passive mass transfer in cell culture simulated in a computer model.

Yakimovich A, Gumpert H, Burckhardt CJ, Lütschg VA, Jurgeit A, Sbalzarini IF, Greber UF.

J Virol. 2012 Sep;86(18):10123-37. doi: 10.1128/JVI.01102-12. Epub 2012 Jul 11.

22.

Energy landscapes of atomic clusters as black box optimization benchmarks.

Müller CL, Sbalzarini IF.

Evol Comput. 2012 Winter;20(4):543-73. doi: 10.1162/EVCO_a_00086. Epub 2012 Aug 31.

PMID:
22779442
23.

Active flows cluster cell surface proteins.

Sbalzarini IF.

Dev Cell. 2012 Jun 12;22(6):1121-2. doi: 10.1016/j.devcel.2012.05.015.

24.

Discreteness-induced concentration inversion in mesoscopic chemical systems.

Ramaswamy R, González-Segredo N, Sbalzarini IF, Grima R.

Nat Commun. 2012 Apr 10;3:779. doi: 10.1038/ncomms1775.

PMID:
22491327
25.

Discrete region competition for unknown numbers of connected regions.

Cardinale J, Paul G, Sbalzarini IF.

IEEE Trans Image Process. 2012 Aug;21(8):3531-45. doi: 10.1109/TIP.2012.2192129. Epub 2012 Apr 3.

26.

Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods.

Ramaswamy R, Sbalzarini IF.

J Chem Phys. 2011 Dec 28;135(24):244103. doi: 10.1063/1.3666988.

27.

Global parameter identification of stochastic reaction networks from single trajectories.

Müller CL, Ramaswamy R, Sbalzarini IF.

Adv Exp Med Biol. 2012;736:477-98. doi: 10.1007/978-1-4419-7210-1_28.

PMID:
22161347
28.

Histone deacetylase 8 is required for centrosome cohesion and influenza A virus entry.

Yamauchi Y, Boukari H, Banerjee I, Sbalzarini IF, Horvath P, Helenius A.

PLoS Pathog. 2011 Oct;7(10):e1002316. doi: 10.1371/journal.ppat.1002316. Epub 2011 Oct 27.

29.

High-resolution cell outline segmentation and tracking from phase-contrast microscopy images.

Ambühl ME, Brepsant C, Meister JJ, Verkhovsky AB, Sbalzarini IF.

J Microsc. 2012 Feb;245(2):161-70. doi: 10.1111/j.1365-2818.2011.03558.x. Epub 2011 Oct 17.

30.

Dynamic measurement of the height and volume of migrating cells by a novel fluorescence microscopy technique.

Bottier C, Gabella C, Vianay B, Buscemi L, Sbalzarini IF, Meister JJ, Verkhovsky AB.

Lab Chip. 2011 Nov 21;11(22):3855-63. doi: 10.1039/c1lc20807a. Epub 2011 Oct 3.

PMID:
21964858
31.

Noise-induced modulation of the relaxation kinetics around a non-equilibrium steady state of non-linear chemical reaction networks.

Ramaswamy R, Sbalzarini IF, González-Segredo N.

PLoS One. 2011 Jan 28;6(1):e16045. doi: 10.1371/journal.pone.0016045.

32.

Proteome sequence features carry signatures of the environmental niche of prokaryotes.

Smole Z, Nikolic N, Supek F, Šmuc T, Sbalzarini IF, Krisko A.

BMC Evol Biol. 2011 Jan 26;11:26. doi: 10.1186/1471-2148-11-26.

33.

A partial-propensity formulation of the stochastic simulation algorithm for chemical reaction networks with delays.

Ramaswamy R, Sbalzarini IF.

J Chem Phys. 2011 Jan 7;134(1):014106. doi: 10.1063/1.3521496.

PMID:
21218996
34.

Intrinsic noise alters the frequency spectrum of mesoscopic oscillatory chemical reaction systems.

Ramaswamy R, Sbalzarini IF.

Sci Rep. 2011;1:154. doi: 10.1038/srep00154. Epub 2011 Nov 11.

35.

Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans.

Awile O, Krisko A, Sbalzarini IF, Zagrovic B.

PLoS Comput Biol. 2010 Jul 15;6(7):e1000854. doi: 10.1371/journal.pcbi.1000854.

36.

Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images.

Helmuth JA, Paul G, Sbalzarini IF.

BMC Bioinformatics. 2010 Jul 7;11:372. doi: 10.1186/1471-2105-11-372.

37.

A partial-propensity variant of the composition-rejection stochastic simulation algorithm for chemical reaction networks.

Ramaswamy R, Sbalzarini IF.

J Chem Phys. 2010 Jan 28;132(4):044102. doi: 10.1063/1.3297948.

38.

A Lagrangian particle method for reaction-diffusion systems on deforming surfaces.

Bergdorf M, Sbalzarini IF, Koumoutsakos P.

J Math Biol. 2010 Nov;61(5):649-63. doi: 10.1007/s00285-009-0315-2. Epub 2009 Dec 18.

PMID:
20020130
39.

A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks.

Ramaswamy R, González-Segredo N, Sbalzarini IF.

J Chem Phys. 2009 Jun 28;130(24):244104. doi: 10.1063/1.3154624.

40.

In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble.

Müller CL, Sbalzarini IF, van Gunsteren WF, Zagrović B, Hünenberger PH.

J Chem Phys. 2009 Jun 7;130(21):214904. doi: 10.1063/1.3140090.

PMID:
19508095
41.

Shape reconstruction of subcellular structures from live cell fluorescence microscopy images.

Helmuth JA, Burckhardt CJ, Greber UF, Sbalzarini IF.

J Struct Biol. 2009 Jul;167(1):1-10. doi: 10.1016/j.jsb.2009.03.017. Epub 2009 Apr 7.

PMID:
19358891
42.

Thermophoretic motion of water nanodroplets confined inside carbon nanotubes.

Zambrano HA, Walther JH, Koumoutsakos P, Sbalzarini IF.

Nano Lett. 2009 Jan;9(1):66-71. doi: 10.1021/nl802429s.

PMID:
19105740
43.

A novel supervised trajectory segmentation algorithm identifies distinct types of human adenovirus motion in host cells.

Helmuth JA, Burckhardt CJ, Koumoutsakos P, Greber UF, Sbalzarini IF.

J Struct Biol. 2007 Sep;159(3):347-58. Epub 2007 Apr 14.

PMID:
17532228
44.

Simulations of (an)isotropic diffusion on curved biological surfaces.

Sbalzarini IF, Hayer A, Helenius A, Koumoutsakos P.

Biophys J. 2006 Feb 1;90(3):878-85. Epub 2005 Nov 11.

45.

Single-particle tracking of murine polyoma virus-like particles on live cells and artificial membranes.

Ewers H, Smith AE, Sbalzarini IF, Lilie H, Koumoutsakos P, Helenius A.

Proc Natl Acad Sci U S A. 2005 Oct 18;102(42):15110-5. Epub 2005 Oct 11.

46.

Feature point tracking and trajectory analysis for video imaging in cell biology.

Sbalzarini IF, Koumoutsakos P.

J Struct Biol. 2005 Aug;151(2):182-95.

PMID:
16043363
47.

Septin-dependent compartmentalization of the endoplasmic reticulum during yeast polarized growth.

Luedeke C, Frei SB, Sbalzarini I, Schwarz H, Spang A, Barral Y.

J Cell Biol. 2005 Jun 20;169(6):897-908.

48.

Effects of organelle shape on fluorescence recovery after photobleaching.

Sbalzarini IF, Mezzacasa A, Helenius A, Koumoutsakos P.

Biophys J. 2005 Sep;89(3):1482-92. Epub 2005 Jun 10.

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