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Items: 1 to 20 of 30

1.

Bidirectional Propagation of Signals and Nutrients in Fungal Networks via Specialized Hyphae.

Schmieder SS, Stanley CE, Rzepiela A, van Swaay D, Sabotič J, Nørrelykke SF, deMello AJ, Aebi M, Künzler M.

Curr Biol. 2019 Jan 21;29(2):217-228.e4. doi: 10.1016/j.cub.2018.11.058. Epub 2019 Jan 3.

PMID:
30612903
2.

AutoTube: a novel software for the automated morphometric analysis of vascular networks in tissues.

Montoya-Zegarra JA, Russo E, Runge P, Jadhav M, Willrodt AH, Stoma S, Nørrelykke SF, Detmar M, Halin C.

Angiogenesis. 2019 May;22(2):223-236. doi: 10.1007/s10456-018-9652-3. Epub 2018 Oct 28.

3.

Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction.

Rzepiela AJ, Ghosh S, Breda J, Vina-Vilaseca A, Syed AP, Gruber AJ, Eschbach K, Beisel C, van Nimwegen E, Zavolan M.

Mol Syst Biol. 2018 Aug 27;14(8):e8266. doi: 10.15252/msb.20188266.

4.

Quantitative spatial analysis of haematopoiesis-regulating stromal cells in the bone marrow microenvironment by 3D microscopy.

Gomariz A, Helbling PM, Isringhausen S, Suessbier U, Becker A, Boss A, Nagasawa T, Paul G, Goksel O, Székely G, Stoma S, Nørrelykke SF, Manz MG, Nombela-Arrieta C.

Nat Commun. 2018 Jun 28;9(1):2532. doi: 10.1038/s41467-018-04770-z.

5.

High-Resolution Cryoelectron Microscopy Structure of the Cyclic Nucleotide-Modulated Potassium Channel MloK1 in a Lipid Bilayer.

Kowal J, Biyani N, Chami M, Scherer S, Rzepiela AJ, Baumgartner P, Upadhyay V, Nimigean CM, Stahlberg H.

Structure. 2018 Jan 2;26(1):20-27.e3. doi: 10.1016/j.str.2017.11.012. Epub 2017 Dec 14.

6.

VEGF-A Regulates Cellular Localization of SR-BI as Well as Transendothelial Transport of HDL but Not LDL.

Velagapudi S, Yalcinkaya M, Piemontese A, Meier R, Nørrelykke SF, Perisa D, Rzepiela A, Stebler M, Stoma S, Zanoni P, Rohrer L, von Eckardstein A.

Arterioscler Thromb Vasc Biol. 2017 May;37(5):794-803. doi: 10.1161/ATVBAHA.117.309284. Epub 2017 Mar 30.

7.

Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform.

Versari C, Stoma S, Batmanov K, Llamosi A, Mroz F, Kaczmarek A, Deyell M, Lhoussaine C, Hersen P, Batt G.

J R Soc Interface. 2017 Feb;14(127). pii: 20160705. doi: 10.1098/rsif.2016.0705.

8.

Hypoxia Induces a HIF-1-Dependent Transition from Collective-to-Amoeboid Dissemination in Epithelial Cancer Cells.

Lehmann S, Te Boekhorst V, Odenthal J, Bianchi R, van Helvert S, Ikenberg K, Ilina O, Stoma S, Xandry J, Jiang L, Grenman R, Rudin M, Friedl P.

Curr Biol. 2017 Feb 6;27(3):392-400. doi: 10.1016/j.cub.2016.11.057. Epub 2017 Jan 12.

9.

Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99].

Breda J, Rzepiela AJ, Gumienny R, van Nimwegen E, Zavolan M.

Methods. 2016 Jul 15;104:204-205. doi: 10.1016/j.ymeth.2015.12.016. Epub 2016 Jan 13. No abstract available.

10.

In Vivo Fluorescence Imaging of the Activity of CEA TCB, a Novel T-Cell Bispecific Antibody, Reveals Highly Specific Tumor Targeting and Fast Induction of T-Cell-Mediated Tumor Killing.

Lehmann S, Perera R, Grimm HP, Sam J, Colombetti S, Fauti T, Fahrni L, Schaller T, Freimoser-Grundschober A, Zielonka J, Stoma S, Rudin M, Klein C, Umana P, Gerdes C, Bacac M.

Clin Cancer Res. 2016 Sep 1;22(17):4417-27. doi: 10.1158/1078-0432.CCR-15-2622. Epub 2016 Apr 26.

11.

Quantifying the strength of miRNA-target interactions.

Breda J, Rzepiela AJ, Gumienny R, van Nimwegen E, Zavolan M.

Methods. 2015 Sep 1;85:90-99. doi: 10.1016/j.ymeth.2015.04.012. Epub 2015 Apr 16.

12.

Communication: Microsecond peptide dynamics from nanosecond trajectories: a Langevin approach.

Rzepiela AJ, Schaudinnus N, Buchenberg S, Hegger R, Stock G.

J Chem Phys. 2014 Dec 28;141(24):241102. doi: 10.1063/1.4904894.

PMID:
25554123
13.

Modeling dynamics of cell-to-cell variability in TRAIL-induced apoptosis explains fractional killing and predicts reversible resistance.

Bertaux F, Stoma S, Drasdo D, Batt G.

PLoS Comput Biol. 2014 Oct 23;10(10):e1003893. doi: 10.1371/journal.pcbi.1003893. eCollection 2014 Oct.

14.

Bridging the gaps in systems biology.

Cvijovic M, Almquist J, Hagmar J, Hohmann S, Kaltenbach HM, Klipp E, Krantz M, Mendes P, Nelander S, Nielsen J, Pagnani A, Przulj N, Raue A, Stelling J, Stoma S, Tobin F, Wodke JA, Zecchina R, Jirstrand M.

Mol Genet Genomics. 2014 Oct;289(5):727-34. doi: 10.1007/s00438-014-0843-3. Epub 2014 Apr 13. Review.

PMID:
24728588
15.

Data driven Langevin modeling of biomolecular dynamics.

Schaudinnus N, Rzepiela AJ, Hegger R, Stock G.

J Chem Phys. 2013 May 28;138(20):204106. doi: 10.1063/1.4804302.

PMID:
23742453
16.

STL-based analysis of TRAIL-induced apoptosis challenges the notion of type I/type II cell line classification.

Stoma S, Donzé A, Bertaux F, Maler O, Batt G.

PLoS Comput Biol. 2013;9(5):e1003056. doi: 10.1371/journal.pcbi.1003056. Epub 2013 May 9.

17.

Harmonic oscillator in heat bath: exact simulation of time-lapse-recorded data and exact analytical benchmark statistics.

Nørrelykke SF, Flyvbjerg H.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Apr;83(4 Pt 1):041103. Epub 2011 Apr 4.

PMID:
21599111
18.

STSE: Spatio-Temporal Simulation Environment Dedicated to Biology.

Stoma S, Fröhlich M, Gerber S, Klipp E.

BMC Bioinformatics. 2011 Apr 28;12:126. doi: 10.1186/1471-2105-12-126.

19.

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites.

Rzepiela AJ, Louhivuori M, Peter C, Marrink SJ.

Phys Chem Chem Phys. 2011 Jun 14;13(22):10437-48. doi: 10.1039/c0cp02981e. Epub 2011 Apr 15.

PMID:
21494747
20.

Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes.

Schäfer LV, de Jong DH, Holt A, Rzepiela AJ, de Vries AH, Poolman B, Killian JA, Marrink SJ.

Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1343-8. doi: 10.1073/pnas.1009362108. Epub 2011 Jan 4.

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