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Items: 1 to 50 of 69

1.

Prediction and quantification of bacterial biofilm detachment using Glazier-Graner-Hogeweg method based model simulations.

Sheraton MV, Melnikov VR, Sloot PMA.

J Theor Biol. 2019 Dec 7;482:109994. doi: 10.1016/j.jtbi.2019.109994. Epub 2019 Sep 2.

PMID:
31487498
2.

[Complexity of disease; a modern view in times of ageing populations and multimorbidity].

Olde Rikkert MGM, van Zuijlen PPM, de Kleuver M, van Reekum A, Hoekstra AG, Sloot PMA.

Ned Tijdschr Geneeskd. 2019 Aug 19;163. pii: D3970. Dutch.

PMID:
31433143
3.

Boolean network modeling of β-cell apoptosis and insulin resistance in type 2 diabetes mellitus.

Dutta P, Ma L, Ali Y, Sloot PMA, Zheng J.

BMC Syst Biol. 2019 Apr 5;13(Suppl 2):36. doi: 10.1186/s12918-019-0692-0.

4.

Supplemented Alkaline Phosphatase Supports the Immune Response in Patients Undergoing Cardiac Surgery: Clinical and Computational Evidence.

Presbitero A, Mancini E, Brands R, Krzhizhanovskaya VV, Sloot PMA.

Front Immunol. 2018 Oct 11;9:2342. doi: 10.3389/fimmu.2018.02342. eCollection 2018.

5.

A study on the dynamics of temporary HIV treatment to assess the controversial outcomes of clinical trials: An in-silico approach.

Mancini E, Quax R, De Luca A, Fidler S, Stohr W, Sloot PMA.

PLoS One. 2018 Jul 18;13(7):e0200892. doi: 10.1371/journal.pone.0200892. eCollection 2018.

6.

Categorical and Geographical Separation in Science.

Sienkiewicz J, Soja K, Hołyst JA, Sloot PMA.

Sci Rep. 2018 May 29;8(1):8253. doi: 10.1038/s41598-018-26511-4.

7.

Mesoscopic Energy Minimization Drives Pseudomonas aeruginosa Biofilm Morphologies and Consequent Stratification of Antibiotic Activity Based on Cell Metabolism.

Sheraton MV, Yam JKH, Tan CH, Oh HS, Mancini E, Yang L, Rice SA, Sloot PMA.

Antimicrob Agents Chemother. 2018 Apr 26;62(5). pii: e02544-17. doi: 10.1128/AAC.02544-17. Print 2018 May.

8.

Survey-based socio-economic data from slums in Bangalore, India.

Roy D, Palavalli B, Menon N, King R, Pfeffer K, Lees M, Sloot PMA.

Sci Data. 2018 Jan 9;5:170200. doi: 10.1038/sdata.2017.200.

9.

Erratum to: The influence of memory on indoor environment exploration: A numerical study.

Viswanathan V, Lees M, Sloot PMA.

Behav Res Methods. 2017 Aug;49(4):1569. doi: 10.3758/s13428-016-0781-6. No abstract available.

PMID:
28342068
10.

Nonparametric estimation of Fisher information from real data.

Har-Shemesh O, Quax R, Miñano B, Hoekstra AG, Sloot PM.

Phys Rev E. 2016 Feb;93(2):023301. doi: 10.1103/PhysRevE.93.023301. Epub 2016 Feb 8.

PMID:
26986433
11.

The influence of memory on indoor environment exploration: A numerical study.

Viswanathan V, Lees M, Sloot PM.

Behav Res Methods. 2016 Jun;48(2):621-39. doi: 10.3758/s13428-015-0604-1. Erratum in: Behav Res Methods. 2017 Mar 24;:.

12.

Temperature affects the silicate morphology in a diatom.

Javaheri N, Dries R, Burson A, Stal LJ, Sloot PMA, Kaandorp JA.

Sci Rep. 2015 Jun 26;5:11652. doi: 10.1038/srep11652.

13.

A novel feature-based approach to extract drug-drug interactions from biomedical text.

Bui QC, Sloot PM, van Mulligen EM, Kors JA.

Bioinformatics. 2014 Dec 1;30(23):3365-71. doi: 10.1093/bioinformatics/btu557. Epub 2014 Aug 20.

PMID:
25143286
14.

Time-frequency methods for structural health monitoring.

Pyayt AL, Kozionov AP, Mokhov II, Lang B, Meijer RJ, Krzhizhanovskaya VV, Sloot PM.

Sensors (Basel). 2014 Mar 12;14(3):5147-73. doi: 10.3390/s140305147.

15.

The relative ineffectiveness of criminal network disruption.

Duijn PA, Kashirin V, Sloot PM.

Sci Rep. 2014 Feb 28;4:4238. doi: 10.1038/srep04238.

16.

Short-term forecasting of Taiwanese earthquakes using a universal model of fusion-fission processes.

Cheong SA, Tan TL, Chen CC, Chang WL, Liu Z, Chew LY, Sloot PM, Johnson NF.

Sci Rep. 2014 Jan 10;4:3624. doi: 10.1038/srep03624.

17.

Superinfection with drug-resistant HIV is rare and does not contribute substantially to therapy failure in a large European cohort.

Bartha I, Assel M, Sloot PM, Zazzi M, Torti C, Schülter E, De Luca A, Sönnerborg A, Abecasis AB, Van Laethem K, Rosi A, Svärd J, Paredes R, van de Vijver DA, Vandamme AM, Müller V.

BMC Infect Dis. 2013 Nov 12;13:537. doi: 10.1186/1471-2334-13-537.

18.

The diminishing role of hubs in dynamical processes on complex networks.

Quax R, Apolloni A, Sloot PM.

J R Soc Interface. 2013 Sep 4;10(88):20130568. doi: 10.1098/rsif.2013.0568. Print 2013 Nov 6.

19.
20.

A Simulation Framework to Investigate in vitro Viral Infection Dynamics.

Bankhead A 3rd, Mancini E, Sims AC, Baric RS, McWeeney S, Sloot PM.

J Comput Sci. 2013 May 1;4(3):127-134.

21.

Promoter sequence determines the relationship between expression level and noise.

Carey LB, van Dijk D, Sloot PM, Kaandorp JA, Segal E.

PLoS Biol. 2013;11(4):e1001528. doi: 10.1371/journal.pbio.1001528. Epub 2013 Apr 2.

22.

Cost-effectiveness of pre-exposure prophylaxis (PrEP) in preventing HIV-1 infections in rural Zambia: a modeling study.

Nichols BE, Boucher CA, van Dijk JH, Thuma PE, Nouwen JL, Baltussen R, van de Wijgert J, Sloot PM, van de Vijver DA.

PLoS One. 2013;8(3):e59549. doi: 10.1371/journal.pone.0059549. Epub 2013 Mar 18.

23.

Noise enhances information transfer in hierarchical networks.

Czaplicka A, Holyst JA, Sloot PM.

Sci Rep. 2013;3:1223. doi: 10.1038/srep01223. Epub 2013 Feb 6.

24.

Combining epidemiological and genetic networks signifies the importance of early treatment in HIV-1 transmission.

Zarrabi N, Prosperi M, Belleman RG, Colafigli M, De Luca A, Sloot PM.

PLoS One. 2012;7(9):e46156. doi: 10.1371/journal.pone.0046156. Epub 2012 Sep 28.

25.

A robust approach to extract biomedical events from literature.

Bui QC, Sloot PM.

Bioinformatics. 2012 Oct 15;28(20):2654-61. doi: 10.1093/bioinformatics/bts487. Epub 2012 Aug 1.

PMID:
22859502
26.

HIV reservoirs and immune surveillance evasion cause the failure of structured treatment interruptions: a computational study.

Mancini E, Castiglione F, Bernaschi M, de Luca A, Sloot PM.

PLoS One. 2012;7(4):e36108. doi: 10.1371/journal.pone.0036108. Epub 2012 Apr 27.

27.

Increasing risk behaviour can outweigh the benefits of antiretroviral drug treatment on the HIV incidence among men-having-sex-with-men in Amsterdam.

Mei S, Quax R, van de Vijver D, Zhu Y, Sloot PM.

BMC Infect Dis. 2011 May 11;11:118. doi: 10.1186/1471-2334-11-118.

28.

A hybrid approach to extract protein-protein interactions.

Bui QC, Katrenko S, Sloot PM.

Bioinformatics. 2011 Jan 15;27(2):259-65. doi: 10.1093/bioinformatics/btq620. Epub 2010 Nov 8.

PMID:
21062765
29.

Comparison of HIV-1 genotypic resistance test interpretation systems in predicting virological outcomes over time.

Frentz D, Boucher CA, Assel M, De Luca A, Fabbiani M, Incardona F, Libin P, Manca N, Müller V, O Nualláin B, Paredes R, Prosperi M, Quiros-Roldan E, Ruiz L, Sloot PM, Torti C, Vandamme AM, Van Laethem K, Zazzi M, van de Vijver DA.

PLoS One. 2010 Jul 9;5(7):e11505. doi: 10.1371/journal.pone.0011505.

30.

Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks.

van Dijk D, Ertaylan G, Boucher CA, Sloot PM.

BMC Syst Biol. 2010 Jul 15;4:96. doi: 10.1186/1752-0509-4-96.

31.

Exploring cancer stem cell niche directed tumor growth.

Sottoriva A, Sloot PM, Medema JP, Vermeulen L.

Cell Cycle. 2010 Apr 15;9(8):1472-9. Epub 2010 Apr 15.

PMID:
20372084
32.

Extracting causal relations on HIV drug resistance from literature.

Bui QC, Nualláin BO, Boucher CA, Sloot PM.

BMC Bioinformatics. 2010 Feb 23;11:101. doi: 10.1186/1471-2105-11-101.

33.

Cancer stem cell tumor model reveals invasive morphology and increased phenotypical heterogeneity.

Sottoriva A, Verhoeff JJ, Borovski T, McWeeney SK, Naumov L, Medema JP, Sloot PM, Vermeulen L.

Cancer Res. 2010 Jan 1;70(1):46-56. doi: 10.1158/0008-5472.CAN-09-3663.

34.

Multi-scale modelling in computational biomedicine.

Sloot PM, Hoekstra AG.

Brief Bioinform. 2010 Jan;11(1):142-52. doi: 10.1093/bib/bbp038. Epub 2009 Dec 22. Review.

PMID:
20028713
35.

Simulations of time harmonic blood flow in the Mesenteric artery: comparing finite element and lattice Boltzmann methods.

Axner L, Hoekstra AG, Jeays A, Lawford P, Hose R, Sloot PM.

Biomed Eng Online. 2009 Oct 2;8:23. doi: 10.1186/1475-925X-8-23.

36.

Calcium homeostasis and signaling in yeast cells and cardiac myocytes.

Cui J, Kaandorp JA, Sloot PM, Lloyd CM, Filatov MV.

FEMS Yeast Res. 2009 Dec;9(8):1137-47. doi: 10.1111/j.1567-1364.2009.00552.x. Epub 2009 Jul 16. Review.

37.

HIV decision support: from molecule to man.

Sloot PM, Coveney PV, Ertaylan G, Müller V, Boucher CA, Bubak M.

Philos Trans A Math Phys Eng Sci. 2009 Jul 13;367(1898):2691-703. doi: 10.1098/rsta.2009.0043.

PMID:
19487205
38.

A hybrid agent-based approach for modeling microbiological systems.

Guo Z, Sloot PM, Tay JC.

J Theor Biol. 2008 Nov 21;255(2):163-75. doi: 10.1016/j.jtbi.2008.08.008. Epub 2008 Aug 15.

PMID:
18775440
39.

Introduction to the special section on BioGrid: biomedical computations on the grid.

Huang CH, Konagaya A, Lanza V, Sloot PM.

IEEE Trans Inf Technol Biomed. 2008 Mar;12(2):133-7. No abstract available.

PMID:
18416025
40.

Understanding the complex dynamics of stock markets through cellular automata.

Qiu G, Kandhai D, Sloot PM.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Apr;75(4 Pt 2):046116. Epub 2007 Apr 26.

PMID:
17500970
41.

Simulating time harmonic flows with the lattice Boltzmann method.

Axner L, Hoekstra AG, Sloot PM.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Mar;75(3 Pt 2):036709. Epub 2007 Mar 27.

PMID:
17500828
42.

Mesoscopic simulations of systolic flow in the human abdominal aorta.

Artoli AM, Hoekstra AG, Sloot PM.

J Biomech. 2006;39(5):873-84.

PMID:
16488226
43.

A Grid-based HIV expert system.

Sloot PM, Boukhanovsky AV, Keulen W, Tirado-Ramos A, Boucher CA.

J Clin Monit Comput. 2005 Oct;19(4-5):263-78.

PMID:
16328942
44.

Numerical simulation and measurement of liquid hold-up in biporous media containing discrete stagnant zones.

Kandhai D, Tallarek U, Hlushkou D, Hoekstra A, Sloot PM, Van As H.

Philos Trans A Math Phys Eng Sci. 2002 Mar 15;360(1792):521-34.

PMID:
16214692
45.

Equilibrium spherically curved two-dimensional Lennard-Jones systems.

Voogd JM, Sloot PM, van Dantzig R.

J Chem Phys. 2005 Aug 22;123(8):084105.

PMID:
16164280
46.

Morphogenesis of the branching reef coral Madracis mirabilis.

Kaandorp JA, Sloot PM, Merks RM, Bak RP, Vermeij MJ, Maier C.

Proc Biol Sci. 2005 Jan 22;272(1559):127-33.

47.

Polyp oriented modelling of coral growth.

Merks RM, Hoekstra AG, Kaandorp JA, Sloot PM.

J Theor Biol. 2004 Jun 21;228(4):559-76.

PMID:
15178203
48.

Simulation and analysis of flow patterns around the scleractinian coral Madracis mirabilis (Duchassaing and Michelotti).

Kaandorp JA, Koopman EA, Sloot PM, Bak RP, Vermeij MJ, Lampmann LE.

Philos Trans R Soc Lond B Biol Sci. 2003 Sep 29;358(1437):1551-7.

49.

Yang-Lee zeros of the Q-state Potts model on recursive lattices.

Ghulghazaryan RG, Ananikian NS, Sloot PM.

Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Oct;66(4 Pt 2):046110. Epub 2002 Oct 14.

PMID:
12443262
50.

Influence of stagnant zones on transient and asymptotic dispersion in macroscopically homogeneous porous media.

Kandhai D, Hlushkou D, Hoekstra AG, Sloot PM, Van As H, Tallarek U.

Phys Rev Lett. 2002 Jun 10;88(23):234501. Epub 2002 May 24.

PMID:
12059367

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