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Scientific Publications
You may find here a selection of some of ViroLab recent peer-reviewed published output.

DocumentsDate added

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file icon Evolution of a novel 5-amino-acid insertion in the beta3-beta4 loop of HIV-1 reverse transcriptasehot!
Huigen MC, de Graaf L, Eggink D, Schuurman R, Müller V, Stamp A, Stammers DK, Boucher CA, Nijhuis M. Evolution of a novel 5-amino-acid insertion in the beta3-beta4 loop of HIV-1 reverse transcriptase. Virology. 2007 Aug 1;364(2):395-406.
file icon Resistance to newly approved and investigational protease inhibitorshot!
Resistance to newly approved and investigational protease inhibitors. De Luca A. Curr Opin HIV AIDS. 2007 Mar;2(2):130-6.
file icon Estimating the relative contribution of dNTP pool imbalance and APOBEC3G/3Fhot!
Deforche K, Camacho R, Laethem KV, Shapiro B, Moreau Y, Rambaut A, Vandamme AM, Lemey P. Estimating the relative contribution of dNTP pool imbalance and APOBEC3G/3F editing to HIV evolution in vivo. J Comput Biol. 2007 Oct;14(8):1105-14.
file icon No response to first-line tenofovir+lamivudine+efavirenz despite optimization according to baseline hot!
Van Laethem K, De Munter P, Schrooten Y, Verbesselt R, Van Ranst M, Van Wijngaerden E, Vandamme AM. No response to first-line tenofovir+lamivudine+efavirenz despite optimization according to baseline resistance testing: impact of resistant minority variants on efficacy of low genetic barrier drugs. J Clin Virol. 2007 May;39(1):43-7.
file icon Interactive N-Body Simulations On the Gridhot!
K.J. Rycerz; A. Tirado-Ramos; A. Gualandris; S.F. Portegies Zwart; M.T. Bubak and P.M.A. Sloot: Interactive N-Body Simulations On the Grid: HLA Versus MPI, International Journal of High Performance Computing Applications, (Selected papers from EuroPVM/MPI 2005 conference, Sorrento, Italy, 18-21 September 2005) vol. 21, nr 2 pp. 210-221. SAGE Publications, 2007.
file icon Characterization of JC virus in cerebrospinal fluid from HIV-1 infected patients with progressive...hot!
Marzocchetti A, Sanguinetti M, Giambenedetto SD, Cingolani A, Fadda G, Cauda R, De Luca A. Characterization of JC virus in cerebrospinal fluid from HIV-1 infected patients with progressive multifocal leukoencephalopathy: insights into viral pathogenesis and disease prognosis. J Neurovirol. 2007 Aug;13(4):338-46.
file icon Association of HIV-1 replication capacity with treatment outcomes in patients with virologic treatmehot!
De Luca A, Weidler J, Di Giambendetto S, Coakley E, Cingolani A, Bates M, Lie Y, Pesano R, Cauda R, Schapiro J. Association of HIV-1 replication capacity with treatment outcomes in patients with virologic treatment failure. Journal of Acquired Immune Deficiency Syndrome 2007 Aug 1; 45(4):411-7.
file icon Recombination confounds the early evolutionary history of human immunodeficiency virus type 1hot!
Abecasis AB, Lemey P, Vidal N, de Oliveira T, Peeters M, Camacho R, Shapiro B, Rambaut A, Vandamme AM. Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form. J Virol. 2007 Aug;81(16):8543-51.
file icon Bayesian network analysis of resistance pathways against HIV-1 protease inhibitorshot!
Deforche K, Camacho R, Grossman Z, Silander T, Soares MA, Moreau Y, Shafer RW, Van Laethem K, Carvalho AP, Wynhoven B, Cane P, Snoeck J, Clarke J, Sirivichayakul S, Ariyoshi K, Holguin A, Rudich H, Rodrigues R, Bouzas MB, Cahn P, Brigido LF, Soriano V, Sugiura W, Phanuphak P, Morris L, Weber J, Pillay D, Tanuri A, Harrigan PR, Shapiro JM, Katzenstein DA, Kantor R, Vandamme AM. Bayesian network analysis of resistance pathways against HIV-1 protease inhibitors. Infect Genet Evol. 2007 Jun;7(3):382-90.
file icon Impact of genetic variation of HIV-1 on drug resistance developmenthot!
Snoeck J, Vandamme A-M & Camacho RJ Impact of genetic variation of HIV-1 on drug resistance development. Future Virology, May 2007, Vol. 2, No. 3, Pages 303-310.
file icon Insights into a Mutation-Assisted Lateral Drug Escape Mechanism from the HIV-1hot!
Insights into a Mutation-Assisted Lateral Drug Escape Mechanism from the HIV-1 Protease Active Site Sadiq et al., Biochemistry, 2007, 46, 14865-14877
file icon Monitoring of Component-Based Applicationshot!
Monitoring of Component-Based Applications Eryk Ciepiela; Master of Science Thesis supervised by Marian Bubak; AGH University of Science and Technology, June 2007, Krakow, Poland
file icon Optimization of Grid Application Executionhot!
Optimization of Grid Application Execution Joanna Kocot, Iwona Ryszka; Master of Science Thesis supervised by Marian Bubak; AGH University of Science and Technology, June 2007, Krakow, Poland
file icon Virolab: a distributed Decision Support System for Viral Disease Treatmenthot!
Virolab: a distributed Decision Support System for Viral Disease Treatment Peter M.A. Sloot, Alfredo Tirados-Ramos, Gokan Ertaylan, Breanndan O Nuallain, D.van de Vijver, Charels Boucher and Marian Bubak, Grakow 2007 Grid orkshop October 15-17, 2007, Crakow, Poland, pp 33-34
file icon GScript Editor as Part of the ViroLab Presentation Layerhot!
GScript Editor as Part of the ViroLab Presentation Layer W. Funika and P. Pegiel, , in: M. Bubak, M. Turala, and K. Wiatr (Eds.). Proceedings of Cracow\'06 Grid Workshop, Oct 15-18, 2006, Cracow, Poland, ACC Cyfronet AGH, 2007, pp. 320-327.
file icon From Monitoring Data to Experiment Information -- Monitoring of Grid Scientific Workflows.hot!
From Monitoring Data to Experiment Information -- Monitoring of Grid Scientific Workflows. B. Balis, M. Bubak, and M. Pelczar. In G. Fox, K. Chiu, and R. Buyya, editors, Third IEEE International Conference on e-Science and Grid Computing, e-Science 2007, Bangalore, India, 10-13 December 2007, pages 187-194. IEEE Computer Society, 2007.
file icon Antiretroviral resistance in different HIV-1 subtypeshot!
Camacho RJ, Vandamme AM. Antiretroviral resistance in different HIV-1 subtypes: impact on therapy outcomes and resistance testing interpretation. Curr Opin HIV AIDS. 2007 Mar;2(2):123-9.
file icon Analysis of HIV-1 pol sequences using Bayesian networks: implications for drug resistancehot!
Deforche K, Silander T, Camacho R, Grossman Z, Soares M, Van Laethem K, Kantor R, Moreau Y, Vandamme AM., non-B workgroup. Analysis of HIV-1 pol sequences using Bayesian networks: implications for drug resistance. Bioinformatics 2006 Dec 15;22(24):2975-9. Epub. 2006 Oct 4.
file icon Experiments with distributed component computing across Grid boundarieshot!
M. Malawski, M. Bubak, M. Placek, D. Kurzyniec, V. Sunderam. Experiments with distributed component computing across Grid boundaries. In Proceedings of the HPC-GECO/CompFrame workshop in conjunction with HPDC 2006, Paris, 2006.
file icon A Conceptual Grid Architecture for Interactive Biomedical Applicationshot!
Tirado Ramos, P.M.A. Sloot. A Conceptual Grid Architecture for Interactive Biomedical Applications 19th IEEE International Symposium on Computer-Based Medical Systems (CBMS\'06), pp. 762-767. IEEE, Salt Lake City, USA, 2006.
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