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

Documents

Untangling Pathways to Tipranavir Resistance in Patients Infected with Various HIV-1 Sub-types (...)
Kristof Theys, Raphael Z. Sangeda, Ricardo Camacho, Bonaventura Clotet, Kristel Van Laethem, Maurizio Zazzi, Anders Sönnerborg, Rolf Kaiser, Andrea De Luca, Carlo Torti, Annemarie M.J. Wensing, Grzegorz Stanczak, Marek Linka, Mario Poljak, Snjezana Zidovec Lepej, Eric Van Wijngaerden, Chris Verhofstede, Soo-Yon Rhee and Anne-Mieke Vandamme. Untangling Pathways to Tipranavir Resistance in Patients Infected with Various HIV-1 Sub-types, for the EHR, ViroLab, EuResist and BREACH projects, 12th European AIDS Conference November 11-14 2009, Cologne, Germany.
Untangling Pathways to Tipranavir Resistance in HIV-1 Treatment Experienced Patients from (...)
Sangeda R.Z., Theys K, Camacho R, Clotet B, Van Laethem K, Zazzi M, Sönnerborg A, Kaiser R, De Luca A, Torti C, Wensing A.M.J, Stanczak G, Linka M,Poljak M, Lepej S.Z, Van Wijngaerden E, Verhofstede C, Rhee S-Y, Vandamme A-M. Untangling Pathways to Tipranavir Resistance in HIV-1 Treatment Experienced Patients from Various Subtypes, for the EHR, ViroLab, EuResist and BARC projects. International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology, 7-11 September 2009, Rotterdam, The Netherlands.
Comparing the prevalence of tipranavir resistance mutations in naïve, PI experienced and (...)
Pieter Libin, Stijn Imbrechts, Gertjan Beheydt, Kristof Theys, Raphael Sangeda, Kristof Theys, Ricardo Camacho, Bonaventura Clotet, Kristel Van Lae-them, Maurizio Zazzi, Anders, Sönnerborg, Rolf Kaiser, Andrea De Luca, Carlo Torti, Wensing, A.M.J., Grzegorz Stanczak, Marek Linka, Mario Poljak, Snjezana Zidovec Lepej, Eric Van Wijngaerden, Chris Verhofstede, Soo-Yon Rhee, Anne-Mieke Vandamme. Comparing the prevalence of tipranavir resistance mutations in naïve, PI experienced and ti-pranavir experienced patients, for the EHR, ViroLab, EuResist and BREACH projects. International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology, 7-11 September 2009, Rotterdam, The Netherlands.
Provenance Tracking and End-User Oriented Query Construction
B. Balis, M. Bubak, M. Pelczar, J. Wach. Provenance Tracking and End-User Oriented Query Construction, In: M. Cannataro (Ed.) Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare, Information Science Reference, 2009, IGI Global.
Virtual Laboratory for Collaborative Applications
Bubak M, Malawski M, Gubala T, Kasztelnik M, Nowakowski P, Harezlak D, Bartynski T, Kocot J, Ciepiela E, Funika W, Krol D, Balis B, Assel M, Tirado-Ramos A. Virtual Laboratory for Collaborative Applications. In: Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare (Cannataro M ed.), IGI Global, 2009, pp. 531-551.
Distinguishing epidemiological dependent from treatment (resistance) dependent HIV mutations
Schietgat L, K Theys, J Ramon, H Blockeel, and AM Vandamme. Distinguishing epidemiological dependent from treatment (resistance) dependent HIV mutations: Problem Statement. Ecml, 2008.
ViroLab Security and Virtual Organization Infrastructure
Jan Meizner, Maciej Malawski, Eryk Ciepiela, Marek Kasztelnik, Daniel Harezlak, Piotr Nowakowski, Dariusz Krol, Tomasz Gubała, Włodzimierz Funika, Marian Bubak, Tomasz Mikołajczyk, Paweł Płaszczak, Krzysztof Wilk, and Matthias Assel: "ViroLab Security and Virtual Organization Infrastructure" in: Y. Dou, R. Gruber, and J. Joller (Eds.): APPT 2009, Advanced Parallel Processing Technologies 8th International Symposium, APPT 2009, Rapperswil, Switzerland, August 24-25, 2009 Proceedings, LNCS 5737, pp. 230–245, Springer-Verlag, 2009.
Monitoring infrastructure for Grid scientific workflows
B. Balis, M. Bubak. Monitoring infrastructure for Grid scientific workflows in 3rd Workshop on Workflows in Support of Large-Scale Science during SuperComputing 08 The International Conference for High Performance Computing, Networking, Storage and Analysis, November 2008 Austin, Texas, IEEE 2008.
Environment for Collaborative Development and Execution of Virtual Laboratory Applications
W. Funika, D. Harezlak, D. Krol, M. Bubak. Environment for Collaborative Development and Execution of Virtual Laboratory Applications. In: Lecture Notes in Computer Science 5103 (Bubak M, van Albada D G, Dongarra J, Sloot P M A eds.), Springer-Verlag, 2008, pp. 246-458.
A Security Framework for Dynamic Collaborative Working Environments
Assel M, Wesner S, Kipp A. A Security Framework for Dynamic Collaborative Working Environments. Identity in the Information Society, 2009 (accepted for publication).
Complex Agent Networks explaining the HIV epidemic among homosexual men in Amsterdam
A.M. Shan; P.M.A. Sloot; R. Quax; Y. Zhu and W. Wang: Complex Agent Networks explaining the HIV epidemic among homosexual men in Amsterdam, Mathematics and Computers in Simulation, (submitted). 2009.
Invocation of operations from script-based grid applications
M. Malawski, T. Bartynski, and M. Bubak, "Invocation of operations from script-based grid applications," Future Generation Computer Systems, vol. In Press, Accepted Manuscript, 2009.
A comparison of three computational modelling methods for the prediction of virological response...
Wang D, Larder B, Revell A, Montaner J, Harrigan R, De Wolf F, Lange J, Wegner S, Ruiz L, Pérez-Elías MJ, Emery S, Gatell J, D'Arminio Monforte A, Torti C, Zazzi M, Lane C. A comparison of three computational modelling methods for the prediction of virological response to combination HIV therapy. Artif Intell Med. 2009 Sep;47(1):63-74.
Predictive value of HIV-1 genotypic resistance test interpretation algorithms.
Rhee SY, Fessel WJ, Liu TF, Marlowe NM, Rowland CM, Rode RA, Vandamme AM, Van Laethem K, Brun-Vezinet F, Calvez V, Taylor J, Hurley L, Horberg M, Shafer RW. Predictive value of HIV-1 genotypic resistance test interpretation algorithms. J Infect Dis. 2009 Aug 1;200(3):453-63.
African descent is associated with slower CD4 cell count decline in treatment-naive patients of(...)
Müller V, von Wyl V, Yerly S, Böni J, Klimkait T, Bürgisser P, Ledergerber B, Günthard HF, Bonhoeffer S; Swiss HIV Cohort Study. African descent is associated with slower CD4 cell count decline in treatment-naive patients of the Swiss HIV Cohort Study. AIDS. 2009 Jun 19;23(10):1269-76.
Increasing clinical virulence in two decades of the Italian HIV epidemic
Müller V, Maggiolo F, Suter F, Ladisa N, De Luca A, Antinori A, Sighinolfi L, Quiros-Roldan E, Carosi G, Torti C. Increasing clinical virulence in two decades of the Italian HIV epidemic. PLoS Pathog. 2009 May;5(5):e1000454.
Discordant genotypic interpretation and phenotypic role of protease mutations in HIV-1 subtypes B...
Santos AF, Abecasis AB, Vandamme AM, Camacho RJ, Soares MA. Discordant genotypic interpretation and phenotypic role of protease mutations in HIV-1 subtypes B and G. J Antimicrob Chemother. Mar;63(3):593-9.
Are mutations in HIV type-1 reverse transcriptase 245 codon predictive of abacavir (...)
Bracciale L, Santangelo R, Fanti I, Prosperi M, Colafigli M, Di Giambenedetto S, Marchetti S, Di Franco A, Cauda R, De Luca A. Are mutations in HIV type-1 reverse transcriptase 245 codon predictive of abacavir hypersensitivity reaction? Antivir Ther. 2009;14(1):99-101.
Investigation of expert rule bases, logistic regression, and non-linear machine learning (...)
Prosperi MC, Altmann A, Rosen-Zvi M, Aharoni E, Borgulya G, Bazso F, Sànnerborg A, Schülter E, Struck D, Ulivi G, Vandamme AM, Vercauteren J, Zazzi M; EuResist and Virolab study groups. Investigation of expert rule bases, logistic regression, and non-linear machine learning techniques for predicting response to antiretroviral treatment. Antivir Ther. 2009;14(3):433-42.
Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance
Bennett DE, Camacho RJ, Otelea D, Kuritzkes DR, Fleury H, Kiuchi M, Heneine W, Kantor R, Jordan MR, Schapiro JM, Vandamme AM, Sandstrom P, Boucher CA, van de Vijver D, Rhee SY, Liu TF, Pillay D, Shafer RW. Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. PLoS One. 2009;4(3):e4724.
The rise and fall of K65R in a Portuguese HIV-1 Drug Resistance database, despite continuously (...)
Theys K., J. Vercauteren, A Abecasis, P. Libin, K. Deforche, AM Vandamme and R. Camacho. The rise and fall of K65R in a Portuguese HIV-1 Drug Resistance database, despite continuously increasing use of Tenofovir. Infection, Genetics and Evolution 2009 Jul;9(4):683-8.
Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach
Paraskevis D, Pybus O, Magiorkinis G, Hatzakis A, Wensing AM, van de Vijver DA, Albert J, Angarano G, Asjö B, Balotta C, Boeri E, Camacho R, Chaix ML, Coughlan S, Costagliola D, De Luca A, de Mendoza C, Derdelinckx I, Grossman Z, Hamouda O, Hoepelman I, Horban A, Korn K, Kücherer C, Leitner T, Loveday C, Macrae E, Maljkovic-Berry I, Meyer L, Nielsen C, Op de Coul EL, Ormaasen V, Perrin L, Puchhammer-Stöckl E, Ruiz L, Salminen MO, Schmit JC, Schuurman R, Soriano V, Stanczak J, Stanojevic M, Struck D, Van Laethem K, Violin M, Yerly S, Zazzi M, Boucher CA, Vandamme AM; SPREAD Programme. Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach. Retrovirology. 2009 May 20;6:49.
Algorithms for the interpretation of HIV-1 genotypic drug resistance information
Vercauteren J, Vandamme AM. Algorithms for the interpretation of HIV-1 genotypic drug resistance information. Antiviral Res. 2006 Sep;71(2-3):335-42.
Towards Context-Sensitive Data Access For Distributed Data Resources within Collaborative(...)
Assel M, Jiang T. Towards Context-Sensitive Data Access For Distributed Data Resources within Collaborative Working Environments. eChallenges Conference 2009, Istanbul, Turkey, 2009 (in press).
Towards semantic-based monitoring of ProActive.
Wlodzimierz Funika, Dennis Caromel, Pawel Koperek and M. Kupisz. Towards semantic-based monitoring of ProActive. Accepted for CoreGRID 2009 Workshop in conjunction with EuroPar 2009, August 24, 2009, Delft, Netherlands.
Simulating Individual-Based Models of Epidemics in Hierarchical Networks
R. Quax; D.A. Bader and P.M.A. Sloot: Simulating Individual-Based Models of Epidemics in Hierarchical Networks, in G. Allen; J. Nabrzyski; E. Seidel; G.D. van Albada; J.J. Dongarra and P.M.A. Sloot, editors, Computational Science - ICCS 2009: 9th International Conference, Baton Rouge, LA, USA, Proceedings, Part I, in series Lecture Notes in Computer Science, vol. 5544, pp. 725-734. Springer, Berlin, Heidelberg, May 2009.
Effect of human immunodeficiency virus type 1 protease inhibitor therapy and subtype on (...)
Palma AC, Abecasis AB, Vercauteren J, Carvalho AP, Cabanas J, Vandamme AM, Camacho RJ. Effect of human immunodeficiency virus type 1 protease inhibitor therapy and subtype on development of resistance in subtypes B and G. Infect Genet Evol. 2009 Jul 2.
The convenience of flow cytometry for HLA-B*5701 screening to prevent abacavir hypersensitivity(...)
Airo P, Scarsi M, Malagoli A, Carella G, Izzo I, Carosi G, Torti C. The convenience of flow cytometry for HLA-B*5701 screening to prevent abacavir hypersensitivity reactions. J Acquir Immune Defic Syndr. 2009 Jul 1;51(3):361-2.
A standardized framework for accurate, high-throughput genotyping of recombinant and (...)
Alcantara LC, Cassol S, Libin P, Deforche K, Pybus OG, Van Ranst M, Galvão-Castro B, Vandamme AM, de Oliveira T. A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W634-42.
Bioinformatics tools for the investigation of emerging and re-emerging infectious diseases
Vandamme AM. Bioinformatics tools for the investigation of emerging and re-emerging infectious diseases. Introduction. Infect Genet Evol. 2009 Jul;9(4):671.
Pharmacokinetic variability of antiretroviral drugs and correlation with virological outcome (...)
Fabbiani M, Di Giambenedetto S, Bracciale L, Bacarelli A, Ragazzoni E, Cauda R, Navarra P, De Luca A. Pharmacokinetic variability of antiretroviral drugs and correlation with virological outcome: 2 years of experience in routine clinical practice. J Antimicrob Chemother. 2009 Jul;64(1):109-17.
Therapy-selected mutations at RT position 215 counteract selection of K65R in HIV-2-infected patient
JC Silva, AC Miranda, MF Gonçalves, E Valadas, K Mansinho, K Van Laethem, A-M Vandamme, P Gomes and RJ Camacho on behalf of the Portuguese HIV-2 Study Group. Therapy-selected mutations at RT position 215 counteract selection of K65R in HIV-2-infected patients. Presented at the International Drug Resistance Workshop, abstract 88, 9-13 June 2009, Fort Meyers, USA. Antiviral Therapy 2009; 14 Suppl 1:A105.
Meta-Model and Framework for Application-Level Interaction Protocols
Eryk Ciepiela, Maciej Malawski and Marian Bubak. Meta-Model and Framework for Application-Level Interaction Protocols, 2nd International Workshop on Real Time Online Interactive Applications on the Grid (ROIA 2009) in conjunction with Euro-Par 2009, to be published in Lecture Notes in Computer Science, Springer, 2009.
Circulating HIV Type 1 Drug Resistance Will Have Limited Impact on the Effectiveness of Preexposure
Van de Vijver DAMC, Derdelinckx I, Boucher CAB, Circulating HIV-1 drug resistance will have limited impact on the effectiveness of Pre-Exposure Prophylaxis among young women in Zimbabwe. J Infect Dis 2009; 199: 1310-1317
Computational e-Science: Studying complex systems in silico
P.M.A. Sloot; D. Frenkel; H.A. Van der Vorst; A. van Kampen; H.E. Bal; P. Klint; R.M.M. Mattheij; J. van Wijk; J. Schaye; H.-J. Langevelde; R.H. Bisseling; B. Smit; E. Valenteyn; H.J. Sips; J.B.T.M. Roerdink and K.G. Langedoen: Computational e-Science: Studying complex systems in silico. A National Coordinated Initiative. White Paper., . February 2007.
Quality of Service on the Grid with User Level Scheduling
J. Mos'cicki; M.T. Bubak; H.C. Lee; A. Muraru and P.M.A. Sloot: Quality of Service on the Grid with User Level Scheduling, in M.T. Bubak; M.Turala and K. Wiatr, editors, CGW'06 Proceedings, pp. 119-129. Cracow, Poland, July 2007. ISBN 83-915141-7-X.
A complex automata model of HIV-1 co-receptor tropism: Understanding mutation rate pressure
G. Ertaylan and P.M.A. Sloot: A complex automata model of HIV-1 co-receptor tropism: Understanding mutation rate pressure, in Reviews in Antiretroviral Therapy, . Washington D.C., USA, December 2007.
in Distributed, High-Performance and Grid Computing in Computational Biology
W. Dubizky; A Schuster; P.M.A. Sloot; M. Schroeder and M. Romberg: in Distributed, High-Performance and Grid Computing in Computational Biology, (Sublibrary: Lecture Notes in Bioinformatics) in series Lecture Notes in Computer Science, vol. 4360, pp. 1-190. Springer, Berlin, Heidelberg, January 2007. ISSN 0302-9743; ISBN-10 3-540-69841-8.
Collaborative Virtual Laboratory for e-Health
M.T. Bubak; T. Gubala; M. Kasztelnik; M. Malawski; P. Nowakowski and P.M.A. Sloot: Collaborative Virtual Laboratory for e-Health, in P. Cunningham and M. Cunningham, editors, Expanding the Knowledge Economy: Issues, Applications, Case Studies, eChallenges e-2007 Conference Proceedings, pp. 537-544. IOS Press, Amsterdam, 2007. ISBN 978-1-58603-801-4 (paper), ISBN: 978-1-905824-05-2 (CD).
Grid-based Interactive Decision Support in BioMedicine
A. Tirado-Ramos; P.M.A. Sloot and M.T. Bubak: Grid-based Interactive Decision Support in BioMedicine, in T. El-Ghazali and A.Y. Zomaya, editors, Grids for Bioinformatics and Computational Biology, pp. 225-246. John Wiley and Sons, USA, January 2008.
A Collaborative Decision Support System in Viral Disease Treatment
P.M.A. Sloot; P.V. Coveney; M.T. Bubak; A.-M. Vandamme; B. Ó Nualláin; D. van de Vijver and C.A.B. Boucher: Virolab: A Collaborative Decision Support System in Viral Disease Treatment, Reviews in Antiviral Therapy, vol. 3, pp. 4-7. Virology Education, 2008. ISSN 1872-437X.
Stochastic simulation of HIV population dynamics through complex network modelling
P.M.A. Sloot; S.V. Ivanov; A.V. Boukhanovsky; D.A.M.C. van de Vijver and C.A.B. Boucher: Stochastic simulation of HIV population dynamics through complex network modelling, International Journal of Computer Mathematics, vol. 85, nr 8 pp. 1175-1187. Taylor & Francis, 2008. (DOI: 10.1080/00207160701750583)
VIROLAB: from the molecule to the man
P.M.A. Sloot: VIROLAB: from the molecule to the man, eStrategies Projects, nr 4 pp. 53-55. British Publishers Ltd, 2008.
Using HLA and Grid for Distributed Multiscale Simulations
K.J. Rycerz; M.T. Bubak and P.M.A. Sloot: Using HLA and Grid for Distributed Multiscale Simulations, in R. Wyrzykowski; K. Karczewski; J.J. Dongarra and J. Wasniewski, editors, Parallel Processing and Applied Mathematics: 7th International Conference, PPAM 2007, Gdansk, Poland, September 9-12, 2007 Revised Selected Papers, in series Lecture Notes in Computer Science, vol. 4967, pp. 780-787. Springer, Berlin, Heidelberg, May 2008. 978-3-540-68105-2. (DOI: 10.1007/978-3-540-68111-3)
Dynamic Interactions in HLA Component Model for Multiscale Simulations
K.J. Rycerz; P.M.A. Sloot and M.T. Bubak: Dynamic Interactions in HLA Component Model for Multiscale Simulations, in M.T. Bubak; G.D. van Albada; J.J. Dongarra and P.M.A. Sloot, editors, Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part II, in series Lecture Notes in Computer Science, vol. 5102, pp. 217-226. Springer, Berlin, Heidelberg, June 2008. 978-3-540-69386-4.
Problem solving environment for distributed interactive applications
K.J. Rycerz; M.T. Bubak; P.M.A. Sloot and V.S. Getov: Problem solving environment for distributed interactive applications, in S. Gorlatch; M.T. Bubak and T. Priol, editors, Achievements in European Research on Grid Systems - CoreGRID Integration Workshop 2006 (Selected Papers), pp. 55-66. Springer, 2008. ISBN-13 978-0-387-72811-7.
Modeling of Complex Systems by Cellular Automata
J. Kroc and P.M.A. Sloot: Modeling of Complex Systems by Cellular Automata, in J.R. Rabuñal; J. Dorado and A. Pazos, editors, Encyclopedia of Artificial Intelligence, . Information Science Reference, May 2008. ISBN: 978-1-59904-849-9.
Towards Distributed Petascale Computing
A.G. Hoekstra; S.F. Portegies Zwart; M.T. Bubak and P.M.A. Sloot: Towards Distributed Petascale Computing, Chapter 8, in D. Bader, editor, Petascale Computing: Algorithms and Applications, pp. 147-164. Chapman & Hall, mar 2008. ISBN: 9781584889090, ISBN 10: 1584889098.
A hybrid agent-based approach for modeling microbiological systems
Z. Guo; P.M.A. Sloot and J.C. Tay: A hybrid agent-based approach for modeling microbiological systems, J. of Theor. Biology, vol. 255, nr 2 pp. 163-175. Nov. 2008. (DOI: 10.1016/j.jtbi.2008.08.008)
A complex automata model of HIV-1 coreceptor tropism: mutation rate verified
G. Ertaylan and P.M.A. Sloot: A complex automata model of HIV-1 coreceptor tropism: mutation rate verified, in M.T. Bubak; M. Turala and K. Wiatr, editors, CGW'07 proceedings, (abstract) pp. 85-85. Krakow, Poland, October 2008. ISBN 978-83-915141-9-1.
HIV Decision Support: From Molecule to Man
P.M.A. Sloot; P. Coveney; G. Ertaylan; V. Müller; C. Boucher and M.T. Bubak: HIV Decision Support: From Molecule to Man, Phil . Trans. R. Soc.A, (in press ) vol. 367, nr 1898 . 2009.
Semantic Integration for Research Environments
T. Guballa; M.T. Bubak and P.M.A. Sloot: Chapter XXVI: Semantic Integration for Research Environments, in M. Cannataro, editor, Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare, . IGI Publishing, Medical Information Science Reference, may 2009. ISBN: 978-1-60566-374-6.
Robust supervised and unsupervised statistical learning for HIV type 1 coreceptor usage analysis
Prosperi MC, Fanti I, Ulivi G, Micarelli A, De Luca A, Zazzi M. Robust supervised and unsupervised statistical learning for HIV type 1 coreceptor usage analysis. AIDS Res Hum Retroviruses. 2009 Mar;25(3):305-14.
Virological suppression reduces clinical progression in patients with multiclass-resistant HIVtype 1
Bracciale L, Di Giambenedetto S, Colafigli M, La Torre G, Prosperi M, Santangelo R, Marchetti S, Cauda R, Fadda G, De Luca A. Virological suppression reduces clinical progression in patients with multiclass-resistant HIV type 1. AIDS Res Hum Retroviruses. 2009 Mar;25(3):261-7.
Genetic analysis of HIV type 1 strains from newly infected untreated patients in cyprus: high (...)
Kousiappa I, van de Vijver DA, Demetriades I, Kostrikis LG. Genetic analysis of HIV type 1 strains from newly infected untreated patients in cyprus: high genetic diversity and low prevalence of drug resistance. AIDS Res Hum Retroviruses. 2009 Jan;25(1):23-35.
Implications of HIV-1 M group polymorphisms on integrase inhibitor efficacy and resistance (...)
Loizidou EZ, Kousiappa I, Zeinalipour-Yazdi CD, Van de Vijver DA, Kostrikis LG. Implications of HIV-1 M group polymorphisms on integrase inhibitor efficacy and resistance: genetic and structural in silico analyses. Biochemistry. 2009 Jan 13;48(1):4-6.
Approaching Fine-grain Access Control for Distributed Biomedical Databases within Virtual (...)
Assel M, Kalyoncu O, Pan Y. Approaching Fine-grain Access Control for Distributed Biomedical Databases within Virtual Environments. In: Proc. 8th Cracow Grid Workshop, Kraków, Poland, 2009, pp. 311-319.
The magnitude of interferon-gamma responses to human cytomegalovirus is predictive for HIV-1 (...)
Darwich L, Cabrera C, Romeu J, Martinez-Picado J, Esté JA, Tural C, Bellido R, Clotet B, Angulo A, Ruiz L, Bofill M. The magnitude of interferon-gamma responses to human cytomegalovirus is predictive for HIV-1 disease progression. J Acquir Immune Defic Syndr. 2008 Dec 15;49(5):507-12.
Comparative Genomics in AIDS Research
Lemey P, Deforche K and Vandamme A-M. Comparative Genomics in AIDS Research. In ‘Comparative Genomics. Basic and Applied Research’, (J.R. Brown, ed.), CRC Press, Taylor & Francis Group, pp219-244, 2008.
An ontology model for execution records of Grid scientific applications
B. Balis, M. Bubak. An ontology model for execution records of Grid scientific applications in 4th International Conference on Semantics, Knowledge and Grid SKG 2008, December 2008, Beijing, China, pp. 34-41, IEEE 2008.
Provenance Querying for End-Users: A Drug Resistance Case Study
B. Balis, M. Bubak, M. Pelczar, J. Wach. Provenance Querying for End-Users: A Drug Resistance Case Study. In: Lecture Notes in Computer Science 5103 (Bubak M, van Albada D G, Dongarra J, Sloot P M A eds.), Springer-Verlag, 2008, pp. 80-89.
An Event-Based Approach to Reducing Coupling in Large-Scale Applications
B. Kowalewski, M. Bubak, B. Balis. An Event-Based Approach to Reducing Coupling in Large-Scale Applications. In: Lecture Notes in Computer Science 5103 (Bubak M, van Albada D G, Dongarra J, Sloot P M A eds.), Springer-Verlag, 2008, pp. 358-367.
A Tool for Building Collaborative Applications by Invocation of Grid Operations
M. Malawski, T. Bartynski, M. Bubak. A Tool for Building Collaborative Applications by Invocation of Grid Operations. In: Lecture Notes in Computer Science 5103 (Bubak M, van Albada D G, Dongarra J, Sloot P M A eds.), Springer-Verlag, 2008, pp. 243-252.
Integrating and Accessing Medical Data Resources within the ViroLab Virtual Laboratory
Assel M, Nowakowski P, Bubak M. Integrating and Accessing Medical Data Resources within the ViroLab Virtual Laboratory. In: Lecture Notes in Computer Science 5103 (Bubak M, van Albada D G, Dongarra J, Sloot P M A eds.), Springer-Verlag, 2008, pp. 90-99.
Data Management and Integration within Collaborative Working Environments
Assel M, Kipp A. Data Management and Integration within Collaborative Working Environments. In: Proc. 10th International Conference on Enterprise Information Systems, Barcelona, Spain, 2008, pp. 258-263.
Dynamic Access Control Management for Distributed Biomedical Data Resources
Assel M, Kalyoncu O. Dynamic Access Control Management for Distributed Biomedical Data Resources. In: Collaboration and the Knowledge Economy: Issues, Applications, Case Studies (Cunningham P, Cunningham M eds.), IOS Press, 2008, pp. 1593-1599.
Provenance Tracking and Querying in ViroLab
B. Balis, M. Bubak, M. Pelczar, J. Wach; Provenance Tracking and Querying in ViroLab, in Cracow Grid Workshop 2007 Workshop Proceedings, pp.71-76, ACC CYFRONET AGH 2008.
Bayesian network analyses of resistance pathways against efavirenz and nevirapine
Deforche K, Camacho RJ, Grossman Z, Soares MA, Van Laethem K, Katzenstein DA, Harrigan PR, Kantor R, Shafer R, Vandamme AM; non-B Workgroup. Bayesian network analyses of resistance pathways against efavirenz and nevirapine. AIDS. 2008 Oct 18;22(16):2107-15.
A king in the CASTLE?
Torti C, Frank I. A king in the CASTLE? Optimum initial HIV protease inhibitor. Lancet. 2008 Aug 23;372(9639):604-6.
Has HIV evolved to induce immune pathogenesis?
Bartha I, Simon P, Müller V. Has HIV evolved to induce immune pathogenesis? Trends Immunol. 2008 Jul;29(7):322-8.
Understanding the changing prevalence of K65R. AIDS Rev
Theys K, Vandamme AM. Understanding the changing prevalence of K65R. AIDS Rev. 2008 Apr-Jun;10(2):125.
A flexible framework for exposing legacy codes as services
B. Balis, M. Bubak, M. Wegiel. LGF: A flexible framework for exposing legacy codes as services, Future Generation Computer Systems, Volume 24, Issue 7, July 2008, Elsevier, pp. 711-719.
Impact of HIV-1 protease mutations A71V/T and T74S on M89I/V-mediated protease inhibitor(...)
Gonzalez LM, Santos AF, Abecasis AB, Van Laethem K, Soares EA, Deforche K, Tanuri A, Camacho R, Vandamme AM, Soares MA. Impact of HIV-1 protease mutations A71V/T and T74S on M89I/V-mediated protease inhibitor resistance in subtype G isolates. J Antimicrob Chemother. 2008 Jun;61(6):1201-4.
Risk of early virological failure of once-daily tenofovir-emtricitabine plus twice-daily (...)
Lapadula G, Costarelli S, Quiros-Roldan E, Calabresi A, Izzo I, Carosi G, Torti C. Risk of early virological failure of once-daily tenofovir-emtricitabine plus twice-daily nevirapine in antiretroviral therapy-naive HIV-infected patients. Clin Infect Dis. 2008 Apr 1;46(7):1127-9.
Introduction to the special section on BioGrid: biomedical computations on the grid
Huang CH, Konagaya A, Lanza V, Sloot PM. Introduction to the special section on BioGrid: biomedical computations on the grid. IEEE Trans Inf Technol Biomed. 2008 Mar;12(2):133-7.
EuroSIDA Study Group. Modelled in vivo HIV fitness under drug selective pressure and estimated (...)
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Multi-Science Decision Support for HIV Drug Resistance Treatment
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HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments
Ho YS, Abecasis AB, Theys K, Deforche K, Dwyer DE, Charleston M, Vandamme AM, Saksena NK. HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments. Virol J. 2008 Jan 23;5:14.
Plasma HIV load and proviral DNA decreases after two standard antiretroviral regimens in ...
Torti C, Quiros-Roldan ME, Cologni G, Nichelatti M, Ceresoli F, Pinti M, Nasi M, Cossarizza A, Lapadula G, Costarelli S, Manca N, Gargiulo F, Magoni M, Carosi G. Plasma HIV load and proviral DNA decreases after two standard antiretroviral regimens in HIV-positive patients naïve to antiretrovirals. Curr HIV Res. 2008 Jan;6(1):43-8.
Vandamme Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressu
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Sequence alignment in HIV computational analysis
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User-Oriented Querying over Repositories of Data and Provenance
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De Luca A, Giambenedetto SD, Trotta MP, Colafigli M, Prosperi M, Ruiz L, Baxter J, Clevenbergh P, Cauda R, Perno CF, Antinori A. Improved interpretation of genotypic changes in the HIV-1 reverse transcriptase coding region that determine the virological response to didanosine. J Infect Dis. 2007 Dec 1;196(11):1645-53. Epub 2007 Oct 26.
No evidence of relation between peripheral neuropathy and presence of hemochromatosis gene(...)
Costarelli S, Torti C, Gatta LB, Tinelli C, Lapadula G, Quiros-Roldan E, Izzo I, Castelnuovo F, Biasiotto G, Arosio P, Carosi G. No evidence of relation between peripheral neuropathy and presence of hemochromatosis gene mutations in HIV-1-positive patients. J Acquir Immune Defic Syndr. 2007 Oct 1;46(2):255-6.
Evolution of a novel 5-amino-acid insertion in the beta3-beta4 loop of HIV-1 reverse transcriptase
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.
Resistance to newly approved and investigational protease inhibitors
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Estimating the relative contribution of dNTP pool imbalance and APOBEC3G/3F
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No response to first-line tenofovir+lamivudine+efavirenz despite optimization according to baseline
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Interactive N-Body Simulations On the Grid
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Characterization of JC virus in cerebrospinal fluid from HIV-1 infected patients with progressive...
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.
Association of HIV-1 replication capacity with treatment outcomes in patients with virologic treatme
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.
Recombination confounds the early evolutionary history of human immunodeficiency virus type 1
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Bayesian network analysis of resistance pathways against HIV-1 protease inhibitors
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Impact of genetic variation of HIV-1 on drug resistance development
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Insights into a Mutation-Assisted Lateral Drug Escape Mechanism from the HIV-1
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Monitoring of Component-Based Applications
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Optimization of Grid Application Execution
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GScript Editor as Part of the ViroLab Presentation Layer
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From Monitoring Data to Experiment Information -- Monitoring of Grid Scientific Workflows.
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Antiretroviral resistance in different HIV-1 subtypes
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Analysis of HIV-1 pol sequences using Bayesian networks: implications for drug resistance
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Experiments with distributed component computing across Grid boundaries
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A Conceptual Grid Architecture for Interactive Biomedical Applications
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A Grid Service for Management of Multiple HLA Federate Processes Parallel Processing and Applied...
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Application of parallel computing to stochastic parameter estimation in environmental models Compute
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Problem-Solving Environments for Biological Morphogenesis Comput
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Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity
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The calculated genetic barrier for antiretroviral drug resistance substitutions...
van de Vijver DA, Wensing AM, Angarano G, Asjö B, Balotta C, Boeri E, Camacho R, Chaix ML, Costagliola D, De Luca A, Derdelinckx I, Grossman Z, Hamouda O, Hatzakis A, Hemmer R, Hoepelman A, Horban A, Korn K, Kücherer C, Leitner T, Loveday C, MacRae E, Maljkovic I, de Mendoza C, Meyer L, Nielsen C, Op de Coul EL, Ormaasen V, Paraskevis D, Perrin L, Puchhammer-Stöckl E, Ruiz L, Salminen M, Schmit JC, Schneider F, Schuurman R, Soriano V, Stanczak G, Stanojevic M, Vandamme AM, Van Laethem K, Violin M, Wilbe K, Yerly S, Zazzi M, Boucher CA. The calculated genetic barrier for antiretroviral drug resistance substitutions is largely similar for different HIV-1 subtypes. J Acquir Immune Defic Syndr. 2006 Mar;41(3):352-60.
Interpreting resistance data for HIV-1 therapy management--know the limitations
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Discordances between interpretation algorithms for genotypic resistance to protease and reverse tran
Snoeck J, Kantor R, Shafer RW, Van Laethem K, Deforche K, Carvalho AP, Wynhoven B, Soares MA, Cane P, Clarke J, Pillay C, Sirivichayakul S, Ariyoshi K, Holguin A, Rudich H, Rodrigues R, Bouzas MB, Brun-Vezinet F, Reid C, Cahn P, Brigido LF, Grossman Z, Soriano V, Sugiura W, Phanuphak P, Morris L, Weber J, Pillay D, Tanuri A, Harrigan RP, Camacho R, Schapiro JM, Katzenstein D, Vandamme AM. Discordances between interpretation algorithms for genotypic resistance to protease and reverse transcriptase inhibitors of human immunodeficiency virus are subtype dependent. Antimicrob Agents Chemother. 2006 Feb;50(2):694-701.