Papers

HIV prevalence and route of transmission in Turkish immigrants living in North-Rhine Westphalia, Germany.
Schülter E, Oette M, Balduin M, Reuter S, Rockstroh J, Fätkenheuer G, Esser S, Lengauer T, Agacfidan A, Pfister H, Kaiser R, Akgül B.
In: PMID: 21461764 [PubMed - in process]. Link

HIV-1 mutational pathways under multidrug therapy
Glenn Lawyer, André Altmann, Alexander Thielen, Maurizio Zazzi, Anders Sönnerborg and Thomas Lengauer
In: AIDS Research and Therapy 2011, 8:26 doi:10.1186/1742-6405-8-26. Link

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE Study). Zazzi M, Kaiser R, Sönnerborg A, Struck D, Altmann A, Prosperi M, Rosen-Zvi M, Petroczi A, Peres Y, Schülter E, Boucher CA, Brun-Vezinet F, Harrigan PR, Morris L, Obermeier M, Perno CF, Phanuphak P, Pillay D, Shafer RW, Vandamme A-M, Van Laethem K, Wensing AMJ, Lengauer T, Incardona F.
In: HIV Med, 2011 Apr; 12(4):211-218. first published online HIV Med, August 2010. Link

Low rate of virological failure and maintenance of susceptibility to HIV-1 protease inhibitors with first-line lopinavir/ritonavir-based antiretroviral treatment in clinical practice Prosperi MC, Zazzi M, Punzi G, Monno L, Colao G, Corsi P, Di Giambenedetto S, Meini G, Ghisetti V, Bonora S, Pecorari M, Gismondo MR, Bagnarelli P, Carli T, De Luca A; ARCA Collaborative Group. In: J Med Virol, 2010 Dec; 82(12):1996-2003. Link

Antiretroviral therapy optimisation without genotype resistance testing: a perspective on treatment history based models Prosperi MC, Rosen-Zvi M, Altmann A, Zazzi M, Di Giambenedetto S, Kaiser R, Schülter E, Struck D, Sloot P, van de Vijver DA, Vandamme AM, Sönnerborg A; EuResist study group; Virolab study group. In: PLoS One, 2010 Oct 29; 5(10):e13753. Link

Changing patterns in HIV-1 non-B clades prevalence and diversity in Italy over three decades Lai A, Riva C, Marconi A, Balestrieri M, Razzolini F, Meini G, Vicenti I, Rosi A, Saladini F, Caramma I, Franzetti M, Galli A, Galli M, Violin M, Zazzi M, Balotta C. In: HIV Med, 2010 Oct 1; 11(9):593-602.

Comparison of HIV-1 Genotypic Resistance Test Interpretation Systems in virological outcomes over time Dineke Frentz, Charles A. B. Boucher, Matthias Assel, Andrea De Luca, Massimiliano Fabbiani, Francesca Incardona, Pieter Libin, Nino Manca, Viktor Müller, Breanndán Ó. Nualláin, Roger Paredes, Mattia Prosperi, Eugenia Quiros-Roldan, Lidia Ruiz, Peter M. A. Sloot, Carlo Torti, Anne-Mieke Vandamme, Kristel Van Laethem, Maurizio Zazzi, and David A. M. C. van de Vijver. In: PLoS One. 2010; 5(7): e11505. Published online 2010 July 9. doi: 10.1371/journal.pone.0011505. Link

Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile, gp120 V3-loop RNA and DNA genotyping Prosperi MC, Bracciale L, Fabbiani M, Di Giambenedetto S, Razzolini F, Meini G, Colafigli M, Marzocchetti A, Cauda R, Zazzi M, De Luca A. In: Retrovirology, 2010 Jun 30; 7:56.

Impact of remote versus local sampling on sensitivity of genotypic antiretroviral resistance testing Balestrieri M, Marconi A, Meini G, Rosi A, Saladini F, Vicenti I, Razzolini F, Zazzi M. In: J Clin Microbiol, 2010 Jun; 48(6):2321-2.

Permutation importance: a corrected feature importance measure Altmann A., Tolosi L., Sander O. and Lengauer T. In: Bioinformatics, 15 May 2010; 26: 1340-1347 Link

Impact of extensive HIV-1 variability on molecular diagnosis in the Congo basin Bruzzone B, Ventura A, Bisio F, Mboungou FA, Miguel LM, Saladini F, Zazzi M, Icardi G, De Maria A, Viscoli C. In: J Clin Virol, 2010 Apr; 47(4):372-5.

Detection of drug resistance mutations at low plasma HIV-1 RNA load in a European multi-centre cohort study Mattia CF Prosperi, Nicola Mackie, Simona Di Giambenedetto, Maurizio Zazzi, Ricardo Camacho, Iuri Fanti, Carlo Torti, Anders Sonnerborg, Rolf Kaiser, Francisco M Codoñer, Kristel Van Laethem, Loveleen Bansi, David AMC van de Vijver, Anna Maria Geretti and Andrea De Luca. 2011 May 30. [Epub ahead of print]

Only slight impact of predicted replicative capacity for therapy response prediction Weisser H., Altmann A., Sierra S., Incardona F., Struck D., Sönnerborg A., Kaiser R., Zazzi M., Tschochner M., Walter H., Lengauer T. In: PLoS ONE 2010 Feb 3;5(2):e9044. Link

Chasing the AIDS Virus Lengauer T., Altmann A., Thielen A. and Kaiser R. In: Communications of the ACM 53, 3 (2010) 66-74.

Bioinformatische Unterstützung der Auswahl von HIV-Therapien Lengauer T., Altmann A., Thielen A. In: Informatik-Spektrum (2009) vol. 32 (4) 320-331

Computerjagd auf das AIDSVirus Lengauer T. and Kaiser R In: Spektrum der Wissenschaft (2009) vol. August 2009. pp. 62-67

Evolution of raltegravir resistance during therapy Sichtig N., Sierra S., Kaiser R., Däumer M., Reuter S. Schülter E., Altmann A., Fätkenheuer G., Dittmer U., Pfister H. and Esser S. In: J Antimicrob Chemother (2009) vol. 64 (1) pp. 25-32 Link

An alternative methodology for the prediction of adherence to anti HIV treatment Richard Thompson, Penelope Bidgood, Andrea Petróczi, James CW Denholm-Price, Mark D Fielder and The EuResist Network Study Group In: AIDS Research and Therapy 2009, 6:9 (June 01, 2009) The article Link

Advantages of Predicted Phenotypes and Statistical Learning Models in Inferring Virological Response to Antiretroviral Therapy from HIV Genotype Altmann A., Sing T., Vermeiren H., Winters B., Van Craenenbroeck E., Van der Borght K., Rhee S-Y, Shafer R.W., Schülter E., Kaiser R., Peres Y., Sönnerborg A., Fessel W.J., Incardona F., Zazzi M., Bacheler L., Van Vlijmen H., Lengauer T. In: Antiviral Therapy (2009), 14:273-283. Link

Investigation of expert rule bases, logistic regression, and non-linear machine learning techniques for predicting response to antiretroviral treatment. 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; the EuResist and Virolab study groups. In: Antiviral Therapy (2009); 14(3):433-442. Link

Stochastic modelling of genotypic drug-resistance for human immunodeficiency virus towards long-term combination therapy optimization Prosperi M.C., D'Autilia R., Incardona F., De Luca A., Zazzi M., Ulivi G. In: Bioinformatics (2009); 25:1040-7 Link

Predicting the Response to Combination Antiretroviral Therapy: Retrospective Validation of geno2pheno-THEO on a Large Clinical Database Altmann A., Däumer M., Beerenwinkel N., Peres Y., Schülter E., Büch J., Rhee S-Y, Sönnerborg A., Fessel W.J., Shafer R.W., Zazzi M., Kaiser R., Lengauer T. In: Journal of Infectious Diseases, 2009 Apr 1;199(7):999-1006. Link

HIV-1 Drug Resistance Prediction and Therapy Optimization: A Case Study for the Application of Classification and Clustering Methods Rosen-Zvi M., Aharoni E., Selbig J., Biehl M. et al. In: Similarity-Based Clustering, LNAI 5400, pp. 185–201, 2009, Springer-Verlag, Berlin Heidelberg Link

Selecting anti-HIV therapies based on a variety of genomic and clinical factors Rosen-Zvi M., Altmann A., Prosperi M., Aharoni E. et al. In: Bioinformatics 2008; 24: i399-406, special issue for ISMB 2008, Oxford University Press Link

Antiretroviral treatment response prediction engines at work: the EuResist project Zazzi M. and Incardona F. In: Reviews in Antiviral Therapy - volume 2; 2008

Comparison of Classifier Fusion Methods for Predicting Response to Anti HIV-1 Therapy Altmann A., Rosen-Zvi M., Prosperi M., Aharoni E., et al. In: PLoS ONE 1 October 2008 Volume 3 Issue 10 e3470 Link

Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance Altmann A., Beerenwinkel N., Sing T., Savenkov I., Däumer M., Kaiser R., Rhee S-Y., Fessel WJ., Shafer R, Lengauer T. In: Antiviral Therapy (2007) 12(2), 169-178 Link

Mutagenetic tree Fisher kernel improves prediction of drug resistance from viral genotype Sing T., Beerenwinkel N. In: Advances in Neural Information Processing Systems: NIPS 2006, MIT Press, 2006

Bioinformatics-assisted anti-HIV therapy Lengauer T., Sing T. In: Nat. Rev. Microbiol. 4(10), 790-797 (October 2006) Link

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