De Luca A, Pezzotti P, Boucher C, Döring M, Incardona F, Kaiser R, Lengauer T, Pfeifer N, Schülter E, Vandamme AM, Zazzi M, Geretti AM for the EucoHIV Study Group, Clinical use, efficacy, and durability of maraviroc for antiretroviral therapy in routine care: a European survey, PONE-D-19-18216R1 Epub ahead of print 2019

Aralaguppe SG, Ambikan AT, Ashokkumar M, Kumar MM, Hanna LE, Amogne W, Sönnerborg A, Neogi U. MiDRMpol: A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors. Viruses 2019; 11: 806.  doi:10.3390/v11090806

Saladini F, Giannini A, Boccuto A, Dragoni F, Appendino A, Albanesi E, Vicenti I, Zazzi M. Comparable in vitro activity of second-generation HIV-1 integrase strand transfer inhibitors (INSTIs) on HIV-1 clinical isolates with INSTI resistance mutations. Antimicrob Agents Chemother. 2019 Oct 14.  [Epub ahead of print] doi: 10.1128/AAC.01717-19 pmid: 3161136

Sarfo FSCastelnuovo BFanti IFeldt TIncardona FKaiser RLwanga IMarrone GSonnerborg ATufa TBZazzi MDe Luca A. "Longer-term effectiveness of protease-inhibitor-based second line antiretroviral therapy in four large sub-Saharan African clinics." J Infect. 2019 May;78(5):402-408. doi: 10.1016/j.


Neshumaev DLebedev AMalysheva MBoyko ASkudarnov SOzhmegova EAntonova AKazennova EBobkova MMolecular Surveillance of HIV-1 Infection in Krasnoyarsk Region, Russia: Epidemiology, Phylodynamics and PhylogeographyCurr HIV Res. 2019;17(2):114-125. doi: 10.2174/1570162X17666190618155816.


Döring, M., et al. (2018). "geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data." Nucleic Acids Research: gky349-gky349.


Neogi U, Singh K, Aralaguppe SG, Rogers LC, Njenda DT, Sarafianos SG, Hejdeman B, Sönnerborg A. Ex vivo antiretroviral potency of newer integrase strand transfer inhibitors cabotegravir and bictegravir in HIV-1 non-B subtypes AIDS. 2018 Feb 20;32(4):469-476. doi: 10.1097/QAD.0000000000001726.


Olson A, Bannert N, Sönnerborg A, de Mendoza C, Price M, Zangerle R, Chaix ML, Prins M, Kran AB, Gill J, Paraskevis D, Porter K; for CASCADE Collaboration in EuroCoord. Temporal trends of transmitted HIV drug resistance in a multinational seroconversion AIDS. 2018 Jan 14;32(2):161-169. doi: 10.1097/QAD.0000000000001689. PMID: 29112061.


Andersson E, Nordquist A, Esbjörnsson J, Flamholc L, Gisslén M, Hejdeman B, Norrgren H, Svedhem V, Wendahl S, Albert J, Sönnerborg A. Increasing prevalence of transmitted drug resistance in migrants from Sub Saharan Africa diagnosed with HIV in Sweden. AIDS. 2018 Jan 24. doi: 10.1097/QAD.0000000000001763. [Epub ahead of print]. PMID: 29369826.



Heger, E., et al. (2017). "Results of the first international HIV-1 coreceptor proficiency panel test." J Clin Virol 93: 53-56.


Kalaghatgi, P. and T. Lengauer (2017). "Computing phylogenetic trees using topologically related minimum spanning trees." Journal of Graph Algorithms and Applications 21(6): 1003-1025.


Lengauer, T. (2017). Modeling viral infections and the development of drug resistance. Crossing Boundaries in Science: Modeling Nature and Society – Can we control the world? Y. Borchert and J. Fritsch. Halle, Deutsche Akademie der Naturforscher Leopoldina – Nationale Akademie der Wissenschaften: 96-102.


Pironti, A., et al. (2017). "Using drug exposure for predicting drug resistance - A data-driven genotypic interpretation tool." PLoS ONE 12(4): e0174992.


Pironti, A., et al. (2017). "Determination of Phenotypic Resistance Cutoffs From Routine Clinical Data." J Acquir Immune Defic Syndr 74(5): e129-e137.


Vinken L, Fransen K, Pineda-Peña AC, Alexiev I, Balotta C, Debaisieux L, Devaux C, García Ribas S, Gomes P, Incardona F, Kaiser R, Ruelle J, Sayan M, Paraschiv S, Paredes R, Peeters M, Sonnerborg A, Vancutsem E, Van den Wijngaert S, Van Ranst M, Verhofstede C, Vandamme AM, Lemey P, Van Laethem K. HIV-1 sub-subtype F1 outbreak among MSM in Belgium. Virus Evol. 2017 Mar 5;3(Suppl 1). pii: vew036.020. doi: 10.1093/ve/vew036.020. eCollection 2017 Mar.


Worku Kalu A, Fikrie Telele N, Gebreselasie S, Fekade D, Abdurahman S, Marrone G, Sönnerborg A. Prediction of coreceptor usage by five bioinformatics tools in a large Ethiopian HIV-1 subtype C cohort. PLoS One 2017 2017 Aug 25;12(8):e0182384. doi: 10.1371/journal.pone.0182384. eCollection 2017.


Neogi U, Siddik AB, Kalaghatgi P, Gisslén M, Bratt G, Marrone G, Sonnerborg A. Recent increased identification and transmission of HIV-1 unique recombinant forms in Sweden. Sci Rep. 2017 Jul 25;7(1):6371. doi: 10.1038/s41598-017-06860-2.


Svärd J, Mugusi S, Mloka D, Neogi U, Zazzi M, Incardona F, Mugusi F, Sönnerborg A. Drug Resistance Testing through Remote Genotyping and Predicted Treatment Options in Human Immunodeficiency Virus Type 1 Infected Tanzanian Subjects Failing First or Second Line Antiretroviral Therapy. PLoS One 2017 Jun 5;12(6):e0178942. doi: 10.1371/journal.pone.0178942. eCollection 2017.

HIV Type 1 Integrase Natural Polymorphisms in Viral Variants Circulating in FSU Countries. Lapovok, Laga, Kazennova, Bobkova, Curr HIV Res. 2017 Aug 15. [Epub ahead of print]

PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context. Pieter Libin, Ewout Vanden Eynden, Francesca Incardona, Ann Nowé, Antonia Bezenchek, EucoHIV study group, Anders Sönnerborg, Anne-Mieke Vandamme, Kristof Theys and Guy Baele. Bioinformatics, Accepted for publication August 2017

Determination of Phenotypic Resistance Cutoffs From Routine Clinical Data Pironti, Alejandro MSc; Walter, Hauke Dr med; Pfeifer, Nico Dr rer nat; Knops, Elena Dr rer nat; Lübke, Nadine Dr rer nat; Büch, Joachim Dr phil; Di Giambenedetto, Simona MD; Kaiser, Rolf Dr rer nat; Lengauer, Thomas Dr phil, PhD; The EuResist Network Study Group

JAIDS Journal of Acquired Immune Deficiency Syndromes: 15 April 2017 - Volume 74 - Issue 5 - p e129–e137

Monophylogenetic HIV-1C epidemic in Ethiopia is dominated by CCR5-tropic viruses–an analysis of a prospective country-wide cohort, Amare Worku Kalu, Nigus Fikrie Telele, Solomon Gebreselasie, Daniel Fekade, Samir Abdurahman, Gaetano Marrone and Anders Sönnerborg - BMC Infectious Diseases, Jan 2017, DOI: 10.1186/s12879-016-2163-1


Magiorkinis G, Angelis K, Mamais I, Katzourakis A, Hatzakis A, Albert J, Lawyer G, Hamouda O, Struck D, Vercauteren J, Wensing A, Alexiev I, Åsjö B, Balotta C, Gomes P, Camacho RJ, Coughlan S, Griskevicius A, Grossman Z, Horban A, Kostrikis LG, Lepej SJ, Liitsola K, Linka M, Nielsen C, Otelea D, Paredes R, Poljak M, Puchhammer-Stöckl E, Schmit JC, Sönnerborg A, Staneková D, Stanojevic M, Boucher CA; SPREAD program, Nikolopoulos G, Vasylyeva T, Friedman SR, van de Vijver D, Angarano G, Chaix ML, de Luca A, Korn K, Loveday C, Soriano V, Yerly S, Zazzi M, Vandamme AM, Paraskevis D. The global spread of HIV-1 subtype B epidemic. Infect Genet Evol. 2016 Jun 2. pii: S1567-1348(16)30223-4. doi: 10.1016/j.meegid.2016.05.041. [Epub ahead of print].

New findings in HCV genotype distribution in selected West European, Russian and Israeli regions. || Kartashev VDöring MNieto LColetta EKaiser RSierra SHCV EuResist Study group. || J Clin Virol. 2016 Aug;81:82-9. doi: 10.1016/j.jcv.2016.05.010. Epub 2016 May 24. 

A data-driven approach for the determination of HIV-2 coreceptor usage enables epidemiological studies and clinical decision support, in print in Retrovirology || M. Döring, P. Borrego, J. Büch, A, Martins, G. Friedrich, R.J. Camacho, J. Eberle, R. Kaier, T. Lengauer, N. Taveria, N. Pfeifer || 2016

Global epidemiology of drug resistance after failure of WHO recommended first-line regimens for adult HIV-1 infection: a multicentre retrospective cohort study. TenoRes Study Group || Lancet Infect Dis. 2016 May;16(5):565-75. doi: 10.1016/S1473-3099(15)00536-8. PMID: 26831472

Determination of phenotypic resistance cutoffs from routine clinical data, in print in Journal of the Acquired Immune Deficiency Syndrome || A. Pironti, H. Walter, N. Pfeifer, E. Knops, N. Lübke, J. Büch, S. Di Gamberetto, R. Kaiser, T. Lengauer || 2016

Family-joining: a fast distance-based method for constructing generally labeled trees, in print in Molecular Biology and Evolution || P. Kalaghatgi, N. Pfeifer, T. Lengauer || 2016

Geno2pheno[HCV] – A Web-based Interpretation System to Support Hepatitis C Treatment Decisions in the Era of Direct-Acting Antiviral Agents || P. Kalaghatgi; A. M. Sikorski; E. Knops; D. Rupp; S. Sierra; E. Heger; M. Neumann-Fraune; B. Beggel; A. Walker; J. Timm; H. Walter; M. Obermeier; R. Kaiser; R. Bartenschlager; T. Lengauer || PLOS ONE 11, 5 (2016) e0155869

Improved darunavir genotypic mutation score predicting treatment response for patients infected with HIV-1 subtype B and non-subtype B receiving a salvage regimen || De Luca, P. Flandre, D. Dunn, M. Zazzi, A Wensing, M. M. Santoro, H. F. Gunthard, L. Wittkop, T. Kordossis, F. Garcia, A. Castagna, A. Cozzi-Lepri, D. Churchill, S. De Wit, N. H. Brockmeyer, A. Imaz, C. Mussini, N. Obel, C. F. Perno, B. Roca, P. Reiss, E. Schuelter, C. Torti, A. van Sighem, R. Zangerle and D. Descamps on behalf of CHAIN and COHERE in EuroCoord†

J Antimicrob Chemother 2016; 71: 1352–1360 doi:10.1093/jac/dkv465 Advance Access publication 28 January 2016

Sub-Epidemics Explain Localized High Prevalence of Reduced Susceptibility to Rilpivirine in Treatment-Naive HIV-1-Infected Patients: Subtype and Geographic Compartmentalization of Baseline Resistance Mutations || Theys K, Van Laethem K, Gomes P, Baele G, Pineda-Peña AC, Vandamme AM, Camacho RJ, Abecasis AB || AIDS Res Hum Retroviruses. 2016 May;32(5):427-33. doi: 10.1089/AID.2015.0095. PMID: 26651266


Proviral DNA as target for HIV-1 resistance analysis || N. Lübke, S. Sierra, V. Di Cristanziano, E. Schülter, B. O. Jensen, M. Oette, T. Lengauer, R. Kaiser || Intervirology 58, 3 (2015), 184-189.

Factors influencing the efficacy of rilpivirine on HIV-1 subtype C in low- and middle-income countries || Neogi U, Häggblom A, Singh K, Rogers L, Rao SD, Amogne W, Schülter E, Zazzi M, Arnold E, Sarafianos S, Sonnerborg A || J Antimicrob Chemother, 71(2):367-71. [PMID: 26518047] (2015)

Parameters influencing baseline HIV-1 genotypic tropism testing related to clinical outcome in patients on Maraviroc || S. Sierra, J.N. Dybowski, A. Pironti, D. Heider, L. Güney, A. Thielen, S. Reuter, S. Esser, G. Fätkenheuer, T. Lengauer, D. Hoffmann, H. Pfister, B. Jensen, R. Kaiser || PLOSONE 10, 5 (2015) e0125502.

Effects of sequence alterations on results from genotypic tropism testing || A. Pironti, N. Pfeifer, S. Sierra, R. Kaiser, T. Lengauer, || Journal of Clinical Virology 65 (2015) 68-73.

Predicted residual activity of rilpivirine in HIV-1 infected patients failing therapy including NNRTIs efavirenz or nevirapine ||
Theys K, Camacho RJ, Gomes P, Vandamme AM, Rhee SY; Portuguese HIV-1 Resistance Study Group || Clin Microbiol Infect. 2015 Jun;21(6):607.e1-8. doi: 10.1016/j.cmi.2015.02.011. Epub 2015 Feb 19. PMID: 25704446

Efficacy of etravirine combined with darunavir or other ritonavir-boosted protease inhibitors in HIV-1-infected patients: an observational study using pooled European cohort data. || Vingerhoets J1, Calvez VFlandre PMarcelin AGCeccherini-Silberstein FPerno CFMercedes Santoro MBateson RNelson MCozzi-Lepri AGrarup JLundgren JIncardona FKaiser RSonnerborg AClotet BParedes RGünthard HFLedergerber BHoogstoel ANijs STambuyzer LLavreys LOpsomer MEtravirine Cohort Study Group.

HIV Med. 2015 May;16(5):297-306. doi: 10.1111/hiv.12218. Epub 2015 Jan 14.



HIV-1 Gag C-terminal amino acid substitutions emerging under selective pressure of protease inhibitors in patient populations infected with different HIV-1 subtypes || Li G, Verheyen J, Theys K, Piampongsant S, Van Laethem K, Vandamme AM. || Retrovirology. 2014 Sep 25;11:79. doi: 10.1186/s12977-014-0079-7. PMID: 25253273

Association between HIV-1 coreceptor usage and resistance to broadly neutralizing antibodies || N. Pfeifer, H. Walter, T. Lengauer,
|| Journal of the Acquired Immune Deficiency Syndrome 67 2 (2014) 107-112.

Novel tetra-peptide insertion in Gag-p6 ALIX-binding motif in HIV-1 subtype C associated with protease inhibitor failure in Indian patients || Neogi U, Rao SD, Bontell I, Verheyen J, Rao VR, Gore SC, Soni N, Shet A, Schülter E, Ekstrand ML, Wondwossen A, Kaiser R, Madhusudhan MS, Prasad VR, Sönnerborg A. || AIDS. 2014 Aug 6. [Epub ahead of print].

Cost-efficient HIV-1 drug resistance surveillance using multiplexed high throughput amplicon sequencing: Implications for use in low and middle income countries || Ekici H, Rao S, Sönnerborg A, Ramprasad V, Gupta R; Neogi U. || [Epub ahead of print].

Patterns of transmitted HIV drug resistance in Europe vary by risk group || Frentz D, van de Vijver A.B D.A.M.C, Abecasis A, Albert J, Hamouda O, Kücherer C, Struck D, Schmit JC, Vercauteren J, Asjö B, Balotta C, Beshkov D, Camacho RJ, Clotet B, Coughlan S, Griskevicius A, Grossman Z, Horban A, Kolupajeva T, Korn K, Kostrikis LG, Liitsola K, Linka M, Nielsen C, Otelea D, Paraskevis D, Paredes R, Poljak M, Puchhammer-Stöckl E, Sönnerborg A, Stanekova D, Stanojevic M, A.-M. Vandamme, Wensing AMJ, Boucher CAB. || PLoS One 2014 Apr 10;9(4):e94495. doi: 10.1371/journal.pone.0094495. eCollection 2014.

Temporal Trends in the Swedish HIV-1 Epidemic: Increase in Non-B Subtypes and Recombinant Forms over Three Decades || Neogi U, Häggblom A, Santacatterina M, Bratt G, Gisslén M, Albert J, Sönnerborg A. || PLoS One. 2014 Jun 12;9(6):e99390. doi: 10.1371/journal.pone.0099390. eCollection 2014.

Decreased phenotypic susceptibility to etravirine in patients with predicted genotypic sensitivity || Agneskog E, Nowak P, Maijgren Steffensson C, Casadellà M, Noguera-Julian M, Paredes R, Källander CF, Sönnerborg A. || PLoS One. 2014 Jul 7;9(7):e101508. doi: 10.1371/journal.pone.0101508. eCollection 2014.



Modelling binding between CCR5 and CXCR4 receptors and their ligands suggests the surface electrostatic potential of the co-receptor to be a key player in the HIV-1 tropism || O. V. Kalinina, N. Pfeifer, T. Lengauer || Retrovirology 10, 11 (2013) 130.

Ambulatory care for HIV-infected patients: differences in outcomes between hospital-based units and private practices: analysis of the RESINA cohort || M. Oette, S. Reuter, R. Kaiser, B. Jensen, T. Lengauer, G. Fätkenheuer, H. Knechten, M. Hower, A, Sagir, H. Pfister, D. Häussinger || For the RESINA Study Group, European Journal of Medical Research 18 (2013) 48.

Full genome ultra-deep pyrosequencing associates G-to-A hypermutation of the hepatitis B virus genome with the natural progression of hepatitis B || B. Beggel, C. Münk, M. Däumer, K. Hauck, D Häussinger, T. Lengauer, A, Ehrhardt || Journal of Viral Hepatitis 20, 12 (2013) 882-889.

Analysis of physicochemical and structural properties determining HIV-1 coreceptor usage || K. Bozek, T. Lengauer, S. Sierra, R. Kaiser, F.S. Domingues || PLoS Computational Biology 9, 3 (2013) e1002977.

Human APOBEC3G/F mediated sequence editing: high prevalence of lethal proviral hypermutations in highly active antiretroviral therapy experienced Indian patients || Neogi U, Shet A, Sahoo PN, Bontell I, Banerjea AC, Ekstrand M, Sönnerborg A. || J Int AIDS Soc. 2013 Feb 25;16:18472. doi: 10.7448/IAS.16.1.18472.

Trends in antiretroviral therapy and prevalence of HIV drug resistance mutations in Sweden 1997-2011 || Bontell I, Häggblom A, Bratt G, Albert J, Sönnerborg A. || PLoS One 2013;8(3):e59337. doi: 10.1371/journal.pone.0059337. Epub 2013 Mar 22.

Evaluation of Sequence Ambiguities of the HIV-1 pol gene as a Method to Identify Recent HIV-1 Infection in Transmitted Drug Resistance Surveys || Andersson E, Shao W, Bontell I, Cham F, Cuong DD, Wondwossen A, Morris L, Hunt G, Sönnerborg A, Bertagnolio S, Maldarelli F, Jordan MR. || Infect Genet Evol. 2013 Apr 10. doi:pii: S1567-1348(13)00141-X. 10.1016/j.meegid.2013.03.050. [Epub ahead of print]

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. PMID: 24219163; PubMed Central PMCID: PMC3879221.

RegaDB: community-driven data management and analysis for infectious diseases || Libin P, Beheydt G, Deforche K, Imbrechts S, Ferreira F, Van Laethem K, Theys  K, Carvalho AP, Cavaco-Silva J, Lapadula G, Torti C, Assel M, Wesner S, Snoeck J, Ruelle J, De Bel A, Lacor P, De Munter P, Van Wijngaerden E, Zazzi M, Kaiser R, Ayouba A, Peeters M, de Oliveira T, Alcantara LC, Grossman Z, Sloot P, Otelea D,  Paraschiv S, Boucher C, Camacho RJ, Vandamme AM. || Bioinformatics. 2013 Jun 1;29(11):1477-80. Epub 2013 May 2.

Declining prevalence of HIV-1 drug resistance in antiretroviral treatment-exposed individuals in Western Europe || De Luca A, Dunn D, Zazzi M, Camacho R, Torti C, Fanti I, Kaiser R, Sönnerborg A, Codoñer Francisco M, Van Laethem K, Vandamme AM, Bansi L, Ghisetti V, van de Vijver David AM, Asboe D, Prosperi Mattia CF, Di Giambenedetto S; for the Sehere collaboration in Chain || J Infect Dis. 2013 Apr;207(8):1216-20.

Clinical Evaluation of Rega 8: An Updated Genotypic Interpretation System That Significantly Predicts HIV-Therapy Response || 
Vercauteren J, Beheydt G, Prosperi M, Libin P, Imbrechts S, Camacho R, Clotet  B, De Luca A, Grossman Z, Kaiser R, Sönnerborg A, Torti C, Van Wijngaerden E, Schmit JC, Zazzi M, Geretti AM, Vandamme AM, Van Laethem K. || PLoS One. 2013 Apr 17;8(4):e61436.

HIV-1 subtype is an independent predictor of reverse transcriptase mutation K65R in HIV-1 patients treated with combination antiretroviral therapy including tenofovir. || Theys K, Vercauteren J, Snoeck J, Zazzi M, Camacho R, Torti C, Schülter E, Clotet B, Sönnerborg A, De Luca A, Grossman Z, Struck D, Vandamme AM, Abecasis AB. || Antimicrob Agents Chemother. 2013 Feb;57(2):1053-6. (IF 2012 = 4.565).

HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure. || Sangeda RZ, Theys K, Beheydt G, Rhee SY, Deforche K, Vercauteren J, Libin P, Imbrechts S, Grossman Z, Camacho RJ, Van Laethem K, Pironti A, Zazzi M, Sönnerborg A, Incardona F, De Luca A, Torti C, Ruiz L, Van de Vijver DA, Shafer RW, Bruzzone B, Van Wijngaerden E, Vandamme AM; || Virolab and EuResist Projects.

RegaDB: community-driven data management and analysis for infectious diseases || Pieter Libin, Gertjan Beheydt, Koen Deforche, Stijn Imbrechts, Fossie Ferreira, Kristel Van Laethem, Kristof Theys, Ana Patricia Carvalho, Joana Cavaco-Silva, Giuseppe Lapadula, Carlo Torti, Matthias Assel, Stefan Wesner, Joke Snoeck, Jean Ruelle, Annelies De Bel, Patrick Lacor, Paul De Munter, Eric Van Wijngaerden, Maurizio Zazzi, Rolf Kaiser, Ahidjo Ayouba, Martine Peeters, Tulio de Oliveira, Luiz C. J. Alcantara, Zehava Grossman, Peter Sloot, Dan Otelea, Simona Paraschiv, Charles Boucher, Ricardo J. Camacho, Anne-Mieke Vandamme || Bioinformatics. 2013 Jun 1; 29(11): 1477–1480. Published online 2013 May 2. doi: 10.1093/bioinformatics/btt162 PMCID: PMC3661054

HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure || Sangeda RZ1, Theys K, Beheydt G, Rhee SY, Deforche K, Vercauteren J, Libin P, Imbrechts S, Grossman Z, Camacho RJ, Van Laethem K, Pironti A, Zazzi M, Sönnerborg A, Incardona F, De Luca A, Torti C, Ruiz L, Van de Vijver DA, Shafer RW, Bruzzone B, Van Wijngaerden E, Vandamme AM; Virolab and EuResist Projects. || Infect Genet Evol. 2013 Oct;19:349-60. doi: 10.1016/j.meegid.2013.03.014. Epub 2013 Mar 21. PMID: 23523594

HIV-1 drug resistance: where do polymorphisms fit in? ||  Future Microbiol. 2013 Mar;8(3):303-6. doi: 10.2217/fmb.13.10. Theys K, Abecasis AB, Vandamme AM. || PMID: 23464368 Infect Genet Evol. 2013 Oct;19:349-60. doi: 10.1016/j.meegid.2013.03.014. Epub 2013 Mar 21. PubMed PMID: 23523594.


EuResist Network Study Group. Efficacy of antiretroviral therapy switch in HIV-infected patients: a 10-year analysis of the EuResist || Cohort. Oette M, Schülter E, Rosen-Zvi M, Peres Y, Zazzi M, Sönnerborg A, Struck D, Altmann A, Kaiser R. || Intervirology. 2012;55(2):160-6. Epub 2012 Jan 24

Molecular Epidemiology of HIV-1 subtypes in India: Origin and evolutionary history of the predominant subtype C. || 
Neogi U, Bontell I, Shet A, De Costa A, Gupta S, Diwan V, Laishram RS, Wanchu A, Ranga U, Banerjea AC, Sönnerborg A. || PLoS One 2012;7(6):e39819. Epub 2012 Jun 29.

Etravirine in protease inhibitor-free antiretroviral combination therapies || Schuelter E, Luebke N, Jensen B, Zazzi M, Sönnerborg A, Lengauer T, Incardona F, Camacho R, Schmit J, Clotet B, Kaiser R, Pironti A. || J Int AIDS Soc. 2012 Nov 11;15(6):18260. doi: 10.7448/IAS.15.6.18260

Managing drug resistance in cancer: lessons from HIV therapy || Bock C, Lengauer T. || Nat Rev Cancer. 2012 Jun 7;12(7):494-501. PMID: 22673150.

Targets for inhibition of HIV replication: entry, enzyme action, release and maturation || Sierra S. and Walter H. || Intervirology 55(2) 2012: 88-97.

Bioinformatical assistance of selecting anti-HIV therapies: where do we stand? || T. Lengauer || Intervirology 55-2-2012. Link

Efficacy of antiretroviral therapy switch in HIV-infected patients: a 10-year analysis of the EuResist Cohort || Oette M, Schülter E, Rosen-Zvi M, Peres Y, Zazzi M, Sönnerborg A, Struck D, Altmann A, Kaiser R; EuResist Network Study Group. || Intervirology. 2012;55(2):160-6.

History-alignment models for bias-aware prediction of virological response to HIV combination therapy || Jasmina Bogojeska, Daniel Stockel, Maurizio Zazzi, Rolf Kaiser, Francesca Incardona, Michal Rosen-Zvi, Thomas Lengauer || JMLR W&CP 22: 118-126, AISTATS 2012

Predicting Response to Antiretroviral Treatment by Machine Learning: The EuResist Project || Maurizio Zazzi, Francesca Incardona, Michal Rosen-Zvi, Mattia Prosperi, Thomas Lengauer, Andre Altmann, Anders Sonnerborg, Tamar Lavee, Eugen Schülter, Rolf Kaiser ||
Intervirology Vol. 55, No. 2, 2012 



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. || Med Microbiol Immunol. 2011

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

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]

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. || HIV Med, 2011 Apr; 12(4):211-218. first published online HIV Med, August 2010.



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. || J Med Virol, 2010 Dec; 82(12):1996-2003

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. || PLoS One, 2010 Oct 29; 5(10):e13753

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. || HIV Med, 2010 Oct 1; 11(9):593-602

Expanding the world's largest HIV drug resistance database, EuResist, into an African context || F. Incardona || Tropical Medicine and International Health doi:10.1111/j.1365-3156.2010.02571. volume 15 no 8 pp s1–s32 august 2010

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. || PLoS One. 2010; 5(7): e11505. Published online 2010 July 9. doi: 10.1371/journal.pone.0011505

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. || 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. || 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. || Bioinformatics, 15 May 2010; 26: 1340-1347

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. || J Clin Virol, 2010 Apr; 47(4):372-5

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. || PLoS ONE 2010 Feb 3;5(2):e9044

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

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



Computerjagd auf das AIDSVirus || Lengauer T. and Kaiser R || 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. || J Antimicrob Chemother (2009) vol. 64 (1) pp. 25-32

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 || AIDS Research and Therapy 2009, 6:9 (June 01, 2009) 

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. || Antiviral Therapy (2009), 14:273-283

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. || Antiviral Therapy (2009); 14(3):433-442

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. || Bioinformatics (2009); 25:1040-7

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. || 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. || 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. || Bioinformatics 2008; 24: i399-406, special issue for ISMB 2008, Oxford University Press

Antiretroviral treatment response prediction engines at work: the EuResist project || Zazzi M. and Incardona F. || 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. || PLoS ONE 1 October 2008 Volume 3 Issue 10 e3470

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. || Antiviral Therapy (2007) 12(2), 169-178

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

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