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PAPERS

2022

Miranda MNS, Pingarilho M, Pimentel V, Martins MDRO, Kaiser R, Seguin-Devaux C, Paredes R, Zazzi M, Incardona F, Abecasis AB. Trends of Transmitted and Acquired Drug Resistance in Europe From 1981 to 2019: A Comparison Between the Populations of Late Presenters and Non-late Presenters. Front Microbiol. 2022 Apr 13;13:846943. doi: 10.3389/fmicb.2022.846943. PMID: 35495657; PMCID: PMC9044068..

 

Bavaro DF, De Vito A, Pasculli G, Bouba Y, Magnasco L, Pincino R, Saladini F, Lattanzio R, Corsini R, Arima S, Zazzi M, Incardona F, Rossetti B, Bezenchek A, Vanni B, Di Biagio A. Early versus delayed antiretroviral therapy based on genotypic resistance test: Results from a large retrospective cohort study. J Med Virol. 2022 Mar 31. doi: 10.1002/jmv.27754. Epub ahead of print. PMID: 35355293.

 

Rossetti B, Fabbiani M, Di Carlo D, Incardona F, Abecasis A, Gomes P, Geretti AM, Seguin-Devaux C, Garcia F, Kaiser R, Modica S, Shallvari A, Sönnerborg A, Zazzi M; EuResist Network, INTEGRATE study group. Effectiveness of integrase strand transfer inhibitors in HIV-infected treatment-experienced individuals across Europe. HIV Med. 2022 Feb 24. doi: 10.1111/hiv.13262. Epub ahead of print. PMID: 35199909.

Kuznetsova A, Lebedev A, Gromov K, Kazennova E, Zazzi M, Incardona F, Sönnerborg A, Bobkova M. Pre-existing singleton E138A mutations in the reverse transcriptase gene do not affect the efficacy of first-line antiretroviral therapy regimens using rilpivirine in human immunodeficiency virus-infected patients. Clin Case Rep. 2022 Feb 3;10(2):e05373. doi: 10.1002/ccr3.5373. PMID: 35140966; PMCID: PMC8813671.

2021

 

Rossetti B, Fabbiani M, Di Carlo D, Incardona F, Abecasis A, Gomes P, Geretti AM, Seguin-Devaux C, Garcia F, Kaiser R, Modica S, Shallvari A, Sönnerborg A, Zazzi M; EuResist Network, INTEGRATE study group. Effectiveness of integrase strand transfer inhibitor-based regimens in HIV-infected treatment-naive individuals: results from a European multi-cohort study. J Antimicrob Chemother. 2021 Aug 12;76(9):2394-2399. doi: 10.1093/jac/dkab200. PMID: 34212176.

Borghetti A, Ciccullo A, Lombardi F, Baldin G, Belmonti S, Prosperi M, Incardona F, Heger E, Borghi V, Sönnerborg A, Zazzi M, De Luca A, Di Giambenedetto S. Transmitted drug resistance to NRTIs and risk of virological failure in naïve patients treated with integrase inhibitors. HIV Med. 2021 Jan;22(1):22-27. doi: 10.1111/hiv.12956. Epub 2020 Sep 23. PMID: 32964671.

Miranda MNS, Pingarilho M, Pimentel V, Martins MDRO, Vandamme AM, Bobkova M, Böhm M, Seguin-Devaux C, Paredes R, Rubio R, Zazzi M, Incardona F, Abecasis A. Determinants of HIV-1 Late Presentation in Patients Followed in Europe. Pathogens. 2021 Jul 2;10(7):835. doi: 10.3390/pathogens10070835. PMID: 34357985; PMCID: PMC8308660.

2020

 

Scutari R, Alteri C, Vicenti I, Di Carlo D, Zuccaro V, Incardona F, Borghi V, Bezenchek A, Andreoni M, Antinori A, Perno CF, Cascio A, De Luca A, Zazzi M, Santoro MM; ARCA (Antiviral Response Cohort Analysis) Study Group. Evaluation of HIV-1 integrase resistance emergence and evolution in patients treated with integrase inhibitors. J Glob Antimicrob Resist. 2020 Mar;20:163-169. doi: 10.1016/j.jgar.2019.07.015. Epub 2019 Jul 19. PMID: 31330378.

Emberti Gialloreti L, Basa FB, Moramarco S, Salih AO, Alsilefanee HH, Qadir SA, Bezenchek A, Incardona F, Di Giovanni D, Khorany R, Alhanabadi LHH, Salih SO, Akhshirsh GS, Azeez BS, Tofiq BA, Palombi L. Supporting Iraqi Kurdistan Health Authorities in Post-conflict Recovery: The Development of a Health Monitoring System. Front Public Health. 2020 Jan 30;8:7. doi: 10.3389/fpubh.2020.00007. PMID: 32083050; PMCID: PMC7003511.

2019

 

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; EucoHIV Study Group. Clinical use, efficacy, and durability of maraviroc for antiretroviral therapy in routine care: A European survey. PLoS One. 2019 Nov 21;14(11):e0225381. doi: 10.1371/journal.pone.0225381. PMID: 31751385; PMCID: PMC6874206.

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 Aug 30;11(9):806. doi: 10.3390/v11090806. PMID: 31480341; PMCID: PMC6784143.

Saladini F, Giannini A, Boccuto A, Dragoni F, Appendino A, Albanesi E, Vicenti I, Zazzi M. Comparable In Vitro Activities of Second-Generation HIV-1 Integrase Strand Transfer Inhibitors (INSTIs) on HIV-1 Clinical Isolates with INSTI Resistance Mutations. Antimicrob Agents Chemother. 2019 Dec 20;64(1):e01717-19. doi: 10.1128/AAC.01717-19. PMID: 31611362; PMCID: PMC7187585.

Sarfo FS, Castelnuovo B, Fanti I, Feldt T, Incardona F, Kaiser R, Lwanga I, Marrone G, Sonnerborg A, Tufa TB, Zazzi M, De 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.jinf.2019.03.003. Epub 2019 Mar 6. PMID: 30849438.

Neshumaev D, Lebedev A, Malysheva M, Boyko A, Skudarnov S, Ozhmegova E, Antonova A, Kazennova E, Bobkova M. Molecular Surveillance of HIV-1 Infection in Krasnoyarsk Region, Russia: Epidemiology, Phylodynamics and Phylogeography. Curr HIV Res. 2019;17(2):114-125. doi: 10.2174/1570162X17666190618155816. PMID: 31210113.

Böhm M, Koppe U, Jovanovic L, Tufa Tb, Buch J, Lengauer T, Zazzi M, De Luca A, Sonnerborg A, Incardona F, Bezenchek A, Kaiser R, Doehring M, Lennartz S, Obermeier M. A retrospective analysis of the EuResist data set assessing if NRTI resistance impairs INSTI based treatment with NRTI backbone. HIV MEDICINE 2019;:76-76

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

2018

Döring M, Büch J, Friedrich G, Pironti A, Kalaghatgi P, Knops E, Heger E, Obermeier M, Däumer M, Thielen A, Kaiser R, Lengauer T, Pfeifer N. geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data. Nucleic Acids Res. 2018 Jul 2;46(W1):W271-W277. doi: 10.1093/nar/gky349. PMID: 29718426; PMCID: PMC6031006.

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 type 1 non-B subtypes. AIDS. 2018 Feb 20;32(4):469-476. doi: 10.1097/QAD.0000000000001726. PMID: 29239896; PMCID: PMC5790636.

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 cohort. 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, Marrone G, Norrgren H, Svedhem V, Wendahl S, Albert J, Sönnerborg A. Increase in transmitted drug resistance in migrants from sub-Saharan Africa diagnosed with HIV-1 in Sweden. AIDS. 2018 Apr 24;32(7):877-884. doi: 10.1097/QAD.0000000000001763. PMID: 29369826.

2017

Heger E, Kaiser R, Knops E, Neumann-Fraune M, Schuelter E, Pironti A, Lengauer T, Walter H, Sierra S. Results of the first international HIV-1 coreceptor proficiency panel test. J Clin Virol. 2017 Aug;93:53-56. doi: 10.1016/j.jcv.2017.06.002. Epub 2017 Jun 10. PMID: 28633097.

Pironti A, Pfeifer N, Walter H, Jensen BO, Zazzi M, Gomes P, Kaiser R, Lengauer T. Using drug exposure for predicting drug resistance - A data-driven genotypic interpretation tool. PLoS One. 2017 Apr 10;12(4):e0174992. doi: 10.1371/journal.pone.0174992. PMID: 28394945; PMCID: PMC5386274.

Pironti A, Walter H, Pfeifer N, Knops E, Lübke N, Büch J, Di Giambenedetto S, Kaiser R, Lengauer T; EuResist Network Study Group. Determination of Phenotypic Resistance Cutoffs From Routine Clinical Data. J Acquir Immune Defic Syndr. 2017 Apr 15;74(5):e129-e137. doi: 10.1097/QAI.0000000000001198. PMID: 27787339; PMCID: PMC5351752.

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. A21 HIV-1 sub-subtype F1 outbreak among MSM in Belgium. Virus Evol. 2017 Mar 5;3(Suppl 1):vew036.020. doi: 10.1093/ve/vew036.020. PMID: 28845274; PMCID: PMC5565986.

Kalu AW, Telele NF, 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 Aug 25;12(8):e0182384. doi: 10.1371/journal.pone.0182384. PMID: 28841646; PMCID: PMC5571954.

Neogi U, Siddik AB, Kalaghatgi P, Gisslén M, Bratt G, Marrone G, Sönnerborg 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. PMID: 28744024; PMCID: PMC5527090.

Svärd J, Mugusi S, Mloka D, Neogi U, Meini G, Mugusi F, Incardona F, Zazzi M, 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. PMID: 28582463; PMCID: PMC5459473.

Lapovok I, Laga V, Kazennova E, Bobkova M. HIV Type 1 Integrase Natural Polymorphisms in Viral Variants Circulating in FSU Countries. Curr HIV Res. 2017 Nov 23;15(5):318-326. doi: 10.2174/1570162X15666170815162052. PMID: 28814231.

Libin P, Vanden Eynden E, Incardona F, Nowé A, Bezenchek A; EucoHIV Study Group, Sönnerborg A, Vandamme AM, Theys K, Baele G. PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context. Bioinformatics. 2017 Dec 15;33(24):3993-3995. doi: 10.1093/bioinformatics/btx535. PMID: 28961923; PMCID: PMC5860094.

Pironti A, Walter H, Pfeifer N, Knops E, Lübke N, Büch J, Di Giambenedetto S, Kaiser R, Lengauer T; EuResist Network Study Group. Determination of Phenotypic Resistance Cutoffs From Routine Clinical Data. J Acquir Immune Defic Syndr. 2017 Apr 15;74(5):e129-e137. doi: 10.1097/QAI.0000000000001198. PMID: 27787339; PMCID: PMC5351752.

Kalu AW, Telele NF, Gebreselasie S, Fekade D, Abdurahman S, Marrone G, Sönnerborg A. Monophylogenetic HIV-1C epidemic in Ethiopia is dominated by CCR5-tropic viruses-an analysis of a prospective country-wide cohort. BMC Infect Dis. 2017 Jan 6;17(1):37. doi: 10.1186/s12879-016-2163-1. PMID: 28061826; PMCID: PMC5219668.

Kalaghatgi, P. and T. Lengauer, Computing phylogenetic trees using topologically related minimum spanning trees. Journal of Graph Algorithms and Applications 2017, 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

2016

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, Stylianou DC, Boucher CAB; 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 Dec;46:169-179. doi: 10.1016/j.meegid.2016.05.041. Epub 2016 Jun 2. PMID: 27262355; PMCID: PMC5157885.

Kartashev V, Döring M, Nieto L, Coletta E, Kaiser R, Sierra S; HCV EuResist Study group. New findings in HCV genotype distribution in selected West European, Russian and Israeli regions. J Clin Virol. 2016 Aug;81:82-9. doi: 10.1016/j.jcv.2016.05.010. Epub 2016 May 24. PMID: 27367545.

Döring M, Borrego P, Büch J, Martins A, Friedrich G, Camacho RJ, Eberle J, Kaiser R, Lengauer T, Taveira N, Pfeifer N. A genotypic method for determining HIV-2 coreceptor usage enables epidemiological studies and clinical decision support. Retrovirology. 2016 Dec 20;13(1):85. doi: 10.1186/s12977-016-0320-7. PMID: 27998283; PMCID: PMC5168878.

TenoRes Study Group. Global epidemiology of drug resistance after failure of WHO recommended first-line regimens for adult HIV-1 infection: a multicentre retrospective cohort study. Lancet Infect Dis. 2016 May;16(5):565-575. doi: 10.1016/S1473-3099(15)00536-8. Epub 2016 Jan 29. Erratum in: Lancet Infect Dis. 2016 Jun;16(6):636. Erratum in: Lancet Infect Dis. 2018 Jan;18(1):21. PMID: 26831472; PMCID: PMC4835583.

Pironti A, Walter H, Pfeifer N, Knops E, Lübke N, Büch J, Di Giambenedetto S, Kaiser R, Lengauer T; EuResist Network Study Group. Determination of Phenotypic Resistance Cutoffs From Routine Clinical Data. J Acquir Immune Defic Syndr. 2017 Apr 15;74(5):e129-e137. doi: 10.1097/QAI.0000000000001198. PMID: 27787339; PMCID: PMC5351752.

Kalaghatgi P, Pfeifer N, Lengauer T. Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees. Mol Biol Evol. 2016 Oct;33(10):2720-34. doi: 10.1093/molbev/msw123. Epub 2016 Jul 19. Erratum in: Mol Biol Evol. 2020 Jun 1;37(6):1845. PMID: 27436007; PMCID: PMC5026249.

Kalaghatgi P, Sikorski AM, Knops E, Rupp D, Sierra S, Heger E, Neumann-Fraune M, Beggel B, Walker A, Timm J, Walter H, Obermeier M, Kaiser R, Bartenschlager R, Lengauer T. Geno2pheno[HCV] - A Web-based Interpretation System to Support Hepatitis C Treatment Decisions in the Era of Direct-Acting Antiviral Agents. PLoS One. 2016 May 19;11(5):e0155869. doi: 10.1371/journal.pone.0155869. PMID: 27196673; PMCID: PMC4873220.

De Luca A, Flandre P, Dunn D, Zazzi M, Wensing A, Santoro MM, Günthard HF, Wittkop L, Kordossis T, Garcia F, Castagna A, Cozzi-Lepri A, Churchill D, De Wit S, Brockmeyer NH, Imaz A, Mussini C, Obel N, Perno CF, Roca B, Reiss P, Schülter E, Torti C, van Sighem A, Zangerle R, Descamps D; CHAIN and COHERE in EuroCoord. Improved darunavir genotypic mutation score predicting treatment response for patients infected with HIV-1 subtype B and non-subtype B receiving a salvage regimen. J Antimicrob Chemother. 2016 May;71(5):1352-60. doi: 10.1093/jac/dkv465. Epub 2016 Jan 28. PMID: 26825119; PMCID: PMC5808835.

Theys K, Van Laethem K, Gomes P, Baele G, Pineda-Peña AC, Vandamme AM, Camacho RJ, Abecasis AB. 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. AIDS Res Hum Retroviruses. 2016 May;32(5):427-33. doi: 10.1089/AID.2015.0095. Epub 2016 Jan 29. PMID: 26651266; PMCID: PMC4845676.

2015

Lübke N, Di Cristanziano V, Sierra S, Knops E, Schülter E, Jensen B, Oette M, Lengauer T, Kaiser R. Proviral DNA as a Target for HIV-1 Resistance Analysis. Intervirology. 2015;58(3):184-9. doi: 10.1159/000431093. Epub 2015 Jun 27. PMID: 26139571.

Neogi U, Häggblom A, Singh K, Rogers LC, Rao SD, Amogne W, Schülter E, Zazzi M, Arnold E, Sarafianos SG, Sönnerborg A. Factors influencing the efficacy of rilpivirine in HIV-1 subtype C in low- and middle-income countries. J Antimicrob Chemother. 2016 Feb;71(2):367-71. doi: 10.1093/jac/dkv359. Epub 2015 Oct 30. PMID: 26518047; PMCID: PMC4710214.

Sierra S, Dybowski JN, Pironti A, Heider D, Güney L, Thielen A, Reuter S, Esser S, Fätkenheuer G, Lengauer T, Hoffmann D, Pfister H, Jensen B, Kaiser R. Parameters Influencing Baseline HIV-1 Genotypic Tropism Testing Related to Clinical Outcome in Patients on Maraviroc. PLoS One. 2015 May 13;10(5):e0125502. doi: 10.1371/journal.pone.0125502. PMID: 25970632; PMCID: PMC4430318.

Pironti A, Sierra S, Kaiser R, Lengauer T, Pfeifer N. Effects of sequence alterations on results from genotypic tropism testing. J Clin Virol. 2015 Apr;65:68-73. doi: 10.1016/j.jcv.2015.02.006. Epub 2015 Feb 10. PMID: 25766992.

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

Vingerhoets J, Calvez V, Flandre P, Marcelin AG, Ceccherini-Silberstein F, Perno CF, Mercedes Santoro M, Bateson R, Nelson M, Cozzi-Lepri A, Grarup J, Lundgren J, Incardona F, Kaiser R, Sonnerborg A, Clotet B, Paredes R, Günthard HF, Ledergerber B, Hoogstoel A, Nijs S, Tambuyzer L, Lavreys L, Opsomer M; Etravirine Cohort Study Group. 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. HIV Med. 2015 May;16(5):297-306. doi: 10.1111/hiv.12218. Epub 2015 Jan 14. PMID: 25585664.

2014

 

Li G, Verheyen J, Theys K, Piampongsant S, Van Laethem K, Vandamme AM. HIV-1 Gag C-terminal amino acid substitutions emerging under selective pressure of protease inhibitors in patient populations infected with different HIV-1 subtypes. Retrovirology. 2014 Sep 25;11:79. doi: 10.1186/s12977-014-0079-7. PMID: 25253273; PMCID: PMC4189171.

Pfeifer N, Walter H, Lengauer T. Association between HIV-1 coreceptor usage and resistance to broadly neutralizing antibodies. J Acquir Immune Defic Syndr. 2014 Oct 1;67(2):107-12. doi: 10.1097/QAI.0000000000000283. PMID: 25072615; PMCID: PMC4175123.

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, Sonnerborg A. Novel tetra-peptide insertion in Gag-p6 ALIX-binding motif in HIV-1 subtype C associated with protease inhibitor failure in Indian patients. AIDS. 2014 Sep 24;28(15):2319-22. doi: 10.1097/QAD.0000000000000419. PMID: 25102091; PMCID: PMC4198440.

Ekici H, Rao SD, Sönnerborg A, Ramprasad VL, Gupta R, Neogi U. Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low- and middle-income countries. J Antimicrob Chemother. 2014 Dec;69(12):3349-55. doi: 10.1093/jac/dku278. Epub 2014 Jul 31. PMID: 25085657.

Frentz D, van de Vijver D, Abecasis A, Albert J, Hamouda O, Jørgensen L, Kücherer C, Struck D, Schmit JC, Vercauteren J, Asjö B, Balotta C, Bergin C, Beshkov D, Camacho R, Clotet B, Griskevicius A, Grossman Z, Horban A, Kolupajeva T, Korn K, Kostrikis L, Linka KL, Nielsen C, Otelea D, Paraskevis D, Paredes R, Poljak M, Puchhammer-Stöckl E, Sönnerborg A, Stanekova D, Stanojevic M, Vandamme AM, Boucher C, Wensing A; SPREAD Programme. Patterns of transmitted HIV drug resistance in Europe vary by risk group. PLoS One. 2014 Apr 10;9(4):e94495. doi: 10.1371/journal.pone.0094495. PMID: 24721998; PMCID: PMC3983178.

Neogi U, Häggblom A, Santacatterina M, Bratt G, Gisslén M, Albert J, Sonnerborg A. Temporal trends in the Swedish HIV-1 epidemic: increase in non-B subtypes and recombinant forms over three decades. PLoS One. 2014 Jun 12;9(6):e99390. doi: 10.1371/journal.pone.0099390. PMID: 24922326; PMCID: PMC4055746.

Agneskog E, Nowak P, Maijgren Steffensson C, Casadellà M, Noguera-Julian M, Paredes R, Källander CF, Sönnerborg A. Decreased phenotypic susceptibility to etravirine in patients with predicted genotypic sensitivity. PLoS One. 2014 Jul 7;9(7):e101508. doi: 10.1371/journal.pone.0101508. PMID: 25000302; PMCID: PMC4084891.

2013

 

Kalinina OV, Pfeifer N, Lengauer T. 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. Retrovirology. 2013 Nov 11;10:130. doi: 10.1186/1742-4690-10-130. PMID: 24215935; PMCID: PMC3833284.

Oette M, Reuter S, Kaiser R, Jensen B, Lengauer T, Fätkenheuer G, Knechten H, Hower M, Sagir A, Pfister H, Häussinger D; RESINA study group. Ambulatory care for HIV-infected patients: differences in outcomes between hospital-based units and private practices: analysis of the RESINA cohort. Eur J Med Res. 2013 Nov 21;18(1):48. doi: 10.1186/2047-783X-18-48. PMID: 24262206; PMCID: PMC4177128..

Beggel B, Münk C, Däumer M, Hauck K, Häussinger D, Lengauer T, Erhardt A. Full genome ultra-deep pyrosequencing associates G-to-A hypermutation of the hepatitis B virus genome with the natural progression of hepatitis B. J Viral Hepat. 2013 Dec;20(12):882-9. doi: 10.1111/jvh.12110. Epub 2013 Jun 7. PMID: 24304458.

Bozek K, Lengauer T, Sierra S, Kaiser R, Domingues FS. Analysis of physicochemical and structural properties determining HIV-1 coreceptor usage. PLoS Comput Biol. 2013;9(3):e1002977. doi: 10.1371/journal.pcbi.1002977. Epub 2013 Mar 21. PMID: 23555214; PMCID: PMC3605109.

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

Bontell I, Häggblom A, Bratt G, Albert J, Sönnerborg A. Trends in antiretroviral therapy and prevalence of HIV drug resistance mutations in Sweden 1997-2011. PLoS One. 2013;8(3):e59337. doi: 10.1371/journal.pone.0059337. Epub 2013 Mar 22. PMID: 23533618; PMCID: PMC3606434.

Andersson E, Shao W, Bontell I, Cham F, Cuong do D, Wondwossen A, Morris L, Hunt G, Sönnerborg A, Bertagnolio S, Maldarelli F, Jordan MR. Evaluation of sequence ambiguities of the HIV-1 pol gene as a method to identify recent HIV-1 infection in transmitted drug resistance surveys. Infect Genet Evol. 2013 Aug;18:125-31. doi: 10.1016/j.meegid.2013.03.050. Epub 2013 Apr 11. PMID: 23583545; PMCID: PMC4066879.

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. Superinfection with drug-resistant HIV is rare and does not contribute substantially to therapy failure in a large European cohort. BMC Infect Dis. 2013 Nov 12;13:537. doi: 10.1186/1471-2334-13-537. PMID: 24219163; PMCID: PMC3879221.

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. RegaDB: community-driven data management and analysis for infectious diseases. Bioinformatics. 2013 Jun 1;29(11):1477-80. doi: 10.1093/bioinformatics/btt162. Epub 2013 May 2. PMID: 23645815; PMCID: PMC3661054..

De Luca A, Dunn D, Zazzi M, Camacho R, Torti C, Fanti I, Kaiser R, Sönnerborg A, Codoñer FM, Van Laethem K, Vandamme AM, Bansi L, Ghisetti V, van de Vijver DA, Asboe D, Prosperi MC, Di Giambenedetto S; SEHERE collaboration in Chain. Declining prevalence of HIV-1 drug resistance in antiretroviral treatment-exposed individuals in Western Europe. J Infect Dis. 2013 Apr 15;207(8):1216-20. doi: 10.1093/infdis/jit017. Epub 2013 Jan 11. PMID: 23315324.

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. Clinical evaluation of Rega 8: an updated genotypic interpretation system that significantly predicts HIV-therapy response. PLoS One. 2013 Apr 17;8(4):e61436. doi: 10.1371/journal.pone.0061436. PMID: 23613852; PMCID: PMC3629176.

Theys K, Vercauteren J, Snoeck J, Zazzi M, Camacho RJ, Torti C, Schülter E, Clotet B, Sönnerborg A, De Luca A, Grossman Z, Struck D, Vandamme AM, Abecasis AB. HIV-1 subtype is an independent predictor of reverse transcriptase mutation K65R in HIV-1 patients treated with combination antiretroviral therapy including tenofovir. Antimicrob Agents Chemother. 2013 Feb;57(2):1053-6. doi: 10.1128/AAC.01668-12. Epub 2012 Nov 26. PMID: 23183438; PMCID: PMC3553726.

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. HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure. Infect Genet Evol. 2013 Oct;19:349-60. doi: 10.1016/j.meegid.2013.03.014. Epub 2013 Mar 21. PMID: 23523594.

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. RegaDB: community-driven data management and analysis for infectious diseases. Bioinformatics. 2013 Jun 1;29(11):1477-80. doi: 10.1093/bioinformatics/btt162. Epub 2013 May 2. PMID: 23645815; PMCID: PMC3661054.

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. HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure. Infect Genet Evol. 2013 Oct;19:349-60. doi: 10.1016/j.meegid.2013.03.014. Epub 2013 Mar 21. PMID: 23523594.


Theys K, Abecasis AB, Vandamme AM. HIV-1 drug resistance: where do polymorphisms fit in? Future Microbiol. 2013 Mar;8(3):303-6. doi: 10.2217/fmb.13.10. PMID: 23464368.

2012

Oette M, Schülter E, Rosen-Zvi M, Peres Y, Zazzi M, Sönnerborg A, Struck D, Altmann A, Kaiser R; EuResist Network Study Group. Efficacy of antiretroviral therapy switch in HIV-infected patients: a 10-year analysis of the EuResist Cohort. Intervirology. 2012;55(2):160-6. doi: 10.1159/000332018. Epub 2012 Jan 24. PMID: 22286887.

Neogi U, Bontell I, Shet A, De Costa A, Gupta S, Diwan V, Laishram RS, Wanchu A, Ranga U, Banerjea AC, Sönnerborg A. Molecular epidemiology of HIV-1 subtypes in India: origin and evolutionary history of the predominant subtype C. PLoS One. 2012;7(6):e39819. doi: 10.1371/journal.pone.0039819. Epub 2012 Jun 29. PMID: 22768132; PMCID: PMC3387228.

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

Bock C, Lengauer T. Managing drug resistance in cancer: lessons from HIV therapy. Nat Rev Cancer. 2012 Jun 7;12(7):494-501. doi: 10.1038/nrc3297. PMID: 22673150.

Sierra-Aragón S, Walter H. Targets for inhibition of HIV replication: entry, enzyme action, release and maturation. Intervirology. 2012;55(2):84-97. doi: 10.1159/000331995. Epub 2012 Jan 24. PMID: 22286875.

Lengauer T. Bioinformatical assistance of selecting anti-HIV therapies: where do we stand? Intervirology. 2012;55(2):108-12. doi: 10.1159/000332000. Epub 2012 Jan 24. PMID: 22286878.

Oette M, Schülter E, Rosen-Zvi M, Peres Y, Zazzi M, Sönnerborg A, Struck D, Altmann A, Kaiser R; EuResist Network Study Group. Efficacy of antiretroviral therapy switch in HIV-infected patients: a 10-year analysis of the EuResist Cohort. Intervirology. 2012;55(2):160-6. doi: 10.1159/000332018. Epub 2012 Jan 24. PMID: 22286887.

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


Zazzi M, Incardona F, Rosen-Zvi M, Prosperi M, Lengauer T, Altmann A, Sonnerborg A, Lavee T, Schülter E, Kaiser R. Predicting response to antiretroviral treatment by machine learning: the EuResist project. Intervirology. 2012;55(2):123-7. doi: 10.1159/000332008. Epub 2012 Jan 24. PMID: 22286881.

2011

 

Schülter E, Oette M, Balduin M, Reuter S, Rockstroh J, Fätkenheuer G, Esser S, Lengauer T, Agacfidan A, Pfister H, Kaiser R, Akgül B. HIV prevalence and route of transmission in Turkish immigrants living in North-Rhine Westphalia, Germany. Med Microbiol Immunol. 2011 Nov;200(4):219-23. doi: 10.1007/s00430-011-0193-2. Epub 2011 Apr 2. PMID: 21461764.

Lawyer G, Altmann A, Thielen A, Zazzi M, Sönnerborg A, Lengauer T. HIV-1 mutational pathways under multidrug therapy. AIDS Res Ther. 2011 Jul 27;8:26. doi: 10.1186/1742-6405-8-26. PMID: 21794106; PMCID: PMC3162516.

Prosperi MC, Mackie N, Di Giambenedetto S, Zazzi M, Camacho R, Fanti I, Torti C, Sönnerborg A, Kaiser R, Codoñer FM, Van Laethem K, Bansi L, van de Vijver DA, Geretti AM, De Luca A; SEHERE consortium. Detection of drug resistance mutations at low plasma HIV-1 RNA load in a European multicentre cohort study. J Antimicrob Chemother. 2011 Aug;66(8):1886-96. doi: 10.1093/jac/dkr171. Epub 2011 May 30. PMID: 21624929.


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 AM, van Laethem K, Wensing AM, Lengauer T, Incardona F. Prediction of response to antiretroviral therapy by human experts and by the EuResist data-driven expert system (the EVE study). HIV Med. 2011 Apr;12(4):211-8. doi: 10.1111/j.1468-1293.2010.00871.x. Epub 2010 Aug 19. Erratum in: HIV Med. 2012 Apr;13(4):253. PMID: 20731728.

2010

 

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. 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. J Med Virol. 2010 Dec;82(12):1996-2003. doi: 10.1002/jmv.21927. PMID: 20981785.

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. Antiretroviral therapy optimisation without genotype resistance testing: a perspective on treatment history based models. PLoS One. 2010 Oct 29;5(10):e13753. doi: 10.1371/journal.pone.0013753. Erratum in: PLoS One. 2011;6(4). doi:10.1371/annotation/d0254103-21b9-4078-836b-57ba5bd1c26a. PMID: 21060792; PMCID: PMC2966424.

Lai A, Riva C, Marconi A, Balestrieri M, Razzolini F, Meini G, Vicenti I, Rosi A, Saladini F, Caramma I, Franzetti M, Rossini V, Galli A, Galli M, Violin M, Zazzi M, Balotta C. Changing patterns in HIV-1 non-B clade prevalence and diversity in Italy over three decades. HIV Med. 2010 Oct 1;11(9):593-602. doi: 10.1111/j.1468-1293.2010.00832.x. Epub 2010 Jun 28. PMID: 20408891.

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

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. Comparison of HIV-1 genotypic resistance test interpretation systems in predicting virological outcomes over time. PLoS One. 2010 Jul 9;5(7):e11505. doi: 10.1371/journal.pone.0011505. PMID: 20634893; PMCID: PMC2901338.

Prosperi MC, Bracciale L, Fabbiani M, Di Giambenedetto S, Razzolini F, Meini G, Colafigli M, Marzocchetti A, Cauda R, Zazzi M, De Luca A. Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile, gp120 V3-loop RNA and DNA genotyping. Retrovirology. 2010 Jun 30;7:56. doi: 10.1186/1742-4690-7-56. PMID: 20591141; PMCID: PMC2907304.

Balestrieri M, Marconi A, Meini G, Rosi A, Saladini F, Vicenti I, Razzolini F, Zazzi M. Impact of remote versus local sampling on sensitivity of genotypic antiretroviral resistance testing. J Clin Microbiol. 2010 Jun;48(6):2321-2. doi: 10.1128/JCM.02394-09. Epub 2010 Apr 21. PMID: 20410346; PMCID: PMC2884515.


Altmann A, Toloşi L, Sander O, Lengauer T. Permutation importance: a corrected feature importance measure. Bioinformatics. 2010 May 15;26(10):1340-7. doi: 10.1093/bioinformatics/btq134. Epub 2010 Apr 12. PMID: 20385727.

Bruzzone B, Ventura A, Bisio F, Mboungou FA, Miguel LM, Saladini F, Zazzi M, Icardi G, De Maria A, Viscoli C. Impact of extensive HIV-1 variability on molecular diagnosis in the Congo basin. J Clin Virol. 2010 Apr;47(4):372-5. doi: 10.1016/j.jcv.2010.01.014. Epub 2010 Feb 20. PMID: 20172759.

Weisser H, Altmann A, Sierra S, Incardona F, Struck D, Sönnerborg A, Kaiser R, Zazzi M, Tschochner M, Walter H, Lengauer T. Only slight impact of predicted replicative capacity for therapy response prediction. PLoS One. 2010 Feb 3;5(2):e9044. doi: 10.1371/journal.pone.0009044. PMID: 20140263; PMCID: PMC2815793.

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

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

2009

 

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

Sichtig N, Sierra S, Kaiser R, Däumer M, Reuter S, Schülter E, Altmann A, Fätkenheuer G, Dittmer U, Pfister H, Esser S. Evolution of raltegravir resistance during therapy. J Antimicrob Chemother. 2009 Jul;64(1):25-32. doi: 10.1093/jac/dkp153. Epub 2009 May 14. PMID: 19447792.

Thompson IR, Bidgood P, Petróczi A, Denholm-Price JC, Fielder MD; EuResist Network Study Group. An alternative methodology for the prediction of adherence to anti HIV treatment. AIDS Res Ther. 2009 Jun 1;6:9. doi: 10.1186/1742-6405-6-9. PMID: 19486507; PMCID: PMC2698819.

Altmann A, Sing T, Vermeiren H, Winters B, Van Craenenbroeck E, Van der Borght K, Rhee SY, Shafer RW, Schülter E, Kaiser R, Peres Y, Sönnerborg A, Fessel WJ, Incardona F, Zazzi M, Bacheler L, Van Vlijmen H, Lengauer T. Advantages of predicted phenotypes and statistical learning models in inferring virological response to antiretroviral therapy from HIV genotype. Antivir Ther. 2009;14(2):273-83. PMID: 19430102.

Prosperi MC, Altmann A, Rosen-Zvi M, Aharoni E, Borgulya G, Bazso F, Sönnerborg 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. PMID: 19474477.

Prosperi MC, D'Autilia R, Incardona F, De Luca A, Zazzi M, Ulivi G. Stochastic modelling of genotypic drug-resistance for human immunodeficiency virus towards long-term combination therapy optimization. Bioinformatics. 2009 Apr 15;25(8):1040-7. doi: 10.1093/bioinformatics/btn568. Epub 2008 Oct 31. PMID: 18977781.

Altmann A, Däumer M, Beerenwinkel N, Peres Y, Schülter E, Büch J, Rhee SY, Sönnerborg A, Fessel WJ, Shafer RW, Zazzi M, Kaiser R, Lengauer T. Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database. J Infect Dis. 2009 Apr 1;199(7):999-1006. doi: 10.1086/597305. PMID: 19239365.

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

2008

 

Rosen-Zvi M, Altmann A, Prosperi M, Aharoni E, Neuvirth H, Sönnerborg A, Schülter E, Struck D, Peres Y, Incardona F, Kaiser R, Zazzi M, Lengauer T. Selecting anti-HIV therapies based on a variety of genomic and clinical factors. Bioinformatics. 2008 Jul 1;24(13):i399-406. doi: 10.1093/bioinformatics/btn141. PMID: 18586740; PMCID: PMC2718619.

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

Altmann A, Rosen-Zvi M, Prosperi M, Aharoni E, Neuvirth H, Schülter E, Büch J, Struck D, Peres Y, Incardona F, Sönnerborg A, Kaiser R, Zazzi M, Lengauer T. Comparison of classifier fusion methods for predicting response to anti HIV-1 therapy. PLoS One. 2008;3(10):e3470. doi: 10.1371/journal.pone.0003470. Epub 2008 Oct 21. PMID: 18941628; PMCID: PMC2565127.

Altmann A, Beerenwinkel N, Sing T, Savenkov I, Doumer M, Kaiser R, Rhee SY, Fessel WJ, Shafer RW, Lengauer T. Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance. Antivir Ther. 2007;12(2):169-78. doi: 10.1177/135965350701200202. PMID: 17503659.

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


Lengauer T, Sing T. Bioinformatics-assisted anti-HIV therapy. Nat Rev Microbiol. 2006 Oct;4(10):790-7. doi: 10.1038/nrmicro1477. PMID: 16980939.