Publications

Moramarco S, Cicala MG, Basa F,  Akhshirsh G, Bezenchek, Adhama R, Azeez B S,  Qadir S,  Salih S O,  Alhanabadi L H H, Fanti I,   Tofiq B,  Di Giovanni D,  Emberti Gialloreti L, Scarcella P.  Exploring health needs and the double burden of disease in adults attending public health facilities in the Iraqi Kurdistan. Front. Public Health, 23 October 2025 Sec. Public Health Policy, Volume 13 – 2025. https://doi.org/10.3389/fpubh.2025.1649273

Valik JK, Hedberg P, Nowak P, Blennow O, Dyrdak R, Vesterbacka J, Zetterqvist J, Naucler P. The effect of remdesivir and nirmatrelvir/ritonavir on mortality in patients hospitalized with COVID-19 during the Omicron era – an emulated target trial. Clin Microbiol Infect. 2025 Sep 22:S1198-743X(25)00462-8. doi: 10.1016/j.cmi.2025.09.012. Epub ahead of print. PMID: 40992693.

​​Drobniewski F, Ashmi M, Kusuma D, Ahmad R, Naumovas D, Juozapaitė D, Toscano C, Perea E, Abecasis AB, Viveiros M, Pereira JPV, Jensen BO, Bardeck N, de Morais Caporali JF, Pinto JA, Incardona F, Parczewski M, Serwin K. Determinants of vaccine hesitancy among healthcare workers in an international multicenter study within the EuCARE project. Sci Rep. 2025 Aug 28;15(1):31703. doi: 10.1038/s41598-025-17507-y. PMID: 40877401; PMCID: PMC12394626.

Hedberg P, Serwin K, Francesca Greco M, P V Pereira J, Juozapaite D, De Benedittis S, Bai F, Lübke N, Wienemann T, Fanti I, König F, Pfeifer N, Kaiser R, Zazzi M, Cozzi-Lepri A, Naumovas D, Marchetti G, Parczewski M, Jensen BO, Incardona F, Sönnerborg A, Nauclér P. Bacterial and Viral Coinfections in Adult Patients Hospitalized With COVID-19 Throughout the Pandemic: A Multinational Cohort Study in the EuCARE Project. J Infect Dis. 2025 Jul 11;231(6):e1091-e1101. doi: 10.1093/infdis/jiaf167. PMID: 40176475; PMCID: PMC12247819.

Hedberg P, Af Geijerstam P, Karlsson Valik J, Almgren-Lidman C, Ternhag A, Naucler P. Determinants of post COVID-19 clinic attendance among SARS-CoV-2-infected individuals in Stockholm, Sweden: a population-based cohort study. BMJ Open. 2025 Jun 17;15(6):e098344. doi: 10.1136/bmjopen-2024-098344. PMID: 40527555; PMCID: PMC12182103.

​Shamsara E, König F, Pfeifer N. An informed deep learning model of the Omicron wave and the impact of vaccination. Comput Biol Med. 2025 Jun;191:109968. doi: 10.1016/j.compbiomed.2025.109968. Epub 2025 Apr 9. PMID: 40209576.

Santoro A, Bai F, Greco MF, Rovito R, Sala M, Borghi L, Piscopo K, Vegni E, de Morais Caporali JF, Marinho CC, Leite AS, Santoro MM, Silberstein FC, Iannetta M, Juozapaite D, Strumiliene E, Almeida A, Toscano C, Quinones JAR, Carioti L, Mommo C, Fanti I, Incardona F, Marchetti G; EuCARE POSTCOVID study. Short and long-term trajectories of the post COVID-19 condition: Results from the EuCARE POSTCOVID study. BMC Infect Dis. 2025 Apr 29;25(1):625. doi: 10.1186/s12879-025-10805-w. PMID: 40301791; PMCID: PMC12039296.​

Górska A, Canziani LM, Rinaldi E, Pana ZD, Beale S, Bai F, Boxma-de Klerk BM, de Bruijn S, Donà D, Ekkelenkamp MB, Incardona F, Mallon P, Marchetti GC, Puhan M, Riva A, Simensen VC, Vaillant M, van der Zalm MM, van Kuijk SMJ, Wingerden SV, Judd A, Tacconelli E, Peñalvo JL. Learning from post-COVID-19 condition for epidemic preparedness: a variable catalogue for future post-acute infection syndromes. Clin Microbiol Infect. 2025 Mar;31(3):380-388. doi: 10.1016/j.cmi.2024.12.001. Epub 2024 Dec 9. PMID: 39662824.

Nagarajan P, Zhou J, Di Teodoro G, Incardona F, Seguin-Devaux C, Kaiser R, Abecasis AB, Gomes P, Tao K, Zazzi M, Shafer RW; EuResist Network. Spectrum of Non-Nucleoside Reverse Transcriptase Inhibitor-Associated Drug Resistance Mutations in Persons Living with HIV-1 Receiving Rilpivirine. Viruses. 2024 Oct 31;16(11):1715. doi: 10.3390/v16111715. PMID: 39599830; PMCID: PMC11599002.

Bai F, Santoro A, Hedberg P, Tavelli A, De Benedittis S, de Morais Caporali JF, Marinho CC, Leite AS, Santoro MM, Ceccherini Silberstein F, Iannetta M, Juozapaité D, Strumiliene E, Almeida A, Toscano C, Ruiz-Quiñones JA, Mommo C, Fanti I, Incardona F, Cozzi-Lepri A, Marchetti G; EuCARE Project. The Omicron Variant Is Associated with a Reduced Risk of the Post COVID-19 Condition and Its Main Phenotypes Compared to the Wild-Type Virus: Results from the EuCARE-POSTCOVID-19 Study. Viruses. 2024 Sep 23;16(9):1500. doi: 10.3390/v16091500. PMID: 39339976; PMCID: PMC11437468.

Ozhmegova E.N., Kuznetsova A.I., Lebedev A.V., Antonova A.A., Kim K.V., Munchak Y.M., Tumanov A.S., Kazennova E.V. Efficacy of first-line ART regimens based on tenofovir in HIV-infected patients with pre-existing A62V mutation in reverse transcriptase // Problems of Virology. – 2024. – Vol. 69. – N. 3. – P. 231-240. doi: 10.36233/0507-4088-232

​Di Teodoro G, Pirkl M, Incardona F, Vicenti I, Sönnerborg A, Kaiser R, Palagi L, Zazzi M, Lengauer T. Incorporating temporal dynamics of mutations to enhance the prediction capability of antiretroviral therapy’s outcome for HIV-1. Bioinformatics. 2024 Jun 3;40(6):btae327. doi: 10.1093/bioinformatics/btae327. PMID: 38775719; PMCID: PMC11153833.

Seabra SG, Merca F, Pereira B, Fonseca I, Carvalho AC, Brito V, Alves D, Libin P, Martins MRO, Miranda MNS, Pingarilho M, Pimentel V, Abecasis AB. Serological screening in a large-scale municipal survey in Cascais, Portugal, during the first waves of the COVID-19 pandemic: lessons for future pandemic preparedness efforts. Front Public Health. 2024 Feb 2;12:1326125. doi: 10.3389/fpubh.2024.1326125. PMID: 38371240; PMCID: PMC10869482.

Hedberg P, Parczewski M, Serwin K, Marchetti G, Bai F, Ole Jensen BE, Pereira JPV, Drobniewski F, Reschreiter H, Naumovas D, Ceccherini-Silberstein F, Rubio Quintanares GH, Mwau M, Toscano C, König F, Pfeifer N, Zazzi M, Fanti I, Incardona F, Cozzi-Lepri A, Sönnerborg A, Nauclér P. In-hospital mortality during the wild-type, alpha, delta, and omicron SARS-CoV-2 waves: a multinational cohort study in the EuCARE project. Lancet Reg Health Eur. 2024 Feb 2;38:100855. doi: 10.1016/j.lanepe.2024.100855. PMID: 38476753; PMCID: PMC10928271.

​​Elén S, Björkman P, Zazzi M, Böhm M, Bernal E, Sönnerborg A, Elvstam O; EuResist Network Study Group. Low-level HIV viraemia during antiretroviral therapy: Longitudinal patterns and predictors of viral suppression. HIV Med. 2024 Jan;25(1):107-116. doi: 10.1111/hiv.13541. Epub 2023 Sep 18. PMID: 37721192.

​Bellerba F, Bardeck N, Boehm M, D’Ecclesiis O, Raimondi S, Tomezzoli E, Miranda MS, Alves IM, Alves D, Abecasis A, Gabellone V, Gabrielli E, Vaglio G, Shamsara E, Pfeifer N, Mommo C, Incardona F, Kaiser R, Gandini S. SARS-CoV-2 trends in Italy, Germany and Portugal and school opening during the period of Omicron variant dominance: A quasi experimental study in the EuCARE project. Int J Infect Dis. 2024 Jan;138:63-72. doi: 10.1016/j.ijid.2023.11.002. Epub 2023 Nov 12. PMID: 37956899.

​Fiaschi L, Biba C, Varasi I, Bartolini N, Paletti C, Giammarino F, Saladini F, Zazzi M, Vicenti I. In Vitro Combinatorial Activity of Direct Acting Antivirals and Monoclonal Antibodies against the Ancestral B.1 and BQ.1.1 SARS-CoV-2 Viral Variants. Viruses. 2024 Jan 23;16(2):168. doi: 10.3390/v16020168. PMID: 38399944; PMCID: PMC10892871.

Miranda MNS, Pimentel V, Gomes P, Martins MDRO, Seabra SG, Kaiser R, Böhm M, Seguin-Devaux C, Paredes R, Bobkova M, Zazzi M, Incardona F, Pingarilho M, Abecasis AB. The Role of Late Presenters in HIV-1 Transmission Clusters in Europe. Viruses. 2023 Dec 13;15(12):2418. doi: 10.3390/v15122418. PMID: 38140659; PMCID: PMC10746990.

Varisco B, Bai F, De Benedittis S, Tavelli A, Cozzi-Lepri A, Sala M, Miraglia FG, Santoro MM, Ceccherini-Silberstein F, Shimoni Y, Ravid S, Kozlovski T, König F, Pfeifer N, Shamsara E, Parczewski M, Monforte AD, Incardona F, Mommo C, Marchetti G. EuCARE-POSTCOVID Study: a multicentre cohort study on long-term post-COVID-19 manifestations. BMC Infect Dis. 2023 Oct 13;23(1):684. doi: 10.1186/s12879-023-08595-0. PMID: 37833640; PMCID: PMC10576381.

Weibull Wärnberg A, Brännström J, Elvstam O, Gisslén M, Månsson F, Sönnerborg A, van de Klundert MA. The molecular epidemiology of HIV-1 in Sweden 1996 to 2022, and the influence of migration from Ukraine. Euro Surveill. 2023 Nov;28(48). doi: 10.2807/1560-7917.ES.2023.28.48.2300224. PMID: 38037731.

Hedberg P, Varisco B, Bai F, Sönnerborg A, Naucler P, Pfeifer N, Cozzi-Lepri A, Ceccherini-Silberstein F, Naumovas D, Drobniewski F, Jensen BO, Toscano C, Parczewski M, Quintanares GHR, Mwau M, Pinto JA, Incardona F, Mommo C, Marchetti G. EuCARE-hospitalised study protocol: a cohort study of patients hospitalised with COVID-19 in the EuCARE project. BMC Infect Dis. 2023 Oct 16;23(1):690. doi: 10.1186/s12879-023-08658-2. PMID: 37845624; PMCID: PMC10580565.

Elén S, Björkman P, Zazzi M, Böhm M, Bernal E, Sönnerborg A, Elvstam O; EuResist Network Study Group. Low-level HIV viraemia during antiretroviral therapy: Longitudinal patterns and predictors of viral suppression. HIV Med. 2023 Sep 18. doi: 10.1111/hiv.13541. Epub ahead of print. PMID: 37721192.

Kuo NI, Garcia F, Sönnerborg A, Böhm M, Kaiser R, Zazzi M; EuResist Network study group; Polizzotto M, Jorm L, Barbieri S. Generating synthetic clinical data that capture class imbalanced distributions with generative adversarial networks: Example using antiretroviral therapy for HIV. J Biomed Inform. 2023 Aug;144:104436. doi: 10.1016/j.jbi.2023.104436. Epub 2023 Jul 13. PMID: 37451495.

Vicenti I, Basso M, Pirola N, Bragato B, Rossi MC, Giobbia M, Pascoli S, Vinci A, Caputo S, Varasi I, Biba C, Fiaschi L, Zazzi M, Parisi SG. SARS-CoV-2 Neutralizing Antibodies to B.1 and to BA.5 Variant after Booster Dose of BNT162b2 Vaccine in HIV Patients COVID-Naïve and on Successful Antiretroviral Therapy.Vaccines (Basel). 2023 Apr 20;11(4):871. doi: 10.3390/vaccines11040871. PMID: 37112782; PMCID: PMC10144758.​

Rossetti, B.; Incardona, F.; Di Teodoro, G.; Mommo, C.; Saladini, F.; Kaiser, R.; Sönnerborg, A.; Lengauer, T.; Zazzi, M., on behalf of the EuResist Network. Cohort Profile: A European Multidisciplinary Network for the Fight against HIV Drug Resistance (EuResist Network). Trop. Med. Infect. Dis. 2023, 8, 243. https://doi.org/10.3390/tropicalmed8050243 

Raimondi, S., Gandini, S., Rubio Quintanares, G.H. et al. European Cohorts of patients and schools to Advance Response to Epidemics (EuCARE): a cluster randomised interventional and observational study protocol to investigate the relationship between schools and SARS-CoV-2 infection. BMC Infect Dis 23, 1 (2023). https://doi.org/10.1186/s12879-022-07947-6

Magnasco L, Pincino R, Pasculli G, Bouba Y, Saladini F, Bavaro DF, De Vito A, Lattanzio R, Corsini R, Zazzi M, Incardona F, Rossetti B, Bezenchek A, Borghi V, Di Biagio A. Predictors of Virological Failure Among People Living with HIV Switching from an Effective First-Line Antiretroviral Regimen. AIDS Res Hum Retroviruses. 2022 Jun;38(6):463-471. doi: 10.1089/AID.2021.0016. Epub 2022 Feb 10. PMID: 34969260.

 

Vicenti I, Basso M, Dragoni F, Gatti F, Scaggiante R, Fiaschi L, Parisi SG, Zazzi M. Comparable Post-Vaccination Decay of Neutralizing Antibody Response to Wild-Type and Delta SARS-CoV-2 Variant in Healthcare Workers Recovered from Mild or Asymptomatic Infection. Vaccines (Basel). 2022 Apr 9;10(4):580. doi: 10.3390/vaccines10040580. PMID: 35455329; PMCID: PMC9025891.

 

Dragoni F, Schiaroli E, Micheli V, Fiaschi L, Lai A, Zehender G, Rossetti B, Gismondo MR, Francisci D, Zazzi M, Vicenti I. Impact of SARS-CoV-2 omicron BA.1 and delta AY.4.2 variants on the neutralization by sera of patients treated with different authorized monoclonal antibodies. Clin Microbiol Infect. 2022 Jul;28(7):1037-1039. doi: 10.1016/j.cmi.2022.03.005. Epub 2022 Mar 15. PMID: 35304279; PMCID: PMC8923034.

Parisi SG, Mengoli C, Basso M, Vicenti I, Gatti F, Scaggiante R, Fiaschi L, Giammarino F, Iannetta M, Malagnino V, Zago D, Dragoni F, Zazzi M. Long-TermLongitudinal Analysis of Neutralizing Antibody Response to Three Vaccine Doses in a Real-Life Setting of Previously SARS-CoV-2 Infected Healthcare Workers: A Model for Predicting Response to Further Vaccine Doses. Vaccines (Basel). 2022 Aug 2;10(8):1237. doi: 10.3390/vaccines10081237. PMID: 36016125; PMCID: PMC9416151.

Kuo, N.IH., Polizzotto, M.N., Finfer, S. et al. The Health Gym: synthetic health-related datasets for the development of reinforcement learning algorithms. Sci Data 9, 693 (2022). https://doi.org/10.1038/s41597-022-01784-7

 

Pirkl M, Büch J, Devaux C, Böhm M, Sönnerborg A, Incardona F, Abecasis A, Vandamme AM, Zazzi M, Kaiser R, Lengauer T, The EuResist Network Study Group. Analysis of mutational history of multi-drug resistant genotypes with a mutagenetic tree model. J Med Virol. 2022 Dec 9. doi: 10.1002/jmv.28389. Epub ahead of print. PMID: 36484375.

van de Klundert, M.A.A.; Antonova, A.; Di Teodoro, G.; Ceña Diez, R.; Chkhartishvili, N.; Heger, E.; Kuznetsova, A.; Lebedev, A.; Narayanan, A.; Ozhmegova, E.; Pronin, A.; Shemshura, A.; Tumanov, A.; Pfeifer, N.; Kaiser, R.; Saladini, F.; Zazzi, M.; Incardona, F.; Bobkova, M.; Sönnerborg, A. Molecular Epidemiology of HIV-1 in Eastern Europe and Russia. Viruses 2022, 14, 2099. https://doi.org/10.3390/v14102099

 

Elvstam O, Malmborn K, Elén S, Marrone G, Garcia F, Zazzi M, Sönnerborg A, Böhm M, Seguin-Devaux C, Björkman P. Virologic failure following low-level viremia and viral blips during antiretroviral therapy: results from a European multicenter cohort. Clin Infect Dis. 2022 Sep 14:ciac762. doi: 10.1093/cid/ciac762. Epub ahead of print. PMID: 36100984.

 

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.

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.

Saladini F, Giammarino F, Hosseini BA, Giannini A, Boccuto A, Dragoni F, Vicenti I, Shafer RW, Zazzi M. In vitro cross-resistance to doravirine in a panel of HIV-1 clones harbouring multiple NNRTI resistance mutations. J Antimicrob Chemother. 2021 Jan 1;76(1):130-134. doi: 10.1093/jac/dkaa401. PMID: 32974670; PMCID: PMC8453390.

Bai X, Narayanan A, Nowak P, Ray S, Neogi U, Sönnerborg A. Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy. Front Microbiol. 2021 Jun 25;12:667718. doi: 10.3389/fmicb.2021.667718. PMID: 34248876; PMCID: PMC8267369.

 

 

Saladini F, Giannini A, Giammarino F, Maggiolo F, Vichi F, Corbelli GM, Galli A, Bigoloni A, Poli A, Santoro MM, Zazzi M, Castagna A. In vitro susceptibility to fostemsavir is not affected by long-term exposure to antiviral therapy in MDR HIV-1-infected patients. J Antimicrob Chemother. 2020 Sep 1;75(9):2547-2553. doi: 10.1093/jac/dkaa178. PMID: 32464638.

 

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.

Schlösser M, Kartashev VV, Mikkola VH, Shemshura A, Saukhat S, Kolpakov D, Suladze A, Tverdokhlebova T, Hutt K, Heger E, Knops E, Böhm M, Di Cristanziano V, Kaiser R, Sönnerborg A, Zazzi M, Bobkova M, Sierra S. HIV-1 Sub-Subtype A6: Settings for Normalised Identification and Molecular Epidemiology in the Southern Federal District, Russia. Viruses. 2020 Apr 22;12(4):475. doi: 10.3390/v12040475. PMID: 32331438; PMCID: PMC7232409.

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

Amit Gruber, Chen Yanover, Tal El-Hay, Anders Sönnerborg, Vanni Borghi, Francesca Incardona, Yaara Goldschmidt. Factorial HMMs with Collapsed Gibbs Sampling for Optimizing Long-term HIV Therapy. AISTATS 2018: 317-326

 

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.

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

Mattia C. F. Prosperi, Alejandro Pironti, Francesca Incardona, Giuseppe Tradigo, Maurizio Zazzi. Predicting human-immunodeficiency virus rebound after therapy initiation/switch using genetic, laboratory, and clinical data. BCB 2016: 611-615

 

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.

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.

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.

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.

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.

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.

 

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 I| Communications 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

 

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

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.

EuCARE school project: effectiveness of the Lolli-Methode in managing Covid-19 clusters and positivity rates in schools, Poster presented by Francesca Incardona
Doi G, Bellerba F, Santos A, Lopalco P, Gabellone V, Bardeck N, Rubio Quintanares G, Tucci G, Mainetti M, Andreon C, Mommo C, Fanti I, Abecasis A, Kaiser R, Gandini S,

23rd European Meeting on HIV &Hepatitis 2025

Learning loss and psychological outcomes in schools during the COVID-19 Pandemic: evidence from the EuCARE international cluster randomised trial, Poster presented by Francesca Incardona Bellerba F, Doi G, Tomezzoli E, Raimondi S, Cutica I, Mazzoni D, Martins Alves I, de Oliveira Tomás dos Santos A, Lopalco P, Gabellone V, Bardeck N, Rubio Quintanares G, Andreon C, Mainetti M, Tucci G, Mommo C, Fanti I, Abecasis A, Kaiser R, Incardona F, Gandini S

23rd European Meeting on HIV &Hepatitis 2025

Early Detection of SARS-CoV-2 Variants in a School Cohort Using Next-Generation Sequencing: Insights from the EUCARE Project, Oral presentation by Dr. Ana Abecasis
Santos A, Pimentel V, Alves I, Sebastião C, Miranda M, Seabra S, Raimondi S, Gandini S, Quintanares G, Lopalco P, D’Ecclesiis O, Tomezzoli E, Mommo C, Fanti I, WP4 E, Bellerba F, Kaiser R, Bardeck N, Martins M, Toscano C, Incardona F, Viveiros M, Pingarilho M, Abecasis A
23rd European Meeting on HIV &Hepatitis 2025

Exploring mental health and learning loss of students during the COVID-19 Pandemic: an international study within the EuCARE project, Oral presentation by Dr. Federica Bellerba
Federica Bellerba, Giulia Doi, Elisa Tomezzoli, Sara Raimondi, Ilaria Cutica, Davide Mazzoni, Inês Martins Alves, André Filipe Bruno de Oliveira Tomás dos Santos, Pier Luigi Lopalco, Valeria Gabellone, Nils Bardeck, Gibran Horemheb Rubio Quintanares, Giuseppina Tucci, Chiara Mommo, Iuri Fanti, Ana Abecasis, Rolf Kaiser, Francesca Incardona, Sara Gandini
The Pandemic EVIDENCE Collaboration 2025 International Conference

Effectiveness of the Lolli-methode in managing covid-19 clusters in schools: insights from the EuCARE project, Oral presentation by Dr. Giulia Doi

Giulia Doi, Federica Bellerba, Inês Martins Alves, André Filipe Bruno de Oliveira Tomás dos Santos, Pier Luigi Lopalco, Valeria Gabellone, Nils Bardeck, Gibran Horemheb Rubio Quintanares, Giuseppina Tucci, Chiara Mommo, Iuri Fanti, Ana Abecasis, Rolf Kaiser, Sara Gandini, Francesca Incardona 

The Pandemic EVIDENCE Collaboration 2025 International Conference

Trajectories and Predictors of Post-COVID-19 Condition Persistence: a prospective evaluation in the EuCARE Study, Andrea Santoro, Claudia Acampora, Maria Francesca Greco, V. Sala, Francesca Ceccherini-Silberstein, Iuri Fanti, Francesca Incardona, J. Andrade Pinto, Gibran Horemheb Rubio Quintanares, Cristina Toscano, Alessandro Cozzi-Lepri, Camilla Tincati, Giulia Marchetti on behalf of EuCARE Study Group

17th Italian Conference on AIDS and Antiviral Research (ICAR 2025)

Psychological outcomes and learning loss in students after the COVID-19 pandemic: findings from EuCARE’s SCHOOL studies, Francesca Incardona
Federica Bellerba, Giulia Doi, Inês Martins Alves, André Filipe Bruno de Oliveira Tomás dos Santos, Pier Luigi Lopalco, Valeria Gabellone, Nils Bardeck, Gibran Horemheb Rubio Quintanares, Giuseppina Tucci, Chiara Mommo, Iuri Fanti, Ana Abecasis, Rolf Kaiser, Sara Gandini, Francesca Incardona
17th Italian Conference on AIDS and Antiviral Research (ICAR 2025)

Reduction of post COVID-19 condition during the Omicron wave: results from the EuCARE POSTCOVID Study, Andrea Santoro
Francesca Bai, Alessandro Cozzi-Lepri, Pontus Hedberg, Andrea Santoro, Maria Francesca Greco, Matteo Sala, Julia Fonseca de Morais Caporali, Carolina Coimbra Marinho, Maria Mercedes Santoro, Francesca Ceccherini Silberstein, Dovile Juozapaite, Edita Strumiliene, André Almeida, Cristina Toscano, Jesus Arturo Ruiz Quinones, Chiara Mommo, Iuri Fanti, Francesca Incardona, Giulia Marchetti on behalf of the EuCARE Project
34th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID 2024) 

In-Hospital Mortality During Different SARS-CoV-2 Variant Waves in the EuCARE Multinational Cohort, Pontus Hedberg, Milosz Parczewski, Giulia Marchetti, Björn Jensen, Francis Drobniewski, Daniel Naumovas, Francesca Ceccherini-Silberstein, Gibran Horemheb Rubio Quintanares, Matilu Mwau, Cristina Toscano, Maurizio Zazzi, Alessandro Cozzi-Lepri, Anders Sönnerborg, Pontus Nauclér

Conference on Retroviruses and Opportunistic Infections- CROI 2024

Preliminary results of the Eucare school studies and SARS CoV 2 trends in Italy, Germany and Portugal and school opening during the Omicron variant,  Federica Bellerba, Nils Bardeck, Michael Böhm, Rolf Kaiser, Elisa Tomezzoli, Ana Abecasis, Oriana D’Ecclesiis, Francesca Incardona, Chiara Mommo, Iuri Fanti, Valeria Gabellone, Giulia Vaglio, Pierluigi Lopalco, Marta Pingarilho, Ines Martins Alves, Daniela Alves, Gibran Rubio Horemheb, Martin Pirkl, Sara Gandini 

21st European Meeting on HIV & Hepatitis 2023

Analysis of mutational history of multi-drug resistance with a mutagenetic tree model, Martin Pirkl et al. 

European Meeting on HIV & Hepatitis 2022 (Paris)

Declining incidence of HIV multidrug resistance in Europe, J. Dewandre, J. Vercauteren, A.-M. Vandamme, B. Rossetti, M. Fabbiani, F. Incardona, A. Abecasis, C. Devaux, R. Kaiser, A. Sönnerborg, M. Zazzi, The EuResist Network study group

18th European AIDS Conference (EACS),  2021

 

4-Class Resistance is rare in treatment experienced patients across Europe, M. Zazzi, A.M. Vandamme, B. Rossetti, M. Fabbiani, F. Incardona, K. Theys, A. Abecasis, C. Devaux, R. Kaiser, A. Sönnerborg, G. Pasculli, J. Vercauteren for the EuResist Network study group

CROI 2020

Prevalence and spatiotemporal dynamics of the HIV-1 circulating recombinant form 03_AB (CRF03_AB) in the former Soviet Union, Ozhmegova E, Lebedev A, Pasechnik O, Blokh A, Grezina L, Dementeva N, Sandyreva T, Kazennova E and Bobkova M, 

18th European meeting on HIV and hepatitis, 2020

Susceptibility to HIV – integrase inhibitors in HIV-1 sub subtype A6 isolates, Giannini A, Giammarino F, Antonova A, Ozhmegova E, Kaiser R, Dragoni F, Boccuto A, Vicenti I, Sönnerborg A, Bobkova M, Zazzi M, Saladini F, 

ICAR Conference, 2020,

Poster session “Best of Posters” 18th European Meeting on HIV & Hepatitis,2020

A changing of HIV-1 genetic diversity in Russia during the last two decades: increase of the recombinants prevalence, Antonova A, Kazennova E, Bobkova M, 18th European meeting on HIV and hepatitis, 2020

High throughput sequencing for in depth analysis of pre-treatment HIV-1 drug resistance in Sweden, Andersson E, Ambikan A, Brännström J, Aralaguppe S, Yilmaz A, Albert J, Neogi U, Sönnerborg A. 

6th Nordic HIV and Hepatitis Conference 2019

HTS methodology and the bioinformatic pipeline for A6 HIV-1 sub-sub.type. Anders Sonnerborg et al. 

6th Nordic HIV and Hepatitis Conference 2019

Current trends in HIV genetic diversity in Russia: increased prevalence of unique recombinant variants. Antonova A, Lebedev A, KaBob E.

17th European AIDS Conference – EACS  2019

Analysis of the local HIV-1 epidemic in Vologda Region, Russia: predominance of CRF03_AB and rapid expansion of URFs, Ozhmegova E, Lebedev A, Krylova T, Kirillova I, Dementeva N, Kazennova E, Bobkova M. 

17th European AIDS Conference – EACS  2019

HIV-1 A6 subtype: its challenging identification and Southern Russian molecular epidemiology. Rolf Kaiser et al. 

EACS 2019

Genotypic susceptibility score of NRTI-backbone predicts time to virological failure of InSTIs-based regimens. A. Borghetti, A. Ciccullo, F. Lombardi, G. Baldin, S. Belmonti, M. Prosperi, F. Incardona, E. Heger, V. Borghi, A. Sönnerborg, M. Zazzi, A. De Luca, S. Di Giambenedetto.

CROI 2019

Integrating EuResist database with integrase resistance data for optimized antiretroviral treatment (the INTEGRATE project), Maurizio Zazzi, Ana Abecasis, Marina Bobkova, Carole Devaux, Iuri Fanti, Francesca Incardona, Rolf Kaiser, Gaetano Marrone, Roger Paredes, Stefano Rusconi, Murat Sayan, Anders Sönnerborg and Andrea De Luca for the EuResist Network and the INTEGRATE study group.

EACS 2017

Predicting human-immunodeficiency virus rebound after therapy initiation/switch using genetic, laboratory, and clinical data ||

Mattia Prosperi, Alejandro Pironti, Francesca Incardona, Giuseppe Tradigo, Maurizio Zazzi – BCB ’16 Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics – 2016, Pages 611-615 

HIV superinfection does not contribute to transmitted drug resistance. (Poster) || Bartha I, M Assel, P Sloot, M Zazzi, C Torti, E Schülter, A de Luca, A Sönnerborg, AB. Abecasis, K Van Laethem, A Rosi, J Svärd, R Paredes, DAMC van de Vijver, A-M Vandamme and V Müller. 20th International HIV Dynamics and Evolution Meeting. 8-11 May 2013, Utrecht, The Netherlands.

Transmitted Drug-Resistance Associated Mutations (TDRAMs) in HIV-1 Protease are Correlated with a Faster Pre-Therapy Decline in CD4+ T-Cell Count. (Poster) – Albini L., BM. Cesana, K. Theys, M. Zazzi, C. Boucher, R. Paredes, A. Sonnerborg, AM. Geretti, A-M. Vandamme, C. Torti. 17th International Workshop on HIV Observational Databases. Cavtat, Croatia, 11-13 April 2013.

 

Clinical evaluation of Rega 8: An updated genotypic interpretation system that significantly predicts HIV-therapy response.(Poster) – 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 A-M, Van Laethem K. 11th European Meeting on HIV & Hepatitis – Treatment Strategies & Antiviral Drug Resistance. Rome, Italy, March 20-22, 2013. 

 

A large scale analysis of a subtype-dependent impact of K65R selection in HIV-1 patients treated with cART including TDF (Poster) – Theys K., J. Vercauteren, J. Snoeck,  Z. Grossman, B. Clotet, A. De Luca, R. Kaiser, A. Sonnerborg, C. Torti, J.-C. Schmit, M. Zazzi, R. Camacho, A.-M. Vandamme and A. Abecasis, in collaboration with the EuResist consortium. 10th European Meeting on HIV & Hepatitis – Treatment Strategies & Antiviral Drug Resistance. Barcelona, Spain. 28-30 March, 2012.

Bayesian Network Analysis of Mutational Pathways to Darunavir Resistance (Poster) – Beheydt G, Theys K, Clotet B, Schülter E, Schmit J-C, Sönnerborg A, Zazzi M, Van Laethem K, Camacho R, Vandamme AM. Nineteenth Conference on Retroviruses and Opportunistic Infections. March 5-8, 2012. Seattle. Link

Training and strategy for HIV drug resistance testing in Eastern Africa – Maurizio Zazzi, Genny Meini, Arthur Emary, Nigus Fikrie, Silvia Kadima, Ezekiel Marandu, Doreen Mloka, Sabina Mugusi, Stephen Mutuku, Washington Njogu, Amare Worku, Muhammad Bakari, Daniel Fekade, Ferdinand Mugusi, Matilu Mwau, Mario Toti, Francesca Incardona, Anders Sonnerborg. Sixth EDCTP Forum, 9-12 October 2011, Addis Ababa, Ethiopia

Impact of natural polymorphisms of HIV-1 reverse transcriptase on virologic response to a first line NNRTI-containing HAART – Santoro MM, Svicher V, Cozzi-Lepri A, Fabeni L, Bruzzone B, Mussini C, De Luca A, Andreoni M, Antinori A, Zazzi M, Perno CF, D’Arminio Monforte A, Ceccherini-Silberstein F for Icona Foundation 15th International Workshop on HIV Observational Databases, Praha, 24-26 March 2011

 

Consensus Statement version 1.0 – Vandekerckhove LPR, Wensing AMJ, Kaiser R, Brun-Vézinet F, Clotet B, De Luca A, Dressler S, Garcia F, Geretti AM, Klimkait T, Korn K, Masquelier B, Perno CF, Schapiro JM, Soriano V, Sönnerborg A, Vandamme AM, Verhofstede C, Walter H, Zazzi M and Boucher CAB on behalf of the European Consensus Group on clinical management of tropism testing. European guidelines on clinical management of HIV-1 tropism testing 9th European Workshop on HIV & Hepatitis – Treatment Strategies & Antiviral Drug Resistance, Cyprus. 23-25 March 2011

 

A system to query distributed heterogeneous viral databases – Beheydt G, Schülter E, Imbrechts S, Abecasis A, Codoñer FM, Paraskevis D, Sönnerborg A, Vandamme AM, Kjaer J. – 9th European Workshop on HIV & Hepatitis – Treatment Strategies & Antiviral Drug Resistance. 23-25 March 2011, Cyprus

HIV-1 gp120 substitutions and plasma maraviroc concentration: contribution to virological failure during maraviroc-based salvage therapy – Di Giambenedetto S, Santangelo R, Meini G, Fabbiani M, Prosperi M, Marchetti S, Fortuna S, Navarra P, Fadda G, Cauda R, Zazzi M, De Luca A 9th European Workshop on HIV & Hepatitis – Treatment Strategies & Antiviral Drug Resistance, Cyprus, 23-25 March 2011

 

A computational method for predicting first-line HIV antiretroviral therapy success  – Pironti A, Altmann A, Schulter E, Boch J, Balduin M, Reuter S, Zazzi M, van de Vijver D, Oette M, Kaiser R, Lengauer T 9th European Workshop on HIV & Hepatitis – Treatment Strategies & Antiviral Drug Resistance, Cyprus. 23-25 March 2011

Declining differences in treatment outcome among different patient categories in Europe, 1992-2010 (Abstract O29) (Oral) – Rosen-Zvi M1, Zazzi M2, Incardona F 3, Aaroni E1, Kaiser R 4, Lengauer T 5, Camacho R6, Clotet B 7, Vandamme AM8, Schmit JC9 , Sönnerborg A10 – for the EuResist Network 9th European Workshop on HIV & Hepatitis – Treatment Strategies & Antiviral Drug Resistance, Cyprus, 23-25 March 2011. Reviews in Antiviral Therapy & Infectious Diseases 2:32, 2011.

A prognostic model for estimating the time to virologic failure in HIV-1 infected patients undergoing a new combination antiretroviral therapy regimen – Prosperi MCF, Di Giambenedetto S, Fanti I, Meini G, Bruzzone B, Callegaro A, Penco G, Bagnarelli P, Micheli V, Paolini E, Di Biagio A, Ghisetti V, Di Pietro M, Zazzi M, De Luca A 9th European Workshop on HIV & Hepatitis – Treatment Strategies & Antiviral Drug Resistance, Cyprus, 23-25 March 2011

Consensus statement of the European guidelines on clinical management of HIV-1 tropism testing vs 1.0 – Vandekerckhove LPR, Wensing AMJ, Kaiser R, Brun-Vézinet F, Clotet B, De Luca A, Dressler S, Garcia F, Geretti AM, Klimkait T, Korn K, Masquelier B, Perno CF, Schapiro JM, Soriano V, Sönnerborg AM, Vandamme AM, Verhofstede C, Walter H , Zazzi M, Boucher CAB on behalf of the European Consensus Group on clinical management of tropism testing Tenth International Congress on Drug Therapy in HIV Infection. Glasgow, UK, 7-11 November 2010

The EuResist expert model for customised HAART optimisation: 2010 update and extension to newest compounds (Abstract 06) (Oral) – Pironti A, Sönnerborg A, Zazzi M, Kaiser R, Struck D, Clotet B, Vandamme AM, Incardona F, Lengauer T, Rosen-Zvi T, Prosperi M. Tenth International Congress on Drug Therapy in HIV Infection. Glasgow, UK, 7-11 November 2010

Learning ancestral polytrees for HIV-1 mutation pathways against protease inhibitor (Abstract 64) (Poster) – Nelfinavir Li G, Beheydt G, Bielza C, Larrañaga P, Camacho R, Grossman Z, Torti C, Zazzi M, Prosperi M, Kaiser R, Van Laethem K, De Maeyer M, Jansen M, Vandamme A-M. Ninth European Conference on Computational Biology, Ghent, Belgium, September 26-29, 2010

The genotypic susceptibility score of Rega v8.0.2 after treatment failure (Abstract 12) (Poster) – Beheydt G, Zazzi M, Carvalho AP, Diogo I, Ram D, Rudich H, Camacho R, Grossman Z. 16th International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology, Bethesda, USA, 29 August – 3 September 2010

Estimating the frequency of superinfection in a large European collaborative HIV database (Abstract FRAA0102) (Oral) -Bartha I, Assel M, Sloot P, Zazzi M, Torti C, Kaiser R, de Luca A, Sonnerborg A, Vandamme A, Paredes R, van de Vijver D, Müller V. XVIII International AIDS Conference, Vienna, Austria, July 18-23, 2010

Evaluation of virological response to cART in patients carrying non-B subtype matched for baseline genotype with B subtype – Franzetti M, Casazza G, Meini G, Callegaro AP, Corsi P, Maggiolo F, Boeri E, Paolucci S, Gianotti N, Francisci D, Orani A, Filice G, Carli T, Zazzi M, Balotta C. International HIV & Hepatitis Virus Drug Resistance Workshop and Curative Strategies, Dubrovnik, Croatia, June 8-12, 2010

Study of the Regimen-Specific HIV-1 Genotypic Susceptibility Score after Treatment Failure (Abstract 82) (Poster) – Beheydt G, Zazzi M, Carvalho AP, Diogo I, Ram D, Rudich H, Camacho R, Grossman Z, Van Laethem K, Vandamme A-M. International HIV & Hepatitis Virus Drug Resistance Workshop and Curative Strategies, Dubrovnik, Croatia, June 8-12, 2010. Antiviral Therapy 2010, Vol. 15, Suppl. 2: A99

Pairwise comparison of genotypic coreceptor tropism prediction between one reference center and 10 European laboratories – Sierra S, Balduin M, Zazzi M, Sönnerborg A, Geretti AM, Vandekerckhove L, Verhofstede C, Berg J, Puchhammer-Stöckl E, Simon B, Kessler H, Wolf E, Thielen A, Däumer M, Kaiser R. International HIV & Hepatitis Virus Drug Resistance Workshop and Curative Strategies, Dubrovnik, Croatia, June 8-12, 2010

Specific Genetic Signatures in V3 Base Can Modulate Co-receptor Usage in Vivo, the Interaction with Neutralizing Antibodies, and HIV-1 Cytopathic Effect – Svicher V, Alteri C, Artese A, Costa G, Mercurio F, D’Arrigo R, Alcaro S, Ceccherini F, Bagnarelli P, Antonelli G, Micheli V, Ghisetti V, Gennari W, Baldanti F, Callegaro AP, Bruzzone B, Fadda G, Re MC, De Luca A, Andreoni M, Antinori A, Zazzi M, Canducci F, Clementi M, Angarano G, Parisi S, Lazzarin A, Perno CF on behalf of OSCAR group. International HIV & Hepatitis Virus Drug Resistance Workshop and Curative Strategies, Dubrovnik, Croatia, June 8-12, 2010

The EuResist Expert Model for Customised HAART Optimisation: 2010 Update and Extension to Newest Compounds – Pironti A, Sonnerborg A, Zazzi M, Kaiser R, Struck D, Clotet B, Vandamme A-M, Incardona F, Lengauer T, Rosen-Zvi M, Prosperi M Tenth International Congress on Drug Therapy in HIV Infection. 7-11 November 2010 Glasgow, UK.

The genotypic susceptibility score of Rega v8.0.2 after treatment failure – Beheydt G, Zazzi M, Carvalho AP, Diogo I, Ram D, Rudich H, Camacho R, Grossman Z, Vandamme A-M, Van Laethem K. 16th International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology. 29 August – 03 September 2010, Bethesda, USA

Estimating the frequency of superinfection in a large European collaborative HIV database (Talk) – Bartha I, Assel M, Sloot P, Zazzi M, Torti C, Kaiser R, de Luca A, Sonnerborg A, Vandamme A, Paredes R, van de Vijver D, Müller V. XIII International AIDS Conference. Wien, July 18-23, 2010.

Study of the Regimen-Specific HIV-1 Genotypic Susceptibility Score after Treatment Failure (Talk) – Beheydt G, Zazzi M, Carvalho AP, Diogo I, Ram D, Rudich H, Camacho R, Grossman Z, Van Laethem K, Vandamme A-M. International HIV & Hepatitis Virus Drug Resistance Workshop and Curative Strategies. June 8-12, 2010. Dubrovnik, Croatia.

Rega 8: an improved genotypic interpretation system that significantly predicts HIV-therapy response for B and non-B subtypes (Talk) (Abstract 50) – Beheydt G, Vercauteren J, Libin P, Imbrechts S, Camacho R, Clotet B, De Luca A, Grossman Z, Kaiser R, Sonnerborg A, Torti C, Van Wijngaerden E, Zazzi M, Geretti AM, Vandamme AM, Prosperi M. 8th European HIV Drug Resistance Workshop. 17-19 March 2010. Sorrento, Italy. Reviews in Antiviral Therapy 2010, 1:48-49. Poster

Prediction of response to antiretroviral therapy by human experts and by the EuResist data-driven expert system (the EVE study). (Abstact 45) – Zazzi M, R Kaiser, A Sonnerborg, D Struck, A Altmann, M Prosperi, M Rosen-Zvi, A Petroczi, Y Peres, E Schulter, C Boucher, F Brun-Vezinet, P Harrigan, L Morris, M Obermeier, C Perno, P Phanuphak, D Pillay, R Shafer, A-M Vandamme, K Van Laethem, A Wensing, T Lengauer, F Incardona. 8th European HIV Drug Resistance Workshop. 17-19 March 2010. Sorrento, Italy. Reviews in Antiviral Therapy 2010, 1:43. Oral

Detection of drug resistance mutations (DRM) at low viral load in a European multicohort study (SEHERE) (Abstract and poster) – Prosperi M., Dunn D., Di Giambenedetto S., Zazzi M., Camacho R., Fanti I., Torti C., Sonnerborg A., Kaiser R., Codoñer F., Van Laethem K., Bansi L., Asboe D., van de Vijver D., De Luca A., for the Virolab, Euresist, Chain and Dynanets consortia. 8th European HIV Drug Resistance Workshop, Sorrento (Italy), 2010

New V3-genetic Signatures Modulate Co-receptor Usage in vivo and the Interaction with CCR5 N-terminus (Talk and poster) – Svicher V., Alteri C., Artese A., D’Arrigo R., Cammarota R., Alcaro S., Ceccherini F., Bagnarelli P., Antonelli G., Micheli V., Ghisetti V., Gennari W., Baldanti F., Callegaro A.P., Bruzzone B., Fadda G., Re M.C., De Luca A., Andreoni M., Antinori A., Zazzi M., Clementi M., Angarano G., Parisi S., Lazzarin A., Perno C.F. on behalf of OSCAR group. 8th European HIV Drug Resistance Workshop, Sorrento (Italy), 2010

Application of a probabilistic Optimization Method for Deriving Clinical Cutoffs for (Predicted) Durg Resistance Phenotypes (Poster) – Altmann A., Daumer M., Pironti A., Perner J., Buch J., Torti C., Prosperi M., Kaiser R., Lengauer T. 8th European HIV Drug Resistance Workshop, Sorrento (Italy), 2010

Untangling pathways to tipranavir resistance in patients infected with various HIV-1 subtypes (Abstract) – Theys K., Sangeda R.Z., Camacho R., Clotet B., Van Laethem K., Zazzi M., Sonnerborg 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.for the EHR, Virolab, EuResist and BREACH Projects 12th European AIDS Conference/EACS, Cologne (Germany), November 11-14, 2009, Abstract PE7.4/9

Semi-Supervised Learning for Improving Prediction of HIV Drug Resistance (Talk) – Perner J., Altmann A., Lengauer T. In: Lecture Notes in Informatics, Proceedings of the German Conference on Bioinformatics 2009 (2009) vol. P-157 pp. 55-65

Calendar trends in antiretroviral drug resistance in treatment-experienced patients in Europe (Abstract) – Di Giambenedetto S., Dunn D., Zazzi M., Fanti I., Camacho R., Manca N., Kaiser R., Sonnerborg A., Codoner F.M., Van Laethem K., Bansi L., Ghisetti V., van de Vijver D., Assel M., Prosperi M., De Luca A. on behalf of Virolab, EuResist, Chain 12th European AIDS Conference/EACS, Cologne (Germany), November 11-14, 2009, Abstract PE3.1/8.

Prediction Of Antiretroviral Therapy Outcomes In Poor Resource Countries: Comparison Between Genotype Resistance Testing Based vs. Treatment History Models (Talk, Abstract) – Prosperi M.C.F., Rosen-Zvi M., Altmann A., Aharoni E., Peres Y., Sönnerborg A., Incardona F., Struck D., Kaiser R., Zazzi M. for the EuResist study Group. 5th EDCTP Forum, Arusha (Tanzania), October 12-14, 2009, selected as oral presentation.

Comparing the prevalence of  tipranavir resistance mutations in naïve, PI experienced and tipranavir experienced patients. (Poster) (Abstract 24) – 15th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology, Rotterdam, The Netherlands, 7-11 September 2009.

Untangling Pathways to Tipranavir Resistance in HIV-1 Treatment Experienced Patients from Various Subtypes. (Poster) (Abstract 25) – Sangeda R, 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 SZ, Van Wijngaerden E, Verhofstede C, Rhee S-Y,  Vandamme A-M, for the EHR, Virolab, EuResist and BREACH projects. 15th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology, Rotterdam, The Netherlands, 7-11 September 2009.

Expanding the world’s largest HIV drug resistance database, EuResist, into an African context (Talk, Abstract) – Incardona F., Aris E., Janabi M., Swai A., Mugusi F., Bakari M., Nagu T., Mugusi S., Mloka D., Wondwossen A., Lindquist L., Sönnerborg A., Zazzi M., Kaiser R., Lengauer T., Prosperi M.C.F., Altmann A., Sandstrom E. 5th EDCTP Forum, Arusha (Tanzania), 2009

Do not blame the fitness! – Only slight impact of predicted replicative capacity for therapy response prediction (Abstract) – Altmann A., Weisser H., Incardona F., Sonnerborg A., Zazzi M., Kaiser R., Lengauer T., Walter H. 7th European HIV Drug Resistance workshop, Stockholm (Sweden), March 25-27, 2009, Abstract Presentation

Evaluation of longitudinal fitness landscapes in prediction of treatment outcome in a clinical dataset of HIV-1 treated patients (Abstract) – Sangeda R.Z., Deforche K., Vercauteren J., Libin P., Imbrechts S., Theys K., Grossman Z., Camacho R., Van Laethem K., Zazzi M., Sönnerborg A., Kaiser R., De Luca A., Torti C., Ruiz L., van de Vijver D., Shafer R.W., Van Wijngaerden E., Vandamme A.M. for the Virolab and EuResist projects 7th European HIV Drug Resistance workshop, Stockholm (Sweden), March 25-27, 2009, Abstract Presentation

Keeping models that predict response to antiretroviral therapy up-to-date: fusion of pure data-driven approaches with rules-based methods (Abstract)– Altmann A., Thielen A., Frentz D., Van Laethem K., Bracciale L., Incardorna F., Sönnerborg A., Zazzi M., Kaiser R., Lengauer T. 7th European HIV Drug Resistance workshop, Stockholm (Sweden), March 25-27, 2009, Abstract Presentation

Antiretroviral therapy optimisation without genotype resistance testing: a perspective on treatment history based models (Abstract and poster) – Prosperi M., Rosen_Zvi M., Altmann A., Aharoni E., Peres Y., Sonnerborg A., Incardona F., Struck D., Kaiser R., Zazzi M. 7th European HIV Drug Resistance workshop, Stockholm (Sweden), March 25-27, 2009, Abstract Presentation

Chasing the AIDS Virus – Computational Biology comes to the help of AIDS patients (Talk) – Lengauer T. Keynote at ISMB/ECCB 2009, Stockholm (Sweden), 2009

Chasing the AIDS Virus – Computational Biology comes to the help of AIDS patients (Talk) – Lengauer T. ETH, Zürich (Switzerland), 2009

Do not blame the fitness! – Only slight impact of predicted replicative capacity for therapy response prediction (Talk) – Altmann A. Arevir Meeting, Bonn (Germany), 2009

Predicting virological response using genotypic approaches for Tenofovir (Talk, Abstract) – Frentz D., Boucher C.A.B., Assel M., Bubak M., De Luca A., Incardona F., Libin P., Ruiz L., Sloot P., Torti C., Vandamme A.M., Zazzi M., Van de Vijver D.A.M.C. 7th European HIV Drug Resistance workshop, Stockholm (Sweden), 2009

Predicting virological response by different systems interpreting genotypic HIV-1 drug resistance in a large European cohort (Talk) – Frentz D., Van de Vijver D.A.M.C., Altmann A., Assel M., De Luca A., Libin P., Müller V., Nualláin B. Ó., Prosperi M., Ruiz L., Sloot P., Schülter E., Torti C., Vandamme A.M., Boucher C.A.B. 7th European HIV Drug Resistance workshop, Stockholm (Sweden), 2009

Chasing the AIDS Virus – Computational Biology comes to the help of AIDS patients (Talk) – Lengauer T. Symposium “Systems Biology and Translatiuonal Pneumology”, Mannheim (Germany), 2009

Chasing the AIDS Virus – Computational Biology comes to the help of AIDS patients (Talk) – Lengauer T. University of Leuven, Germany, 2009

Chasing the AIDS Virus – Computational Biology comes to the help of AIDS patients (Talk) – Lengauer T. Freiburg University, Germany, 2009

 

Chasing the AIDS Virus – Computational Biology comes to the help of AIDS patients (Talk) – Lengauer T. Konstanz University, Germany, 2009

Chasing the AIDS Virus – Computational Biology comes to the help of AIDS patients (Talk) – Lengauer T. Hamburg University, Germany, 2009

Multi-task learning for hiv therapy screening – Bickel, Bogojeska, Lengauer and Scheffer Proceedings of the 25th annual International Conference on Machine Learning (ICML 2008), p. 56-63.

Inferring Virological Response from Genotype: With or without predicted phenotypes? (Talk) – Altmann A. Virco, Mechelen (Belgium), 2008

Chasing the AIDS Virus – Computational Biology comes to the help of AIDS patients (Talk) – Lengauer T. Workshop on Machine Learning, NIPS 2008, Vancouver (Canada), 2008

Genotypic methods for predicting HIV tropism (Talk) – Lengauer T. Forth HIV Entry Workshop, Puerto Rico, 2008

Bioinformatics: RESINA, geno2pheno and EuResist (Talk) Altmann A. 2nd HIV Resistance workshop, Robert Koch Institute, Berlin (Germany), 2008

Chasing the AIDS Virus – Computational Biology comes to the help of AIDS patients (Talk) Lengauer T. Heidelberg University, Germany, 2008

Chasing the AIDS Virus – Computational Biology comes to the help of AIDS patients (Talk) Lengauer T. Annual Meeting of the German Society for Fighting Viral Disease (DVV), Cologne (Germany), 2008

Chasing the AIDS Virus – Computational Biology comes to the help of AIDS patients (Talk) Lengauer T. Helmholtz Gymnasium Bonn, Germany, 2008

Sustaining lamivudine/emtricitabine, abacavir, zidovudine or atazanavir from a previous treatment shows a clinical benefit (Abstract and poster) Rosen-Zvi M., Schuelter E., Altmann A., Sierra-Aragon S., Zazzi M., Sonnerborg A., Oette M., Lengauer T., Kaiser R. on behalf of the EuResist Group 17th International HIV Drug Resistance Workshop, Sitges (Spain), June 10-14, 2008, Abstract Presentation

Chasing the AIDS Virus – Computational Biology comes to the help of AIDS patients (Talk) Lengauer T. Annual Meeting, Max Planck Society, Dresden (Germany), 2008

A system that learns from clinical-genomic patients data and generate recommendations on best therapy – the AIDS disease as a case study (Talk)Rosen-Zvi et al. Yearly meeting of information systems in medicine, Israel, 2008

Jagt auf das Virus – Hilfe fuer AIDS Patienten aus dem Computer (transl: “Chasing the Virus – Help for HIV patients from the Computer”) (Invited lecture) Lengauer T., Altmann A. Max Planck annual meeting, Munchen (Germany), 2008

EuResist: an integrated system for management of antiretroviral drug resistance (Talk) Incardona F. Third AREVIR RKI Meeting, Bonn (Germany), 2008

EuResist presentation (Talk) Prosperi M. Third AREVIR RKI Meeting, Bonn (Germany), 2008

Guiding treatment selection: past present and future (Talk) Altmann A. Third AREVIR RKI Meeting, Bonn (Germany), 2008

EuResist project (Talk) Zazzi M. Second Baltic-Swedish HIV Meeting, Tallinn (Hestonia), 2008

Resistance tests (Talk) Kaiser R. Second Baltic-Swedish HIV Meeting, Tallinn (Hestonia), 2008

Bionformatics helps to make sense of resistance (Talk) Lengauer T. Second Baltic-Swedish HIV Meeting”, Tallinn (Hestonia), 2008

Basics of HIV drug resistance and resistance to novel drugs (Talk) Sonnerborg A. Second Baltic-Swedish HIV Meeting”, Tallinn (Hestonia), 2008

The EuResist approach for predicting response to anti HIV-1 therapy Altmann A., Rosen-Zvi M., Prosperi M., Aharoni E., Neuvirth H., Schülter E., Büch J., Peres Y., Incardona F., Sönnerborg A., Kaiser R., Zazzi M., Lengauer T. 6th European HIV Drug Resistance Workshop, 26 to 28 March 2008, Budapest (Hungary), 2008

Sustaining 3TC/FTC, ABC, AZT or ATV from a previous treatment shows a clinical benefit (Poster) Rosen-Zvi et al. XVII International HIV Drug Resistance Workshop, Sitges (Spain), 2008

EuResist presentation (Talk) Rosen-Zvi M. IBM Student Reception, “NIPS conference”, Canada, 2007

Connections between network structure and functionality (Talk) Bazso F. Simonyi-day lecture, Budapest (Hungary), 2007

Data-mining on graphs, with application to mutation data (Talk) Bazso F. Simonyi-day lecture, Budapest (Hungary), 2007

Standard based interoperability middleware helps fight AIDS (Talk) Rosen-Zvi M. HL7 UK Conference: “Making Interoperability Work”, London (UK), 2007

EuResist presentation (Talk) Rosen-Zvi M. Healthcare and Life Sciences Seminar 2007, IBM Haifa Research Lab, Israel, 2007

EuResist presentation (Talk) Zazzi M. First Workshop on Italian HIV Cohorts, Siena (Italy), 2007

EuResist: An integrated system for management of antiretroviral drug resistance (Talk and poster) Incardona F. The World of Health It Conference & Exhibition, Wien (Austria), 2007

Likelihood-based clustering of directed graphs (Talk) Nepusz T., Bazsó F. Proceedings of the IEEE 3rd International Symposium on Computational Intelligence and Intelligent Informatics (March, 28-30, 2007) 1-4244-1158-0/07/$25.00 © 2007 IEEE

Integration of Viral Genomics with Clinical Data to Predict Response to Anti-HIV Treatment (Talk) Aharoni E., Altmann A., Borgulya G., D’autilia R., Incardona F., Kaiser R., Kent C., Lengauer T., Neuvirth H., Peres Y, Petroczi A., Prosperi M., Rosen-Zvi M., Schulter E., Sing T., Sonnerborg A., Thompson R., Zazzi M. Conference Proceedings IST Africa 2007 – Maputo (Mozambique), May 9-11, 2007.

Analysis of Positional Interdependencies of Mutations in Reverse Transcriptase (Poster) Bazsó F., Borgulya G., Zalányi L., Nepusz T. 1st International Symposium on Genetic and Immune Correlates of HIV infection and vaccine-induced immunity, Hungary, 2007

EuResist presentation (Poster) Bazso F. NetSci International Workshop and Conference on Network Science, New York (USA), 2007

EuResist presentation (Talk) Bazso F. Saint Laszlo Hospital, Budapest (Hungary), 2007

EuResist presentation (Abstract and poster) Bazso F. Proceedings of the IEEE 3rd International Symposium on Computational Intelligence and Intelligent Informatics, Agadir (Morocco), 2007

Statistical Comparison of Machine Learning Techniques for Treatment Optimisation of Drug-Resistant HIV-1 Prosperi M., G. Ulivi G., Zazzi M. In: IEEE Computer-Based Medical Systems (June 20-22, 2007)

EuResist presentation (Talk) Lengauer T. 3rd Deutsch-Österreichische AIDS Kongress, 2007

EuResist presentation (Poster) Lengauer T. 16th International HIV Drug resistance workshop, Barbados, 2007

EuResist presentation (Talk) Lengauer T. Bioperspectives, Cologne (Germany), 2007

EuResist presentation (Talk) Lengauer T. AREVIR RKI Annual Meeting hosted by Caesar (Center of advanced European science and research), Bonn (Germany), 2007

Validation of geno2pheno and THEO on a large independent clinical dataset (Talk and Poster) Lengauer T. 5th European HIV Drug Resistance Workshop, Cascais (Portugal), 2007

Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance (Talk) Altmann A., Beerenwinkel N., Sing T., Savenkov I., D¨aumer M., Kaiser R., Rhee S., Fessel J., Shafer R. Statistik (German statistical conference) 2007

EuResist presentation (Talk) Lengauer T. MPG Workshop on System Biology, Berlin (Germany), 2007

EuResist presentation (Talk) Lengauer T. CMBI, Nijmegen (Netherlands), 2007

EuResist: European data – European interpretation systems (Talk) Rosen-Zvi M., Aharoni E., Altmann A., Kaiser R., Lengauer T., Neuvirth H., Prosperi M., Bazsó F., Incardona F., Zazzi M. AREVIR RKI Annual Meeting hosted by Caesar (Center of advanced European science and research), Bonn (Germany), 2007, Expanded Abstract in the European Journal of Medical Research

EuResist: Integrating and exchanging European HIV data (Talk) Peres Y., Bergroth T., Denholm-Price J., Incardona F., Kaiser R., Kent C., Prosperi M., Schuelter E., Sonnerborg A., Zazzi M. AREVIR RKI Annual Meeting hosted by Caesar (Center of advanced European science and research), Bonn (Germany), 2007, Expanded Abstract in the European Journal of Medical Research

Geno2pheno-THEO: predicting response to combination ART on a large independent dataset (Abstract) Altmann A., Däumer M., Sing T., Beerenwinkel N., Schülter E., Peres Y., Sonnerborg A., Zazzi M., Kaiser R., Lengauer T. AREVIR-GENAFOR Meeting, Bonn (Germany), April 19-20, 2007, Abstract Presentation.

Exploration of multiple modeling techniques for prediction of response to treatment (Abstract) Zazzi M., Aharoni E., Altmann A., Bazsó F., Bidgood P., Borgulya G., Denholm-Price J., Fielder M., Kaiser R., Kent C., Lengauer T., Nepusz T., Neuvirth H., Peres Y., Petroczi A., Prosperi M., Romano L., Rosen-Zvi M., Schuelter E., Sing T., Sonnerborg A., Thompson R., Ulivi G., Zalányi L., Incardona F., EuResist Study Group. 5th European HIV Drug Resistance Workshop, Cascais (Portugal), March 28-30, 2007, Abstract Presentation.

The Euresist: clinical genomic analysis of HIV treatments (Talk) Rosen-Zvi M. Dagstuhl seminar on Similarity based Clustering and its Applications in Medicine and Biology, Germany, 2007

EuResist presentation (Talk) Kaiser R. AREVIR RKI Annual Meeting hosted by Caesar (Center of advanced European science and research), Bonn (Germany), 2007

HIV resistance testing and prediction of new therapies (Talk) Sonnerborg A. Centre Infectious Diseases – West-Tallinn Central Hospital, Tallinn (Hestonia), 2007

EuResist presentation (Talk) Zazzi M. Swedish HIV cohort meeting, Sweden, 2007

EuResist presentation (Talk) Zazzi M. Annual Italian ARCA meeting, Italy, 2007

Detection of HIV minority variants, HIV-gag-mutations and resistance to antiretroviral drugs (Talks) Rolf K. 5th European HIV Drug Resistance Workshop. Cascais (Portugal), 2007

EuResist: exploration of multiple modelling techniques for prediction of response to treatment (Talk and poster) Zazzi M. 5th European HIV Drug Resistance Workshop. Cascais (Portugal), 2007

EuResist presentation (Talk) Incardona F. International Symposium on Biomedical Informatics in Europe, Barcelona Biomedical Research Park (PRBB), Barcelona (Spain), 2007

Modellazione delle dinamiche di resistenza selettiva dell’HIV ed ottimizzazione terapeutica (Talk) Incardona F. CNR-IASI, Rome (Italy), 2007

Consistent dimensionality reduction scheme and its application to clinical HIV data (Abstract) Rosen-Zvi M., Neuvirth H., Aharoni E., Zazzi M., Tishby N. NIPS 2006 workshop: Novel Applications of Dimensionality Reduction, Whistler (Canada), December 9, 2006, Abstract Presentation

Consistent dimensionality reduction scheme and its application to clinical HIV data (Talk) Rosen-Zvi M. Learning Club at the Hebrew University Jerusalem, Israel, 2006

The AREVIR-Project and EuResist; The contribution of mutations in the gag-region of HIV with respect to resistance (Talk) Kaiser R. University of Utrecht, Utrecht (Holand), 2006

EuResist presentation (Poster) Rosen-Zvi M. “Novel Applications of Dimensionality Reduction” workshop, The NIPS conference, Vancouver (Canada), 2006

Improved prediction of HIV resistance in-vitro by biochemical-driven models (Talk) Rosen-Zvi M. “New Problems and Methods in Computational Biology” workshop, The NIPS conference, Vancouver (Canada), 2006

CGL7 – The Seventh Layer of Clinical Genomics (Talk and Poster) Rosen-Zvi M. IBM Watson Institute Workshop on Personalized Medicine: The Role of Multimodal Medical Informatics, December 2006, Hawthorne (USA), 2006

MD-Towards the Development of Prognosis Prediction in HIV Patients: Statistical Analysis of a Merged European HIV Database (Poster) Petroczi A. St. George’s Research Day, St. George’s Hospital, Tooting, London (UK), 2006

EuResist presentation (Invited lecture) Sonnerborg A. Swedish Medical Association Annual meeting, Sweden, 2006

HIV-GRADE and geno2pheno interpretation system (Talk) Kaiser R. geno2pheno, RKI, Berlin (Germany), 2006

EuResist presentation (Talk) Sonnerborg A. EMEA assessors meeting, Uppsala (Sweden), 2006

Improved prediction of response to antiretroviral combination therapy using evolutionary models (Talk) Altmann A. IST 2006, November 22, Helsinki (Finland), 2006

Learning from HIV clinical-genomic data with a Generative-Discriminative approach (Talk) Rosen-Zvi M. (joint work with Aharoni E., Neuvirth-Telem H., Zazzi M., Tishby T.) IST 2006, November 22, Helsinki (Finland), 2006

Jensen-Shannon semi-supervised learning and its application to clinical HIV data (Talk) Rosen-Zvi M. Biomedical informatics for optimized treatment of infectious diseases, Helsinki (Finland), 2006

Challenges for optimization of treatment of infectious diseases (Talk) Zazzi M. Biomedical informatics for optimized treatment of infectious diseases, Helsinki (Finland), 2006

EuResist: Integration of viral genomics with clinical data to predict response to anti-HIV treatment (Talk) Rosen-Zvi M. Seminar “Oltre i Confini dell’Ospedale”, Bologna (Italy), 2006

EuResist presentation (Talk) Lengauer T. RWTH Aachen University, Aachen (Germany), 2006

EuResist presentation (Invited lecture) Sonnerborg A. Annual Clinical Sciences Lectures, Karolinska University Hospital, Stockholm (Sweden), 2006

EuResist presentation (Talk) Lengauer T. Bioinformatics Munich Workshop: From Genomes to Systems Biology, Munich (Germany), 2006

EuResist presentation (Talk) Lengauer T. Workshop on Innovative Technologies in the Preventive Health Sector, Enschede (Netherlands), 2006

EuResist presentation (Talk) Lengauer T. Workshop on Bioinformatics and Modeling in Biomedicine, Luxembourg, 2006 Use of resistance data in regulatory issues (Talk) Sonnerborg A. European Medicines Evaluation Agency (EMEA), London (UK), 2006 Studies of resistance guided therapy (Talk) Sonnerborg A.

EuResist presentation at the Swedish West Regional HIV meeting, Sweden, 2006 EuResist presentation (Talk) Lengauer T. Workshop Wissenschaft für jedermann, Deutsches Museum, Munich (Germany), 2006 Resistenz und Resensitivierung bei PIs (Talk) Kaiser R. Resistenzworkshop, Frankfurt a.M. (Germany), 2006

EuResist presentation (Talk) Altmann A. Workshop “Clinical relevance of HIV evolutionary pathways and the genetic barrier to drug resistance”, German society for medical computer science, biometrics and epidemiology, Leipzig (Germany), 2006

Salvage therapies from virologists point of view (Talk) Kaiser R. Der Haarte Alltag, Frankfurt a.M. (Germany), 2006

Bioinformatic analysis in HIV resistance (Talk) Sonnerborg A. EuResist presentation at the Division of Infectious Diseases, Karolinska University Hospital, Stockholm (Sweden), 2006

EuResist presentation (Talk) Lengauer T. Informatik überzeugt, Paderborn (Germany), 2006

EuResist presentation (Talk) Bazso F. HIV specialists of the Semmelweiss University, Budapest (Hungary), 2006

AIDS Forschung in Saarbrücken – Wie Bioinformatiker den Patienten helfen können (Talk) Nacht der Informatik, Saarbrücken (Germany), 2006

EuResist presentation (Talk and Poster) Incardona F. ICT for Bio conference, Brussels (Belgium), 2006

Resistance to new drugs (Talk) Kaiser R. Summary of the International Ressitance Meeting at the Post Sitges Meeting, Frankfurt a.M. (Germany), 2006

Statistical analysis of a merged European HIV database: towards the development of prognosis prediction in HIV patients (Talk) Petroczi A. EuResist presentation at the Kingston University Postgraduate Research Day, Kingston (UK), 2006

p7/p1 and p1/p6-gag cleavage site are associated with specific PR mutations and PI resistance profiles (Poster) Kaiser R. International HIV Resistance Meeting, Sitges (Spain), 2006

The EuResist Initiative: Integration of Viral Genomics with Clinical Data to Predict Response of HIV Patients to Treatment (Talk) Rosen-Zvi M. Machine Learning Seminar, IBM Haifa Lab Israel, Haifa (Israel), 2006

Biomedical Information Integration for Clinical Genomics (Talk) Rosen-Zvi M. Information Technology for Public Health Seminar, IBM Haifa Lab Israel, Haifa (Israel), 2006

HIV-Resistance testing in clinical practice (Talk) Kaiser R. Molekular Diagnostics Meeting, Graz (Germany), 2006

EuResist presentation (Talk and Poster) Lengauer T. CUBIC-CDFD, Cologne (Germany), 2006

Detection of Minor variants of HIV-Strains (Talk and Poster) Zazzi M., Kaiser R. 4th European Workshop on HIV Drug Resistance, Munich (Germany), 2006

Analyse von HIV-Minoritäten-Varianten (Talk) Kaiser R. Jahrestagung der Gesellschaft für Virologie, Munich (Germany), 2006

Resistenztestung in clinical setting (Talk) Kaiser R. EuResist presentation at the Chariteé Berlin, Insitut für Virologie, Berlin (Germany), 2006

EuResist presentation (Talk) Lengauer T. Workshop on Systems Biology, Berlin (Germany), 2006

Evolution of HIV-strains in different patients originating from a single source (Talk) Kaiser R. HIV Abseits der Standards, Zoologic Garden, Cologne (Germany), 2006