1. Simen BB, Braverman MS, Abbate I, Aerssens J, Bidet Y, Bouchez O, Gabriel C, Izopet J, Kessler HH, Stelzl E, Di Giallonardo F, Schlapbach R, Radonic A, Paredes R, Recordon-Pinson P, Sakwa J, St John EP, Schmitz-Agheguian GG, Metzner KJ, Däumer MP; 454 HIV Alphastudy Group. An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing. J Virol Methods. 2014 Apr 13;204C:31-37. doi: 10.1016/j.jviromet.2014.04.007. [Epub ahead of print] PubMed PMID: 24731928.
  1. Pou C, Codoñer FM, Thielen A, Bellido R, Pérez-Álvarez S, Cabrera C, Dalmau J, Curriu M, Lie Y, Noguera-Julian M, Puig J, Martínez-Picado J, Blanco J, Coakley E, Däumer M, Clotet B, Paredes R. HIV-1 tropism testing in subjects achieving undetectable HIV-1 RNA: diagnostic accuracy, viral evolution and compartmentalization. PLoS One. 2013 Aug 1;8(8):e67085. doi: 10.1371/journal.pone.0067085. Print 2013. PubMed PMID: 23936293; PubMed Central PMCID: PMC3731261.
  1. 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. PubMed PMID: 24304458.
  1. Dietz J, Schelhorn SE, Fitting D, Mihm U, Susser S, Welker MW, Füller C, Däumer M, Teuber G, Wedemeyer H, Berg T, Lengauer T, Zeuzem S, Herrmann E, Sarrazin C. Deep sequencing reveals mutagenic effects of ribavirin during monotherapy of HCV genotype 1-infected patients. J Virol. 2013 Mar 27. [Epub ahead of print] PubMed PMID: 23536652.
  1. Portsmouth S, Valluri SR, Däumer M, Thiele B, Valdez H, Lewis M, Craig C, Thielen A, James I, Demarest J, Heera J. Correlation between genotypic (V3 population sequencing) and phenotypic (Trofile ES) methods of characterizing co-receptor usage of HIV-1 from 200 treatment-naive HIV patients screened for Study A4001078. Antiviral Res. 2013 Jan;97(1):60-5. doi: 10.1016/j.antiviral.2012.11.002. Epub 2012 Nov 16. PubMed PMID: 23165088.
  1. Zagordi O, Däumer M, Beisel C, Beerenwinkel N. Read length versus depth of coverage for viral quasispecies reconstruction. PLoS One. 2012;7(10):e47046. doi: 10.1371/journal.pone.0047046. Epub 2012 Oct 3. PubMed PMID: 23056573; PubMed Central PMCID: PMC3463535.
  1. McGovern RA, Thielen A, Portsmouth S, Mo T, Dong W, Woods CK, Zhong X, Brumme CJ, Chapman D, Lewis M, James I, Heera J, Valdez H, Harrigan PR. Population-based sequencing of the V3-loop can predict the virological response to maraviroc in treatment-naive patients of the MERIT trial. J Acquir Immune Defic Syndr. 2012
  1. Swenson LC, Däumer M, Paredes R. Next-generation sequencing to assess HIV tropism. Curr Opin HIV AIDS. 2012 Sep;7(5):478-85. doi: 10.1097/COH.0b013e328356e9da. Review. PubMed PMID: 22832710.
  1. Ebert, C., Knauer, F., Spielberger, B., Thiele, B., Hohmann, U. (2012): Estimating wild boar (Sus scrofa L.) population size using faecal DNA and capture-recapture modelling. Wildlife Biology 18, 142-152.
  1. Ebert, C., Sandrini, J., Spielberger, B., Thiele, B., Hohmann, U. (2012): Non-invasive genetic approaches for estimation of ungulate population size: a study on roe deer (Capreolus capreolus) based on faeces. Animal Biodiversity and Conservation 35.2, 267-275.
  1. Kolodziej, K., Schulz, H.K., Theissinger, K., Ebert, C., Hohmann, U., Schulz, R. (2012): Comparison of established methods for quantifying genotyping error rates in wildlife forensics. Conservation Genetic Resources. DOI 10.1007/s12686-012-9729-z
  1. Thielen A, Lengauer T. Geno2pheno[454]: a Web server for the prediction of HIV-1 coreceptor usage from next-generation sequencing data. Intervirology. 2012;55(2):113-7. doi: 10.1159/000332002. Epub 2012 Jan 24. PubMed PMID: 22286879.
  1. Swenson LC, Mo T, Dong WW, Zhong X, Woods CK, Thielen A, Jensen MA, Knapp DJ, Chapman D, Portsmouth S, Lewis M, James I, Heera J, Valdez H, Harrigan PR. Deep V3 sequencing for HIV type 1 tropism in treatment-naive patients: a reanalysis of the MERIT trial of maraviroc. Clin Infect Dis. 2011 Oct;53(7):732-42. doi: 10.1093/cid/cir493. PubMed PMID: 21890778.
  1. 10: Codoñer FM, Pou C, Thielen A, García F, Delgado R, Dalmau D, Álvarez-Tejado M, Ruiz L, Clotet B, Paredes R. Added value of deep sequencing relative to population sequencing in heavily pre-treated HIV-1-infected subjects. PLoS One. 2011;6(5):e19461. doi: 10.1371/journal.pone.0019461. Epub 2011 May 13. PubMed PMID: 21602929; PubMed Central PMCID: PMC3094345.
  1. Heger E, Thielen A, Gilles R, Obermeier M, Lengauer T, Kaiser R, Trapp S. APOBEC3G/F as one possible driving force for co-receptor switch of the human immunodeficiency virus-1. Med Microbiol Immunol. 2012 Feb;201(1):7-16. doi: 10.1007/s00430-011-0199-9. Epub 2011 May 15. PubMed PMID: 21573951.
  1. Thielen A, Lengauer T, Swenson LC, Dong WW, McGovern RA, Lewis M, James I, Heera J, Valdez H, Harrigan PR. Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially. Antivir Ther. 2011;16(3):319-28. doi: 10.3851/IMP1769. PubMed PMID: 21555814.
  1. 14: Swenson LC, Mo T, Dong WW, Zhong X, Woods CK, Jensen MA, Thielen A, Chapman D, Lewis M, James I, Heera J, Valdez H, Harrigan PR. Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients. J Infect Dis. 2011 Jan 15;203(2):237-45. doi: 10.1093/infdis/jiq030. PubMed PMID: 21288824; PubMed Central PMCID: PMC3071057.
  1. Däumer M, Kaiser R, Klein R, Lengauer T, Thiele B, Thielen A. Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis. BMC Med Inform Decis Mak. 2011 May 13;11:30. doi: 10.1186/1472-6947-11-30. PubMed PMID: 21569501; PubMed Central PMCID: PMC3112379.
  1. Holcomb CL, Höglund B, Anderson MW, Blake LA, Böhme I, Egholm M, Ferriola D, Gabriel C, Gelber SE, Goodridge D, Hawbecker S, Klein R, Ladner M, Lind C, Monos D, Pando MJ, Pröll J, Sayer DC, Schmitz-Agheguian G, Simen BB, Thiele B, Trachtenberg EA, Tyan DB, Wassmuth R, White S, Erlich HA. A multi-site study using high-resolution HLA genotyping by next generation sequencing. Tissue Antigens. 2011 Mar;77(3):206-17. doi: 10.1111/j.1399-0039.2010.01606.x.
  1. Ebert, C., Marell, R.-R., Rahlfs, M., Spielberger, B., Hohmann, U., Thiele, B.: Estimating red deer (Cervus elaphus) population size by genotyping faeces: a non-invasive approach. Oral presentation at the XXXth Congress of the International Union of Game Biologists (IUGB) 5th – 9th September 2011 in Barcelona. Abstract book p. 96. (Eds.: Puigcerver, M., Teijeiro, J., Buner, F.)
  1. Hohmann, U., Ebert, C., Huckschlag, D., Marell, R.-R., Rahlfs, M., Spielberger, B., Thiele, B.: Calibrating harvest rates. Ungulate management of a harvested wild boar and red deer population by using non-invasive population estimates in Germany. Oral presentation at the XXXth Congress of the International Union of Game Biologists (IUGB) 5th – 9th September 2011 in Barcelona. Abstract book p. 99. (Eds.: Puigcerver, M., Teijeiro, J., Buner, F.)
  1. Ebert, C., Knauer, F., Spielberger, C., Thiele, B., Hohmann, U.: Estimating wild boar (Sus scrofa ) population size using faecal DNA and capture-recapture modelling – recent developments. Oral presentation at the 9th International Symposium on Wild Boar and other Suids, 2nd – 6th September 2012. Abstract book p. 30
  1. Sester M, Giehl C, McNerney R, Kampmann B, Walzl G, Cuch P, Wingfield C, Lange C, Migliori GB, Kritski AL, Meyerhans A; European Network for global cooperation in the field of AIDS and TB (EUCO-Net). Challenges and perspectives for improved management of HIV/Mycobacterium tuberculosis co-infection. Eur Respir J. 2010 Dec;36(6):1242-7. doi: 10.1183/09031936.00040910. PubMed PMID: 21119204.
  1. Knoepfel SA, Di Giallonardo F, Däumer M, Thielen A, Metzner KJ. In-depth analysis of G-to-A hypermutation rate in HIV-1 env DNA induced by endogenous APOBEC3 proteins using massively parallel sequencing. J Virol Methods. 2011 Feb;171(2):329-38. doi: 10.1016/j.jviromet.2010.11.016. Epub 2010 Nov 24. PubMed PMID: 21111003.
  1. Zagordi O, Klein R, Däumer M, Beerenwinkel N. Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Res. 2010 Nov;38(21):7400-9. doi: 10.1093/nar/gkq655. Epub 2010 Jul 29. PubMed PMID: 20671025; PubMed Central PMCID: PMC2995073.
  1. Codoñer FM, Pou C, Thielen A, García F, Delgado R, Dalmau D, Santos JR, Buzón MJ, Martínez-Picado J, Alvarez-Tejado M, Clotet B, Ruiz L, Paredes R. Dynamic escape of pre-existing raltegravir-resistant HIV-1 from raltegravir selection pressure. Antiviral Res. 2010 Dec;88(3):281-6. doi: 10.1016/j.antiviral.2010.09.016. Epub 2010 Sep 29. PubMed PMID: 20883724.
  1. Däumer M, Awerkiew S, Aragón SS, Kartashev V, Poplavskaja T, Klein R, Sichtig N, Thiele B, Lengauer T, Roomp K, Pfister H, Kaiser R. Selection of thymidine analogue resistance mutational patterns in children infected from a common HIV type 1 subtype G source. AIDS Res Hum Retroviruses. 2010 Mar;26(3):275-8. doi: 10.1089/aid.2009.0233.
  1. McGovern RA, Thielen A, Mo T, Dong W, Woods CK, Chapman D, Lewis M, James I, Heera J, Valdez H, Harrigan PR. Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies. AIDS. 2010 Oct 23;24(16):2517-25. doi: 10.1097/QAD.0b013e32833e6cfb. PubMed PMID: 20736814.
  1. Kamp C, Wolf T, Bravo IG, Kraus B, Krause B, Neumann B, Winskowsky G, Thielen A, Werner A, Schnierle BS. Decreased HIV diversity after allogeneic stem cell transplantation of an HIV-1 infected patient: a case report. Virol J. 2010 Mar 8;7:55. doi: 10.1186/1743-422X-7-55. PubMed PMID: 20210988; PubMed Central PMCID: PMC2845567
  1. Swenson LC, Moores A, Low AJ, Thielen A, Dong W, Woods C, Jensen MA, Wynhoven B, Chan D, Glascock C, Harrigan PR. Improved detection of CXCR4-using HIV by V3 genotyping: application of population-based and “deep” sequencing to plasma RNA and proviral DNA. J Acquir Immune Defic Syndr. 2010 Aug;54(5):506-10. doi: 10.1097/QAI.0b013e3181d0558f. PubMed PMID: 20512044.
  1. Bader J, Däumer M, Schöni-Affolter F, Böni J, Gorgievski-Hrisoho M, Martinetti G, Thielen A, Klimkait T; Swiss HIV Cohort Study. Therapeutic Immune Recovery and Reduction of CXCR4-Tropic HIV-1. Clin Infect Dis. 2017 Feb 1;64(3):295-300. doi: 10.1093/cid/ciw737. Epub 2016 Nov 12. PMID: 27838645
  1. Mulato A, Hansen D, Thielen A, Porter D, Stepan G, White K, Däumer M, Cihlar T, Yant SR. Rapid In Vitro Evaluation of Antiretroviral Barrier to Resistance at Therapeutic Drug Levels. AIDS Res Hum Retroviruses. 2016 Dec;32(12):1237-1247. Epub 2016 Jul 25. PMID: 27356854
  1. Major T, Gindele R, Szabó Z, Alef T, Thiele B, Bora L, Kis Z, Bárdossy P, Rácz T, Havacs I, Bereczky Z. Evidence for the founder effect of a novel ACVRL1 splice-site mutation in Hungarian hereditary hemorrhagic telangiectasia families. Clin Genet. 2016 Nov;90(5):466-467. doi: 10.1111/cge.12806. Epub 2016 Jun 12. No abstract available. PMID: 27291782
  1. Hofstra LM, Sauvageot N, Albert J, Alexiev I, Garcia F, Struck D, Van de Vijver DAMC, Åsjö B, Beshkov D, Coughlan S, Descamps D, Griskevicius A, Hamouda O, Horban A, Van Kasteren M, Kolupajeva T, Kostrikis LG, Liitsola K, Linka M, Mor O, Nielsen C, Otelea D, Paraskevis D, Paredes R, Poljak M, Puchhammer-Stöckl E, Sönnerborg A, Staneková D, Stanojevic M, Van Laethem K, Zazzi M, Zidovec Lepej S, Boucher CAB, Schmit JC, Wensing AMJ; SPREAD Program., Puchhammer-Stockl E, Sarcletti M, Schmied B, Geit M, Balluch G, Vandamme AM, Vercauteren J, Derdelinckx I, Sasse A, Bogaert M, Ceunen H, De Roo A, De Wit S, Echahidi F, Fransen K, Goffard JC, Goubau P, Goudeseune E, Yombi JC, Lacor P, Liesnard C, Moutschen M, Pierard D, Rens R, Schrooten Y, Vaira D, Vandekerckhove LPR, Van den Heuvel A, Van Der Gucht B, Van Ranst M, Van Wijngaerden E, Vandercam B, Vekemans M, Verhofstede C, Clumeck N, Van Laethem K, Beshkov D, Alexiev I, Lepej SZ, Begovac J, Kostrikis L, Demetriades I, Kousiappa I, Demetriou V, Hezka J, Linka M, Maly M, Machala L, Nielsen C, Jørgensen LB, Gerstoft J, Mathiesen L, Pedersen C, Nielsen H, Laursen A, Kvinesdal B, Liitsola K, Ristola M, Suni J, Sutinen J, Descamps D, Assoumou L, Castor G, Grude M, Flandre P, Storto A, Hamouda O, Kücherer C, Berg T, Braun P, Poggensee G, Däumer M, Eberle J, Heiken H, Kaiser R, Knechten H, Korn K, Müller H, Neifer S, Schmidt B, Walter H, Gunsenheimer-Bartmeyer B, Harrer T, Paraskevis D, Hatzakis A, Zavitsanou A, Vassilakis A, Lazanas M, Chini M, Lioni A, Sakka V, Kourkounti S, Paparizos V, Antoniadou A, Papadopoulos A, Poulakou G, Katsarolis I, Protopapas K, Chryssos G, Drimis S, Gargalianos P, Xylomenos G, Lourida G, Psichogiou M, Daikos GL, Sipsas NV, Kontos A, Gamaletsou MN, Koratzanis G, Sambatakou H, Mariolis H, Skoutelis A, Papastamopoulos V, Georgiou O, Panagopoulos P, Maltezos E, Coughlan S, De Gascun C, Byrne C, Duffy M, Bergin C, Reidy D, Farrell G, Lambert J, O’Connor E, Rochford A, Low J, Coakely P, O’Dea S, Hall W, Mor O, Levi I, Chemtob D, Grossman Z, Zazzi M, de Luca A, Balotta C, Riva C, Mussini C, Caramma I, Capetti A, Colombo MC, Rossi C, Prati F, Tramuto F, Vitale F, Ciccozzi M, Angarano G, Rezza G, Kolupajeva T, Vasins O, Griskevicius A, Lipnickiene V, Schmit JC, Struck D, Sauvageot N, Hemmer R, Arendt V, Michaux C, Staub T, Sequin-Devaux C, Wensing AMJ, Boucher CAB, van de Vijver DAMC, van Kessel A, van Bentum PHM, Brinkman K, Connell BJ, van der Ende ME, Hoepelman IM, van Kasteren M, Kuipers M, Langebeek N, Richter C, Santegoets RMWJ, Schrijnders-Gudde L, Schuurman R, van de Ven BJM, Åsjö B, Kran AB, Ormaasen V, Aavitsland P, Horban A, Stanczak JJ, Stanczak GP, Firlag-Burkacka E, Wiercinska-Drapalo A, Jablonowska E, Maolepsza E, Leszczyszyn-Pynka M, Szata W, Camacho R, Palma C, Borges F, Paixão T, Duque V, Araújo F, Otelea D, Paraschiv S, Tudor AM, Cernat R, Chiriac C, Dumitrescu F, Prisecariu LJ, Stanojevic M, Jevtovic D, Salemovic D, Stanekova D, Habekova M, Chabadová Z, Drobkova T, Bukovinova P, Shunnar A, Truska P, Poljak M, Lunar M, Babic D, Tomazic J, Vidmar L, Vovko T, Karner P, Garcia F, Paredes R, Monge S, Moreno S, Del Amo J, Asensi V, Sirvent JL, de Mendoza C, Delgado R, Gutiérrez F, Berenguer J, Garcia-Bujalance S, Stella N, de Los Santos I, Blanco JR, Dalmau D, Rivero M, Segura F, Elías MJP, Alvarez M, Chueca N, Rodríguez-Martín C, Vidal C, Palomares JC, Viciana I, Viciana P, Cordoba J, Aguilera A, Domingo P, Galindo MJ, Miralles C, Del Pozo MA, Ribera E, Iribarren JA, Ruiz L, de la Torre J, Vidal F, Clotet B, Albert J, Heidarian A, Aperia-Peipke K, Axelsson M, Mild M, Karlsson A, Sönnerborg A, Thalme A, Navér L, Bratt G, Karlsson A, Blaxhult A, Gisslén M, Svennerholm B, Bergbrant I, Björkman P, Säll C, Mellgren Å, Lindholm A, Kuylenstierna N, Montelius R, Azimi F, Johansson B, Carlsson M, Johansson E, Ljungberg B, Ekvall H, Strand A, Mäkitalo S, Öberg S, Holmblad P, Höfer M, Holmberg H, Josefson P, Ryding U. Transmission of HIV Drug Resistance and the Predicted Effect on Current First-line Regimens in Europe. Clin Infect Dis. 2016 Mar 1;62(5):655-663. doi: 10.1093/cid/civ963. Epub 2015 Nov 29. PMID: 26620652
  2. Noguera-Julian M, Cozzi-Lepri A, Di Giallonardo F, Schuurman R, Däumer M, Aitken S, Ceccherini-Silberstein F, D’Arminio Monforte A, Geretti AM, Booth CL, Kaiser R, Michalik C, Jansen K, Masquelier B, Bellecave P, Kouyos RD, Castro E, Furrer H, Schultze A, Günthard HF, Brun-Vezinet F, Metzner KJ, Paredes R; CHAIN Minority HIV-1 Variants Working group.
    Contribution of APOBEC3G/F activity to the development of low-abundance drug-resistant human immunodeficiency virus type 1 variants.
    Clin Microbiol Infect. 2016 Feb;22(2):191-200. doi: 10.1016/j.cmi.2015.10.004. Epub 2015 Oct 23. PMID: 26482266
  1. St John EP, Simen BB, Turenchalk GS, Braverman MS, Abbate I, Aerssens J, Bouchez O, Gabriel C, Izopet J, Meixenberger K, Di Giallonardo F, Schlapbach R, Paredes R, Sakwa J, Schmitz-Agheguian GG, Thielen A, Victor M, Metzner KJ, Däumer MP; 454 HIV-1 Alpha Study Group. A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing. PLoS One. 2016 Jan 12;11(1):e0146687. doi: 10.1371/journal.pone.0146687. eCollection 2016. PMID: 26756901
  1. Porter DP, Daeumer M, Thielen A, Chang S, Martin R, Cohen C, Miller MD, White KL. Emergent HIV-1 Drug Resistance Mutations Were Not Present at Low-Frequency at Baseline in Non-Nucleoside Reverse Transcriptase Inhibitor-Treated Subjects in the STaR Study. Viruses. 2015 Dec 7;7(12):6360-70. doi: 10.3390/v7122943. PMID: 26690199