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Getting more from heterogeneous HIV-1 surveillance data in a high immigration country: estimation of incidence and undiagnosed population size using multiple biomarkers.

Giardina F, Romero-Severson EO, Axelsson M, Svedhem V, Leitner T, Britton T, Albert J.

Int J Epidemiol. 2019 Dec 1;48(6):1795-1803. doi: 10.1093/ije/dyz100.


Phylogenetics in HIV transmission: taking within-host diversity into account.

Leitner T.

Curr Opin HIV AIDS. 2019 May;14(3):181-187. doi: 10.1097/COH.0000000000000536.


Accidental Father-to-Son HIV-1 Transmission During the Seroconversion Period.

Ezeonwumelu I, Bártolo I, Martin F, Abecasis A, Campos T, Romero-Severson EO, Leitner T, Taveira N.

AIDS Res Hum Retroviruses. 2018 Oct;34(10):857-862. doi: 10.1089/AID.2018.0060. Epub 2018 Sep 20.


Time-resolved electron spectroscopy for chemical analysis of photodissociation: Photoelectron spectra of Fe(CO)5, Fe(CO)4, and Fe(CO)3.

Leitner T, Josefsson I, Mazza T, Miedema PS, Schröder H, Beye M, Kunnus K, Schreck S, Düsterer S, Föhlisch A, Meyer M, Odelius M, Wernet P.

J Chem Phys. 2018 Jul 28;149(4):044307. doi: 10.1063/1.5035149.


Phylogenetic patterns recover known HIV epidemiological relationships and reveal common transmission of multiple variants.

Leitner T, Romero-Severson E.

Nat Microbiol. 2018 Sep;3(9):983-988. doi: 10.1038/s41564-018-0204-9. Epub 2018 Jul 30.


The Puzzle of HIV Neutral and Selective Evolution.

Leitner T.

Mol Biol Evol. 2018 Jun 1;35(6):1355-1358. doi: 10.1093/molbev/msy089.


Maltose formation in wheat dough depending on mechanical starch modification and dough hydration.

Hackenberg S, Leitner T, Jekle M, Becker T.

Carbohydr Polym. 2018 Apr 1;185:153-158. doi: 10.1016/j.carbpol.2017.12.064. Epub 2017 Dec 27.


Impact of the HIV-1 genetic background and HIV-1 population size on the evolution of raltegravir resistance.

Fun A, Leitner T, Vandekerckhove L, Däumer M, Thielen A, Buchholz B, Hoepelman AIM, Gisolf EH, Schipper PJ, Wensing AMJ, Nijhuis M.

Retrovirology. 2018 Jan 5;15(1):1. doi: 10.1186/s12977-017-0384-z.


CRISPR/Cas9 delivery with one single adenoviral vector devoid of all viral genes.

Ehrke-Schulz E, Schiwon M, Leitner T, Dávid S, Bergmann T, Liu J, Ehrhardt A.

Sci Rep. 2017 Dec 7;7(1):17113. doi: 10.1038/s41598-017-17180-w.


Partially Reversible Photoinduced Chemical Changes in a Mixed-Ion Perovskite Material for Solar Cells.

Cappel UB, Svanström S, Lanzilotto V, Johansson FOL, Aitola K, Philippe B, Giangrisostomi E, Ovsyannikov R, Leitner T, Föhlisch A, Svensson S, Mårtensson N, Boschloo G, Lindblad A, Rensmo H.

ACS Appl Mater Interfaces. 2017 Oct 11;9(40):34970-34978. doi: 10.1021/acsami.7b10643. Epub 2017 Sep 29.


Donor-Recipient Identification in Para- and Poly-phyletic Trees Under Alternative HIV-1 Transmission Hypotheses Using Approximate Bayesian Computation.

Romero-Severson EO, Bulla I, Hengartner N, Bártolo I, Abecasis A, Azevedo-Pereira JM, Taveira N, Leitner T.

Genetics. 2017 Nov;207(3):1089-1101. doi: 10.1534/genetics.117.300284. Epub 2017 Sep 14.


Communication: Direct evidence for sequential dissociation of gas-phase Fe(CO)5 via a singlet pathway upon excitation at 266 nm.

Wernet P, Leitner T, Josefsson I, Mazza T, Miedema PS, Schröder H, Beye M, Kunnus K, Schreck S, Radcliffe P, Düsterer S, Meyer M, Odelius M, Föhlisch A.

J Chem Phys. 2017 Jun 7;146(21):211103. doi: 10.1063/1.4984774.


The effect of severe grain refinement on the damage tolerance of a superelastic NiTi shape memory alloy.

Leitner T, Sabirov I, Pippan R, Hohenwarter A.

J Mech Behav Biomed Mater. 2017 Jul;71:337-348. doi: 10.1016/j.jmbbm.2017.03.020. Epub 2017 Mar 27.


Phylodynamic Inference across Epidemic Scales.

Volz EM, Romero-Severson E, Leitner T.

Mol Biol Evol. 2017 May 1;34(5):1276-1288. doi: 10.1093/molbev/msx077.


Inference of Transmission Network Structure from HIV Phylogenetic Trees.

Giardina F, Romero-Severson EO, Albert J, Britton T, Leitner T.

PLoS Comput Biol. 2017 Jan 13;13(1):e1005316. doi: 10.1371/journal.pcbi.1005316. eCollection 2017 Jan.


Primate immunodeficiency virus classification and nomenclature: Review.

Foley BT, Leitner T, Paraskevis D, Peeters M.

Infect Genet Evol. 2016 Dec;46:150-158. doi: 10.1016/j.meegid.2016.10.018. Epub 2016 Oct 24. Review.


On the contribution of Angola to the initial spread of HIV-1.

Pineda-Peña AC, Varanda J, Sousa JD, Theys K, Bártolo I, Leitner T, Taveira N, Vandamme AM, Abecasis AB.

Infect Genet Evol. 2016 Dec;46:219-222. doi: 10.1016/j.meegid.2016.08.009. Epub 2016 Aug 10.


Electronic structure dynamics in a low bandgap polymer studied by time-resolved photoelectron spectroscopy.

Cappel UB, Plogmaker S, Terschlüsen JA, Leitner T, Johansson EM, Edvinsson T, Sandell A, Karis O, Siegbahn H, Svensson S, Mårtensson N, Rensmo H, Söderström J.

Phys Chem Chem Phys. 2016 Aug 3;18(31):21921-9. doi: 10.1039/c6cp04136a.


Rare HIV-1 Subtype J Genomes and a New H/U/CRF02_AG Recombinant Genome Suggests an Ancient Origin of HIV-1 in Angola.

Bártolo I, Calado R, Borrego P, Leitner T, Taveira N.

AIDS Res Hum Retroviruses. 2016 Aug;32(8):822-8. doi: 10.1089/AID.2016.0084. Epub 2016 Jun 1.


Phylogenetically resolving epidemiologic linkage.

Romero-Severson EO, Bulla I, Leitner T.

Proc Natl Acad Sci U S A. 2016 Mar 8;113(10):2690-5. doi: 10.1073/pnas.1522930113. Epub 2016 Feb 22.


Cloning and Large-Scale Production of High-Capacity Adenoviral Vectors Based on the Human Adenovirus Type 5.

Ehrke-Schulz E, Zhang W, Schiwon M, Bergmann T, Solanki M, Liu J, Boehme P, Leitner T, Ehrhardt A.

J Vis Exp. 2016 Jan 28;(107):e52894. doi: 10.3791/52894.


Recombination Enhances HIV-1 Envelope Diversity by Facilitating the Survival of Latent Genomic Fragments in the Plasma Virus Population.

Immonen TT, Conway JM, Romero-Severson EO, Perelson AS, Leitner T.

PLoS Comput Biol. 2015 Dec 22;11(12):e1004625. doi: 10.1371/journal.pcbi.1004625. eCollection 2015 Dec.


Recombination elevates the effective evolutionary rate and facilitates the establishment of HIV-1 infection in infants after mother-to-child transmission.

Sanborn KB, Somasundaran M, Luzuriaga K, Leitner T.

Retrovirology. 2015 Nov 16;12:96. doi: 10.1186/s12977-015-0222-0.


Trends of HIV-1 incidence with credible intervals in Sweden 2002-09 reconstructed using a dynamic model of within-patient IgG growth.

Romero-Severson EO, Lee Petrie C, Ionides E, Albert J, Leitner T.

Int J Epidemiol. 2015 Jun;44(3):998-1006. doi: 10.1093/ije/dyv034. Epub 2015 Jul 10.


Dynamic Variation in Sexual Contact Rates in a Cohort of HIV-Negative Gay Men.

Romero-Severson EO, Volz E, Koopman JS, Leitner T, Ionides EL.

Am J Epidemiol. 2015 Aug 1;182(3):255-62. doi: 10.1093/aje/kwv044. Epub 2015 May 20.


PrimerDesign-M: a multiple-alignment based multiple-primer design tool for walking across variable genomes.

Yoon H, Leitner T.

Bioinformatics. 2015 May 1;31(9):1472-4. doi: 10.1093/bioinformatics/btu832. Epub 2014 Dec 17.


Reduced evolutionary rates in HIV-1 reveal extensive latency periods among replicating lineages.

Immonen TT, Leitner T.

Retrovirology. 2014 Oct 16;11:81. doi: 10.1186/s12977-014-0081-0.


A-D-A-type S,N-heteropentacenes: next-generation molecular donor materials for efficient vacuum-processed organic solar cells.

Mishra A, Popovic D, Vogt A, Kast H, Leitner T, Walzer K, Pfeiffer M, Mena-Osteritz E, Bäuerle P.

Adv Mater. 2014 Nov 12;26(42):7217-23. doi: 10.1002/adma.201402448. Epub 2014 Sep 22.


Timing and order of transmission events is not directly reflected in a pathogen phylogeny.

Romero-Severson E, Skar H, Bulla I, Albert J, Leitner T.

Mol Biol Evol. 2014 Sep;31(9):2472-82. doi: 10.1093/molbev/msu179. Epub 2014 May 29.


Single bunch X-ray pulses on demand from a multi-bunch synchrotron radiation source.

Holldack K, Ovsyannikov R, Kuske P, Müller R, Schälicke A, Scheer M, Gorgoi M, Kühn D, Leitner T, Svensson S, Mårtensson N, Föhlisch A.

Nat Commun. 2014 May 30;5:4010. doi: 10.1038/ncomms5010.


Short communication: HIV-1 Nef protein carries multiple epitopes suitable for induction of cellular immunity for an HIV vaccine in Africa.

Kilpeläinen A, Axelsson Robertson R, Leitner T, Sandström E, Maeurer M, Wahren B.

AIDS Res Hum Retroviruses. 2014 Nov;30(11):1065-71. doi: 10.1089/AID.2013.0299. Epub 2014 Jul 16.


Forensic informativity of ~3000 bp of coding sequence of domestic dog mtDNA.

Angleby H, Oskarsson M, Pang J, Zhang YP, Leitner T, Braham C, Arvestad L, Lundeberg J, Webb KM, Savolainen P.

J Forensic Sci. 2014 Jul;59(4):898-908. doi: 10.1111/1556-4029.12504. Epub 2014 May 11.


Neutralization of HIV subtypes A and D by breast milk IgG from women with HIV infection in Uganda.

Palaia JM, McConnell M, Achenbach JE, Gustafson CE, Stoermer KA, Nolan M, Guay LA, Leitner TK, Matovu F, Taylor AW, Fowler MG, Janoff EN.

J Infect. 2014 Mar;68(3):264-72. doi: 10.1016/j.jinf.2013.11.002. Epub 2013 Nov 13.


Monochromatizing and focussing femtosecond high-order harmonic radiation with one optical element.

Ibek M, Leitner T, Erko A, Firsov A, Wernet P.

Rev Sci Instrum. 2013 Oct;84(10):103102. doi: 10.1063/1.4822114.


Evolution of the human immunodeficiency virus type 2 envelope in the first years of infection is associated with the dynamics of the neutralizing antibody response.

Rocha C, Calado R, Borrego P, Marcelino JM, Bártolo I, Rosado L, Cavaco-Silva P, Gomes P, Família C, Quintas A, Skar H, Leitner T, Barroso H, Taveira N.

Retrovirology. 2013 Oct 24;10:110. doi: 10.1186/1742-4690-10-110.


SCoRS--A Method Based on Stability for Feature Selection and Mapping inNeuroimaging [corrected].

Rondina JM, Hahn T, de Oliveira L, Marquand AF, Dresler T, Leitner T, Fallgatter AJ, Shawe-Taylor J, Mourao-Miranda J.

IEEE Trans Med Imaging. 2014 Jan;33(1):85-98. doi: 10.1109/TMI.2013.2281398. Epub 2013 Sep 11. Erratum in: IEEE Trans Med Imaging. 2014 Mar;33(3):794.


A multiple-alignment based primer design algorithm for genetically highly variable DNA targets.

Brodin J, Krishnamoorthy M, Athreya G, Fischer W, Hraber P, Gleasner C, Green L, Korber B, Leitner T.

BMC Bioinformatics. 2013 Aug 21;14:255. doi: 10.1186/1471-2105-14-255.


PCR-induced transitions are the major source of error in cleaned ultra-deep pyrosequencing data.

Brodin J, Mild M, Hedskog C, Sherwood E, Leitner T, Andersson B, Albert J.

PLoS One. 2013 Jul 23;8(7):e70388. doi: 10.1371/journal.pone.0070388. Print 2013.


A hybrid stochastic-deterministic computational model accurately describes spatial dynamics and virus diffusion in HIV-1 growth competition assay.

Immonen T, Gibson R, Leitner T, Miller MA, Arts EJ, Somersalo E, Calvetti D.

J Theor Biol. 2012 Nov 7;312:120-32. doi: 10.1016/j.jtbi.2012.07.005. Epub 2012 Jul 17.


Agent-based and phylogenetic analyses reveal how HIV-1 moves between risk groups: injecting drug users sustain the heterosexual epidemic in Latvia.

Graw F, Leitner T, Ribeiro RM.

Epidemics. 2012 Jun;4(2):104-16. doi: 10.1016/j.epidem.2012.04.002. Epub 2012 May 2.


Quantitative experimental determination of primer-dimer formation risk by free-solution conjugate electrophoresis.

Desmarais SM, Leitner T, Barron AE.

Electrophoresis. 2012 Feb;33(3):483-91. doi: 10.1002/elps.201100452. Epub 2012 Jan 10.


Phylogenetic analysis of the Latvian HIV-1 epidemic.

Balode D, Skar H, Mild M, Kolupajeva T, Ferdats A, Rozentale B, Leitner T, Albert J.

AIDS Res Hum Retroviruses. 2012 Aug;28(8):928-32. doi: 10.1089/AID.2011.0310. Epub 2012 Feb 2.


Daily sampling of an HIV-1 patient with slowly progressing disease displays persistence of multiple env subpopulations consistent with neutrality.

Skar H, Gutenkunst RN, Wilbe Ramsay K, Alaeus A, Albert J, Leitner T.

PLoS One. 2011;6(8):e21747. doi: 10.1371/journal.pone.0021747. Epub 2011 Aug 2.


Guidelines for HIV in court cases.

Leitner T.

Nature. 2011 May 19;473(7347):284. doi: 10.1038/473284a. No abstract available. Erratum in: Nature. 2011 Jul 7;475(7354):37.


Viral linkage in HIV-1 seroconverters and their partners in an HIV-1 prevention clinical trial.

Campbell MS, Mullins JI, Hughes JP, Celum C, Wong KG, Raugi DN, Sorensen S, Stoddard JN, Zhao H, Deng W, Kahle E, Panteleeff D, Baeten JM, McCutchan FE, Albert J, Leitner T, Wald A, Corey L, Lingappa JR; Partners in Prevention HSV/HIV Transmission Study Team.

PLoS One. 2011 Mar 2;6(3):e16986. doi: 10.1371/journal.pone.0016986.


Epitope-specific CD8+ T lymphocytes cross-recognize mutant simian immunodeficiency virus (SIV) sequences but fail to contain very early evolution and eventual fixation of epitope escape mutations during SIV infection.

Cale EM, Hraber P, Giorgi EE, Fischer W, Bhattacharya T, Leitner T, Yeh WW, Gleasner C, Green LD, Han CS, Korber B, Letvin NL.

J Virol. 2011 Apr;85(8):3746-57. doi: 10.1128/JVI.02420-10. Epub 2011 Feb 9.


Dynamics of two separate but linked HIV-1 CRF01_AE outbreaks among injection drug users in Stockholm, Sweden, and Helsinki, Finland.

Skar H, Axelsson M, Berggren I, Thalme A, Gyllensten K, Liitsola K, Brummer-Korvenkontio H, Kivelä P, Spångberg E, Leitner T, Albert J.

J Virol. 2011 Jan;85(1):510-8. doi: 10.1128/JVI.01413-10. Epub 2010 Oct 20.


Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing.

Fischer W, Ganusov VV, Giorgi EE, Hraber PT, Keele BF, Leitner T, Han CS, Gleasner CD, Green L, Lo CC, Nag A, Wallstrom TC, Wang S, McMichael AJ, Haynes BF, Hahn BH, Perelson AS, Borrow P, Shaw GM, Bhattacharya T, Korber BT.

PLoS One. 2010 Aug 20;5(8):e12303. doi: 10.1371/journal.pone.0012303.


Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing.

Hedskog C, Mild M, Jernberg J, Sherwood E, Bratt G, Leitner T, Lundeberg J, Andersson B, Albert J.

PLoS One. 2010 Jul 7;5(7):e11345. doi: 10.1371/journal.pone.0011345.

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