List of works - Thomas Leitner

A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA

scientific article

A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes

scientific article

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

scientific article

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

article

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

scientific article

Biological and genetic evolution of HIV type 1 in two siblings with different patterns of disease progression.

scientific article published on December 2007

Characterization of novel recombinant HIV-1 genomes using the branching index

scientific article published on November 2003

Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching index

scientific article (publication date: September 2008)

Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5' untranslated region (UTR) fails to classify subtypes

scientific article (publication date: 14 December 2006)

Daily Sampling of an HIV-1 Patient with Slowly Progressing Disease Displays Persistence of Multiple env Subpopulations Consistent with Neutrality ⬇️

scientific article published on August 2, 2011

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

scientific article published on 14 September 2017

Dynamic correlation between intrahost HIV-1 quasispecies evolution and disease progression

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Genetic evidence for an East Asian origin of domestic dogs

scientific article (publication date: 22 November 2002)

Guidelines for HIV in court cases

scientific article published in Nature

HIV biological variability unveiled: frequent isolations and chimeric receptors reveal unprecedented variation of coreceptor use.

scientific article published on December 2003

HIV classification using the coalescent theory

scientific article

HIV-2 genetic evolution in patients with advanced disease is faster than that in matched HIV-1 patients

scientific article

Identification of two CRF11-cpx genomes and two preliminary representatives of a new circulating recombinant form (CRF13-cpx) of HIV type 1 in Cameroon.

scientific article published on August 2002

Improved HIV-1 viral load determination based on reverse transcriptase activity recovered from human plasma

scientific article

Inference of Transmission Network Structure from HIV Phylogenetic Trees

scientific article

Inferring transmission heterogeneity using virus genealogies: Estimation and targeted prevention

scientific article published on 03 September 2020

Multiple HIV-1 introductions into the Swedish intravenous drug user population

scientific article published on 08 April 2008

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

scientific article

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

scientific article

Phylodynamic Inference across Epidemic Scales

scientific article

Phylogenetic analysis of the Latvian HIV-1 epidemic

scientific article

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

article

Phylogenetically resolving epidemiologic linkage.

scientific article published on 22 February 2016

Prevalence of drug-resistant HIV-1 variants in untreated individuals in Europe: implications for clinical management

scientific article published on 15 August 2005

Primate immunodeficiency virus classification and nomenclature: Review

scientific article

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

scientific article published on 17 December 2014

Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo

scientific article

Quantitative experimental determination of primer–dimer formation risk by free‐solution conjugate electrophoresis ⬇️

scientific article published on January 10, 2012

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

scientific article

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

scientific article published on 22 December 2015

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

scientific article

Recombination rate and selection strength in HIV intra-patient evolution

scientific article

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

scientific article

Relative dominance of Gag p24-specific cytotoxic T lymphocytes is associated with human immunodeficiency virus control

scientific article

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

scientific article

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

scientific article published on 07 May 2020

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

scientific article

The Calculated Genetic Barrier for Antiretroviral Drug Resistance Substitutions Is Largely Similar for Different HIV-1 Subtypes

article

The Puzzle of HIV Neutral and Selective Evolution

article

The evolutionary rate dynamically tracks changes in HIV-1 epidemics: application of a simple method for optimizing the evolutionary rate in phylogenetic trees with longitudinal data

scientific article (publication date: December 2009)

The role of recombination in the emergence of a complex and dynamic HIV epidemic

scientific article

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

scientific article

Towards Estimation of HIV-1 Date of Infection: A Time-Continuous IgG-Model Shows That Seroconversion Does Not Occur at the Midpoint between Negative and Positive Tests ⬇️

scientific article published on April 16, 2013

Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach

scientific article published on 20 May 2009

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

scientific article

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

scientific article published in June 2015

Unequal evolutionary rates in the human immunodeficiency virus type 1 (HIV-1) pandemic: the evolutionary rate of HIV-1 slows down when the epidemic rate increases

scientific article

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

scientific article

What Should Health Departments Do with HIV Sequence Data?

scientific article published on 12 September 2020

jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1.

scientific article

jpHMM: improving the reliability of recombination prediction in HIV-1.

scientific article published on 14 May 2009

mtDNA data indicate a single origin for dogs south of Yangtze River, less than 16,300 years ago, from numerous wolves

scientific article

List of works by Thomas Leitner

A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA

A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes

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

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

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

Biological and genetic evolution of HIV type 1 in two siblings with different patterns of disease progression.

Characterization of novel recombinant HIV-1 genomes using the branching index

Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching index

Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5' untranslated region (UTR) fails to classify subtypes

Daily Sampling of an HIV-1 Patient with Slowly Progressing Disease Displays Persistence of Multiple env Subpopulations Consistent with Neutrality ⬇️

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

Dynamic correlation between intrahost HIV-1 quasispecies evolution and disease progression

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

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

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

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

Genetic evidence for an East Asian origin of domestic dogs

Guidelines for HIV in court cases

HIV biological variability unveiled: frequent isolations and chimeric receptors reveal unprecedented variation of coreceptor use.

HIV classification using the coalescent theory

HIV-2 genetic evolution in patients with advanced disease is faster than that in matched HIV-1 patients

Identification of two CRF11-cpx genomes and two preliminary representatives of a new circulating recombinant form (CRF13-cpx) of HIV type 1 in Cameroon.

Improved HIV-1 viral load determination based on reverse transcriptase activity recovered from human plasma

Inference of Transmission Network Structure from HIV Phylogenetic Trees

Inferring transmission heterogeneity using virus genealogies: Estimation and targeted prevention

Multiple HIV-1 introductions into the Swedish intravenous drug user population

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

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

Phylodynamic Inference across Epidemic Scales

Phylogenetic analysis of the Latvian HIV-1 epidemic

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

Phylogenetically resolving epidemiologic linkage.

Prevalence of drug-resistant HIV-1 variants in untreated individuals in Europe: implications for clinical management

Primate immunodeficiency virus classification and nomenclature: Review

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

Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo

Quantitative experimental determination of primer–dimer formation risk by free‐solution conjugate electrophoresis ⬇️

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

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

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

Recombination rate and selection strength in HIV intra-patient evolution

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

Relative dominance of Gag p24-specific cytotoxic T lymphocytes is associated with human immunodeficiency virus control

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

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

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

The Calculated Genetic Barrier for Antiretroviral Drug Resistance Substitutions Is Largely Similar for Different HIV-1 Subtypes

The Puzzle of HIV Neutral and Selective Evolution

The evolutionary rate dynamically tracks changes in HIV-1 epidemics: application of a simple method for optimizing the evolutionary rate in phylogenetic trees with longitudinal data

The role of recombination in the emergence of a complex and dynamic HIV epidemic

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

Towards Estimation of HIV-1 Date of Infection: A Time-Continuous IgG-Model Shows That Seroconversion Does Not Occur at the Midpoint between Negative and Positive Tests ⬇️

Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach

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

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

Unequal evolutionary rates in the human immunodeficiency virus type 1 (HIV-1) pandemic: the evolutionary rate of HIV-1 slows down when the epidemic rate increases

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

What Should Health Departments Do with HIV Sequence Data?

jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1.

jpHMM: improving the reliability of recombination prediction in HIV-1.

mtDNA data indicate a single origin for dogs south of Yangtze River, less than 16,300 years ago, from numerous wolves