Publications by authors named "Thomas Leitner"

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Identifying impacts of contact tracing on HIV epidemiological inference from phylogenetic data.
Michael D Kupperman, Ruian Ke, Thomas Leitner

Virus Evol· October 2025

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wavess: An R package for simulation of adaptive within-host virus sequence evolution.
Narmada Sambaturu, Zena Lapp, Fernando D K Tria, Ethan Romero-Severson, Carmen Molina-París, Thomas Leitner

PLoS Comput Biol· September 2025

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SIV proviruses seeded later in infection are harbored in short-lived CD4 T cells.
Narmada Sambaturu, Emily J Fray, Vivek Hariharan, Fengting Wu, Carolin Zitzmann, Thomas Leitner

Cell Rep· May 2025

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Hypermut 3: identifying specific mutational patterns in a defined nucleotide context that allows multistate characters.
Zena Lapp, Hyejin Yoon, Brian Foley, Thomas Leitner

Bioinform Adv· February 2025

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Identification of 2 Novel Subtypes of Hepatitis C Virus Genotype 8 and a Potential New Genotype Successfully Treated With Direct Acting Antivirals.
Jean L Mbisa, Zena Lapp, David F Bibby, Laura T Phillips, Carmen F Manso, Thomas Leitner

J Infect Dis· December 2024

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Sweden surpasses the UNAIDS 95-95-95 target: estimating HIV-1 incidence, 2003 to 2022.
Erik Lundgren, Macauley Locke, Ethan Romero-Severson, Mira Dimitrijevic, Maria Axelsson, Thomas Leitner

Euro Surveill· October 2024

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Hypermut 3: Identifying specific mutational patterns in a defined nucleotide context that allows multistate characters.
Zena Lapp, Hyejin Yoon, Brian Foley, Thomas Leitner

bioRxiv· October 2024

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Identifying Impacts of Contact Tracing on Epidemiological Inference from Phylogenetic Data.
Michael D Kupperman, Ruian Ke, Thomas Leitner

bioRxiv· September 2024

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The Number and Pattern of Viral Genomic Reassortments are not Necessarily Identifiable from Segment Trees.
Qianying Lin, Emma E Goldberg, Thomas Leitner, Carmen Molina-París, Aaron A King

Mol Biol Evol· June 2024

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A story of viral co-infection, co-transmission and co-feeding in ticks: how to compute an invasion reproduction number.
Giulia Belluccini, Qianying Lin, Bevelynn Williams, Yijun Lou, Zati Vatansever, Thomas Leitner

ArXiv· March 2024

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Eddy Current Position Measurement in Harsh Environments: A Temperature Compensation and Calibration Approach.
Gabriel Gruber, Bernhard Schweighofer, Matthias Berger, Thomas Leitner, Gerald Kloesch

Sensors (Basel)· February 2024

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Inferring Viral Transmission Time from Phylogenies for Known Transmission Pairs.
Emma E Goldberg, Erik J Lundgren, Ethan O Romero-Severson, Thomas Leitner

Mol Biol Evol· January 2024

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Salt-rich versus salt-poor structural scenarios in the central Northern Calcareous Alps: implications for the Hallstatt facies and early Alpine tectonic evolution (Eastern Alps, Austria).
Oscar Fernandez, Hugo Ortner, Diethard Sanders, Bernhard Grasemann, Thomas Leitner

Int J Earth Sci· January 2024

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Inferring viral transmission time from phylogenies for known transmission pairs.
Emma E Goldberg, Erik J Lundgren, Ethan O Romero-Severson, Thomas Leitner

bioRxiv· November 2023

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Last in first out: SIV proviruses seeded later in infection are harbored in short-lived CD4 T cells.
Narmada Sambaturu, Emily J Fray, Fengting Wu, Carolin Zitzmann, Francesco R Simonetti, Thomas Leitner

bioRxiv· November 2023

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A novel candidate hepatitis C virus genotype 4 subtype identified by next generation sequencing full-genome characterization in a patient from Saudi Arabia.
Mariantonietta Di Stefano, Mona H Ismail, Thomas Leitner, Giuseppina Faleo, Marwan Jabr Alwazzeh

Front Microbiol· November 2023

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Modeling the evolution of segment trees reveals deficiencies in current inferential methods for genomic reassortment.
Qianying Lin, Emma E Goldberg, Thomas Leitner, Carmen Molina-París, Aaron A King

bioRxiv· September 2023

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Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies.
Lauren A Castro, Thomas Leitner, Ethan Romero-Severson

Virus Evol· May 2023

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Antiretroviral therapy reveals triphasic decay of intact SIV genomes and persistence of ancestral variants.
Emily J Fray, Fengting Wu, Francesco R Simonetti, Carolin Zitzmann, Narmada Sambaturu, Thomas Leitner

Cell Host Microbe· March 2023

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Molecular and Genetic Characterization of Hepatitis B Virus (HBV) among Saudi Chronically HBV-Infected Individuals.
Mariantonietta Di Stefano, Giuseppina Faleo, Thomas Leitner, Wei Zheng, Yang Zhang

Viruses· February 2023

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Long-Term and Low-Level Envelope C2V3 Stimulation by Highly Diverse Virus Isolates Leads to Frequent Development of Broad and Elite Antibody Neutralization in HIV-1-Infected Individuals.
Francisco Martin, José Maria Marcelino, Claudia Palladino, Inês Bártolo, Susana Tracana, Thomas Leitner

Microbiol Spectr· December 2022

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A deep learning approach to real-time HIV outbreak detection using genetic data.
Michael D Kupperman, Thomas Leitner, Ruian Ke

PLoS Comput Biol· October 2022

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Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification.
Erik Lundgren, Ethan Romero-Severson, Jan Albert, Thomas Leitner

PLoS Comput Biol· August 2022

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Updated HIV-1 Consensus Sequences Change but Stay Within Similar Distance From Worldwide Samples.
Gregorio V Linchangco, Brian Foley, Thomas Leitner

Front Microbiol· January 2022

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Genetic Subtypes and Natural Resistance Mutations in HCV Genotype 4 Infected Saudi Arabian Patients.
Mariantonietta Di Stefano, Mona H Ismail, Thomas Leitner, Giuseppina Faleo, Saada A Elmnan Adem

Viruses· September 2021

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