HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data
Authors
- Emma C. Thomson (ORCID: https://orcid.org/0000-0003-1482-0889)
- Oliver Laeyendecker (ORCID: https://orcid.org/0000-0002-6429-4760)
- Mohammed Limbada (ORCID: https://orcid.org/0000-0002-3736-1462)
- Pia Kivelä (ORCID: https://orcid.org/0000-0002-0678-2694)
- Jairam R. Lingappa (ORCID: https://orcid.org/0000-0001-6191-9828)
- Chris Wymant (ORCID: https://orcid.org/0000-0002-9847-8226)
- Swee Hoe Ong (ORCID: https://orcid.org/0000-0002-3629-5387)
- Ben Berkhout (ORCID: https://orcid.org/0000-0002-1905-8486)
- George MacIntyre-Cockett
- Myron S. Cohen (ORCID: https://orcid.org/0000-0001-5917-9664)
- Helen Ayles (ORCID: https://orcid.org/0000-0003-4108-2842)
- Ronald Moses Galiwango (ORCID: https://orcid.org/0000-0003-3702-5722)
- Nelly Mugo (ORCID: https://orcid.org/0000-0002-2347-006X)
- Margreet Bakker (ORCID: https://orcid.org/0000-0002-3803-3380)
- Barry R. Kosloff (ORCID: https://orcid.org/0000-0002-8074-2586)
- David R. Bonsall (ORCID: https://orcid.org/0000-0002-2542-7559)
- Kholoud Porter (ORCID: https://orcid.org/0000-0002-9226-6206)
- Astrid Gall (ORCID: https://orcid.org/0000-0001-6452-5816)
- Tanya Golubchik (ORCID: https://orcid.org/0000-0003-2765-9828)
- Lucie Abeler‐Dörner (ORCID: https://orcid.org/0000-0003-3662-4192)
- Huldrych F. Günthard (ORCID: https://orcid.org/0000-0002-1142-6723)
- Jan Albert (ORCID: https://orcid.org/0000-0001-9020-0521)
- Jared M. Baeten (ORCID: https://orcid.org/0000-0001-8242-8438)
- Sarah Fidler (ORCID: https://orcid.org/0000-0003-1676-7583)
- Paul Kellam (ORCID: https://orcid.org/0000-0003-3166-4734)
- Roger D. Kouyos (ORCID: https://orcid.org/0000-0002-9220-8348)
- Deogratius Ssemwanga (ORCID: https://orcid.org/0000-0001-9675-4234)
- M. Kate Grabowski (ORCID: https://orcid.org/0000-0002-4451-3436)
- Oliver Ratmann (ORCID: https://orcid.org/0000-0001-8667-4118)
- Joseph Kagaayi (ORCID: https://orcid.org/0000-0003-4101-3038)
- Pontiano Kaleebu
- Joshua T. Herbeck (ORCID: https://orcid.org/0000-0003-4577-7406)
- Susan H. Eshleman (ORCID: https://orcid.org/0000-0002-4587-791X)
- Mark van der Valk
- Marion Cornelissen
- Andrew Mujugira (ORCID: https://orcid.org/0000-0001-6646-6733)
- Jacques Fellay (ORCID: https://orcid.org/0000-0002-8240-939X)
- Connie Celum (ORCID: https://orcid.org/0000-0002-8813-3419)
- Richard Hayes (ORCID: https://orcid.org/0000-0002-1729-9892)
- François Blanquart (ORCID: https://orcid.org/0000-0003-3208-6665)
- David Burns (ORCID: https://orcid.org/0000-0002-3362-865X)
- Ard van Sighem
- Matthew Hall
- Daniela Bezemer
- Laurence Meyer
- Norbert Bannert
- Barbara Gunsenheimer‐Bartmeyer
- Christophe Fraser
- Peter Reiss
Institutions
- University of North Carolina at Chapel Hill (US)
- SIB Swiss Institute of Bioinformatics (CH)
- Centre National de la Recherche Scientifique (FR)
- National Institutes of Health (US)
- European Bioinformatics Institute (GB)
- Karolinska University Hospital (SE)
- Centre for Human Genetics (GB)
- Johns Hopkins University (US)
- Inserm (FR)
- Collège de France (FR)
- University of Washington (US)
- University of Zurich (CH)
- Université Paris Cité (FR)
- Robert Koch Institute (DE)
- Université Paris Sciences et Lettres (FR)
- Université Paris-Saclay (FR)
- Johns Hopkins Medicine (US)
- Helsinki University Hospital (FI)
- Wellcome Sanger Institute (GB)
- Karolinska Institutet (SE)
- Kenya Medical Research Institute (KE)
- University of Zambia (ZM)
- University of Oxford (GB)
- London School of Hygiene & Tropical Medicine (GB)
- Assistance Publique – Hôpitaux de Paris (FR)
- University Hospital of Zurich (CH)
- Centre de recherche en Epidémiologie et Santé des Populations (FR)
- Bellevue Hospital Center (US)
- NIHR Imperial Biomedical Research Centre (GB)
- Centre Interdisciplinaire de Recherche en Biologie (FR)
- Infectious Diseases Institute (UG)
- Rakai Health Sciences Program (UG)
- Stichting HIV Monitoring (NL)
- Amsterdam Institute for Global Health and Development (NL)
- National Clinical Research (US)
- National Institute of Allergy and Infectious Diseases (US)
- Zambart (ZM)
- Amsterdam University Medical Centers (NL)
- Institute for Disease Modeling (US)
- Bicêtre Hospital (FR)
- University College London (GB)
- Imperial College London (GB)
- École Polytechnique Fédérale de Lausanne (CH)
- Makerere University (UG)
- University of Amsterdam (NL)
- Uganda Virus Research Institute (UG)
- University of Lausanne (CH)
Publication Details
- Journal
- BMC Bioinformatics
- Published
- 2025-08-14
- DOI
- https://doi.org/10.1186/s12859-025-06189-y
- Primary Topic
- HIV Research and Treatment
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Bill and Melinda Gates Foundation
- European Research Council
- National Health and Medical Research Council
- National Institute of Allergy and Infectious Diseases