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Ivan Topolsky
Researcher at Swiss Institute of Bioinformatics
Publications - 14
Citations - 339
Ivan Topolsky is an academic researcher from Swiss Institute of Bioinformatics. The author has contributed to research in topics: Medicine & Disease. The author has an hindex of 7, co-authored 9 publications receiving 162 citations. Previous affiliations of Ivan Topolsky include ETH Zurich & University of Basel.
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Posted ContentDOI
Within-patient genetic diversity of SARS-CoV-2
Jack Kuipers,Jack Kuipers,Aashil A. Batavia,Aashil A. Batavia,Kim Philipp Jablonski,Kim Philipp Jablonski,Fritz Bayer,Fritz Bayer,Nico Borgsmüller,Nico Borgsmüller,Arthur Dondi,Arthur Dondi,Monica-Andreea Drăgan,Monica-Andreea Drăgan,Pedro Ferreira,Pedro Ferreira,Katharina Jahn,Katharina Jahn,Lisa Lamberti,Lisa Lamberti,Martin Pirkl,Martin Pirkl,Susana Posada-Cespedes,Susana Posada-Cespedes,Ivan Topolsky,Ivan Topolsky,Ina Nissen,Natascha Santacroce,Elodie Burcklen,Tobias Schär,Vincenzo Capece,Christiane Beckmann,Olivier Kobel,Christoph Noppen,Maurice Redondo,Sarah Nadeau,Sarah Nadeau,Sophie Seidel,Sophie Seidel,Noemi Santamaria de Souza,Christian Beisel,Tanja Stadler,Tanja Stadler,Niko Beerenwinkel,Niko Beerenwinkel +44 more
TL;DR: The diversity of genetic variants coexisting within patients across a cohort of 3939 publicly accessible samples and 749 recently sequenced samples from Switzerland is examined and it is found that a small number of patients carry most of the diversity, and that patients with more diversity tend to be older.
Posted ContentDOI
Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data
Sarah Nadeau,Sarah Nadeau,Christiane Beckmann,Ivan Topolsky,Ivan Topolsky,Timothy G. Vaughan,Timothy G. Vaughan,Emma B. Hodcroft,Emma B. Hodcroft,Tobias Schaer,Ina Nissen,Natascha Santacroce,Elodie Burcklen,Pedro Ferreira,Pedro Ferreira,Kim Philipp Jablonski,Kim Philipp Jablonski,Susana Posada-Cespedes,Susana Posada-Cespedes,Vincenzo Capece,Sophie Seidel,Sophie Seidel,Noemi Santamaria de Souza,Julia M. Martinez-Gomez,Phil F. Cheng,Philipp P. Bosshard,Mitchell P. Levesque,Verena Kufner,Stefan Schmutz,Maryam Zaheri,Michael Huber,Alexandra Trkola,Samuel Cordey,Florian Laubscher,Ana Rita Gonçalves,Karoline Leuzinger,Karoline Leuzinger,Madlen Stange,Alfredo Mari,Tim Roloff,Helena M.B. Seth-Smith,Hans H. Hirsch,Adrian Egli,Maurice Redondo,Olivier Kobel,Christoph Noppen,Niko Beerenwinkel,Niko Beerenwinkel,Richard A. Neher,Richard A. Neher,Christian Beisel,Tanja Stadler,Tanja Stadler +52 more
TL;DR: It is demonstrated that no one lineage became dominant, pointing against evolution towards general lower virulence, and the framework can be applied to quantify evolution and epidemiology in other locations or for other pathogens based on genomic data.
Posted ContentDOI
Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland
Chaoran Chen,Sarah Nadeau,Ivan Topolsky,Marc Manceau,Jana S. Huisman,Jana S. Huisman,Kim Philipp Jablonski,Lara Fuhrmann,David Dreifuss,Katharina Jahn,Christiane Beckmann,Maurice Redondo,Olivier Kobel,Christoph Noppen,Lorenz Risch,Martin Risch,Nadia Wohlwend,Sinem Kas,Thomas Bodmer,Tim Roloff,Tim Roloff,Tim Roloff,Madlen Stange,Madlen Stange,Madlen Stange,Adrian Egli,Adrian Egli,Isabella Eckerle,Isabella Eckerle,Laurent Kaiser,Laurent Kaiser,Rebecca Denes,Mirjam Feldkamp,Ina Nissen,Natascha Santacroce,Elodie Burcklen,Catharine Aquino,Andreia Cabral de Gouvea,Maria Domenica Moccia,Simon Grüter,Timothy Sykes,Lennart Opitz,Griffin White,Laura Neff,Doris Popovic,Andrea Patrignani,Jay Tracy,Ralph Schlapbach,Emmanouil T. Dermitzakis,Keith Harshman,Ioannis Xenarios,Henri Pegeot,Lorenzo Cerutti,Deborah Penet,Anthony Blin,Melyssa Elies,Christian L. Althaus,Christian Beisel,Niko Beerenwinkel,Martin Ackermann,Tanja Stadler +60 more
TL;DR: In this paper, the authors estimate the transmission advantage and the effective reproductive number of B.1.7 through time for data from Switzerland between 14.12.2020 and 11.03.2021.
Posted ContentDOI
V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput sequencing data
TL;DR: V-pipe, a bioinformatics pipeline combining various state-of-the-art statistical models and computational tools for automated end-to-end analyses of raw sequencing reads, is developed and implemented in a modular fashion to facilitate adaptations to the continuously changing technology landscape.
Journal ArticleDOI
Wastewater monitoring of SARS-CoV-2 shows high correlation with COVID-19 case numbers and allowed early detection of the first confirmed B.1.1.529 infection in Switzerland: results of an observational surveillance study.
Claudia Bagutti,Monica Alt Hug,Philippe Heim,Laura Maurer Pekerman,Evelyn Ilg Hampe,Philipp Hübner,Simon Fuchs,Miodrag Savic,Tanja Stadler,Ivan Topolsky,Pelin Icer Baykal,David Dreifuss,Niko Beerenwinkel,Sarah Tschudin Sutter +13 more
TL;DR: In this article , the authors report correlations between SARS-CoV-2 detection in wastewater and the officially recorded COVID-19 case numbers, as well as the validity of such surveillance to detect emerging variants, exemplified by the detection of the B.1.529 variant Omicron in Basel, Switzerland.