Daodu, Richard Olumide; Awotoro, Ebenezer; Ulrich, Jens-Uwe; Kühnert, Denise
CLASV: Rapid Lassa virus lineage assignment with random forest. Journal Article
In: PLoS Negl Trop Dis, vol. 19, iss. 9, pp. e0013512, 2025, ISSN: 1935-2735.
@article{Daodu:25,
title = {CLASV: Rapid Lassa virus lineage assignment with random forest.},
author = {Richard Olumide Daodu and Ebenezer Awotoro and Jens-Uwe Ulrich and Denise Kühnert},
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Gomez, Luis Roger Esquivel; Weber, Ariane; Kocher, Arthur; Kühnert, Denise
Recombination-aware phylogenetic analysis sheds light on the evolutionary origin of SARS-CoV-2. Journal Article
In: Sci. Rep., vol. 14, iss. 1, pp. 541, 2024, ISSN: 2045-2322.
@article{Esquivel:24,
title = {Recombination-aware phylogenetic analysis sheds light on the evolutionary origin of SARS-CoV-2.},
author = {Luis Roger Esquivel Gomez and Ariane Weber and Arthur Kocher and Denise Kühnert},
url = {https://pubmed.ncbi.nlm.nih.gov/38177346/},
doi = {10.1038/s41598-023-50952-1},
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Djakovic, Lara; Hennig, Thomas; Reinisch, Katharina; Milić, Andrea; Whisnant, Adam W; Wolf, Katharina; Weiß, Elena; Haas, Tobias; Grothey, Arnhild; Jürges, Christopher S; Kluge, Michael; Wolf, Elmar; Erhard, Florian; Friedel, Caroline C; Dölken, Lars
The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes. Journal Article
In: Nat Commun, vol. 14, iss. 1, no. 1, pp. 4591, 2023, ISSN: 2041-1723.
@article{Djakovic:23,
title = {The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes.},
author = {Lara Djakovic and Thomas Hennig and Katharina Reinisch and Andrea Milić and Adam W Whisnant and Katharina Wolf and Elena Weiß and Tobias Haas and Arnhild Grothey and Christopher S Jürges and Michael Kluge and Elmar Wolf and Florian Erhard and Caroline C Friedel and Lars Dölken},
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Smith, Maureen Rebecca; Trofimova, Maria; Weber, Ariane; Duport, Yannick; Kühnert, Denise; Kleist, Max
Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020. Journal Article
In: Nat Commun, vol. 12, iss. 1, no. 1, pp. 6009, 2021, ISSN: 2041-1723.
@article{Smith:21,
title = {Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020.},
author = {Maureen Rebecca Smith and Maria Trofimova and Ariane Weber and Yannick Duport and Denise Kühnert and Max Kleist},
doi = {10.1038/s41467-021-26267-y},
issn = {2041-1723},
year = {2021},
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Kocher, Arthur; Papac, Luka; Barquera, Rodrigo; Key, Felix M; Spyrou, Maria A; Hübler, Ron; Rohrlach, Adam B; Aron, Franziska; Stahl, Raphaela; Wissgott, Antje; Bömmel, Florian; Pfefferkorn, Maria; Mittnik, Alissa; Villalba-Mouco, Vanessa; Hansen, Svend; Kitov, Egor P; Dobeš, Miroslav; Ernée, Michal; Meller, Harald; Alt, Kurt W; Prüfer, Kay; Warinner, Christina; Schiffels, Stephan; Stockhammer, Philipp W; Bos, Kirsten; Posth, Cosimo; Herbig, Alexander; Haak, Wolfgang; Krause, Johannes; Kühnert, Denise
Ten millennia of hepatitis B virus evolution. Journal Article
In: Science, vol. 374, iss. 6564, no. 6564, pp. 182–188, 2021, ISSN: 1095-9203.
@article{Kocher:21,
title = {Ten millennia of hepatitis B virus evolution.},
author = {Arthur Kocher and Luka Papac and Rodrigo Barquera and Felix M Key and Maria A Spyrou and Ron Hübler and Adam B Rohrlach and Franziska Aron and Raphaela Stahl and Antje Wissgott and Florian Bömmel and Maria Pfefferkorn and Alissa Mittnik and Vanessa Villalba-Mouco and Svend Hansen and Egor P Kitov and Miroslav Dobeš and Michal Ernée and Harald Meller and Kurt W Alt and Kay Prüfer and Christina Warinner and Stephan Schiffels and Philipp W Stockhammer and Kirsten Bos and Cosimo Posth and Alexander Herbig and Wolfgang Haak and Johannes Krause and Denise Kühnert},
doi = {10.1126/science.abi5658},
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year = {2021},
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Whisnant, Adam W; Jürges, Christopher S; Hennig, Thomas; Wyler, Emanuel; Prusty, Bhupesh; Rutkowski, Andrzej J; L'hernault, Anne; Djakovic, Lara; Göbel, Margarete; Döring, Kristina; Menegatti, Jennifer; Antrobus, Robin; Matheson, Nicholas J; Künzig, Florian W H; Mastrobuoni, Guido; Bielow, Chris; Kempa, Stefan; Liang, Chunguang; Dandekar, Thomas; Zimmer, Ralf; Landthaler, Markus; Grässer, Friedrich; Lehner, Paul J; Friedel, Caroline C; Erhard, Florian; Dölken, Lars
Integrative functional genomics decodes herpes simplex virus 1 Journal Article
In: Nat Commun, vol. 11, iss. 1, pp. 2038, 2020.
@article{Whisnant:20,
title = {Integrative functional genomics decodes herpes simplex virus 1},
author = {Adam W Whisnant and Christopher S Jürges and Thomas Hennig and Emanuel Wyler and Bhupesh Prusty and Andrzej J Rutkowski and Anne L'hernault and Lara Djakovic and Margarete Göbel and Kristina Döring and Jennifer Menegatti and Robin Antrobus and Nicholas J Matheson and Florian W H Künzig and Guido Mastrobuoni and Chris Bielow and Stefan Kempa and Chunguang Liang and Thomas Dandekar and Ralf Zimmer and Markus Landthaler and Friedrich Grässer and Paul J Lehner and Caroline C Friedel and Florian Erhard and Lars Dölken},
doi = {10.1038/s41467-020-15992-5},
year = {2020},
date = {2020-01-01},
journal = {Nat Commun},
volume = {11},
issue = {1},
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Kühnert, Denise; Kouyos, Roger; Shirreff, George; Pečerska, Jūlija; Scherrer, Alexandra U; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Günthard, Huldrych F; Stadler, Tanja; Bonhoeffer, Sebastian; Study, Swiss HIV Cohort
Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics. Journal Article
In: PLoS Pathog, vol. 14, iss. 2, no. 2, pp. e1006895, 2018, ISSN: 1553-7374.
@article{Kuehnert:18,
title = {Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics.},
author = {Denise Kühnert and Roger Kouyos and George Shirreff and Jūlija Pečerska and Alexandra U Scherrer and Jürg Böni and Sabine Yerly and Thomas Klimkait and Vincent Aubert and Huldrych F Günthard and Tanja Stadler and Sebastian Bonhoeffer and Swiss HIV Cohort Study},
doi = {10.1371/journal.ppat.1006895},
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year = {2018},
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Hennig, Thomas; Michalski, Marco; Rutkowski, Andrzej J; Djakovic, Lara; Whisnant, Adam W; Friedl, Marie-Sophie; Jha, Bhaskar Anand; Baptista, Marisa A P; L'Hernault, Anne; Erhard, Florian; Dölken, Lars; Friedel, Caroline C
HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes. Journal Article
In: PLoS Pathog, vol. 14, iss. 3, no. 3, pp. e1006954, 2018, ISSN: 1553-7374.
@article{Hennig:18,
title = {HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes.},
author = {Thomas Hennig and Marco Michalski and Andrzej J Rutkowski and Lara Djakovic and Adam W Whisnant and Marie-Sophie Friedl and Bhaskar Anand Jha and Marisa A P Baptista and Anne L'Hernault and Florian Erhard and Lars Dölken and Caroline C Friedel},
doi = {10.1371/journal.ppat.1006954},
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Bonfert, Thomas; Friedel, Caroline C
Prediction of poly(A) sites by poly(A) read mapping. Journal Article
In: PLoS One, vol. 12, iss. 1, no. 1, pp. e0170914, 2017, ISSN: 1932-6203.
@article{Bonfert:17,
title = {Prediction of poly(A) sites by poly(A) read mapping.},
author = {Thomas Bonfert and Caroline C Friedel},
url = {https://pubmed.ncbi.nlm.nih.gov/28135292/},
doi = {10.1371/journal.pone.0170914},
issn = {1932-6203},
year = {2017},
date = {2017-01-01},
journal = {PLoS One},
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number = {1},
issue = {1},
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Rutkowski, Andrzej J; Erhard, Florian; L'Hernault, Anne; Bonfert, Thomas; Schilhabel, Markus; Crump, Colin; Rosenstiel, Philip; Efstathiou, Stacey; Zimmer, Ralf; Friedel, Caroline C; Dölken, Lars
Widespread disruption of host transcription termination in HSV-1 infection. Journal Article
In: Nat Commun, vol. 6, pp. 7126, 2015, ISSN: 2041-1723.
@article{Rutkowski:15,
title = {Widespread disruption of host transcription termination in HSV-1 infection.},
author = {Andrzej J Rutkowski and Florian Erhard and Anne L'Hernault and Thomas Bonfert and Markus Schilhabel and Colin Crump and Philip Rosenstiel and Stacey Efstathiou and Ralf Zimmer and Caroline C Friedel and Lars Dölken},
doi = {10.1038/ncomms8126},
issn = {2041-1723},
year = {2015},
date = {2015-01-01},
journal = {Nat Commun},
volume = {6},
pages = {7126},
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