Publications
Showing records 1 - 20 (of 87)
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift)
ID
Author
Year
Title
Publisher
4652446
Reichmuth, Martina L.; Hodcroft, Emma B.; Riou, Julien; Neher, Richard A.; Hens, Niel; Althaus, Christian L.
2022
Impact of cross-border-associated cases on the SARS-CoV-2 epidemic in Switzerland during summer 2020 and 2021
Epidemics
4652448
Nadeau, Sarah A.; Vaughan, Timothy G.; Beckmann, Christiane; Topolsky, Ivan; Chen, Chaoran; Hodcroft, Emma; Schär, Tobias; Nissen, Ina; Santacroce, Natascha; Burcklen, Elodie; Ferreira, Pedro; Jablonski, Kim Philipp; Posada-Céspedes, Susana; Capece, Vincenzo; Seidel, Sophie; Santamaria de Souza, Noemi; Martinez-Gomez, Julia M.; Cheng, Phil; Bosshard, Philipp P.; Levesque, Mitchell P.; Kufner, Verena; Schmutz, Stefan; Zaheri, Maryam; Huber, Michael; Trkola, Alexandra; Cordey, Samuel; Laubscher, Florian; Gonçalves, Ana Rita; Aeby, Sébastien; Pillonel, Trestan; Jacot, Damien; Bertelli, Claire; Greub, Gilbert; Leuzinger, Karoline; Stange, Madlen; Mari, Alfredo; Roloff, Tim; Seth-Smith, Helena; Hirsch, Hans H.; Egli, Adrian; Redondo, Maurice; Kobel, Olivier; Noppen, Christoph; du Plessis, Louis; Beerenwinkel, Niko; Neher, Richard A.; Beisel, Christian; Stadler, Tanja
2022
Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data
Science Translational Medicine
4652084
Huisman, Jana S.; Scire, Jérémie; Angst, Daniel C.; Li, Jinzhou; Neher, Richard A.; Maathuis, Marloes H.; Bonhoeffer, Sebastian; Stadler, Tanja
2022
Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2
eLife
4652088
Happi, Christian; Adetifa, Ifedayo; Mbala, Placide; Njouom, Richard; Nakoune, Emmanuel; Happi, Anise; Ndodo, Nnaemeka; Ayansola, Oyeronke; Mboowa, Gerald; Bedford, Trevor; Neher, Richard A.; Roemer, Cornelius; Hodcroft, Emma; Tegally, Houriiyah; O'Toole, Áine; Rambaut, Andrew; Pybus, Oliver; Kraemer, Moritz U. G.; Wilkinson, Eduan; Isidro, Joana; Borges, Vítor; Pinto, Miguel; Gomes, Joăo Paulo; Freitas, Lucas; Resende, Paola C.; Lee, Raphael T. C.; Maurer-Stroh, Sebastian; Baxter, Cheryl; Lessells, Richard; Ogwell, Ahmed E.; Kebede, Yenew; Tessema, Sofonias K.; de Oliveira, Tulio
2022
Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus
PLoS Biology
4652086
Barrat-Charlaix, Pierre; Vaughan, Timothy G.; Neher, Richard A.
2022
TreeKnit: Inferring ancestral reassortment graphs of influenza viruses
PLoS Computational Biology
4652082
Hodcroft, Emma B.; Dyrdak, Robert; Andrés, Cristina; Egli, Adrian; Reist, Josiane; García Martínez de Artola, Diego; Alcoba-Flórez, Julia; Niesters, Hubert G. M.; Antón, Andrés; Poelman, Randy; Reynders, Marijke; Wollants, Elke; Neher, Richard A.; Albert, Jan
2022
Evolution, geographic spreading, and demographic distribution of Enterovirus D68
PLoS Pathogens
4627394
Konings, Frank; Perkins, Mark D.; Kuhn, Jens H.; Pallen, Mark J.; Alm, Erik J.; Archer, Brett N.; Barakat, Amal; Bedford, Trevor; Bhiman, Jinal N.; Caly, Leon; Carter, Lisa L.; Cullinane, Anne; de Oliveira, Tulio; Druce, Julian; El Masry, Ihab; Evans, Roger; Gao, George F.; Gorbalenya, Alexander E.; Hamblion, Esther; Herring, Belinda L.; Hodcroft, Emma; Holmes, Edward C.; Kakkar, Manish; Khare, Shagun; Koopmans, Marion P. G.; Korber, Bette; Leite, Juliana; MacCannell, Duncan; Marklewitz, Marco; Maurer-Stroh, Sebastian; Rico, Jairo Andres Mendez; Munster, Vincent J.; Neher, Richard; Munnink, Bas Oude; Pavlin, Boris I.; Peiris, Malik; Poon, Leo; Pybus, Oliver; Rambaut, Andrew; Resende, Paola; Subissi, Lorenzo; Thiel, Volker; Tong, Suxiang; van der Werf, Sylvie; von Gottberg, Anne; Ziebuhr, John; Van Kerkhove, Maria D.
2021
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse
Nature Microbiology
4627396
Hodcroft, Emma B.; Zuber, Moira; Nadeau, Sarah; Vaughan, Timothy G.; Crawford, Katharine H. D.; Althaus, Christian L.; Reichmuth, Martina L.; Bowen, John E.; Walls, Alexandra C.; Corti, Davide; Bloom, Jesse D.; Veesler, David; Mateo, David; Hernando, Alberto; Comas, Ińaki; González-Candelas, Fernando; SeqCovid-Spain consortium,; Stadler, Tanja; Neher, Richard A.
2021
Spread of a SARS-CoV-2 variant through Europe in the summer of 2020
Nature
4627398
Benschop, Kimberley S. M.; Broberg, Eeva K.; Hodcroft, Emma; Schmitz, Dennis; Albert, Jan; Baicus, Anda; Bailly, Jean-Luc; Baldvinsdottir, Gudrun; Berginc, Natasa; Blomqvist, Soile; Böttcher, Sindy; Brytting, Mia; Bujaki, Erika; Cabrerizo, Maria; Celma, Cristina; Cinek, Ondrej; Claas, Eric C. J.; Cremer, Jeroen; Dean, Jonathan; Dembinski, Jennifer L.; Demchyshyna, Iryna; Diedrich, Sabine; Dudman, Susanne; Dunning, Jake; Dyrdak, Robert; Emmanouil, Mary; Farkas, Agnes; De Gascun, Cillian; Fournier, Guillaume; Georgieva, Irina; Gonzalez-Sanz, Ruben; van Hooydonk-Elving, Jolanda; Jääskeläinen, Anne J.; Jancauskaite, Ruta; Keeren, Kathrin; Fischer, Thea K.; Krokstad, Sidsel; Nikolaeva-Glomb, Lubomira; Novakova, Ludmila; Midgley, Sofie E.; Mirand, Audrey; Molenkamp, Richard; Morley, Ursula; Mossong, Joël; Muralyte, Svajune; Murk, Jean-Luc; Nguyen, Trung; Nordbř, Svein A.; Österback, Riikka; Pas, Suzan; Pellegrinelli, Laura; Pogka, Vassiliki; Prochazka, Birgit; Rainetova, Petra; Van Ranst, Marc; Roorda, Lieuwe; Schuffenecker, Isabelle; Schuurman, Rob; Stoyanova, Asya; Templeton, Kate; Verweij, Jaco J.; Voulgari-Kokota, Androniki; Vuorinen, Tytti; Wollants, Elke; Wolthers, Katja C.; Zakikhany, Katherina; Neher, Richard; Harvala, Heli; Simmonds, Peter
2021
Molecular Epidemiology and Evolutionary Trajectory of Emerging Echovirus 30, Europe
Emerging infectious diseases
4627390
Boehm, Erik; Kronig, Ilona; Neher, Richard A.; Eckerle, Isabella; Vetter, Pauline; Kaiser, Laurent
2021
Novel SARS-CoV-2 variants: the pandemics within the pandemic
Clinical microbiology and infection
4627392
Barrat-Charlaix, Pierre; Huddleston, John; Bedford, Trevor; Neher, Richard A.
2021
Limited Predictability of Amino Acid Substitutions in Seasonal Influenza Viruses
Molecular Biology and Evolution
4627406
Huddleston, John; Hadfield, James; Sibley, Thomas R.; Lee, Jover; Fay, Kairsten; Ilcisin, Misja; Harkins, Elias; Bedford, Trevor; Neher, Richard A.; Hodcroft, Emma B.
2021
Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens
Journal of Open Source Software
4627404
Dyrdak, Robert; Hodcroft, Emma B.; Wahlund, Martina; Neher, Richard A.; Albert, Jan
2021
Interactions between seasonal human coronaviruses and implications for the SARS-CoV-2 pandemic: A retrospective study in Stockholm, Sweden, 2009-2020
Journal of clinical virology
4627402
Goncalves Cabecinhas, Ana Rita; Roloff, Tim; Stange, Madlen; Bertelli, Claire; Huber, Michael; Ramette, Alban; Chen, Chaoran; Nadeau, Sarah; Gerth, Yannick; Yerly, Sabine; Opota, Onya; Pillonel, Trestan; Schuster, Tobias; Metzger, Cesar M. J. A.; Sieber, Jonas; Bel, Michael; Wohlwend, Nadia; Baumann, Christian; Koch, Michel C.; Bittel, Pascal; Leuzinger, Karoline; Brunner, Myrta; Suter-Riniker, Franziska; Berlinger, Livia; Sřgaard, Kirstine K.; Beckmann, Christiane; Noppen, Christoph; Redondo, Maurice; Steffen, Ingrid; Seth-Smith, Helena M. B.; Mari, Alfredo; Lienhard, Reto; Risch, Martin; Nolte, Oliver; Eckerle, Isabella; Martinetti Lucchini, Gladys; Hodcroft, Emma B.; Neher, Richard A.; Stadler, Tanja; Hirsch, Hans H.; Leib, Stephen L.; Risch, Lorenz; Kaiser, Laurent; Trkola, Alexandra; Greub, Gilbert; Egli, Adrian
2021
SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing
Microorganisms
4637535
Aksamentov, Ivan; Roemer, Cornelius; Hodcroft, Emma B.; Neher, Richard A.
2021
Nextclade: clade assignment, mutation calling and quality control for viral genomes
Journal of Open Source Software
4627400
Vogels, Chantal B. F.; Breban, Mallery I.; Ott, Isabel M.; Alpert, Tara; Petrone, Mary E.; Watkins, Anne E.; Kalinich, Chaney C.; Earnest, Rebecca; Rothman, Jessica E.; Goes de Jesus, Jaqueline; Morales Claro, Ingra; Magalhăes Ferreira, Giulia; Crispim, Myuki A. E.; Brazil-UK Cadde Genomic Network,; Singh, Lavanya; Tegally, Houriiyah; Anyaneji, Ugochukwu J.; Network for Genomic Surveillance in South Africa,; Hodcroft, Emma B.; Mason, Christopher E.; Khullar, Gaurav; Metti, Jessica; Dudley, Joel T.; MacKay, Matthew J.; Nash, Megan; Wang, Jianhui; Liu, Chen; Hui, Pei; Murphy, Steven; Neal, Caleb; Laszlo, Eva; Landry, Marie L.; Muyombwe, Anthony; Downing, Randy; Razeq, Jafar; de Oliveira, Tulio; Faria, Nuno R.; Sabino, Ester C.; Neher, Richard A.; Fauver, Joseph R.; Grubaugh, Nathan D.
2021
Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2
PLoS Biology
4607819
Neher, Richard A.; Dyrdak, Robert; Druelle, Valentin; Hodcroft, Emma B.; Albert, Jan
2020
Potential impact of seasonal forcing on a SARS-CoV-2 pandemic
Swiss Medical Weekly
4627410
Bedford, Trevor; Greninger, Alexander L.; Roychoudhury, Pavitra; Starita, Lea M.; Famulare, Michael; Huang, Meei-Li; Nalla, Arun; Pepper, Gregory; Reinhardt, Adam; Xie, Hong; Shrestha, Lasata; Nguyen, Truong N.; Adler, Amanda; Brandstetter, Elisabeth; Cho, Shari; Giroux, Danielle; Han, Peter D.; Fay, Kairsten; Frazar, Chris D.; Ilcisin, Misja; Lacombe, Kirsten; Lee, Jover; Kiavand, Anahita; Richardson, Matthew; Sibley, Thomas R.; Truong, Melissa; Wolf, Caitlin R.; Nickerson, Deborah A.; Rieder, Mark J.; Englund, Janet A.; Seattle Flu Study Investigators,; Hadfield, James; Hodcroft, Emma B.; Huddleston, John; Moncla, Louise H.; Müller, Nicola F.; Neher, Richard A.; Deng, Xianding; Gu, Wei; Federman, Scot; Chiu, Charles; Duchin, Jeffrey S.; Gautom, Romesh; Melly, Geoff; Hiatt, Brian; Dykema, Philip; Lindquist, Scott; Queen, Krista; Tao, Ying; Uehara, Anna; Tong, Suxiang; MacCannell, Duncan; Armstrong, Gregory L.; Baird, Geoffrey S.; Chu, Helen Y.; Shendure, Jay; Jerome, Keith R.
2020
Cryptic transmission of SARS-CoV-2 in Washington state
Science
4613171
Müller, Nicola F.; Wüthrich, Daniel; Goldman, Nina; Sailer, Nadine; Saalfrank, Claudia; Brunner, Myrta; Augustin, Noémi; Seth-Smith, Helena Mb; Hollenstein, Yvonne; Syedbasha, Mohammedyaseen; Lang, Daniela; Neher, Richard A.; Dubuis, Olivier; Naegele, Michael; Buser, Andreas; Nickel, Christian H.; Ritz, Nicole; Zeller, Andreas; Lang, Brian M.; Hadfield, James; Bedford, Trevor; Battegay, Manuel; Schneider-Sliwa, Rita; Egli, Adrian; Stadler, Tanja
2020
Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics
PLoS Pathogens
4627413
Puller, Vadim; Sagulenko, Pavel; Neher, Richard A.
2020
Efficient inference, potential, and limitations of site-specific substitution models
Virus Evolution
Showing records 1 - 20 (of 87)