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Neves, Aitana; Walther, Daniel; Martin-Campos, Trinidad; Barbie, Valerie; Bertelli, Claire; Blanc, Dominique; Bouchet, Gérard; Erard, Frédéric; Greub, Gilbert; Hirsch, Hans H; Huber, Michael; Kaiser, Laurent; Leib, Stephen L; Leuzinger, Karoline; Lazarevic, Vladimir; Mäusezahl, Mirjam; Molina, Jorge; Neher, Richard A; Perreten, Vincent; Ramette, Alban; ... (2023). The Swiss Pathogen Surveillance Platform - towards a nation-wide One Health data exchange platform for bacterial, viral and fungal genomics and associated metadata. Microbial genomics, 9(5) Microbiology Society 10.1099/mgen.0.001001
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; ... (2023). Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data. Science translational medicine, 15(680), eabn7979. American Association for the Advancement of Science 10.1126/scitranslmed.abn7979
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, 41, p. 100654. Elsevier 10.1016/j.epidem.2022.100654
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; ... (2022). Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus [perspective]. PLoS biology, 20(8), e3001769. Public Library of Science 10.1371/journal.pbio.3001769
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, 18(5), e1010515. Public Library of Science 10.1371/journal.ppat.1010515
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, Iñaki; Candelas, Fernando González; Stadler, Tanja; Neher, Richard A (2021). Spread of a SARS-CoV-2 variant through Europe in the summer of 2020. Nature, 595(7869), pp. 707-712. Springer Nature 10.1038/s41586-021-03677-y
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, 6(57), p. 2906. Open Journals 10.21105/joss.02906
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; Magalhães Ferreira, Giulia; Crispim, Myuki A E; Singh, Lavanya; Tegally, Houriiyah; Anyaneji, Ugochukwu J; Hodcroft, Emma B.; Mason, Christopher E; Khullar, Gaurav; Metti, Jessica; ... (2021). Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. PLoS biology, 19(5), e3001236. Public Library of Science 10.1371/journal.pbio.3001236
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; ... (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, 9(4), p. 677. MDPI 10.3390/microorganisms9040677
Egli, Adrian; Blanc, Dominique S; Greub, Gilbert; Keller, Peter Michael; Lazarevic, Vladimir; Lebrand, Aitana; Leib, Stephen; Neher, Richard A; Perreten, Vincent; Ramette, Alban; Schrenzel, Jacques; Stephan, Roger; Wagner, Karolin; Wuethrich, Daniel; Xenarios, Ioannis (2018). Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform. Swiss medical weekly, 148(w14693), w14693. EMH Media 10.4414/smw.2018.14693
