Prof. Dr. Richard Neher

Molari, Marco, Shaw, Liam P., & Neher, Richard A. (2025). Quantifying the Evolutionary Dynamics of Structure and Content in Closely Related E. coli Genomes. Molecular Biology and Evolution, 42(1). https://doi.org/10.1093/molbev/msae272

Barrat-Charlaix, Pierre, & Neher, Richard A. (2024). Eco-evolutionary dynamics of adapting pathogens and host immunity. eLife, 13. https://doi.org/10.7554/eLife.97350

Dyrdak, Robert, Hodcroft, Emma B., Broddesson, Sandra, Grabbe, Malin, Franklin, Hildur, Gisslén, Magnus, Holm, Maricris E., Lindh, Magnus, Nederby-Öhd, Joanna, Ringlander, Johan, Sundqvist, Martin, Neher, Richard A., & Albert, Jan. (2024). Early unrecognised SARS-CoV-2 introductions shaped the first pandemic wave, Sweden, 2020 [Journal-article]. Eurosurveillance, 29(41). https://doi.org/10.2807/1560-7917.ES.2024.29.41.2400021

Goya, Stephanie, Ruis, Christopher, Neher, Richard A., Meijer, Adam, Aziz, Ammar, Hinrichs, Angie S., von Gottberg, Anne, Roemer, Cornelius, Amoako, Daniel G., Acuña, Dolores, McBroome, Jakob, Otieno, James R., Bhiman, Jinal N., Everatt, Josie, Muñoz-Escalante, Juan C., Ramaekers, Kaat, Duggan, Kate, Presser, Lance D., Urbanska, Laura, et al. (2024). Standardized Phylogenetic Classification of Human Respiratory Syncytial Virus below the Subgroup Level. Emerging Infectious Diseases, 30(8), 1631–1641. https://doi.org/10.3201/eid3008.240209

Wegner, Fanny, Cabrera-Gil, Blanca, Tanguy, Araud, Beckmann, Christiane, Beerenwinkel, Niko, Bertelli, Claire, Carrara, Matteo, Cerutti, Lorenzo, Chen, Chaoran, Cordey, Samuel, Dumoulin, Alexis, Plessis, Louis du, Friedli, Marc, Gerth, Yannick, Greub, Gilbert, Härri, Adrian, Hirsch, Hans, Howald, Cedric, Huber, Michael, et al. (2024). How much should we sequence? An analysis of the Swiss SARSCoV-2 surveillance effort. Microbiology Spectrum, 12(5). https://doi.org/10.1128/spectrum.03628-23

Goya, S., Ruis, C., Neher, R. A., Meijer, A., Aziz, A., Hinrichs, A. S., von Gottberg, A., Roemer, C., Amoako, D. G., Acuña, D., McBroome, J., Otieno, J. R., Bhiman, J. N., Everatt, J., Muñoz-Escalante, J. C., Ramaekers, K., Duggan, K., Presser, L. D., Urbanska, L., et al. (2024). The unified proposal for classification of human respiratory syncytial virus below the subgroup level [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.02.13.24302237

Germuskova, Zoja, Sosa, Elisa, Lagos, Amaya Campillay, Aamot, Hege Vangstein, Beale, Mathew A., Bertelli, Claire, Björkmann, Jonas, Couto, Natacha, Feige, Lena, Greub, Gilbert, Hallbäck, Erika Tång, Hodcroft, Emma B., Harmsen, Dag, Jacob, Laurent, Jolley, Keith A., Kahles, Andre, Mather, Alison E., Neher, Richard A., Neves, Aitana, et al. (2024, January 1). Conference report: the first bacterial genome sequencing pan-European network conference. Microbes and Infection. https://doi.org/10.1016/j.micinf.2024.105410

Lustig, Gila, Ganga, Yashica, Rodel, Hylton E, Tegally, Houriiyah, Khairallah, Afrah, Jackson, Laurelle, Cele, Sandile, Khan, Khadija, Jule, Zesuliwe, Reedoy, Kajal, Karim, Farina, Bernstein, Mallory, Ndung’u, Thumbi, Moosa, Mahomed-Yunus S, Archary, Derseree, De Oliveira, Tulio, Lessells, Richard, Neher, Richard A, Abdool Karim, Salim S, & Sigal, Alex. (2024). SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations. Virus Evolution, 10(1). https://doi.org/10.1093/ve/vead075

Sigal, Alex, Neher, Richard A., & Lessells, Richard J. (2024). The consequences of SARS-CoV-2 within-host persistence. Nature Reviews Microbiology. https://doi.org/10.1038/s41579-024-01125-y

Sollier, Julie, Basler, Marek, Broz, Petr, Dittrich, Petra S., Drescher, Knut, Egli, Adrian, Harms, Alexander, Hierlemann, Andreas, Hiller, Sebastian, King, Carolyn G., McKinney, John D., Moran-Gilad, Jacob, Neher, Richard A., Page, Malcolm G. P., Panke, Sven, Persat, Alexandre, Picotti, Paola, Rentsch, Katharina M., Rivera-Fuentes, Pablo, et al. (2024). Revitalizing antibiotic discovery and development through in vitro modelling of in-patient conditions. Nature Microbiology, 9(1), 1–3. https://doi.org/10.1038/s41564-023-01566-w

Khan, Khadija, Lustig, Gila, Römer, Cornelius, Reedoy, Kajal, Jule, Zesuliwe, Karim, Farina, Ganga, Yashica, Bernstein, Mallory, Baig, Zainab, Jackson, Laurelle, Mahlangu, Boitshoko, Mnguni, Anele, Nzimande, Ayanda, Stock, Nadine, Kekana, Dikeledi, Ntozini, Buhle, van Deventer, Cindy, Marshall, Terry, Manickchund, Nithendra, et al. (2023). Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-43703-3

Shaw, Liam P., & Neher, Richard A. (2023). Visualizing and quantifying structural diversity around mobile resistance genes. Microbial Genomics, 9(12). https://doi.org/10.1099/mgen.0.001168

O’Toole, Á., Neher, R. A., Ndodo, N., Borges, V., Gannon, B., Gomes, J. P., Groves, N., King, D. J., Maloney, D., Lemey, P., Lewandowski, K., Loman, N., Myers, R., Omah, I. F., Suchard, M. A., Worobey, M., Chand, M., Ihekweazu, C., Ulaeto, D., et al. (2023). APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016 [Journal-article]. Science, 382(6670), 595–600. https://doi.org/10.1126/science.adg8116

Borges, V., Duque, M. P., Martins, J. V., Vasconcelos, P., Ferreira, R., Sobral, D., Pelerito, A., de Carvalho, I. L., Núncio, M. S., Borrego, M. J., Roemer, C., Neher, R. A., O’Driscoll, M., Rocha, R., Lopo, S., Neves, R., Palminha, P., Coelho, L., Nunes, A., et al. (2023). Viral genetic clustering and transmission dynamics of the 2022 mpox outbreak in Portugal. Nature Medicine, 29(10), 2509–2517. https://doi.org/10.1038/s41591-023-02542-x

Inzaule, S. C., Siedner, M. J., Little, S. J., Avila-Rios, S., Ayitewala, A., Bosch, R. J., Calvez, V., Ceccherini-Silberstein, F., Charpentier, C., Descamps, D., Eshleman, S. H., Fokam, J., Frenkel, L. M., Gupta, R. K., Ioannidis, J. P. A., Kaleebu, P., Kantor, R., Kassaye, S. G., Kosakovsky Pond, S. L., et al. (2023). Recommendations on data sharing in HIV drug resistance research. PLoS Medicine, 20(9 September). https://doi.org/10.1371/journal.pmed.1004293

Shaw, L. P., & Neher, R. A. (2023). Visualizing and quantifying structural diversity around mobile AMR genes [Posted-content]. bioRxiv. https://doi.org/10.1101/2023.08.07.551646

Noll, N., Molari, M., Shaw, L. P., & Neher, R. A. (2023). PanGraph: scalable bacterial pan-genome graph construction. Microbial Genomics, 9(6). https://doi.org/10.1099/mgen.0.001034

Bloom, J. D., Beichman, A. C., Neher, R. A., & Harris, K. (2023). Evolution of the SARS-CoV-2 Mutational Spectrum. Molecular Biology and Evolution, 40(4). https://doi.org/10.1093/molbev/msad085

Dadonaite, B., Crawford, K. H. D., Radford, C. E., Farrell, A. G., Yu, T. C., Hannon, W. W., Zhou, P., Andrabi, R., Burton, D. R., Liu, L., Ho, D. D., Chu, H. Y., Neher, R. A., & Bloom, J. D. (2023). A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike. Cell, 186(6), 1263–1278. https://doi.org/10.1016/j.cell.2023.02.001

Bloom, J. D., & Neher, R. A. (2023). Fitness effects of mutations to SARS-CoV-2 proteins [Posted-content]. bioRxiv. https://doi.org/10.1101/2023.01.30.526314

O’Toole, Á., Neher, R. A., Ndodo, N., Borges, V., Gannon, B., Gomes, J. P., Groves, N., King, D. J., Maloney, D., Lemey, P., Lewandowski, K., Loman, N., Myers, R., Suchard, M. A., Worobey, M., Chand, M., Ihekweazu, C., Ulaeto, D., Adetifa, I., & Rambaut, A. (2023). Putative APOBEC3 deaminase editing in MPXV as evidence for sustained human transmission since at least 2016 [Posted-content]. bioRxiv. https://doi.org/10.1101/2023.01.23.525187

Bloom, J. D., & Neher, R. A. (2023). Fitness effects of mutations to SARS-CoV-2 proteins. Virus Evolution, 9(2). https://doi.org/10.1093/ve/vead055

Druelle, V., & Neher, R. A. (2023). Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates. Virus Evolution, 9(1). https://doi.org/10.1093/ve/veac118

Lee, J., Hadfield, J., Black, A., Sibley, T. R., Neher, R. A., Bedford, T., & Huddleston, J. (2023). Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition. Frontiers in Bioinformatics, 3. https://doi.org/10.3389/fbinf.2023.1069487

Neves, A., Walther, D., Martin-Campos, T., Barbie, V., Bertelli, C., Blanc, D., Bouchet, G., Erard, F., Greub, G., Hirsch, H. H., Huber, M., Kaiser, L., Leib, S. L., Leuzinger, K., Lazarevic, V., Mäusezahl, M., Molina, J., Neher, R. A., Perreten, V., et al. (2023). The Swiss Pathogen Surveillance Platform – towards a nationwide One Health data exchange platform for bacterial, viral and fungal genomics and associated metadata. Microbial Genomics, 9(5). https://doi.org/10.1099/mgen.0.001001

Bloom, Jesse D, Beichman, Annabel C, Neher, Richard A, & Harris, Kelley. (2022). Evolution of the SARS-CoV-2 mutational spectrum [Posted-content]. bioRxiv. https://doi.org/10.1101/2022.11.19.517207

Barrat-Charlaix, Pierre, Vaughan, Timothy G., & Neher, Richard A. (2022). TreeKnit: Inferring ancestral reassortment graphs of influenza viruses. PLoS Computational Biology, 18(8), e1010394. https://doi.org/10.1371/journal.pcbi.1010394

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, et al. (2022). Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus. PLoS Biology, 20(8), e3001769. https://doi.org/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. https://doi.org/10.1371/journal.ppat.1010515

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, 11, 50. https://doi.org/10.7554/elife.71345

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., et al. (2022). Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data. Science Translational Medicine, 15(680), eabn7979. https://doi.org/10.1126/scitranslmed.abn7979

Neher, R. A. (2022). Contributions of adaptation and purifying selection to SARS-CoV-2 evolution. Virus Evolution, 8(2). https://doi.org/10.1093/ve/veac113

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, 100654. https://doi.org/10.1016/j.epidem.2022.100654

Barrat-Charlaix, Pierre, Vaughan, Timothy G., & Neher, Richard A. (2021). TreeKnit: Inferring Ancestral Reassortment Graphs of influenza viruses [Posted-content]. bioRxiv. https://doi.org/10.1101/2021.12.20.473456

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, 6(67), 3773. https://doi.org/10.21105/joss.03773

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, 38(7), 2767–2777. https://doi.org/10.1093/molbev/msab065

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, et al. (2021). Molecular Epidemiology and Evolutionary Trajectory of Emerging Echovirus 30, Europe. Emerging infectious diseases, 27(6), 1616–1626. https://doi.org/10.3201/eid2706.203096

Bloom, Jesse D., Chan, Yujia Alina, Baric, Ralph S., Bjorkman, Pamela J., Cobey, Sarah, Deverman, Benjamin E., Fisman, David N., Gupta, Ravindra, Iwasaki, Akiko, Lipsitch, Marc, Medzhitov, Ruslan, Neher, Richard A., Nielsen, Rasmus, Patterson, Nick, Stearns, Tim, van Nimwegen, Erik, Worobey, Michael, & Relman, David A. (2021). Investigate the origins of COVID-19. Science, 372(6543), 694. https://doi.org/10.1126/science.abj0016

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, 27(8), 1109–1117. https://doi.org/10.1016/j.cmi.2021.05.022

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, 136(March), 104754. https://doi.org/10.1016/j.jcv.2021.104754

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., et al. (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), 9040677. https://doi.org/10.3390/microorganisms9040677

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, 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, 595(7869), 707–712. https://doi.org/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), 4. https://doi.org/10.21105/joss.02906

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, et al. (2021). SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse. Nature Microbiology, 6(7), 821–823. https://doi.org/10.1038/s41564-021-00932-w

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., Brazil-UK Cadde Genomic Network, Singh, Lavanya, Tegally, Houriiyah, Anyaneji, Ugochukwu J., Network for Genomic Surveillance in South Africa, Hodcroft, Emma B., et al. (2021). Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. PLoS Biology, 19(5), e3001236. https://doi.org/10.1371/journal.pbio.3001236

Huisman, Jana S., Scire, Jérémie, Angst, Daniel C., Li, Jinzhou, Neher, Richard A., Maathuis, Marloes H., Bonhoeffer, Sebastian, & Stadler, Tanja. (2020). Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2 [Posted-content]. medRxiv. https://doi.org/10.1101/2020.11.26.20239368

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, González Candelas, Fernando, Stadler, Tanja, & Neher, Richard A. (2020). Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020 [Posted-content]. medRxiv. https://doi.org/10.1101/2020.10.25.20219063

Dyrdak, R., Hodcroft, E. B., Wahlund, M., Neher, R. A., & Albert, J. (2020). Interactions between seasonal human coronaviruses and implications for the SARS-CoV-2 pandemic: A retrospective study in Stockholm, Sweden, 2009-2020 [Posted-content]. medRxiv . https://doi.org/10.1101/2020.10.01.20205096

Barrat-Charlaix, Pierre, Huddleston, John, Bedford, Trevor, & Neher, Richard A. (2020). Limited predictability of amino acid substitutions in seasonal influenza viruses [Posted-content]. bioRxiv. https://doi.org/10.1101/2020.07.31.231100

Morris, Dylan H., Petrova, Velislava N., Rossine, Fernando W., Parker, Edyth, Grenfell, Bryan T., Neher, Richard A., Levin, Simon A., & Russell, Colin A. (2020). Asynchrony between virus diversity and antibody selection limits influenza virus evolution [Posted-content]. bioRxiv. https://doi.org/10.1101/2020.04.27.064915

Jackson, Laurelle, Cele, Sandile, Lustig, Gila, Giandhari, Jennifer, de Oliveira, Tulio, Neher, Richard A., & Sigal, Alex. (2020). Complementation can maintain a quasispecies of drug sensitive and resistant HIV [Posted-content]. bioRxiv. https://doi.org/10.1101/2020.04.20.051854

Egli, Adrian, Goldman, Nina, Müller, Nicola F., Brunner, Myrta, Wüthrich, Daniel, Tschudin-Sutter, Sarah, Hodcroft, Emma, Neher, Richard, Saalfrank, Claudia, Hadfield, James, Bedford, Trevor, Syedbasha, Mohammedyaseen, Vogel, Thomas, Augustin, Noémie, Bauer, Jan, Sailer, Nadine, Amar-Sliwa, Nadezhda, Lang, Daniela, Seth-Smith, Helena M.B., et al. (2020). High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters [Posted-content]. bioRxiv. https://doi.org/10.1101/2020.04.03.023135

Neher, Richard A., Dyrdak, Robert, Druelle, Valentin, Hodcroft, Emma B., & Albert, Jan. (2020). Potential impact of seasonal forcing on a SARS-CoV-2 pandemic [Posted-content]. medRxiv. https://doi.org/10.1101/2020.02.13.20022806

Puller, Vadim, Sagulenko, Pavel, & Neher, Richard A. (2020). Efficient inference, potential, and limitations of site-specific substitution models [Posted-content]. bioRxiv. https://doi.org/10.1101/2020.01.18.911255

Alm, Erik, Broberg, Eeva K., Connor, Thomas, Hodcroft, Emma B., Komissarov, Andrey B., Maurer-Stroh, Sebastian, Melidou, Angeliki, Neher, Richard A., O’Toole, Áine, & Pereyaslov, Dmitriy. (2020). Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. Eurosurveillance, 25(32), 7–14. https://doi.org/10.2807/1560-7917.es.2020.25.32.2001410

Battegay, Manuel, Kuehl, Richard, Tschudin-Sutter, Sarah, Hirsch, Hans H., Widmer, Andreas F., & Neher, Richard A. (2020). 2019-novel Coronavirus (2019-nCoV): estimating the case fatality rate - a word of caution. Swiss Medical Weekly, 150, w20203. https://doi.org/10.4414/smw.2020.20203

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., et al. (2020). Cryptic transmission of SARS-CoV-2 in Washington state. Science, 370(6516), 571–575. https://doi.org/10.1126/science.abc0523

Fauver, Joseph R., Petrone, Mary E., Hodcroft, Emma B., Shioda, Kayoko, Ehrlich, Hanna Y., Watts, Alexander G., Vogels, Chantal B. F., Brito, Anderson F., Alpert, Tara, Muyombwe, Anthony, Razeq, Jafar, Downing, Randy, Cheemarla, Nagarjuna R., Wyllie, Anne L., Kalinich, Chaney C., Ott, Isabel M., Quick, Joshua, Loman, Nicholas J., Neugebauer, Karla M., et al. (2020). Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States. Cell, 181(5), 990–996. https://doi.org/10.1016/j.cell.2020.04.021

Huddleston, John, Barnes, John R., Rowe, Thomas, Xu, Xiyan, Kondor, Rebecca, Wentworth, David E., Whittaker, Lynne, Ermetal, Burcu, Daniels, Rodney Stuart, McCauley, John W., Fujisaki, Seiichiro, Nakamura, Kazuya, Kishida, Noriko, Watanabe, Shinji, Hasegawa, Hideki, Barr, Ian, Subbarao, Kanta, Barrat-Charlaix, Pierre, Neher, Richard A., & Bedford, Trevor. (2020). Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution. eLife, 9, e60067. https://doi.org/10.7554/elife.60067

Mavian, Carla, Pond, Sergei Kosakovsky, Marini, Simone, Magalis, Brittany Rife, Vandamme, Anne-Mieke, Dellicour, Simon, Scarpino, Samuel V., Houldcroft, Charlotte, Villabona-Arenas, Julian, Paisie, Taylor K., Trovão, Nídia S., Boucher, Christina, Zhang, Yun, Scheuermann, Richard H., Gascuel, Olivier, Lam, Tommy Tsan-Yuk, Suchard, Marc A., Abecasis, Ana, Wilkinson, Eduan, et al. (2020). Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. Proceedings of the National Academy of Sciences of the United States of America, 117(23), 12522–12523. https://doi.org/10.1073/pnas.2007295117

Morris, Dylan H., Petrova, Velislava N., Rossine, Fernando W., Parker, Edyth, Grenfell, Bryan T., Neher, Richard A., Levin, Simon A., & Russell, Colin A. (2020). Asynchrony between virus diversity and antibody selection limits influenza virus evolution. eLife, 9, e62105. https://doi.org/10.7554/elife.62105

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., et al. (2020). Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics. PLoS Pathogens, 16(11), e1008984. https://doi.org/10.1371/journal.ppat.1008984

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, 150, w20224. https://doi.org/10.4414/smw.2020.20224

Noll, Nicholas B., Aksamentov, Ivan, Druelle, Valentin, Badenhorst, Abrie, Ronzani, Bruno, Jefferies, Gavin, Albert, Jan, & Neher, Richard A. (2020). COVID-19 Scenarios: an interactive tool to explore the spread and associated morbidity and mortality of SARS-CoV-2. medRxiv. https://doi.org/10.1101/2020.05.05.20091363

Puller, Vadim, Sagulenko, Pavel, & Neher, Richard A. (2020). Efficient inference, potential, and limitations of site-specific substitution models. Virus Evolution, 6(2), veaa066. https://doi.org/10.1093/ve/veaa066

Salathé, Marcel, Althaus, Christian L., Neher, Richard, Stringhini, Silvia, Hodcroft, Emma, Fellay, Jacques, Zwahlen, Marcel, Senti, Gabriela, Battegay, Manuel, Wilder-Smith, Annelies, Eckerle, Isabella, Egger, Matthias, & Low, Nicola. (2020). COVID-19 epidemic in Switzerland: on the importance of testing, contact tracing and isolation. Swiss Medical Weekly, 150, w20225. https://doi.org/10.4414/smw.2020.20225

Bedford, Trevor, Huddleston, John, Potter, Barney, & Neher, Richard A. (2019). Seasonal influenza circulation patterns and projections for September 2019 to September 2020 [Posted-content]. bioRxiv. https://doi.org/10.1101/780627

Potter, Barney I., Garten, Rebecca, Hadfield, James, Huddleston, John, Barnes, John, Rowe, Thomas, Guo, Lizheng, Xu, Xiyan, Neher, Richard A., Bedford, Trevor, & Wentworth, David. (2019). Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season [Posted-content]. bioRxiv. https://doi.org/10.1101/543322

Carvajal-Yepes, M., Cardwell, K., Nelson, A., Garrett, K. A., Giovani, B., Saunders, D. G. O., Kamoun, S., Legg, J. P., Verdier, V., Lessel, J., Neher, R. A., Day, R., Pardey, P., Gullino, M. L., Records, A. R., Bextine, B., Leach, J. E., Staiger, S., & Tohme, J. (2019). A global surveillance system for crop diseases. Science, 364(6447), 1237–1239. https://doi.org/10.1126/science.aaw1572

Cunrath, Olivier, Meinel, Dominik M., Maturana, Pauline, Fanous, Joseph, Buyck, Julien M., Saint Auguste, Pamela, Seth-Smith, Helena M. B., Körner, Jonas, Dehio, Christoph, Trebosc, Vincent, Kemmer, Christian, Neher, Richard, Egli, Adrian, & Bumann, Dirk. (2019). Quantitative contribution of efflux to multi-drug resistance of clinical Escherichia coli and Pseudomonas aeruginosa strains. EBioMedicine, 41, 479–487. https://doi.org/10.1016/j.ebiom.2019.02.061

Dyrdak, Robert, Mastafa, Monika, Hodcroft, Emma B., Neher, Richard A., & Albert, Jan. (2019). Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing. Virus Evolution, 5(1), vez007. https://doi.org/10.1093/ve/vez007

Egli, Adrian, Koch, Daniel, Danuser, Jürg, Hendriksen, Rene S., Driesen, Susanne, Schmid, Diana Coman, Neher, Richard, Mäusezahl, Mirjam, Seth-Smith, Helena M. B., Bloemberg, Guido, Tschudin-Sutter, Sarah, Endimiani, Andrea, Perreten, Vincent, Greub, Gilbert, Schrenzel, Jacques, & Stephan, Roger. (2019). Symposium report: One Health meets sequencing. Microbes and Infection, 22(1), 1–7. https://doi.org/10.1016/j.micinf.2019.07.004

Potter, Barney I., Kondor, Rebecca, Hadfield, James, Huddleston, John, Barnes, John, Rowe, Thomas, Guo, Lizheng, Xu, Xiyan, Neher, Richard A., Bedford, Trevor, & Wentworth, David E. (2019). Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season. Virus Evolution, 5(2). https://doi.org/10.1093/ve/vez046

Wüthrich, Daniel, Lang, Daniela, Müller, Nicola F., Neher, Richard A., Stadler, Tanja, & Egli, Adrian. (2019). Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses. Journal of Virological Methods, 266, 30–33. https://doi.org/10.1016/j.jviromet.2019.01.009

Yan, Le, Neher, Richard A., & Shraiman, Boris I. (2019). Phylodynamic theory of persistence, extinction and speciation of rapidly adapting pathogens. eLife, 8, e44205. https://doi.org/10.7554/elife.44205

Noll, Nicholas, Urich, Eric, Wüthrich, Daniel, Hinic, Vladimira, Egli, Adrian, & Neher, Richard A. (2018). Resolving structural diversity of Carbapenemase-producing gram-negative bacteria using single molecule sequencing [Posted-content]. bioRxiv. https://doi.org/10.1101/456897

Yan, Le, Neher, Richard A., & Shraiman, Boris I. (2018). Phylodynamics of rapidly adapting pathogens: extinction and speciation of a Red Queen [Posted-content]. bioRxiv. https://doi.org/10.1101/455444

Dyrdak, Robert, Mastafa, Monika, Hodcroft, Emma B., Neher, Richard A., & Albert, Jan. (2018). Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing [Posted-content]. bioRxiv. https://doi.org/10.1101/420836

Neher, Richard A. (2018). Efficient estimation of evolutionary rates by covariance aware regression [Posted-content]. bioRxiv. https://doi.org/10.1101/408005

Neher, Richard A., & Bedford, Trevor. (2018). Real-time analysis and visualization of pathogen sequence data [Posted-content]. bioRxiv. https://doi.org/10.1101/286187

Bedford, Trevor, & Neher, Richard A. (2018). Seasonal influenza circulation patterns and projections for Feb 2018 to Feb 2019 [Posted-content]. bioRxiv. https://doi.org/10.1101/271114

Egli, Adrian, Blanc, Dominique S., Greub, Gilbert, Keller, Peter M., 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(49-50), w14693. https://doi.org/10.4414/smw.2018.14693

Hadfield, James, Megill, Colin, Bell, Sidney M., Huddleston, John, Potter, Barney, Callender, Charlton, Sagulenko, Pavel, Bedford, Trevor, & Neher, Richard A. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121–4123. https://doi.org/10.1093/bioinformatics/bty407

Jackson, Laurelle, Hunter, Jessica, Cele, Sandile, Ferreira, Isabella Markham, Young, Andrew C., Karim, Farina, Madansein, Rajhmun, Dullabh, Kaylesh J., Chen, Chih-Yuan, Buckels, Noel J., Ganga, Yashica, Khan, Khadija, Boulle, Mikael, Lustig, Gila, Neher, Richard A., & Sigal, Alex. (2018). Incomplete inhibition of HIV infection results in more HIV infected lymph node cells by reducing cell death. eLife, 7(e30134), 1–24. https://doi.org/10.7554/elife.30134

Javed, Mumina, Ueltzhoeffer, Viola, Heinrich, Maximilian, Siegrist, Hans Justus, Wildermuth, Ronja, Lorenz, Freia-Raphaella, Neher, Richard A., & Willmann, Matthias. (2018). Colistin susceptibility test evaluation of multiple-resistance-level Pseudomonas aeruginosa isolates generated in a morbidostat device. The journal of antimicrobial chemotherapy, 73(12), 3368–3374. https://doi.org/10.1093/jac/dky337

Karasov, Talia L., Almario, Juliana, Friedemann, Claudia, Ding, Wei, Giolai, Michael, Heavens, Darren, Kersten, Sonja, Lundberg, Derek S., Neumann, Manuela, Regalado, Julian, Neher, Richard A., Kemen, Eric, & Weigel, Detlef. (2018). Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales. Cell Host & Microbe, 24(1), 168–179. https://doi.org/10.1016/j.chom.2018.06.011

Neher, Richard A., & Bedford, Trevor. (2018). Real-time analysis and visualization of pathogen sequence data. Journal of Clinical Microbiology, 56(11), e00480–18. https://doi.org/10.1128/jcm.00480-18

Sagulenko, Pavel, Puller, Vadim, & Neher, Richard A. (2018). TreeTime: Maximum-likelihood phylodynamic analysis. Virus Evolution, 4(1), vex042. https://doi.org/10.1093/ve/vex042

Bedford, Trevor, & Neher, Richard A. (2017). Seasonal influenza circulation patterns and projections for Sep 2017 to Sep 2018 [Posted-content]. bioRxiv. https://doi.org/10.1101/191676

Sagulenko, Pavel, Puller, Vadim, & Neher, Richard A. (2017). TreeTime: maximum likelihood phylodynamic analysis [Posted-content]. bioRxiv. https://doi.org/10.1101/153494

Puller, Vadim, Neher, Richard, & Albert, Jan. (2017). Estimating time of HIV-1 infection from next-generation sequence diversity [Posted-content]. bioRxiv. https://doi.org/10.1101/129387

Bedford, Trevor, & Neher, Richard A. (2017). Seasonal influenza circulation patterns and projections for 2017-2018 [Posted-content]. bioRxiv. https://doi.org/10.1101/113035

Ding, Wei, Baumdicker, Franz, & Neher, Richard A. (2017). panX: pan-genome analysis and exploration. Nucleic Acids Research, 46(1), e5. https://doi.org/10.1093/nar/gkx977

Morris, Dylan H., Gostic, Katelyn M., Pompei, Simone, Bedford, Trevor, Łuksza, Marta, Neher, Richard A., Grenfell, Bryan T., Lässig, Michael, & McCauley, John W. (2017). Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology. Trends in Microbiology, 26(2), 102–118. https://doi.org/10.1016/j.tim.2017.09.004

Puller, Vadim, Neher, Richard, & Albert, Jan. (2017). Estimating time of HIV-1 infection from next-generation sequence diversity. PLoS Computational Biology, 13(10), e1005775. https://doi.org/10.1371/journal.pcbi.1005775

Regenbogen, Bianca, Willmann, Matthias, Steglich, Matthias, Bunk, Boyke, Nübel, Ulrich, Peter, Silke, & Neher, Richard A. (2017). Rapid and consistent evolution of colistin resistance in XDR Pseudomonas aeruginosa during morbidostat culture. Antimicrobial Agents and Chemotherapy, 61(9), e00043–17. https://doi.org/10.1128/aac.00043-17

You, Yuan, Sawikowska, Aneta, Neumann, Manuela, Posé, David, Capovilla, Giovanna, Langenecker, Tobias, Neher, Richard A., Krajewski, Pawel, & Schmid, Markus. (2017). Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering. Nature Communications, 8, 15120. https://doi.org/10.1038/ncomms15120

Zanini, Fabio, Puller, Vadim, Brodin, Johanna, Albert, Jan, & Neher, Richard A. (2017). In vivo mutation rates and the landscape of fitness costs of HIV-1. Virus Evolution, 3(1), vex003. https://doi.org/10.1093/ve/vex003

Regenbogen, B., Willmann, M., Steglich, M., Bunk, B., Nübel, U., Peter, S., & Neher, R. A. (2016, October 14). Rapid and consistent evolution of colistin resistance in<i>Pseudomonas aeruginosa</i>during morbidostat culture [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/080960

Bedford, T., & Neher, R. A. (2016, September 21). Seasonal influenza circulation patterns and projections for 2016-2017 [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/076638