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Hodcroft, Emma B. and Dyrdak, Robert and Andrés, Cristina and Egli, Adrian and Reist, Josiane and García Martínez de Artola, Diego and Alcoba-Flórez, Julia and Niesters, Hubert G. M. and Antón, Andrés and Poelman, Randy and Reynders, Marijke and Wollants, Elke and Neher, Richard A. and Albert, Jan. (2022) Evolution, geographic spreading, and demographic distribution of Enterovirus D68. PLoS Pathogens, 18 (5). e1010515.

Huisman, Jana S. and Scire, Jérémie and Angst, Daniel C. and Li, Jinzhou and Neher, Richard A. and Maathuis, Marloes H. and Bonhoeffer, Sebastian and Stadler, Tanja. (2022) Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2. eLife, 11. p. 50.

Barrat-Charlaix, Pierre and Vaughan, Timothy G. and Neher, Richard A.. (2022) TreeKnit: Inferring ancestral reassortment graphs of influenza viruses. PLoS Computational Biology, 18 (8). e1010394.

Happi, Christian and Adetifa, Ifedayo and Mbala, Placide and Njouom, Richard and Nakoune, Emmanuel and Happi, Anise and Ndodo, Nnaemeka and Ayansola, Oyeronke and Mboowa, Gerald and Bedford, Trevor and Neher, Richard A. and Roemer, Cornelius and Hodcroft, Emma and Tegally, Houriiyah and O'Toole, Áine and Rambaut, Andrew and Pybus, Oliver and Kraemer, Moritz U. G. and Wilkinson, Eduan and Isidro, Joana and Borges, Vítor and Pinto, Miguel and Gomes, João Paulo and Freitas, Lucas and Resende, Paola C. and Lee, Raphael T. C. and Maurer-Stroh, Sebastian and Baxter, Cheryl and Lessells, Richard and Ogwell, Ahmed E. and Kebede, Yenew and Tessema, Sofonias K. and de Oliveira, Tulio. (2022) Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus. PLoS Biology, 20 (8). e3001769.

Reichmuth, Martina L. and Hodcroft, Emma B. and Riou, Julien and Neher, Richard A. and Hens, Niel and 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.

Nadeau, Sarah A. and Vaughan, Timothy G. and Beckmann, Christiane and Topolsky, Ivan and Chen, Chaoran and Hodcroft, Emma and Schär, Tobias and Nissen, Ina and Santacroce, Natascha and Burcklen, Elodie and Ferreira, Pedro and Jablonski, Kim Philipp and Posada-Céspedes, Susana and Capece, Vincenzo and Seidel, Sophie and Santamaria de Souza, Noemi and Martinez-Gomez, Julia M. and Cheng, Phil and Bosshard, Philipp P. and Levesque, Mitchell P. and Kufner, Verena and Schmutz, Stefan and Zaheri, Maryam and Huber, Michael and Trkola, Alexandra and Cordey, Samuel and Laubscher, Florian and Gonçalves, Ana Rita and Aeby, Sébastien and Pillonel, Trestan and Jacot, Damien and Bertelli, Claire and Greub, Gilbert and Leuzinger, Karoline and Stange, Madlen and Mari, Alfredo and Roloff, Tim and Seth-Smith, Helena and Hirsch, Hans H. and Egli, Adrian and Redondo, Maurice and Kobel, Olivier and Noppen, Christoph and du Plessis, Louis and Beerenwinkel, Niko and Neher, Richard A. and Beisel, Christian and Stadler, Tanja. (2022) Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data. Science Translational Medicine, 15 (680). eabn7979.

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

Boehm, Erik and Kronig, Ilona and Neher, Richard A. and Eckerle, Isabella and Vetter, Pauline and Kaiser, Laurent. (2021) Novel SARS-CoV-2 variants: the pandemics within the pandemic. Clinical microbiology and infection, 27 (8). pp. 1109-1117.

Barrat-Charlaix, Pierre and Huddleston, John and Bedford, Trevor and Neher, Richard A.. (2021) Limited Predictability of Amino Acid Substitutions in Seasonal Influenza Viruses. Molecular Biology and Evolution , 38 (7). pp. 2767-2777.

Konings, Frank and Perkins, Mark D. and Kuhn, Jens H. and Pallen, Mark J. and Alm, Erik J. and Archer, Brett N. and Barakat, Amal and Bedford, Trevor and Bhiman, Jinal N. and Caly, Leon and Carter, Lisa L. and Cullinane, Anne and de Oliveira, Tulio and Druce, Julian and El Masry, Ihab and Evans, Roger and Gao, George F. and Gorbalenya, Alexander E. and Hamblion, Esther and Herring, Belinda L. and Hodcroft, Emma and Holmes, Edward C. and Kakkar, Manish and Khare, Shagun and Koopmans, Marion P. G. and Korber, Bette and Leite, Juliana and MacCannell, Duncan and Marklewitz, Marco and Maurer-Stroh, Sebastian and Rico, Jairo Andres Mendez and Munster, Vincent J. and Neher, Richard and Munnink, Bas Oude and Pavlin, Boris I. and Peiris, Malik and Poon, Leo and Pybus, Oliver and Rambaut, Andrew and Resende, Paola and Subissi, Lorenzo and Thiel, Volker and Tong, Suxiang and van der Werf, Sylvie and von Gottberg, Anne and Ziebuhr, John and Van Kerkhove, Maria D.. (2021) SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse. Nature Microbiology, 6 (7). pp. 821-823.

Hodcroft, Emma B. and Zuber, Moira and Nadeau, Sarah and Vaughan, Timothy G. and Crawford, Katharine H. D. and Althaus, Christian L. and Reichmuth, Martina L. and Bowen, John E. and Walls, Alexandra C. and Corti, Davide and Bloom, Jesse D. and Veesler, David and Mateo, David and Hernando, Alberto and Comas, Iñaki and González-Candelas, Fernando and SeqCovid-Spain consortium, and Stadler, Tanja and Neher, Richard A.. (2021) Spread of a SARS-CoV-2 variant through Europe in the summer of 2020. Nature, 595 (7869). pp. 707-712.

Benschop, Kimberley S. M. and Broberg, Eeva K. and Hodcroft, Emma and Schmitz, Dennis and Albert, Jan and Baicus, Anda and Bailly, Jean-Luc and Baldvinsdottir, Gudrun and Berginc, Natasa and Blomqvist, Soile and Böttcher, Sindy and Brytting, Mia and Bujaki, Erika and Cabrerizo, Maria and Celma, Cristina and Cinek, Ondrej and Claas, Eric C. J. and Cremer, Jeroen and Dean, Jonathan and Dembinski, Jennifer L. and Demchyshyna, Iryna and Diedrich, Sabine and Dudman, Susanne and Dunning, Jake and Dyrdak, Robert and Emmanouil, Mary and Farkas, Agnes and De Gascun, Cillian and Fournier, Guillaume and Georgieva, Irina and Gonzalez-Sanz, Ruben and van Hooydonk-Elving, Jolanda and Jääskeläinen, Anne J. and Jancauskaite, Ruta and Keeren, Kathrin and Fischer, Thea K. and Krokstad, Sidsel and Nikolaeva-Glomb, Lubomira and Novakova, Ludmila and Midgley, Sofie E. and Mirand, Audrey and Molenkamp, Richard and Morley, Ursula and Mossong, Joël and Muralyte, Svajune and Murk, Jean-Luc and Nguyen, Trung and Nordbø, Svein A. and Österback, Riikka and Pas, Suzan and Pellegrinelli, Laura and Pogka, Vassiliki and Prochazka, Birgit and Rainetova, Petra and Van Ranst, Marc and Roorda, Lieuwe and Schuffenecker, Isabelle and Schuurman, Rob and Stoyanova, Asya and Templeton, Kate and Verweij, Jaco J. and Voulgari-Kokota, Androniki and Vuorinen, Tytti and Wollants, Elke and Wolthers, Katja C. and Zakikhany, Katherina and Neher, Richard and Harvala, Heli and Simmonds, Peter. (2021) Molecular Epidemiology and Evolutionary Trajectory of Emerging Echovirus 30, Europe. Emerging infectious diseases, 27 (6). pp. 1616-1626.

Vogels, Chantal B. F. and Breban, Mallery I. and Ott, Isabel M. and Alpert, Tara and Petrone, Mary E. and Watkins, Anne E. and Kalinich, Chaney C. and Earnest, Rebecca and Rothman, Jessica E. and Goes de Jesus, Jaqueline and Morales Claro, Ingra and Magalhães Ferreira, Giulia and Crispim, Myuki A. E. and Brazil-UK Cadde Genomic Network, and Singh, Lavanya and Tegally, Houriiyah and Anyaneji, Ugochukwu J. and Network for Genomic Surveillance in South Africa, and Hodcroft, Emma B. and Mason, Christopher E. and Khullar, Gaurav and Metti, Jessica and Dudley, Joel T. and MacKay, Matthew J. and Nash, Megan and Wang, Jianhui and Liu, Chen and Hui, Pei and Murphy, Steven and Neal, Caleb and Laszlo, Eva and Landry, Marie L. and Muyombwe, Anthony and Downing, Randy and Razeq, Jafar and de Oliveira, Tulio and Faria, Nuno R. and Sabino, Ester C. and Neher, Richard A. and Fauver, Joseph R. and Grubaugh, Nathan D.. (2021) Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. PLoS Biology, 19 (5). e3001236.

Goncalves Cabecinhas, Ana Rita and Roloff, Tim and Stange, Madlen and Bertelli, Claire and Huber, Michael and Ramette, Alban and Chen, Chaoran and Nadeau, Sarah and Gerth, Yannick and Yerly, Sabine and Opota, Onya and Pillonel, Trestan and Schuster, Tobias and Metzger, Cesar M. J. A. and Sieber, Jonas and Bel, Michael and Wohlwend, Nadia and Baumann, Christian and Koch, Michel C. and Bittel, Pascal and Leuzinger, Karoline and Brunner, Myrta and Suter-Riniker, Franziska and Berlinger, Livia and Søgaard, Kirstine K. and Beckmann, Christiane and Noppen, Christoph and Redondo, Maurice and Steffen, Ingrid and Seth-Smith, Helena M. B. and Mari, Alfredo and Lienhard, Reto and Risch, Martin and Nolte, Oliver and Eckerle, Isabella and Martinetti Lucchini, Gladys and Hodcroft, Emma B. and Neher, Richard A. and Stadler, Tanja and Hirsch, Hans H. and Leib, Stephen L. and Risch, Lorenz and Kaiser, Laurent and Trkola, Alexandra and Greub, Gilbert and 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, 9 (4). p. 9040677.

Dyrdak, Robert and Hodcroft, Emma B. and Wahlund, Martina and Neher, Richard A. and 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). p. 104754.

Huddleston, John and Hadfield, James and Sibley, Thomas R. and Lee, Jover and Fay, Kairsten and Ilcisin, Misja and Harkins, Elias and Bedford, Trevor and Neher, Richard A. and Hodcroft, Emma B.. (2021) Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. Journal of Open Source Software, 6 (57). p. 4.

Aksamentov, Ivan and Roemer, Cornelius and Hodcroft, Emma B. and Neher, Richard A.. (2021) Nextclade: clade assignment, mutation calling and quality control for viral genomes. Journal of Open Source Software, 6 (67). p. 3773.

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

Neher, Richard A. and Dyrdak, Robert and Druelle, Valentin and Hodcroft, Emma B. and Albert, Jan. (2020) Potential impact of seasonal forcing on a SARS-CoV-2 pandemic. Swiss Medical Weekly, 150. w20224.

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

Fauver, Joseph R. and Petrone, Mary E. and Hodcroft, Emma B. and Shioda, Kayoko and Ehrlich, Hanna Y. and Watts, Alexander G. and Vogels, Chantal B. F. and Brito, Anderson F. and Alpert, Tara and Muyombwe, Anthony and Razeq, Jafar and Downing, Randy and Cheemarla, Nagarjuna R. and Wyllie, Anne L. and Kalinich, Chaney C. and Ott, Isabel M. and Quick, Joshua and Loman, Nicholas J. and Neugebauer, Karla M. and Greninger, Alexander L. and Jerome, Keith R. and Roychoudhury, Pavitra and Xie, Hong and Shrestha, Lasata and Huang, Meei-Li and Pitzer, Virginia E. and Iwasaki, Akiko and Omer, Saad B. and Khan, Kamran and Bogoch, Isaac I. and Martinello, Richard A. and Foxman, Ellen F. and Landry, Marie L. and Neher, Richard A. and Ko, Albert I. and Grubaugh, Nathan D.. (2020) Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States. Cell, 181 (5). pp. 990-996.e5.

Mavian, Carla and Pond, Sergei Kosakovsky and Marini, Simone and Magalis, Brittany Rife and Vandamme, Anne-Mieke and Dellicour, Simon and Scarpino, Samuel V. and Houldcroft, Charlotte and Villabona-Arenas, Julian and Paisie, Taylor K. and Trovão, Nídia S. and Boucher, Christina and Zhang, Yun and Scheuermann, Richard H. and Gascuel, Olivier and Lam, Tommy Tsan-Yuk and Suchard, Marc A. and Abecasis, Ana and Wilkinson, Eduan and de Oliveira, Tulio and Bento, Ana I. and Schmidt, Heiko A. and Martin, Darren and Hadfield, James and Faria, Nuno and Grubaugh, Nathan D. and Neher, Richard A. and Baele, Guy and Lemey, Philippe and Stadler, Tanja and Albert, Jan and Crandall, Keith A. and Leitner, Thomas and Stamatakis, Alexandros and Prosperi, Mattia and Salemi, Marco. (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). pp. 12522-12523.

Alm, Erik and Broberg, Eeva K. and Connor, Thomas and Hodcroft, Emma B. and Komissarov, Andrey B. and Maurer-Stroh, Sebastian and Melidou, Angeliki and Neher, Richard A. and O'Toole, Áine and Pereyaslov, Dmitriy. (2020) Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. Eurosurveillance, 25 (32). p. 2001410.

Müller, Nicola F. and Wüthrich, Daniel and Goldman, Nina and Sailer, Nadine and Saalfrank, Claudia and Brunner, Myrta and Augustin, Noémi and Seth-Smith, Helena Mb and Hollenstein, Yvonne and Syedbasha, Mohammedyaseen and Lang, Daniela and Neher, Richard A. and Dubuis, Olivier and Naegele, Michael and Buser, Andreas and Nickel, Christian H. and Ritz, Nicole and Zeller, Andreas and Lang, Brian M. and Hadfield, James and Bedford, Trevor and Battegay, Manuel and Schneider-Sliwa, Rita and Egli, Adrian and Stadler, Tanja. (2020) Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics. PLoS Pathogens, 16 (11). e1008984.

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

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

Bedford, Trevor and Greninger, Alexander L. and Roychoudhury, Pavitra and Starita, Lea M. and Famulare, Michael and Huang, Meei-Li and Nalla, Arun and Pepper, Gregory and Reinhardt, Adam and Xie, Hong and Shrestha, Lasata and Nguyen, Truong N. and Adler, Amanda and Brandstetter, Elisabeth and Cho, Shari and Giroux, Danielle and Han, Peter D. and Fay, Kairsten and Frazar, Chris D. and Ilcisin, Misja and Lacombe, Kirsten and Lee, Jover and Kiavand, Anahita and Richardson, Matthew and Sibley, Thomas R. and Truong, Melissa and Wolf, Caitlin R. and Nickerson, Deborah A. and Rieder, Mark J. and Englund, Janet A. and Seattle Flu Study Investigators, and Hadfield, James and Hodcroft, Emma B. and Huddleston, John and Moncla, Louise H. and Müller, Nicola F. and Neher, Richard A. and Deng, Xianding and Gu, Wei and Federman, Scot and Chiu, Charles and Duchin, Jeffrey S. and Gautom, Romesh and Melly, Geoff and Hiatt, Brian and Dykema, Philip and Lindquist, Scott and Queen, Krista and Tao, Ying and Uehara, Anna and Tong, Suxiang and MacCannell, Duncan and Armstrong, Gregory L. and Baird, Geoffrey S. and Chu, Helen Y. and Shendure, Jay and Jerome, Keith R.. (2020) Cryptic transmission of SARS-CoV-2 in Washington state. Science, 370 (6516). pp. 571-575.

Puller, Vadim and Sagulenko, Pavel and Neher, Richard A.. (2020) Efficient inference, potential, and limitations of site-specific substitution models. Virus Evolution, 6 (2). veaa066.

Wüthrich, Daniel and Lang, Daniela and Müller, Nicola F. and Neher, Richard A. and Stadler, Tanja and Egli, Adrian. (2019) Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses. Journal of Virological Methods, 266. pp. 30-33.

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

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

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

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

Yan, Le and Neher, Richard A. and Shraiman, Boris I.. (2019) Phylodynamic theory of persistence, extinction and speciation of rapidly adapting pathogens. eLife, 8. e44205.

Potter, Barney I. and Kondor, Rebecca and Hadfield, James and Huddleston, John and Barnes, John and Rowe, Thomas and Guo, Lizheng and Xu, Xiyan and Neher, Richard A. and Bedford, Trevor and 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). vez046.

Sagulenko, Pavel and Puller, Vadim and Neher, Richard A.. (2018) TreeTime: Maximum-likelihood phylodynamic analysis. Virus Evolution, 4 (1, vex042). pp. 1-9.

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

Hadfield, James and Megill, Colin and Bell, Sidney M. and Huddleston, John and Potter, Barney and Callender, Charlton and Sagulenko, Pavel and Bedford, Trevor and Neher, Richard A.. (2018) Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34 (23). pp. 4121-4123.

Karasov, Talia L. and Almario, Juliana and Friedemann, Claudia and Ding, Wei and Giolai, Michael and Heavens, Darren and Kersten, Sonja and Lundberg, Derek S. and Neumann, Manuela and Regalado, Julian and Neher, Richard A. and Kemen, Eric and Weigel, Detlef. (2018) Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales. Cell Host & Microbe, 24 (1). pp. 168-179.e4.

Neher, Richard A. and Bedford, Trevor. (2018) Real-time analysis and visualization of pathogen sequence data. Journal of clinical microbiology, 56 (11, ). e00480-18.

Javed, Mumina and Ueltzhoeffer, Viola and Heinrich, Maximilian and Siegrist, Hans Justus and Wildermuth, Ronja and Lorenz, Freia-Raphaella and Neher, Richard A. and 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). pp. 3368-3374.

Egli, Adrian and Blanc, Dominique S. and Greub, Gilbert and Keller, Peter M. and Lazarevic, Vladimir and Lebrand, Aitana and Leib, Stephen and Neher, Richard A. and Perreten, Vincent and Ramette, Alban and Schrenzel, Jacques and Stephan, Roger and Wagner, Karolin and Wuethrich, Daniel and 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.

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

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

Regenbogen, Bianca and Willmann, Matthias and Steglich, Matthias and Bunk, Boyke and Nübel, Ulrich and Peter, Silke and 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.

Puller, Vadim and Neher, Richard and Albert, Jan. (2017) Estimating time of HIV-1 infection from next-generation sequence diversity. PLoS Computational Biology, 13 (10). e1005775.

Ding, Wei and Baumdicker, Franz and Neher, Richard A.. (2017) panX: pan-genome analysis and exploration. Nucleic acids research. p. 12.

Morris, Dylan H. and Gostic, Katelyn M. and Pompei, Simone and Bedford, Trevor and Łuksza, Marta and Neher, Richard A. and Grenfell, Bryan T. and Lässig, Michael and McCauley, John W.. (2017) Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology. Trends in Microbiology, 26 (2). p. 17.

Zanini, Fabio and Brodin, Johanna and Albert, Jan and Neher, Richard A.. (2016) Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing. Virus Research , 239. pp. 106-114.

Brodin, Johanna and Zanini, Fabio and Thebo, Lina and Lanz, Christa and Bratt, Göran and Neher, Richard A. and Albert, Jan. (2016) Establishment and stability of the latent HIV-1 DNA reservoir. eLife, 5. p. 15.

Boullé, Mikaël and Müller, Thorsten G. and Dähling, Sabrina and Ganga, Yashica and Jackson, Laurelle and Mahamed, Deeqa and Oom, Lance and Lustig, Gila and Neher, Richard A. and Sigal, Alex. (2016) HIV Cell-to-Cell Spread Results in Earlier Onset of Viral Gene Expression by Multiple Infections per Cell. PLoS Pathogens, 12 (11). e1005964.

Neher, Richard A. and Bedford, Trevor and Daniels, Rodney S. and Russell, Colin A. and Shraiman, Boris I.. (2016) Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses. Proceedings of the National Academy of Sciences of the United States of America, 113 (12). pp. 1701-1709.

Hassouna, I. and Ott, C. and Wüstefeld, L. and Offen, N. and Neher, R. A. and Mitkovski, M. and Winkler, D. and Sperling, S. and Fries, L. and Goebbels, S. and Vreja, I. C. and Hagemeyer, N. and Dittrich, M. and Rossetti, M. F. and Kröhnert, K. and Hannke, K. and Boretius, S. and Zeug, A. and Höschen, C. and Dandekar, T. and Dere, E. and Neher, E. and Rizzoli, S. O. and Nave, K.-A. and Sirén, A.-L. and Ehrenreich, H.. (2016) Revisiting adult neurogenesis and the role of erythropoietin for neuronal and oligodendroglial differentiation in the hippocampus. Molecular Psychiatry, 21 (12). pp. 1752-1767.

Zanini, Fabio and Brodin, Johanna and Thebo, Lina and Lanz, Christa and Bratt, Göran and Albert, Jan and Neher, Richard A.. (2015) Population genomics of intrapatient HIV-1 evolution. eLife, 4. p. 26.

Neher, Richard A. and Bedford, Trevor. (2015) nextflu: real-time tracking of seasonal influenza virus evolution in humans. Bioinformatics, 31 (21). pp. 3546-3548.

Brodin, Johanna and Hedskog, Charlotte and Heddini, Alexander and Benard, Emmanuel and Neher, Richard A. and Mild, Mattias and Albert, Jan. (2015) Challenges with using primer IDs to improve accuracy of next generation sequencing. PLoS ONE, 10 (3). e0119123.

Neher, Richard A. and Russell, Colin A. and Shraiman, Boris I.. (2014) Predicting evolution from the shape of genealogical trees. eLife, 3. p. 18.

Good, Benjamin H. and Walczak, Aleksandra M. and Neher, Richard A. and Desai, Michael M.. (2014) Genetic diversity in the interference selection limit. PLoS Genetics, 10 (3). e1004222.

Rödelsperger, Christian and Neher, Richard A. and Weller, Andreas M. and Eberhardt, Gabi and Witte, Hanh and Mayer, Werner E. and Dieterich, Christoph and Sommer, Ralf J.. (2014) Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data. Genetics, 196 (4). pp. 1153-1165.

Kessinger, Taylor A. and Perelson, Alan S. and Neher, Richard A.. (2013) Inferring HIV Escape Rates from Multi-Locus Genotype Data. Frontiers in Immunology, 4. p. 252.

Neher, Richard A. and Kessinger, Taylor A. and Shraiman, Boris I.. (2013) Coalescence and genetic diversity in sexual populations under selection. Proceedings of the National Academy of Sciences, 110 (39). pp. 15836-15841.

Mukherjee, Amrita and Neher, Richard A. and Renault, Andrew D.. (2013) Quantifying the range of a lipid phosphate signal in vivo. Journal of Cell Science, 126. pp. 5453-5464.

Zanini, Fabio and Neher, Richard A.. (2013) Quantifying selection against synonymous mutations in HIV-1 env evolution. Journal of virology, 87 (21). pp. 11843-11850.

Ganusov, Vitaly V. and Neher, Richard A. and Perelson, Alan S.. (2013) Mathematical modeling of escape of HIV from cytotoxic T lymphocyte responses. International Journal of Statistical Mechanics, 2013. P01010.

Neher, Richard A. and Hallatschek, Oskar. (2013) Genealogies of rapidly adapting populations. Proceedings of the National Academy of Sciences, 110 (2). pp. 437-442.

Neher, Richard A.. (2013) Genetic Draft, Selective Interference, and Population Genetics of Rapid Adaptation. Annual Review of Ecology, Evolution, and Systematics, 44. pp. 195-215.

Zanini, Fabio and Neher, Richard A.. (2012) FFPopSim: an efficient forward simulation package for the evolution of large populations. Bioinformatics, 28 (24). pp. 3332-3333.

Goyal, Sidhartha and Balick, Daniel J. and Jerison, Elizabeth R. and Neher, Richard A. and Shraiman, Boris I. and Desai, Michael M.. (2012) Dynamic mutation-selection balance as an evolutionary attractor. Genetics, 191 (4). pp. 1309-1319.

Neher, Richard A. and Shraiman, Boris I.. (2012) Fluctuations of fitness distributions and the rate of Muller's ratchet. Genetics, 191 (4). pp. 1283-1293.

Messer, Philipp W. and Neher, Richard A.. (2012) Estimating the strength of selective sweeps from deep population diversity data. Genetics, 191 (2). pp. 593-605.

Schötz, Thomas and Neher, Richard A. and Gerland, Ulrich. (2011) Target search on a dynamic DNA molecule. Physical Review E, 84 (5). 051911.

Neher, R. A. and Shraiman, B. I.. (2011) Genetic draft and quasi-neutrality in large facultatively sexual populations. Genetics, 188 (4). pp. 975-996.

Callahan, Benjamin and Neher, Richard A. and Bachtrog, Doris and Andolfatto, Peter and Shraiman, Boris I.. (2011) Correlated evolution of nearby residues in Drosophilid proteins. PLoS Genetics, 7 (2). e1001315.

Neher, Richard A. and Leitner, Thomas. (2010) Recombination rate and selection strength in HIV intra-patient evolution. PLoS Computational Biology, 6 (1). e1000660.

Neher, R. A. and Shraiman, B. I. and Fisher, D. S.. (2010) Rate of adaptation in large sexual populations. Genetics, 184 (2). pp. 467-481.

Neher, Richard A. and Mitkovski, Miso and Kirchhoff, Frank and Neher, Erwin and Theis, Fabian J. and Zeug, André. (2009) Blind source separation techniques for the decomposition of multiply labeled fluorescence images. Biophysical Journal, 96 (9). pp. 3791-3800.

Neher, Richard A. and Shraiman, Boris I.. (2009) Competition between recombination and epistasis can cause a transition from allele to genotype selection. Proceedings of the National Academy of Sciences, 106 (16). pp. 6866-6871.

Neher, Richard A. and Möbius, Wolfram and Frey, Erwin and Gerland, Ulrich. (2007) Optimal flexibility for conformational transitions in macromolecules. Physical Review Letters, 99 (17). p. 178101.

Kühner, Ferdinand and Morfill, Julia and Neher, Richard A. and Blank, Kerstin and Gaub, Hermann E.. (2007) Force-induced DNA slippage. Biophysical Journal, 92 (7). pp. 2491-2497.

Möbius, Wolfram and Neher, Richard A. and Gerland, Ulrich. (2006) Kinetic accessibility of buried DNA sites in nucleosomes. Physical Review Letters, 97 (20). p. 208102.

Neher, Richard A. and Gerland, Ulrich. (2006) Intermediate phase in DNA melting. Physical Review E, 73 (3). 030902.

Neher, Richard A. and Gerland, Ulrich. (2005) DNA as a programmable viscoelastic nanoelement. Biophysical Journal, 89 (6). pp. 3846-3855.

Neher, Richard A. and Gerland, Ulrich. (2004) Dynamics of force-induced DNA slippage. Physical Review Letters, 93 (19). p. 198102.

Neher, Richard A. and Neher, Erwin. (2004) Applying spectral fingerprinting to the analysis of FRET images. Microscopy Research and Technique, 64 (2). pp. 185-195.

Neher, Richard and Neher, Erwin. (2004) Optimizing imaging parameters for the separation of multiple labels in a fluorescence image. Journal of Microscopy, 213 (1). pp. 46-62.

Preprint

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