Items where contributor is "Neher, Richard A"

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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.