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

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.

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.

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.

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; 10 Kemmer, Christian; Neher, Richard; Egli, Adrian; Bumann, Dirk; 19 (2019). Quantitative contribution of efflux to multi-drug resistance of clinical Escherichia coli and Pseudomonas aeruginosa strains. EBioMedicine, 41, 479-487.

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.

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), vez046.


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.

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.

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

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.e4.

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.

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.

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


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.

Ding, Wei; Baumdicker, Franz; Neher, Richard A. (2017). panX: pan-genome analysis and exploration. Nucleic acids research, 46 (1), e5.

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

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.

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.

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.


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

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

Boullé, Mikaël; Müller, Thorsten G.; Dähling, Sabrina; Ganga, Yashica; Jackson, Laurelle; Mahamed, Deeqa; Oom, Lance; Lustig, Gila; Neher, Richard A.; 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.; Bedford, Trevor; Daniels, Rodney S.; Russell, Colin A.; 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), E1701-9.

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


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

Neher, Richard A.; Bedford, Trevor (2015). nextflu: real-time tracking of seasonal influenza virus evolution in humans. Bioinformatics, 31 (21), 3546-8.

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


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

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

Rödelsperger, Christian; Neher, Richard A.; Weller, Andreas M.; Eberhardt, Gabi; Witte, Hanh; Mayer, Werner E.; Dieterich, Christoph; Sommer, Ralf J. (2014). Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data. Genetics, 196 (4), 1153-65.


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

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

Neher, Richard A.; Kessinger, Taylor A.; Shraiman, Boris I. (2013). Coalescence and genetic diversity in sexual populations under selection. Proceedings of the National Academy of Sciences, 110 (39), 15836-41.

Mukherjee, Amrita; Neher, Richard A.; Renault, Andrew D. (2013). Quantifying the range of a lipid phosphate signal in vivo. Journal of Cell Science, 126 (Pt23), 5453-64.

Zanini, Fabio; Neher, Richard A. (2013). Quantifying selection against synonymous mutations in HIV-1 env evolution. Journal of virology, 87 (21), 11843-50.

Neher, Richard A.; Hallatschek, Oskar (2013). Genealogies of rapidly adapting populations. Proceedings of the National Academy of Sciences, 110 (2), 437-42.

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


Zanini, Fabio; Neher, Richard A. (2012). FFPopSim: an efficient forward simulation package for the evolution of large populations. Bioinformatics, 28 (24), 3332-3.

Goyal, Sidhartha; Balick, Daniel J.; Jerison, Elizabeth R.; Neher, Richard A.; Shraiman, Boris I.; Desai, Michael M. (2012). Dynamic mutation-selection balance as an evolutionary attractor. Genetics, 191 (4), 1309-19.

Neher, Richard A.; Shraiman, Boris I. (2012). Fluctuations of fitness distributions and the rate of Muller's ratchet. Genetics, 191 (4), 1283-93.

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


Schötz, Thomas; Neher, Richard A.; Gerland, Ulrich (2011). Target search on a dynamic DNA molecule. Physical Review E, 84 (5Pt1), 051911.

Neher, R. A.; Shraiman, B. I. (2011). Genetic draft and quasi-neutrality in large facultatively sexual populations. Genetics, 188 (4), 975-96.

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


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

Neher, R. A.; Shraiman, B. I.; Fisher, D. S. (2010). Rate of adaptation in large sexual populations. Genetics, 184 (2), 467-81.


Neher, Richard A.; Mitkovski, Miso; Kirchhoff, Frank; Neher, Erwin; Theis, Fabian J.; Zeug, André (2009). Blind source separation techniques for the decomposition of multiply labeled fluorescence images. Biophysical Journal, 96 (9), 3791-800.

Neher, Richard A.; 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), 6866-71.


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

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


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

Neher, Richard A.; Gerland, Ulrich (2006). Intermediate phase in DNA melting. Physical Review E, 73 (3Pt1), 030902.


Neher, Richard A.; Gerland, Ulrich (2005). DNA as a programmable viscoelastic nanoelement. Biophysical Journal, 89 (6), 3846-55.


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

Neher, Richard A.; Neher, Erwin (2004). Applying spectral fingerprinting to the analysis of FRET images. Microscopy Research and Technique, 64 (2), 185-95.

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

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