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Bloom, J. D., Chan, Y. A., Baric, R. S., Bjorkman, P. J., Cobey, S., Deverman, B. E., Fisman, D. N., Gupta, R., Iwasaki, A., Lipsitch, M., Medzhitov, R., Neher, R. A., Nielsen, R., Patterson, N., Stearns, T., van Nimwegen, E., Worobey, M. and Relman, D. A. (2021) ‘Investigate the origins of COVID-19’, Science, 372(6543), p. 694. doi: 10.1126/science.abj0016.   edoc
Battegay, M., Kuehl, R., Tschudin-Sutter, S., Hirsch, H. H., Widmer, A. F. and Neher, R. A. (2020) ‘2019-novel Coronavirus (2019-nCoV): estimating the case fatality rate - a word of caution’, Swiss medical weekly, 150, p. w20203. doi: 10.4414/smw.2020.20203.   
Neher, R. A., Dyrdak, R., Druelle, V., Hodcroft, E. B. and Albert, J. (2020) ‘Potential impact of seasonal forcing on a SARS-CoV-2 pandemic’, Swiss medical weekly, 150, p. w20224. doi: 10.4414/smw.2020.20224.   
Salathé, M., Althaus, C. L., Neher, R., Stringhini, S., Hodcroft, E., Fellay, J., Zwahlen, M., Senti, G., Battegay, M., Wilder-Smith, A., Eckerle, I., Egger, M. and Low, N. (2020) ‘COVID-19 epidemic in Switzerland: on the importance of testing, contact tracing and isolation’, Swiss medical weekly, 150, p. w20225. doi: 10.4414/smw.2020.20225.   
Fauver, J. R., Petrone, M. E., Hodcroft, E. B., Shioda, K., Ehrlich, H. Y., Watts, A. G., Vogels, C. B. F., Brito, A. F., Alpert, T., Muyombwe, A., Razeq, J., Downing, R., Cheemarla, N. R., Wyllie, A. L., Kalinich, C. C., Ott, I. M., Quick, J., Loman, N. J., Neugebauer, K. M., Greninger, A. L., Jerome, K. R., Roychoudhury, P., Xie, H., Shrestha, L., Huang, M.-L., Pitzer, V. E., Iwasaki, A., Omer, S. B., Khan, K., Bogoch, I. I., Martinello, R. A., Foxman, E. F., Landry, M. L., Neher, R. A., Ko, A. I. and Grubaugh, N. 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. doi: 10.1016/j.cell.2020.04.021.   
Alm, E., Broberg, E. K., Connor, T., Hodcroft, E. B., Komissarov, A. B., Maurer-Stroh, S., Melidou, A., Neher, R. A., O’Toole, Áine, Pereyaslov, D., European Region sequencing laboratories, W. H. O., Gisaid EpiCoV group, T. members of the working group are listed in the I. ., European Region sequencing laboratories, W. H. O. and Gisaid EpiCoV group* (2020) ‘Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020’, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 25(32), p. 2001410. doi: 10.2807/1560-7917.ES.2020.25.32.2001410.   
Midgley, S. E., Benschop, K., Dyrdak, R., Mirand, A., Bailly, J.-L., Bierbaum, S., Buderus, S., Böttcher, S., Eis-Hübinger, A.-M., Hönemann, M., Jensen, V. V., Hartling, U. B., Henquell, C., Panning, M., Thomsen, M. K., Hodcroft, E. B. and Meijer, A. (2020) ‘Co-circulation of multiple enterovirus D68 subclades, including a novel B3 cluster, across Europe in a season of expected low prevalence, 2019/20’, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 25(2), p. 1900749. doi: 10.2807/1560-7917.ES.2020.25.2.1900749.   
Mavian, C., Pond, S. K., Marini, S., Magalis, B. R., Vandamme, A.-M., Dellicour, S., Scarpino, S. V., Houldcroft, C., Villabona-Arenas, J., Paisie, T. K., Trovão, N. S., Boucher, C., Zhang, Y., Scheuermann, R. H., Gascuel, O., Lam, T. T.-Y., Suchard, M. A., Abecasis, A., Wilkinson, E., de Oliveira, T., Bento, A. I., Schmidt, H. A., Martin, D., Hadfield, J., Faria, N., Grubaugh, N. D., Neher, R. A., Baele, G., Lemey, P., Stadler, T., Albert, J., Crandall, K. A., Leitner, T., Stamatakis, A., Prosperi, M. and Salemi, M. (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. doi: 10.1073/pnas.2007295117.   
Egli, A., Koch, D., Danuser, J., Hendriksen, R. S., Driesen, S., Schmid, D. C., Neher, R., Mäusezahl, M., Seth-Smith, H. M. B., Bloemberg, G., Tschudin-Sutter, S., Endimiani, A., Perreten, V., Greub, G., Schrenzel, J. and Stephan, R. (2019) ‘Symposium report: One Health meets sequencing’, Microbes and Infection, 22(1), pp. 1–7. doi: 10.1016/j.micinf.2019.07.004.   edoc | Open Access
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. and Tohme, J. (2019) ‘A global surveillance system for crop diseases’, Science, 364(6447), pp. 1237–1239. doi: 10.1126/science.aaw1572.   edoc
Wüthrich, D., Lang, D., Müller, N. F., Neher, R. A., Stadler, T. and Egli, A. (2019) ‘Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses’, Journal of Virological Methods, 266, pp. 30–33. doi: 10.1016/j.jviromet.2019.01.009.   edoc | Open Access
Yan, L., Neher, R. A. and Shraiman, B. I. (2019) ‘Phylodynamic theory of persistence, extinction and speciation of rapidly adapting pathogens’, eLife, 8, p. e44205. doi: 10.7554/eLife.44205.   edoc | Open Access
Dyrdak, R., Mastafa, M., Hodcroft, E. B., Neher, R. A. and Albert, J. (2019) ‘Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing’, Virus Evolution, 5(1), p. vez007. doi: 10.1093/ve/vez007.   edoc | Open Access
Cunrath, O., Meinel, D. M., Maturana, P., Fanous, J., Buyck, J. M., Saint Auguste, P., Seth-Smith, H. M. B., Körner, J., Dehio, C., Trebosc, V., Kemmer, C., Neher, R., Egli, A. and Bumann, D. (2019) ‘Quantitative contribution of efflux to multi-drug resistance of clinical Escherichia coli and Pseudomonas aeruginosa strains’, EBioMedicine, 41, pp. 479–487. doi: 10.1016/j.ebiom.2019.02.061.   edoc | Open Access
Egli, A., Blanc, D. S., Greub, G., Keller, P. M., Lazarevic, V., Lebrand, A., Leib, S., Neher, R. A., Perreten, V., Ramette, A., Schrenzel, J., Stephan, R., Wagner, K., Wuethrich, D. and Xenarios, I. (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), p. w14693. doi: 10.4414/smw.2018.14693.   edoc | Open Access
Jackson, L., Hunter, J., Cele, S., Ferreira, I. M., Young, A. C., Karim, F., Madansein, R., Dullabh, K. J., Chen, C.-Y., Buckels, N. J., Ganga, Y., Khan, K., Boulle, M., Lustig, G., Neher, R. A. and Sigal, A. (2018) ‘Incomplete inhibition of HIV infection results in more HIV infected lymph node cells by reducing cell death’, eLife, 7(e30134), pp. 1–24. doi: 10.7554/eLife.30134.   edoc | Open Access
Sagulenko, P., Puller, V. and Neher, R. A. (2018) ‘TreeTime: Maximum-likelihood phylodynamic analysis’, Virus Evolution, 4(1, vex042), pp. 1–9. doi: 10.1093/ve/vex042.   edoc | Open Access
Javed, M., Ueltzhoeffer, V., Heinrich, M., Siegrist, H. J., Wildermuth, R., Lorenz, F.-R., Neher, R. A. and Willmann, M. (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. doi: 10.1093/jac/dky337.   edoc | Open Access
Neher, R. A. and Bedford, T. (2018) ‘Real-time analysis and visualization of pathogen sequence data’, Journal of clinical microbiology, 56(11, ), pp. e00480–18. doi: 10.1128/JCM.00480-18.   edoc | Open Access
Karasov, T. L., Almario, J., Friedemann, C., Ding, W., Giolai, M., Heavens, D., Kersten, S., Lundberg, D. S., Neumann, M., Regalado, J., Neher, R. A., Kemen, E. and Weigel, D. (2018) ‘Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales’, Cell Host & Microbe, 24(1), pp. 168–179.e4. doi: 10.1016/j.chom.2018.06.011.   edoc | Open Access
Hadfield, J., Megill, C., Bell, S. M., Huddleston, J., Potter, B., Callender, C., Sagulenko, P., Bedford, T. and Neher, R. A. (2018) ‘Nextstrain: real-time tracking of pathogen evolution’, Bioinformatics, 34(23), pp. 4121–4123. doi: 10.1093/bioinformatics/bty407.   edoc | Open Access
Morris, D. H., Gostic, K. M., Pompei, S., Bedford, T., Łuksza, M., Neher, R. A., Grenfell, B. T., Lässig, M. and McCauley, J. W. (2017) ‘Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology’, Trends in Microbiology, 26(2), p. 17. doi: 10.1016/j.tim.2017.09.004.   edoc | Open Access
Ding, W., Baumdicker, F. and Neher, R. A. (2017) ‘panX: pan-genome analysis and exploration’, Nucleic acids research, p. 12. doi: 10.1093/nar/gkx977.   edoc | Open Access
Puller, V., Neher, R. and Albert, J. (2017) ‘Estimating time of HIV-1 infection from next-generation sequence diversity’, PLoS Computational Biology, 13(10), p. e1005775. doi: 10.1371/journal.pcbi.1005775.   edoc | Open Access
You, Y., Sawikowska, A., Neumann, M., Posé, D., Capovilla, G., Langenecker, T., Neher, R. A., Krajewski, P. and Schmid, M. (2017) ‘Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering’, Nature Communications, 8, p. 15120. doi: 10.1038/ncomms15120.   edoc | Open Access
Zanini, F., Puller, V., Brodin, J., Albert, J. and Neher, R. A. (2017) ‘In vivo mutation rates and the landscape of fitness costs of HIV-1’, Virus Evolution, 3(1), p. vex003. doi: 10.1093/ve/vex003.   edoc | Open Access
Regenbogen, B., Willmann, M., Steglich, M., Bunk, B., Nübel, U., Peter, S. and Neher, R. A. (2017) ‘Rapid and consistent evolution of colistin resistance in XDR Pseudomonas aeruginosa during morbidostat culture’, Antimicrobial agents and chemotherapy, 61(9), pp. e00043–17. doi: 10.1128/AAC.00043-17.   edoc | Open Access
Zanini, F., Brodin, J., Albert, J. and Neher, R. A. (2016) ‘Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing’, Virus Research , 239, pp. 106–114. doi: 10.1016/j.virusres.2016.12.009.   edoc
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. 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. doi: 10.1038/mp.2015.212.   edoc | Open Access
Neher, R. A., Bedford, T., Daniels, R. S., Russell, C. A. and Shraiman, B. 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. doi: 10.1073/pnas.1525578113.   edoc | Open Access
Boullé, M., Müller, T. G., Dähling, S., Ganga, Y., Jackson, L., Mahamed, D., Oom, L., Lustig, G., Neher, R. A. and Sigal, A. (2016) ‘HIV Cell-to-Cell Spread Results in Earlier Onset of Viral Gene Expression by Multiple Infections per Cell’, PLoS Pathogens, 12(11), p. e1005964. doi: 10.1371/journal.ppat.1005964.   edoc | Open Access
Brodin, J., Zanini, F., Thebo, L., Lanz, C., Bratt, G., Neher, R. A. and Albert, J. (2016) ‘Establishment and stability of the latent HIV-1 DNA reservoir’, eLife, 5, p. 15. doi: 10.7554/eLife.18889.   edoc | Open Access
Neher, R. A. and Bedford, T. (2015) ‘nextflu: real-time tracking of seasonal influenza virus evolution in humans’, Bioinformatics, 31(21), pp. 3546–3548. doi: 10.1093/bioinformatics/btv381.   edoc | Open Access
Brodin, J., Hedskog, C., Heddini, A., Benard, E., Neher, R. A., Mild, M. and Albert, J. (2015) ‘Challenges with using primer IDs to improve accuracy of next generation sequencing’, PLoS ONE, 10(3), p. e0119123. doi: 10.1371/journal.pone.0119123.   edoc | Open Access
Zanini, F., Brodin, J., Thebo, L., Lanz, C., Bratt, G., Albert, J. and Neher, R. A. (2015) ‘Population genomics of intrapatient HIV-1 evolution’, eLife, 4, p. 26. doi: 10.7554/eLife.11282.   edoc | Open Access
Good, B. H., Walczak, A. M., Neher, R. A. and Desai, M. M. (2014) ‘Genetic diversity in the interference selection limit’, PLoS Genetics, 10(3), p. e1004222. doi: 10.1371/journal.pgen.1004222.   edoc | Open Access
Rödelsperger, C., Neher, R. A., Weller, A. M., Eberhardt, G., Witte, H., Mayer, W. E., Dieterich, C. and Sommer, R. J. (2014) ‘Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data’, Genetics, 196(4), pp. 1153–1165. doi: 10.1534/genetics.113.159855.   edoc | Open Access
Neher, R. A., Russell, C. A. and Shraiman, B. I. (2014) ‘Predicting evolution from the shape of genealogical trees’, eLife, 3, p. 18. doi: 10.7554/eLife.03568.   edoc | Open Access
Neher, R. A. (2013) ‘Genetic Draft, Selective Interference, and Population Genetics of Rapid Adaptation’, Annual Review of Ecology, Evolution, and Systematics, 44, pp. 195–215. doi: 10.1146/annurev-ecolsys-110512-135920 .   edoc | Open Access
Neher, R. A. and Hallatschek, O. (2013) ‘Genealogies of rapidly adapting populations’, Proceedings of the National Academy of Sciences, 110(2), pp. 437–442. doi: 10.1073/pnas.1213113110.   edoc | Open Access
Neher, R. A., Kessinger, T. A. and Shraiman, B. I. (2013) ‘Coalescence and genetic diversity in sexual populations under selection’, Proceedings of the National Academy of Sciences, 110(39), pp. 15836–15841. doi: 10.1073/pnas.1309697110.   edoc | Open Access
Ganusov, V. V., Neher, R. A. and Perelson, A. S. (2013) ‘Mathematical modeling of escape of HIV from cytotoxic T lymphocyte responses’, International Journal of Statistical Mechanics, 2013, p. P01010. doi: 10.1088/1742-5468/2013/01/P01010.   edoc | Open Access
Zanini, F. and Neher, R. A. (2013) ‘Quantifying selection against synonymous mutations in HIV-1 env evolution’, Journal of virology, 87(21), pp. 11843–11850. doi: 10.1128/JVI.01529-13.   edoc | Open Access
Mukherjee, A., Neher, R. A. and Renault, A. D. (2013) ‘Quantifying the range of a lipid phosphate signal in vivo’, Journal of Cell Science, 126, pp. 5453–5464. doi: 10.1242/jcs.136176.   edoc | Open Access
Kessinger, T. A., Perelson, A. S. and Neher, R. A. (2013) ‘Inferring HIV Escape Rates from Multi-Locus Genotype Data’, Frontiers in Immunology, 4, p. 252. doi: 10.3389/fimmu.2013.00252.   edoc | Open Access
Zanini, F. and Neher, R. A. (2012) ‘FFPopSim: an efficient forward simulation package for the evolution of large populations’, Bioinformatics, 28(24), pp. 3332–3333. doi: 10.1093/bioinformatics/bts633.   edoc | Open Access
Messer, P. W. and Neher, R. A. (2012) ‘Estimating the strength of selective sweeps from deep population diversity data’, Genetics, 191(2), pp. 593–605. doi: 10.1534/genetics.112.138461.   edoc | Open Access
Goyal, S., Balick, D. J., Jerison, E. R., Neher, R. A., Shraiman, B. I. and Desai, M. M. (2012) ‘Dynamic mutation-selection balance as an evolutionary attractor’, Genetics, 191(4), pp. 1309–1319. doi: 10.1534/genetics.112.141291.   edoc | Open Access
Neher, R. A. and Shraiman, B. I. (2012) ‘Fluctuations of fitness distributions and the rate of Muller’s ratchet’, Genetics, 191(4), pp. 1283–1293. doi: 10.1534/genetics.112.141325.   edoc | Open Access
Schötz, T., Neher, R. A. and Gerland, U. (2011) ‘Target search on a dynamic DNA molecule’, Physical Review E, 84(5), p. 51911. doi: 10.1103/PhysRevE.84.051911.   edoc | Open Access
Callahan, B., Neher, R. A., Bachtrog, D., Andolfatto, P. and Shraiman, B. I. (2011) ‘Correlated evolution of nearby residues in Drosophilid proteins’, PLoS Genetics, 7(2), p. e1001315. doi: 10.1371/journal.pgen.1001315.   edoc | Open Access
Neher, R. A. and Shraiman, B. I. (2011) ‘Genetic draft and quasi-neutrality in large facultatively sexual populations’, Genetics, 188(4), pp. 975–996. doi: 10.1534/genetics.111.128876.   edoc | Open Access
Neher, R. A. and Leitner, T. (2010) ‘Recombination rate and selection strength in HIV intra-patient evolution’, PLoS Computational Biology, 6(1), p. e1000660. doi: 10.1371/journal.pcbi.1000660.   edoc | Open Access
Neher, R. A., Shraiman, B. I. and Fisher, D. S. (2010) ‘Rate of adaptation in large sexual populations’, Genetics, 184(2), pp. 467–481. doi: 10.1534/genetics.109.109009.   edoc | Open Access
Neher, R. A., Mitkovski, M., Kirchhoff, F., Neher, E., Theis, F. J. and Zeug, A. (2009) ‘Blind source separation techniques for the decomposition of multiply labeled fluorescence images’, Biophysical Journal, 96(9), pp. 3791–3800. doi: 10.1016/j.bpj.2008.10.068.   edoc | Open Access
Neher, R. A. and Shraiman, B. 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. doi: 10.1073/pnas.0812560106.   edoc | Open Access
Neher, R. A., Möbius, W., Frey, E. and Gerland, U. (2007) ‘Optimal flexibility for conformational transitions in macromolecules’, Physical Review Letters, 99(17), p. 178101. doi: 10.1103/PhysRevLett.99.178101.   edoc | Open Access
Kühner, F., Morfill, J., Neher, R. A., Blank, K. and Gaub, H. E. (2007) ‘Force-induced DNA slippage’, Biophysical Journal, 92(7), pp. 2491–2497. doi: 10.1529/biophysj.106.095836.   edoc | Open Access
Neher, R. A. and Gerland, U. (2006) ‘Intermediate phase in DNA melting’, Physical Review E, 73(3), p. 30902. doi: 10.1103/PhysRevE.73.030902.   edoc | Open Access
Möbius, W., Neher, R. A. and Gerland, U. (2006) ‘Kinetic accessibility of buried DNA sites in nucleosomes’, Physical Review Letters, 97(20), p. 208102. doi: 10.1103/PhysRevLett.97.208102.   edoc | Open Access
Neher, R. A. and Gerland, U. (2005) ‘DNA as a programmable viscoelastic nanoelement’, Biophysical Journal, 89(6), pp. 3846–3855. doi: 10.1529/biophysj.105.068866.   edoc | Open Access
Neher, R. A. and Neher, E. (2004) ‘Applying spectral fingerprinting to the analysis of FRET images’, Microscopy Research and Technique, 64(2), pp. 185–195. doi: 10.1002/jemt.20078.   edoc
Neher, R. A. and Gerland, U. (2004) ‘Dynamics of force-induced DNA slippage’, Physical Review Letters, 93(19), p. 198102. doi: 10.1103/PhysRevLett.93.198102.   edoc | Open Access