Publications

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. und Stephan, R. (2019) «Symposium report: One Health meets sequencing», Microbes and Infection. Elsevier, 22(1), S. 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. und Tohme, J. (2019) «A global surveillance system for crop diseases», Science. American Association for the Advancement of Science, 364(6447), S. 1237-1239. doi: 10.1126/science.aaw1572.   edoc
Wüthrich, D., Lang, D., Müller, N. F., Neher, R. A., Stadler, T. und Egli, A. (2019) «Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses», Journal of Virological Methods. Elsevier, 266, S. 30-33. doi: 10.1016/j.jviromet.2019.01.009.   edoc | Open Access
Yan, L., Neher, R. A. und Shraiman, B. I. (2019) «Phylodynamic theory of persistence, extinction and speciation of rapidly adapting pathogens», eLife. eLife Sciences Publications , 8, S. e44205. doi: 10.7554/eLife.44205.   edoc | Open Access
Dyrdak, R., Mastafa, M., Hodcroft, E. B., Neher, R. A. und Albert, J. (2019) «Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing», Virus Evolution. Oxford University Press, 5(1), S. 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. und Bumann, D. (2019) «Quantitative contribution of efflux to multi-drug resistance of clinical Escherichia coli and Pseudomonas aeruginosa strains», EBioMedicine. Elsevier, 41, S. 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. und 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. EMH Schweizerischer Arzteverlag , 148(49-50), S. 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. und Sigal, A. (2018) «Incomplete inhibition of HIV infection results in more HIV infected lymph node cells by reducing cell death», eLife. eLife Sciences Publications , 7(e30134), S. 1-24. doi: 10.7554/eLife.30134.   edoc | Open Access
Sagulenko, P., Puller, V. und Neher, R. A. (2018) «TreeTime: Maximum-likelihood phylodynamic analysis», Virus Evolution. Oxford University Press, 4(1, vex042), S. 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. und Willmann, M. (2018) «Colistin susceptibility test evaluation of multiple-resistance-level Pseudomonas aeruginosa isolates generated in a morbidostat device», The journal of antimicrobial chemotherapy. Oxford University Press, 73(12), S. 3368-3374. doi: 10.1093/jac/dky337.   edoc
Neher, R. A. und Bedford, T. (2018) «Real-time analysis and visualization of pathogen sequence data», Journal of clinical microbiology. American Society for Microbiology, 56(11, ), S. 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. und Weigel, D. (2018) «Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales», Cell Host & Microbe. Cell Press, 24(1), S. 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. und Neher, R. A. (2018) «Nextstrain: real-time tracking of pathogen evolution», Bioinformatics. Oxford University Press, 34(23), S. 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. und McCauley, J. W. (2017) «Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology», Trends in Microbiology. Elsevier, 26(2), S. 17. doi: 10.1016/j.tim.2017.09.004.   edoc | Open Access
Ding, W., Baumdicker, F. und Neher, R. A. (2017) «panX: pan-genome analysis and exploration», Nucleic acids research, 46(1), S. 12. doi: 10.1093/nar/gkx977.   edoc | Open Access
Puller, V., Neher, R. und Albert, J. (2017) «Estimating time of HIV-1 infection from next-generation sequence diversity», PLoS Computational Biology. Library of Science, 13(10), S. 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. und Schmid, M. (2017) «Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering», Nature Communications. Nature Publishing Group, 8, S. 15120. doi: 10.1038/ncomms15120.   edoc | Open Access
Zanini, F., Puller, V., Brodin, J., Albert, J. und Neher, R. A. (2017) «In vivo mutation rates and the landscape of fitness costs of HIV-1», Virus Evolution. Oxford University Press, 3(1), S. vex003. doi: 10.1093/ve/vex003.   edoc | Open Access
Regenbogen, B., Willmann, M., Steglich, M., Bunk, B., Nübel, U., Peter, S. und Neher, R. A. (2017) «Rapid and consistent evolution of colistin resistance in XDR Pseudomonas aeruginosa during morbidostat culture», Antimicrobial agents and chemotherapy. American Society for Microbiology, 61(9), S. e00043-17. doi: 10.1128/AAC.00043-17.   edoc | Open Access
Zanini, F., Brodin, J., Albert, J. und Neher, R. A. (2016) «Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing», Virus Research . Elsevier, 239, S. 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. und Ehrenreich, H. (2016) «Revisiting adult neurogenesis and the role of erythropoietin for neuronal and oligodendroglial differentiation in the hippocampus», Molecular Psychiatry. Nature Publishing Group, 21(12), S. 1752-1767. doi: 10.1038/mp.2015.212.   edoc | Open Access
Neher, R. A., Bedford, T., Daniels, R. S., Russell, C. A. und 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. National Academy of Sciences, 113(12), S. 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. und Sigal, A. (2016) «HIV Cell-to-Cell Spread Results in Earlier Onset of Viral Gene Expression by Multiple Infections per Cell», PLoS Pathogens. Public Library of Science, 12(11), S. e1005964. doi: 10.1371/journal.ppat.1005964.   edoc | Open Access
Brodin, J., Zanini, F., Thebo, L., Lanz, C., Bratt, G., Neher, R. A. und Albert, J. (2016) «Establishment and stability of the latent HIV-1 DNA reservoir», eLife, 5, S. 15. doi: 10.7554/eLife.18889.   edoc | Open Access
Neher, R. A. und Bedford, T. (2015) «nextflu: real-time tracking of seasonal influenza virus evolution in humans», Bioinformatics. Oxford University Press, 31(21), S. 3546-3548. doi: 10.1093/bioinformatics/btv381.   edoc | Open Access
Brodin, J., Hedskog, C., Heddini, A., Benard, E., Neher, R. A., Mild, M. und Albert, J. (2015) «Challenges with using primer IDs to improve accuracy of next generation sequencing», PLoS ONE. Public Library of Science, 10(3), S. e0119123. doi: 10.1371/journal.pone.0119123.   edoc | Open Access
Zanini, F., Brodin, J., Thebo, L., Lanz, C., Bratt, G., Albert, J. und Neher, R. A. (2015) «Population genomics of intrapatient HIV-1 evolution», eLife, 4, S. 26. doi: 10.7554/eLife.11282.   edoc | Open Access
Good, B. H., Walczak, A. M., Neher, R. A. und Desai, M. M. (2014) «Genetic diversity in the interference selection limit», PLoS Genetics. Public Library of Science, 10(3), S. 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. und Sommer, R. J. (2014) «Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data», Genetics. Genetics Society of America, 196(4), S. 1153-1165. doi: 10.1534/genetics.113.159855.   edoc | Open Access
Neher, R. A., Russell, C. A. und Shraiman, B. I. (2014) «Predicting evolution from the shape of genealogical trees», eLife, 3, S. 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. Annual Reviews, 44, S. 195-215. doi: 10.1146/annurev-ecolsys-110512-135920 .   edoc | Open Access
Neher, R. A. und Hallatschek, O. (2013) «Genealogies of rapidly adapting populations», Proceedings of the National Academy of Sciences. National Academy of Sciences, 110(2), S. 437-442. doi: 10.1073/pnas.1213113110.   edoc | Open Access
Neher, R. A., Kessinger, T. A. und Shraiman, B. I. (2013) «Coalescence and genetic diversity in sexual populations under selection», Proceedings of the National Academy of Sciences. National Academy of Sciences, 110(39), S. 15836-15841. doi: 10.1073/pnas.1309697110.   edoc | Open Access
Ganusov, V. V., Neher, R. A. und Perelson, A. S. (2013) «Mathematical modeling of escape of HIV from cytotoxic T lymphocyte responses», International Journal of Statistical Mechanics. Hindawi, 2013, S. P01010. doi: 10.1088/1742-5468/2013/01/P01010.   edoc | Open Access
Zanini, F. und Neher, R. A. (2013) «Quantifying selection against synonymous mutations in HIV-1 env evolution», Journal of virology. American Society of Microbiology, 87(21), S. 11843-11850. doi: 10.1128/JVI.01529-13.   edoc | Open Access
Mukherjee, A., Neher, R. A. und Renault, A. D. (2013) «Quantifying the range of a lipid phosphate signal in vivo», Journal of Cell Science. Company of Biologists, 126(Pt 23), S. 5453-5464. doi: 10.1242/jcs.136176.   edoc | Open Access
Kessinger, T. A., Perelson, A. S. und Neher, R. A. (2013) «Inferring HIV Escape Rates from Multi-Locus Genotype Data», Frontiers in Immunology. Frontiers Media, 4, S. 252. doi: 10.3389/fimmu.2013.00252.   edoc | Open Access
Zanini, F. und Neher, R. A. (2012) «FFPopSim: an efficient forward simulation package for the evolution of large populations», Bioinformatics. Oxford University Press, 28(24), S. 3332-3333. doi: 10.1093/bioinformatics/bts633.   edoc | Open Access
Messer, P. W. und Neher, R. A. (2012) «Estimating the strength of selective sweeps from deep population diversity data», Genetics. Genetics Society of America, 191(2), S. 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. und Desai, M. M. (2012) «Dynamic mutation-selection balance as an evolutionary attractor», Genetics. Genetics Society of America, 191(4), S. 1309-1319. doi: 10.1534/genetics.112.141291.   edoc | Open Access
Neher, R. A. und Shraiman, B. I. (2012) «Fluctuations of fitness distributions and the rate of Muller’s ratchet», Genetics. Genetics Society of America, 191(4), S. 1283-1293. doi: 10.1534/genetics.112.141325.   edoc | Open Access
Schötz, T., Neher, R. A. und Gerland, U. (2011) «Target search on a dynamic DNA molecule», Physical Review E. American Physical Society, 84(5), S. 51911. doi: 10.1103/PhysRevE.84.051911.   edoc | Open Access
Callahan, B., Neher, R. A., Bachtrog, D., Andolfatto, P. und Shraiman, B. I. (2011) «Correlated evolution of nearby residues in Drosophilid proteins», PLoS Genetics. Public Library of Science, 7(2), S. e1001315. doi: 10.1371/journal.pgen.1001315.   edoc | Open Access
Neher, R. A. und Shraiman, B. I. (2011) «Genetic draft and quasi-neutrality in large facultatively sexual populations», Genetics. Genetics Society of America, 188(4), S. 975-996. doi: 10.1534/genetics.111.128876.   edoc | Open Access
Neher, R. A. und Leitner, T. (2010) «Recombination rate and selection strength in HIV intra-patient evolution», PLoS Computational Biology. Library of Science, 6(1), S. e1000660. doi: 10.1371/journal.pcbi.1000660.   edoc | Open Access
Neher, R. A., Shraiman, B. I. und Fisher, D. S. (2010) «Rate of adaptation in large sexual populations», Genetics. Genetics Society of America, 184(2), S. 467-481. doi: 10.1534/genetics.109.109009.   edoc | Open Access
Neher, R. A., Mitkovski, M., Kirchhoff, F., Neher, E., Theis, F. J. und Zeug, A. (2009) «Blind source separation techniques for the decomposition of multiply labeled fluorescence images», Biophysical Journal. Biophysical Society, 96(9), S. 3791-3800. doi: 10.1016/j.bpj.2008.10.068.   edoc | Open Access
Neher, R. A. und 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. National Academy of Sciences, 106(16), S. 6866-6871. doi: 10.1073/pnas.0812560106.   edoc | Open Access
Neher, R. A., Möbius, W., Frey, E. und Gerland, U. (2007) «Optimal flexibility for conformational transitions in macromolecules», Physical Review Letters. American Physical Society, 99(17), S. 178101. doi: 10.1103/PhysRevLett.99.178101.   edoc | Open Access
Kühner, F., Morfill, J., Neher, R. A., Blank, K. und Gaub, H. E. (2007) «Force-induced DNA slippage», Biophysical Journal. Biophysical Society, 92(7), S. 2491-2497. doi: 10.1529/biophysj.106.095836.   edoc | Open Access
Neher, R. A. und Gerland, U. (2006) «Intermediate phase in DNA melting», Physical Review E. American Physical Society, 73(3), S. 30902. doi: 10.1103/PhysRevE.73.030902.   edoc | Open Access
Möbius, W., Neher, R. A. und Gerland, U. (2006) «Kinetic accessibility of buried DNA sites in nucleosomes», Physical Review Letters. American Physical Society, 97(20), S. 208102. doi: 10.1103/PhysRevLett.97.208102.   edoc | Open Access
Neher, R. A. und Gerland, U. (2005) «DNA as a programmable viscoelastic nanoelement», Biophysical Journal. Biophysical Society, 89(6), S. 3846-3855. doi: 10.1529/biophysj.105.068866.   edoc | Open Access
Neher, R. A. und Neher, E. (2004) «Applying spectral fingerprinting to the analysis of FRET images», Microscopy Research and Technique. Wiley, 64(2), S. 185-195. doi: 10.1002/jemt.20078.   edoc
Neher, R. A. und Gerland, U. (2004) «Dynamics of force-induced DNA slippage», Physical Review Letters. American Physical Society, 93(19), S. 198102. doi: 10.1103/PhysRevLett.93.198102.   edoc | Open Access
Neher, R. und Neher, E. (2004) «Optimizing imaging parameters for the separation of multiple labels in a fluorescence image», Journal of Microscopy. Wiley, 213(1), S. 46-62. doi: 10.1111/j.1365-2818.2004.01262.x.   edoc