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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. und Relman, D. A. (2021) „Investigate the origins of COVID-19“, Science, 372(6543), S. 694. 10.1126/science.abj0016.   edoc
Barrat-Charlaix, P., Huddleston, J., Bedford, T. und Neher, R. A. (2021) „Limited Predictability of Amino Acid Substitutions in Seasonal Influenza Viruses“, Molecular biology and evolution, 38(7), S. 2767–2777. 10.1093/molbev/msab065.   
Dyrdak, R., Hodcroft, E. B., Wahlund, M., Neher, R. A. und Albert, J. (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 : the official publication of the Pan American Society for Clinical Virology, 136, S. 104754. 10.1016/j.jcv.2021.104754.   
Boehm, E., Kronig, I., Neher, R. A., Eckerle, I., Vetter, P., Kaiser, L. und Geneva Centre for Emerging Viral Diseases (2021) „Novel SARS-CoV-2 variants: the pandemics within the pandemic“, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, 27(8), S. 1109–1117. 10.1016/j.cmi.2021.05.022.   
Benschop, K. S. M., Broberg, E. K., Hodcroft, E., Schmitz, D., Albert, J., Baicus, A., Bailly, J.-L., Baldvinsdottir, G., Berginc, N., Blomqvist, S., Böttcher, S., Brytting, M., Bujaki, E., Cabrerizo, M., Celma, C., Cinek, O., Claas, E. C. J., Cremer, J., Dean, J., Dembinski, J. L., Demchyshyna, I., Diedrich, S., Dudman, S., Dunning, J., Dyrdak, R., Emmanouil, M., Farkas, A., De Gascun, C., Fournier, G., Georgieva, I., Gonzalez-Sanz, R., van Hooydonk-Elving, J., Jääskeläinen, A. J., Jancauskaite, R., Keeren, K., Fischer, T. K., Krokstad, S., Nikolaeva-Glomb, L., Novakova, L., Midgley, S. E., Mirand, A., Molenkamp, R., Morley, U., Mossong, J., Muralyte, S., Murk, J.-L., Nguyen, T., Nordbø, S. A., Österback, R., Pas, S., Pellegrinelli, L., Pogka, V., Prochazka, B., Rainetova, P., Van Ranst, M., Roorda, L., Schuffenecker, I., Schuurman, R., Stoyanova, A., Templeton, K., Verweij, J. J., Voulgari-Kokota, A., Vuorinen, T., Wollants, E., Wolthers, K. C., Zakikhany, K., Neher, R., Harvala, H. und Simmonds, P. (2021) „Molecular Epidemiology and Evolutionary Trajectory of Emerging Echovirus 30, Europe“, Emerging infectious diseases, 27(6), S. 1616–1626. 10.3201/eid2706.203096.   
Vogels, C. B. F., Breban, M. I., Ott, I. M., Alpert, T., Petrone, M. E., Watkins, A. E., Kalinich, C. C., Earnest, R., Rothman, J. E., Goes de Jesus, J., Morales Claro, I., Magalhães Ferreira, G., Crispim, M. A. E., Brazil-UK Cadde Genomic Network, Singh, L., Tegally, H., Anyaneji, U. J., Network for Genomic Surveillance in South Africa, Hodcroft, E. B., Mason, C. E., Khullar, G., Metti, J., Dudley, J. T., MacKay, M. J., Nash, M., Wang, J., Liu, C., Hui, P., Murphy, S., Neal, C., Laszlo, E., Landry, M. L., Muyombwe, A., Downing, R., Razeq, J., de Oliveira, T., Faria, N. R., Sabino, E. C., Neher, R. A., Fauver, J. R. und Grubaugh, N. D. (2021) „Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2“, PLoS biology, 19(5), S. e3001236. 10.1371/journal.pbio.3001236.   
Huddleston, J., Hadfield, J., Sibley, T. R., Lee, J., Fay, K., Ilcisin, M., Harkins, E., Bedford, T., Neher, R. A. und Hodcroft, E. B. (2021) „Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens“, Journal of open source software, 6(57), S. 4. 10.21105/joss.02906.   
Konings, F., Perkins, M. D., Kuhn, J. H., Pallen, M. J., Alm, E. J., Archer, B. N., Barakat, A., Bedford, T., Bhiman, J. N., Caly, L., Carter, L. L., Cullinane, A., de Oliveira, T., Druce, J., El Masry, I., Evans, R., Gao, G. F., Gorbalenya, A. E., Hamblion, E., Herring, B. L., Hodcroft, E., Holmes, E. C., Kakkar, M., Khare, S., Koopmans, M. P. G., Korber, B., Leite, J., MacCannell, D., Marklewitz, M., Maurer-Stroh, S., Rico, J. A. M., Munster, V. J., Neher, R., Munnink, B. O., Pavlin, B. I., Peiris, M., Poon, L., Pybus, O., Rambaut, A., Resende, P., Subissi, L., Thiel, V., Tong, S., van der Werf, S., von Gottberg, A., Ziebuhr, J. und Van Kerkhove, M. D. (2021) „SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse“, Nature microbiology, 6(7), S. 821–823. 10.1038/s41564-021-00932-w.   
Hodcroft, E. B., Zuber, M., Nadeau, S., Vaughan, T. G., Crawford, K. H. D., Althaus, C. L., Reichmuth, M. L., Bowen, J. E., Walls, A. C., Corti, D., Bloom, J. D., Veesler, D., Mateo, D., Hernando, A., Comas, I., González-Candelas, F., SeqCovid-Spain consortium, Stadler, T. und Neher, R. A. (2021) „Spread of a SARS-CoV-2 variant through Europe in the summer of 2020“, Nature, 595(7869), S. 707–712. 10.1038/s41586-021-03677-y.   
Goncalves Cabecinhas, A. R., Roloff, T., Stange, M., Bertelli, C., Huber, M., Ramette, A., Chen, C., Nadeau, S., Gerth, Y., Yerly, S., Opota, O., Pillonel, T., Schuster, T., Metzger, C. M. J. A., Sieber, J., Bel, M., Wohlwend, N., Baumann, C., Koch, M. C., Bittel, P., Leuzinger, K., Brunner, M., Suter-Riniker, F., Berlinger, L., Søgaard, K. K., Beckmann, C., Noppen, C., Redondo, M., Steffen, I., Seth-Smith, H. M. B., Mari, A., Lienhard, R., Risch, M., Nolte, O., Eckerle, I., Martinetti Lucchini, G., Hodcroft, E. B., Neher, R. A., Stadler, T., Hirsch, H. H., Leib, S. L., Risch, L., Kaiser, L., Trkola, A., Greub, G. und Egli, A. (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), S. 9040677. 10.3390/microorganisms9040677.   
Morris, D. H., Petrova, V. N., Rossine, F. W., Parker, E., Grenfell, B. T., Neher, R. A., Levin, S. A. und Russell, C. A. (2020) „Asynchrony between virus diversity and antibody selection limits influenza virus evolution“, eLife, 9, S. e62105. 10.7554/eLife.62105.   edoc | Open Access
Huddleston, J., Barnes, J. R., Rowe, T., Xu, X., Kondor, R., Wentworth, D. E., Whittaker, L., Ermetal, B., Daniels, R. S., McCauley, J. W., Fujisaki, S., Nakamura, K., Kishida, N., Watanabe, S., Hasegawa, H., Barr, I., Subbarao, K., Barrat-Charlaix, P., Neher, R. A. und Bedford, T. (2020) „Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution“, eLife, 9, S. e60067. 10.7554/eLife.60067.   edoc | Open Access
Bedford, T., Greninger, A. L., Roychoudhury, P., Starita, L. M., Famulare, M., Huang, M.-L., Nalla, A., Pepper, G., Reinhardt, A., Xie, H., Shrestha, L., Nguyen, T. N., Adler, A., Brandstetter, E., Cho, S., Giroux, D., Han, P. D., Fay, K., Frazar, C. D., Ilcisin, M., Lacombe, K., Lee, J., Kiavand, A., Richardson, M., Sibley, T. R., Truong, M., Wolf, C. R., Nickerson, D. A., Rieder, M. J., Englund, J. A., Seattle Flu Study Investigators, Hadfield, J., Hodcroft, E. B., Huddleston, J., Moncla, L. H., Müller, N. F., Neher, R. A., Deng, X., Gu, W., Federman, S., Chiu, C., Duchin, J. S., Gautom, R., Melly, G., Hiatt, B., Dykema, P., Lindquist, S., Queen, K., Tao, Y., Uehara, A., Tong, S., MacCannell, D., Armstrong, G. L., Baird, G. S., Chu, H. Y., Shendure, J. und Jerome, K. R. (2020) „Cryptic transmission of SARS-CoV-2 in Washington state“, Science (New York, N.Y.), 370(6516), S. 571–575. 10.1126/science.abc0523.   
Puller, V., Sagulenko, P. und Neher, R. A. (2020) „Efficient inference, potential, and limitations of site-specific substitution models“, Virus evolution, 6(2), S. veaa066. 10.1093/ve/veaa066.   
Battegay, M., Kuehl, R., Tschudin-Sutter, S., Hirsch, H. H., Widmer, A. F. und Neher, R. A. (2020) „2019-novel Coronavirus (2019-nCoV): estimating the case fatality rate - a word of caution“, Swiss medical weekly, 150, S. w20203. 10.4414/smw.2020.20203.   
Neher, R. A., Dyrdak, R., Druelle, V., Hodcroft, E. B. und Albert, J. (2020) „Potential impact of seasonal forcing on a SARS-CoV-2 pandemic“, Swiss medical weekly, 150, S. w20224. 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. und Low, N. (2020) „COVID-19 epidemic in Switzerland: on the importance of testing, contact tracing and isolation“, Swiss medical weekly, 150, S. w20225. 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. und Grubaugh, N. D. (2020) „Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States“, Cell, 181(5), S. 990–996.e5. 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. und 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), S. 2001410. 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. und 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), S. 1900749. 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. und 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), S. 12522–12523. 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. und Stephan, R. (2019) „Symposium report: One Health meets sequencing“, Microbes and Infection, 22(1), S. 1–7. 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, 364(6447), S. 1237–1239. 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, 266, S. 30–33. 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, 8, S. e44205. 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, 5(1), S. vez007. 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, 41, S. 479–487. 10.1016/j.ebiom.2019.02.061.   edoc | Open Access
Potter, B. I., Kondor, R., Hadfield, J., Huddleston, J., Barnes, J., Rowe, T., Guo, L., Xu, X., Neher, R. A., Bedford, T. und Wentworth, D. E. (2019) „Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season“, Virus evolution, 5(2), S. vez046. 10.1093/ve/vez046.   
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, 148(49-50), S. w14693. 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, 7(e30134), S. 1–24. 10.7554/eLife.30134.   edoc | Open Access
Sagulenko, P., Puller, V. und Neher, R. A. (2018) „TreeTime: Maximum-likelihood phylodynamic analysis“, Virus Evolution, 4(1, vex042), S. 1–9. 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, 73(12), S. 3368–3374. 10.1093/jac/dky337.   edoc | Open Access
Neher, R. A. und Bedford, T. (2018) „Real-time analysis and visualization of pathogen sequence data“, Journal of clinical microbiology, 56(11, ), S. e00480–18. 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, 24(1), S. 168–179.e4. 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, 34(23), S. 4121–4123. 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, 26(2), S. 17. 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, S. 12. 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, 13(10), S. e1005775. 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, 8, S. 15120. 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, 3(1), S. vex003. 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, 61(9), S. e00043–17. 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 , 239, S. 106–114. 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, 21(12), S. 1752–1767. 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, 113(12), S. 1701–1709. 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, 12(11), S. e1005964. 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. 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, 31(21), S. 3546–3548. 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, 10(3), S. e0119123. 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. 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, 10(3), S. e1004222. 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, 196(4), S. 1153–1165. 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. 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, S. 195–215. 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, 110(2), S. 437–442. 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, 110(39), S. 15836–15841. 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, 2013, S. P01010. 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, 87(21), S. 11843–11850. 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, 126, S. 5453–5464. 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, 4, S. 252. 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, 28(24), S. 3332–3333. 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, 191(2), S. 593–605. 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, 191(4), S. 1309–1319. 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, 191(4), S. 1283–1293. 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, 84(5), S. 51911. 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, 7(2), S. e1001315. 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, 188(4), S. 975–996. 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, 6(1), S. e1000660. 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, 184(2), S. 467–481. 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, 96(9), S. 3791–3800. 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, 106(16), S. 6866–6871. 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, 99(17), S. 178101. 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, 92(7), S. 2491–2497. 10.1529/biophysj.106.095836.   edoc | Open Access
Neher, R. A. und Gerland, U. (2006) „Intermediate phase in DNA melting“, Physical Review E, 73(3), S. 30902. 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, 97(20), S. 208102. 10.1103/PhysRevLett.97.208102.   edoc | Open Access
Neher, R. A. und Gerland, U. (2005) „DNA as a programmable viscoelastic nanoelement“, Biophysical Journal, 89(6), S. 3846–3855. 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, 64(2), S. 185–195. 10.1002/jemt.20078.   edoc
Neher, R. A. und Gerland, U. (2004) „Dynamics of force-induced DNA slippage“, Physical Review Letters, 93(19), S. 198102. 10.1103/PhysRevLett.93.198102.   edoc | Open Access