Items where Division is "05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Computational Modeling of Biological Processes (Neher)"

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Bloom, Jesse D. and Chan, Yujia Alina and Baric, Ralph S. and Bjorkman, Pamela J. and Cobey, Sarah and Deverman, Benjamin E. and Fisman, David N. and Gupta, Ravindra and Iwasaki, Akiko and Lipsitch, Marc and Medzhitov, Ruslan and Neher, Richard A. and Nielsen, Rasmus and Patterson, Nick and Stearns, Tim and van Nimwegen, Erik and Worobey, Michael and Relman, David A.. (2021) Investigate the origins of COVID-19. Science, 372 (6543). p. 694.


Huddleston, John and Barnes, John R. and Rowe, Thomas and Xu, Xiyan and Kondor, Rebecca and Wentworth, David E. and Whittaker, Lynne and Ermetal, Burcu and Daniels, Rodney Stuart and McCauley, John W. and Fujisaki, Seiichiro and Nakamura, Kazuya and Kishida, Noriko and Watanabe, Shinji and Hasegawa, Hideki and Barr, Ian and Subbarao, Kanta and Barrat-Charlaix, Pierre and Neher, Richard A. and Bedford, Trevor. (2020) Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution. eLife, 9. e60067.

Morris, Dylan H. and Petrova, Velislava N. and Rossine, Fernando W. and Parker, Edyth and Grenfell, Bryan T. and Neher, Richard A. and Levin, Simon A. and Russell, Colin A.. (2020) Asynchrony between virus diversity and antibody selection limits influenza virus evolution. eLife, 9. e62105.


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.

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.

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.

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.

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.


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.

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.

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.

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.

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.

Sagulenko, Pavel and Puller, Vadim and Neher, Richard A.. (2018) TreeTime: Maximum-likelihood phylodynamic analysis. Virus Evolution, 4 (1, vex042). pp. 1-9.


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.

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.

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.

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.

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.


Boullé, Mikaël and Müller, Thorsten G. and Dähling, Sabrina and Ganga, Yashica and Jackson, Laurelle and Mahamed, Deeqa and Oom, Lance and Lustig, Gila and Neher, Richard A. and 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.

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

Hassouna, I. and Ott, C. and Wüstefeld, L. and Offen, N. and Neher, R. A. and Mitkovski, M. and Winkler, D. and Sperling, S. and Fries, L. and Goebbels, S. and Vreja, I. C. and Hagemeyer, N. and Dittrich, M. and Rossetti, M. F. and Kröhnert, K. and Hannke, K. and Boretius, S. and Zeug, A. and Höschen, C. and Dandekar, T. and Dere, E. and Neher, E. and Rizzoli, S. O. and Nave, K.-A. and 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.

Neher, Richard A. and Bedford, Trevor and Daniels, Rodney S. and Russell, Colin A. and 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). pp. 1701-1709.

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


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

Neher, Richard A. and Bedford, Trevor. (2015) nextflu: real-time tracking of seasonal influenza virus evolution in humans. Bioinformatics, 31 (21). pp. 3546-3548.

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


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

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

Rödelsperger, Christian and Neher, Richard A. and Weller, Andreas M. and Eberhardt, Gabi and Witte, Hanh and Mayer, Werner E. and Dieterich, Christoph and Sommer, Ralf J.. (2014) Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data. Genetics, 196 (4). pp. 1153-1165.


Ganusov, Vitaly V. and Neher, Richard A. and 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. and Perelson, Alan S. and Neher, Richard A.. (2013) Inferring HIV Escape Rates from Multi-Locus Genotype Data. Frontiers in Immunology, 4. p. 252.

Mukherjee, Amrita and Neher, Richard A. and Renault, Andrew D.. (2013) Quantifying the range of a lipid phosphate signal in vivo. Journal of Cell Science, 126. pp. 5453-5464.

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

Neher, Richard A. and Hallatschek, Oskar. (2013) Genealogies of rapidly adapting populations. Proceedings of the National Academy of Sciences, 110 (2). pp. 437-442.

Neher, Richard A. and Kessinger, Taylor A. and Shraiman, Boris I.. (2013) Coalescence and genetic diversity in sexual populations under selection. Proceedings of the National Academy of Sciences, 110 (39). pp. 15836-15841.

Zanini, Fabio and Neher, Richard A.. (2013) Quantifying selection against synonymous mutations in HIV-1 env evolution. Journal of virology, 87 (21). pp. 11843-11850.


Goyal, Sidhartha and Balick, Daniel J. and Jerison, Elizabeth R. and Neher, Richard A. and Shraiman, Boris I. and Desai, Michael M.. (2012) Dynamic mutation-selection balance as an evolutionary attractor. Genetics, 191 (4). pp. 1309-1319.

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

Neher, Richard A. and Shraiman, Boris I.. (2012) Fluctuations of fitness distributions and the rate of Muller's ratchet. Genetics, 191 (4). pp. 1283-1293.

Zanini, Fabio and Neher, Richard A.. (2012) FFPopSim: an efficient forward simulation package for the evolution of large populations. Bioinformatics, 28 (24). pp. 3332-3333.


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

Neher, R. A. and Shraiman, B. I.. (2011) Genetic draft and quasi-neutrality in large facultatively sexual populations. Genetics, 188 (4). pp. 975-996.

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


Neher, R. A. and Shraiman, B. I. and Fisher, D. S.. (2010) Rate of adaptation in large sexual populations. Genetics, 184 (2). pp. 467-481.

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


Neher, Richard A. and Mitkovski, Miso and Kirchhoff, Frank and Neher, Erwin and Theis, Fabian J. and Zeug, André. (2009) Blind source separation techniques for the decomposition of multiply labeled fluorescence images. Biophysical Journal, 96 (9). pp. 3791-3800.

Neher, Richard A. and 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). pp. 6866-6871.


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

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


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

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


Neher, Richard A. and Gerland, Ulrich. (2005) DNA as a programmable viscoelastic nanoelement. Biophysical Journal, 89 (6). pp. 3846-3855.


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

Neher, Richard A. and Neher, Erwin. (2004) Applying spectral fingerprinting to the analysis of FRET images. Microscopy Research and Technique, 64 (2). pp. 185-195.

This list was generated on Wed Jan 19 03:52:02 2022 CET.