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

Article

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.