Publications of RA Neher

Puller, V.; Sagulenko, P.; Neher, R.: Efficient inference, potential, and limitations of site-specific substitution models. Virus Evolution 6 (2), veaa066 (2020)

Hadfield, J.; Megill, C.; Bell, S.; Huddleston, J.; Potter, B.; Callender, C.; Sagulenko, P.; Bedford, T.; Neher, R.: Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 34 (23), pp. 4121 - 4123 (2018)

Karasov, T.; Almario, J.; Friedemann, C.; Ding, W.; Giolai, M.; Heavens, D.; Kersten, S.; Lundberg, D.; Neumann, M.; Regalado, J. et al.; Neher, R.; Kemen, E.; Weigel, D.: Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales. Cell Host & Microbe 24 (1), pp. 168 - 179 (2018)

Ding, W.; Baumdicker, F.; Neher, R.: panX: pan-genome analysis and exploration. Nucleic Acids Research (London) 46 (1), e5 (2018)

Sagulenko, P.; Puller, V.; Neher, R.: TreeTime: Maximum-likelihood phylodynamic analysis. Virus Evolution 4 (1), vex042 (2018)

Puller, V.; Neher, R.; Albert, J.: Estimating time of HIV-1 infection from next-generation sequence diversity. PLoS Computational Biology 13 (10), e1005775 (2017)

Dößelmann, B.; Willmann, M.; Steglich, M.; Bunk, B.; Nübel, U.; Peter, S.; Neher, R.: Rapid and Consistent Evolution of Colistin Resistance in Extensively Drug-Resistant Pseudomonas aeruginosa during Morbidostat Culture. Antimicrobial Agents and Chemotherapy 61 (9), e00043-17 (2017)

Zanini, F.; Brodin, J.; Albert, J.; Neher, R.: Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing. Virus Research 239, pp. 106 - 114 (2017)

You, Y.; Sawikowska, A.; Neumann, M.; Posé, D.; Capovilla, G.; Langenecker, T.; Neher, R.; Krajewski, P.; Schmid, M.: Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering. Nature Communications 8, 15120 (2017)

Zanini, F.; Puller, V.; Brodin, J.; Albert, J.; Neher, R.: In vivo mutation rates and the landscape of fitness costs of HIV-1. Virus Evolution 3 (1), vex003 (2017)

Hassouna, I.; Ott, C.; Wüstefeld, L.; Offen, N.; Neher, R.; Mitkovski, M.; Winkler, D.; Sperling, S.; Fries, L.; Goebbels, S. et al.; Vreja, I.; Hagemeyer, N.; Dittrich, M.; Rossetti, M.; Kröhnert, K.; Hannke, K.; Boretius, S.; Zeug, A.; Höschen, C.; Dandekar, T.; Dere, E.; Neher, E.; Rizzoli, S.; Nave, K.; Sirén, A.; Ehrenreich, H.: Revisiting adult neurogenesis and the role of erythropoietin for neuronal and oligodendroglial differentiation in the hippocampus. Molecular Psychiatry 21 (12), pp. 1752 - 1767 (2016)

Boullé, M.; Müller, T.; Dähling, S.; Ganga, Y.; Jackson, L.; Mahamed, D.; Oom, L.; Lustig, G.; Neher, R.; Sigal, A.: HIV Cell-to-Cell Spread Results in Earlier Onset of Viral Gene Expression by Multiple Infections per Cell. PLoS Pathogens 12 (11), e1005964 (2016)

Brodin, J.; Zanini, F.; Thebo, L.; Lanz, C.; Bratt, G.; Neher, R.; Albert, J.: Establishment and stability of the latent HIV-1 DNA reservoir. eLife 5, e18889 (2016)

Neher, R.; Bedford, T.; Daniels, R.; Russell, C.; Shraiman, B.: 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. E1701 - E1709 (2016)

Zanini, F.; Brodin, J.; Thebo, L.; Lanz, C.; Bratt, G.; Albert, J.; Neher, R.: Population genomics of intrapatient HIV-1 evolution. eLife 4, e11282 (2015)

Neher, R.; Bedford, T.: nextflu: real-time tracking of seasonal influenza virus evolution in humans. Bioinformatics 31 (21), pp. 3546 - 3548 (2015)

Brodin, J.; Hedskog, C.; Heddini, A.; Benard, E.; Neher, R.; Mild, M.; Albert, J.: Challenges with using primer IDs to improve accuracy of next generation sequencing. PLoS One 10 (3), e0119123 (2015)

Neher, R.; Russell, C.; Shraiman, B.: Predicting evolution from the shape of genealogical trees. eLife 3, e03568 (2014)

Rödelsperger, C.; Neher, R.; Weller, A.; Eberhardt, G.; Witte, H.; Mayer, W.; Dieterich, C.; Sommer, R.: Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data. Genetics 196 (4), pp. 1153 - 1165 (2014)

Good, B.; Walczak, A.; Neher, R.; Desai, M.: Genetic diversity in the interference selection limit. PLoS Genetics 10 (3), e1004222 (2014)