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TreeTime: Maximum-likelihood phylodynamic analysis.
Sagulenko P, Puller V, Neher RA. Sagulenko P, et al. Among authors: neher ra. Virus Evol. 2018 Jan 8;4(1):vex042. doi: 10.1093/ve/vex042. eCollection 2018 Jan. Virus Evol. 2018. PMID: 29340210 Free PMC article.
FFPopSim: an efficient forward simulation package for the evolution of large populations.
Zanini F, Neher RA. Zanini F, et al. Among authors: neher ra. Bioinformatics. 2012 Dec 15;28(24):3332-3. doi: 10.1093/bioinformatics/bts633. Epub 2012 Oct 24. Bioinformatics. 2012. PMID: 23097421 Free PMC article.
Inferring HIV Escape Rates from Multi-Locus Genotype Data.
Kessinger TA, Perelson AS, Neher RA. Kessinger TA, et al. Among authors: neher ra. Front Immunol. 2013 Sep 3;4:252. doi: 10.3389/fimmu.2013.00252. eCollection 2013. Front Immunol. 2013. PMID: 24027569 Free PMC article.
Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing.
Zanini F, Brodin J, Albert J, Neher RA. Zanini F, et al. Among authors: neher ra. Virus Res. 2017 Jul 15;239:106-114. doi: 10.1016/j.virusres.2016.12.009. Epub 2016 Dec 27. Virus Res. 2017. PMID: 28039047 Review.
In vivo mutation rates and the landscape of fitness costs of HIV-1.
Zanini F, Puller V, Brodin J, Albert J, Neher RA. Zanini F, et al. Among authors: neher ra. Virus Evol. 2017 Mar 2;3(1):vex003. doi: 10.1093/ve/vex003. eCollection 2017 Jan. Virus Evol. 2017. PMID: 28458914 Free PMC article.
Estimating time of HIV-1 infection from next-generation sequence diversity.
Puller V, Neher R, Albert J. Puller V, et al. Among authors: neher r. PLoS Comput Biol. 2017 Oct 2;13(10):e1005775. doi: 10.1371/journal.pcbi.1005775. eCollection 2017 Oct. PLoS Comput Biol. 2017. PMID: 28968389 Free PMC article.
panX: pan-genome analysis and exploration.
Ding W, Baumdicker F, Neher RA. Ding W, et al. Among authors: neher ra. Nucleic Acids Res. 2018 Jan 9;46(1):e5. doi: 10.1093/nar/gkx977. Nucleic Acids Res. 2018. PMID: 29077859 Free PMC article.
Nextstrain: real-time tracking of pathogen evolution.
Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, Sagulenko P, Bedford T, Neher RA. Hadfield J, et al. Among authors: neher ra. Bioinformatics. 2018 Dec 1;34(23):4121-4123. doi: 10.1093/bioinformatics/bty407. Bioinformatics. 2018. PMID: 29790939 Free PMC article.
Real-Time Analysis and Visualization of Pathogen Sequence Data.
Neher RA, Bedford T. Neher RA, et al. J Clin Microbiol. 2018 Oct 25;56(11):e00480-18. doi: 10.1128/JCM.00480-18. Print 2018 Nov. J Clin Microbiol. 2018. PMID: 30135232 Free PMC article. Review.
Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing.
Dyrdak R, Mastafa M, Hodcroft EB, Neher RA, Albert J. Dyrdak R, et al. Among authors: neher ra. Virus Evol. 2019 Apr 24;5(1):vez007. doi: 10.1093/ve/vez007. eCollection 2019 Jan. Virus Evol. 2019. PMID: 31037220 Free PMC article.
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