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Phylodynamic theory of persistence, extinction and speciation of rapidly adapting pathogens.

Yan L, Neher RA, Shraiman BI.

Elife. 2019 Sep 18;8. pii: e44205. doi: 10.7554/eLife.44205.


Symposium report: One Health meets sequencing.

Egli A, Koch D, Danuser J, Hendriksen RS, Driesen S, Schmid DC, Neher R, Mäusezahl M, Seth-Smith HMB, Bloemberg G, Tschudin-Sutter S, Endimiani A, Perreten V, Greub G, Schrenzel J, Stephan R.

Microbes Infect. 2019 Aug 8. pii: S1286-4579(19)30083-8. doi: 10.1016/j.micinf.2019.07.004. [Epub ahead of print] No abstract available.


A global surveillance system for crop diseases.

Carvajal-Yepes M, Cardwell K, Nelson A, Garrett KA, Giovani B, Saunders DGO, Kamoun S, Legg JP, Verdier V, Lessel J, Neher RA, Day R, Pardey P, Gullino ML, Records AR, Bextine B, Leach JE, Staiger S, Tohme J.

Science. 2019 Jun 28;364(6447):1237-1239. doi: 10.1126/science.aaw1572. No abstract available.


Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing.

Dyrdak R, Mastafa M, Hodcroft EB, Neher RA, Albert J.

Virus Evol. 2019 Apr 24;5(1):vez007. doi: 10.1093/ve/vez007. eCollection 2019 Jan.


Quantitative contribution of efflux to multi-drug resistance of clinical Escherichia coli and Pseudomonas aeruginosa strains.

Cunrath O, Meinel DM, Maturana P, Fanous J, Buyck JM, Saint Auguste P, Seth-Smith HMB, Körner J, Dehio C, Trebosc V, Kemmer C, Neher R, Egli A, Bumann D.

EBioMedicine. 2019 Mar;41:479-487. doi: 10.1016/j.ebiom.2019.02.061. Epub 2019 Mar 7.


Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses.

Wüthrich D, Lang D, Müller NF, Neher RA, Stadler T, Egli A.

J Virol Methods. 2019 Apr;266:30-33. doi: 10.1016/j.jviromet.2019.01.009. Epub 2019 Jan 21.


Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform.

Egli A, Blanc DS, Greub G, Keller PM, Lazarevic V, Lebrand A, Leib S, Neher RA, Perreten V, Ramette A, Schrenzel J, Stephan R, Wagner K, Wuethrich D, Xenarios I.

Swiss Med Wkly. 2018 Dec 15;148:w14693. doi: 10.4414/smw.2018.14693. eCollection 2018 Dec 3.


Colistin susceptibility test evaluation of multiple-resistance-level Pseudomonas aeruginosa isolates generated in a morbidostat device.

Javed M, Ueltzhoeffer V, Heinrich M, Siegrist HJ, Wildermuth R, Lorenz FR, Neher RA, Willmann M.

J Antimicrob Chemother. 2018 Dec 1;73(12):3368-3374. doi: 10.1093/jac/dky337.


Real-Time Analysis and Visualization of Pathogen Sequence Data.

Neher RA, Bedford T.

J Clin Microbiol. 2018 Oct 25;56(11). pii: e00480-18. doi: 10.1128/JCM.00480-18. Print 2018 Nov. Review.


Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales.

Karasov TL, Almario J, Friedemann C, Ding W, Giolai M, Heavens D, Kersten S, Lundberg DS, Neumann M, Regalado J, Neher RA, Kemen E, Weigel D.

Cell Host Microbe. 2018 Jul 11;24(1):168-179.e4. doi: 10.1016/j.chom.2018.06.011.


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.

Bioinformatics. 2018 Dec 1;34(23):4121-4123. doi: 10.1093/bioinformatics/bty407.


Incomplete inhibition of HIV infection results in more HIV infected lymph node cells by reducing cell death.

Jackson L, Hunter J, Cele S, Ferreira IM, Young AC, Karim F, Madansein R, Dullabh KJ, Chen CY, Buckels NJ, Ganga Y, Khan K, Boulle M, Lustig G, Neher RA, Sigal A.

Elife. 2018 Mar 20;7. pii: e30134. doi: 10.7554/eLife.30134.


Detection of the Malaria causing Plasmodium Parasite in Saliva from Infected Patients using Topoisomerase I Activity as a Biomarker.

Hede MS, Fjelstrup S, Lötsch F, Zoleko RM, Klicpera A, Groger M, Mischlinger J, Endame L, Veletzky L, Neher R, Simonsen AKW, Petersen E, Mombo-Ngoma G, Stougaard M, Ho YP, Labouriau R, Ramharter M, Knudsen BR.

Sci Rep. 2018 Mar 7;8(1):4122. doi: 10.1038/s41598-018-22378-7.


Using Patient Demographics and Statistical Modeling to Predict Knee Tibia Component Sizing in Total Knee Arthroplasty.

Ren AN, Neher RE, Bell T, Grimm J.

J Arthroplasty. 2018 Jun;33(6):1732-1736. doi: 10.1016/j.arth.2018.01.031. Epub 2018 Jan 31.


TreeTime: Maximum-likelihood phylodynamic analysis.

Sagulenko P, Puller V, Neher RA.

Virus Evol. 2018 Jan 8;4(1):vex042. doi: 10.1093/ve/vex042. eCollection 2018 Jan.


Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology.

Morris DH, Gostic KM, Pompei S, Bedford T, Łuksza M, Neher RA, Grenfell BT, Lässig M, McCauley JW.

Trends Microbiol. 2018 Feb;26(2):102-118. doi: 10.1016/j.tim.2017.09.004. Epub 2017 Oct 30. Review.


panX: pan-genome analysis and exploration.

Ding W, Baumdicker F, Neher RA.

Nucleic Acids Res. 2018 Jan 9;46(1):e5. doi: 10.1093/nar/gkx977.


Estimating time of HIV-1 infection from next-generation sequence diversity.

Puller V, Neher R, Albert J.

PLoS Comput Biol. 2017 Oct 2;13(10):e1005775. doi: 10.1371/journal.pcbi.1005775. eCollection 2017 Oct.


Rapid and Consistent Evolution of Colistin Resistance in Extensively Drug-Resistant Pseudomonas aeruginosa during Morbidostat Culture.

Dößelmann B, Willmann M, Steglich M, Bunk B, Nübel U, Peter S, Neher RA.

Antimicrob Agents Chemother. 2017 Aug 24;61(9). pii: e00043-17. doi: 10.1128/AAC.00043-17. Print 2017 Sep.


Sagittal tibiotalar translation and clinical outcomes in mobile and fixed-bearing total ankle replacement.

Usuelli FG, Manzi L, Brusaferri G, Neher RE, Guelfi M, Maccario C.

Foot Ankle Surg. 2017 Jun;23(2):95-101. doi: 10.1016/j.fas.2016.08.005. Epub 2016 Aug 26.


Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering.

You Y, Sawikowska A, Neumann M, Posé D, Capovilla G, Langenecker T, Neher RA, Krajewski P, Schmid M.

Nat Commun. 2017 May 17;8:15120. doi: 10.1038/ncomms15120.


In vivo mutation rates and the landscape of fitness costs of HIV-1.

Zanini F, Puller V, Brodin J, Albert J, Neher RA.

Virus Evol. 2017 Mar 2;3(1):vex003. doi: 10.1093/ve/vex003. eCollection 2017 Jan.


Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing.

Zanini F, Brodin J, Albert J, Neher RA.

Virus Res. 2017 Jul 15;239:106-114. doi: 10.1016/j.virusres.2016.12.009. Epub 2016 Dec 27. Review.


Establishment and stability of the latent HIV-1 DNA reservoir.

Brodin J, Zanini F, Thebo L, Lanz C, Bratt G, Neher RA, Albert J.

Elife. 2016 Nov 15;5. pii: e18889. doi: 10.7554/eLife.18889.


HIV Cell-to-Cell Spread Results in Earlier Onset of Viral Gene Expression by Multiple Infections per Cell.

Boullé M, Müller TG, Dähling S, Ganga Y, Jackson L, Mahamed D, Oom L, Lustig G, Neher RA, Sigal A.

PLoS Pathog. 2016 Nov 3;12(11):e1005964. doi: 10.1371/journal.ppat.1005964. eCollection 2016 Nov.


Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses.

Neher RA, Bedford T, Daniels RS, Russell CA, Shraiman BI.

Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):E1701-9. doi: 10.1073/pnas.1525578113. Epub 2016 Mar 7.


Revisiting adult neurogenesis and the role of erythropoietin for neuronal and oligodendroglial differentiation in the hippocampus.

Hassouna I, Ott C, Wüstefeld L, Offen N, Neher RA, Mitkovski M, Winkler D, Sperling S, Fries L, Goebbels S, Vreja IC, Hagemeyer N, Dittrich M, Rossetti MF, Kröhnert K, Hannke K, Boretius S, Zeug A, Höschen C, Dandekar T, Dere E, Neher E, Rizzoli SO, Nave KA, Sirén AL, Ehrenreich H.

Mol Psychiatry. 2016 Dec;21(12):1752-1767. doi: 10.1038/mp.2015.212. Epub 2016 Jan 26.


Population genomics of intrapatient HIV-1 evolution.

Zanini F, Brodin J, Thebo L, Lanz C, Bratt G, Albert J, Neher RA.

Elife. 2015 Dec 11;4. pii: e11282. doi: 10.7554/eLife.11282.


nextflu: real-time tracking of seasonal influenza virus evolution in humans.

Neher RA, Bedford T.

Bioinformatics. 2015 Nov 1;31(21):3546-8. doi: 10.1093/bioinformatics/btv381. Epub 2015 Jun 26.


Challenges with using primer IDs to improve accuracy of next generation sequencing.

Brodin J, Hedskog C, Heddini A, Benard E, Neher RA, Mild M, Albert J.

PLoS One. 2015 Mar 5;10(3):e0119123. doi: 10.1371/journal.pone.0119123. eCollection 2015.


Predicting evolution from the shape of genealogical trees.

Neher RA, Russell CA, Shraiman BI.

Elife. 2014 Nov 11;3. doi: 10.7554/eLife.03568.


Genetic diversity in the interference selection limit.

Good BH, Walczak AM, Neher RA, Desai MM.

PLoS Genet. 2014 Mar 27;10(3):e1004222. doi: 10.1371/journal.pgen.1004222. eCollection 2014 Mar.


Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data.

Rödelsperger C, Neher RA, Weller AM, Eberhardt G, Witte H, Mayer WE, Dieterich C, Sommer RJ.

Genetics. 2014 Apr;196(4):1153-65. doi: 10.1534/genetics.113.159855. Epub 2014 Jan 17.


Inferring HIV Escape Rates from Multi-Locus Genotype Data.

Kessinger TA, Perelson AS, Neher RA.

Front Immunol. 2013 Sep 3;4:252. doi: 10.3389/fimmu.2013.00252. eCollection 2013.


Coalescence and genetic diversity in sexual populations under selection.

Neher RA, Kessinger TA, Shraiman BI.

Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15836-41. doi: 10.1073/pnas.1309697110. Epub 2013 Sep 9.


Quantifying the range of a lipid phosphate signal in vivo.

Mukherjee A, Neher RA, Renault AD.

J Cell Sci. 2013 Dec 1;126(Pt 23):5453-64. doi: 10.1242/jcs.136176. Epub 2013 Sep 4.


Quantifying selection against synonymous mutations in HIV-1 env evolution.

Zanini F, Neher RA.

J Virol. 2013 Nov;87(21):11843-50. doi: 10.1128/JVI.01529-13. Epub 2013 Aug 28.


Mathematical modeling of escape of HIV from cytotoxic T lymphocyte responses.

Ganusov VV, Neher RA, Perelson AS.

J Stat Mech. 2013 Jan 1;2013:P01010.


Genealogies of rapidly adapting populations.

Neher RA, Hallatschek O.

Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):437-42. doi: 10.1073/pnas.1213113110. Epub 2012 Dec 26.


FFPopSim: an efficient forward simulation package for the evolution of large populations.

Zanini F, Neher RA.

Bioinformatics. 2012 Dec 15;28(24):3332-3. doi: 10.1093/bioinformatics/bts633. Epub 2012 Oct 24.


Dynamic mutation-selection balance as an evolutionary attractor.

Goyal S, Balick DJ, Jerison ER, Neher RA, Shraiman BI, Desai MM.

Genetics. 2012 Aug;191(4):1309-19. doi: 10.1534/genetics.112.141291. Epub 2012 Jun 1.


Fluctuations of fitness distributions and the rate of Muller's ratchet.

Neher RA, Shraiman BI.

Genetics. 2012 Aug;191(4):1283-93. doi: 10.1534/genetics.112.141325. Epub 2012 May 29.


Estimating the strength of selective sweeps from deep population diversity data.

Messer PW, Neher RA.

Genetics. 2012 Jun;191(2):593-605. doi: 10.1534/genetics.112.138461. Epub 2012 Apr 4.


Target search on a dynamic DNA molecule.

Schötz T, Neher RA, Gerland U.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Nov;84(5 Pt 1):051911. Epub 2011 Nov 17.


Genetic draft and quasi-neutrality in large facultatively sexual populations.

Neher RA, Shraiman BI.

Genetics. 2011 Aug;188(4):975-96. doi: 10.1534/genetics.111.128876. Epub 2011 May 30.


Correlated evolution of nearby residues in Drosophilid proteins.

Callahan B, Neher RA, Bachtrog D, Andolfatto P, Shraiman BI.

PLoS Genet. 2011 Feb;7(2):e1001315. doi: 10.1371/journal.pgen.1001315. Epub 2011 Feb 24.


Recombination rate and selection strength in HIV intra-patient evolution.

Neher RA, Leitner T.

PLoS Comput Biol. 2010 Jan 29;6(1):e1000660. doi: 10.1371/journal.pcbi.1000660.


Rate of adaptation in large sexual populations.

Neher RA, Shraiman BI, Fisher DS.

Genetics. 2010 Feb;184(2):467-81. doi: 10.1534/genetics.109.109009. Epub 2009 Nov 30.


Blind source separation techniques for the decomposition of multiply labeled fluorescence images.

Neher RA, Mitkovski M, Kirchhoff F, Neher E, Theis FJ, Zeug A.

Biophys J. 2009 May 6;96(9):3791-800. doi: 10.1016/j.bpj.2008.10.068.


Competition between recombination and epistasis can cause a transition from allele to genotype selection.

Neher RA, Shraiman BI.

Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6866-71. doi: 10.1073/pnas.0812560106. Epub 2009 Apr 6.

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