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Items: 1 to 50 of 57

1.

The utility of fitness landscapes and big data for predicting evolution.

de Visser JAGM, Elena SF, Fragata I, Matuszewski S.

Heredity (Edinb). 2018 Nov;121(5):401-405. doi: 10.1038/s41437-018-0128-4. Epub 2018 Aug 20. No abstract available.

2.

Unraveling the causes of adaptive benefits of synonymous mutations in TEM-1 β-lactamase.

Zwart MP, Schenk MF, Hwang S, Koopmanschap B, de Lange N, van de Pol L, Nga TTT, Szendro IG, Krug J, de Visser JAGM.

Heredity (Edinb). 2018 Nov;121(5):406-421. doi: 10.1038/s41437-018-0104-z. Epub 2018 Jul 2.

3.

[Polymicrobial infections: ecosystems with special properties].

de Vos MGJ, de Visser JAGM, Rossen JWA, Zwaan BJ.

Ned Tijdschr Geneeskd. 2018;162:D2224. Dutch.

PMID:
29543145
4.

Local Fitness Landscapes Predict Yeast Evolutionary Dynamics in Directionally Changing Environments.

Gorter FA, Aarts MGM, Zwaan BJ, de Visser JAGM.

Genetics. 2018 Jan;208(1):307-322. doi: 10.1534/genetics.117.300519. Epub 2017 Nov 15.

5.

Adaptive benefits from small mutation supplies in an antibiotic resistance enzyme.

Salverda MLM, Koomen J, Koopmanschap B, Zwart MP, de Visser JAGM.

Proc Natl Acad Sci U S A. 2017 Nov 28;114(48):12773-12778. doi: 10.1073/pnas.1712999114. Epub 2017 Nov 13.

6.

Nanowire sensors monitor bacterial growth kinetics and response to antibiotics.

Ibarlucea B, Rim T, Baek CK, de Visser JAGM, Baraban L, Cuniberti G.

Lab Chip. 2017 Dec 5;17(24):4283-4293. doi: 10.1039/c7lc00807d.

PMID:
29119168
7.

Genomics of Adaptation Depends on the Rate of Environmental Change in Experimental Yeast Populations.

Gorter FA, Derks MFL, van den Heuvel J, Aarts MGM, Zwaan BJ, de Ridder D, de Visser JAGM.

Mol Biol Evol. 2017 Oct 1;34(10):2613-2626. doi: 10.1093/molbev/msx185.

PMID:
28957501
8.

Mutation supply and the repeatability of selection for antibiotic resistance.

van Dijk T, Hwang S, Krug J, de Visser JAGM, Zwart MP.

Phys Biol. 2017 Aug 21;14(5):055005. doi: 10.1088/1478-3975/aa7f36.

PMID:
28699625
9.

Power provides protection: Genetic robustness in yeast depends on the capacity to generate energy.

Plech M, Tomala K, Tutaj H, Piwcewicz DE, de Visser JAGM, Korona R.

PLoS Genet. 2017 May 11;13(5):e1006768. doi: 10.1371/journal.pgen.1006768. eCollection 2017 May.

10.

Experimental tests of host-virus coevolution in natural killer yeast strains.

Pieczynska MD, Korona R, De Visser JA.

J Evol Biol. 2017 Apr;30(4):773-781. doi: 10.1111/jeb.13044. Epub 2017 Feb 24.

11.

Sex in a test tube: testing the benefits of in vitro recombination.

Pesce D, Lehman N, de Visser JA.

Philos Trans R Soc Lond B Biol Sci. 2016 Oct 19;371(1706). pii: 20150529. doi: 10.1098/rstb.2015.0529. Review.

12.

Diminishing-returns epistasis among random beneficial mutations in a multicellular fungus.

Schoustra S, Hwang S, Krug J, de Visser JA.

Proc Biol Sci. 2016 Aug 31;283(1837). pii: 20161376. doi: 10.1098/rspb.2016.1376.

13.

Dynamics of Adaptation in Experimental Yeast Populations Exposed to Gradual and Abrupt Change in Heavy Metal Concentration.

Gorter FA, Aarts MM, Zwaan BJ, de Visser JA.

Am Nat. 2016 Jan;187(1):110-9. doi: 10.1086/684104.

PMID:
27277407
14.

Rapid multiple-level coevolution in experimental populations of yeast killer and nonkiller strains.

Pieczynska MD, Wloch-Salamon D, Korona R, de Visser JA.

Evolution. 2016 Jun;70(6):1342-53. doi: 10.1111/evo.12945. Epub 2016 May 30.

PMID:
27168531
15.

Lineage Tracking for Probing Heritable Phenotypes at Single-Cell Resolution.

Cottinet D, Condamine F, Bremond N, Griffiths AD, Rainey PB, de Visser JA, Baudry J, Bibette J.

PLoS One. 2016 Apr 14;11(4):e0152395. doi: 10.1371/journal.pone.0152395. eCollection 2016.

16.

Evolution of coexistence in a crowded microplate well.

de Visser JA.

Proc Natl Acad Sci U S A. 2015 Sep 8;112(36):11148-9. doi: 10.1073/pnas.1514399112. Epub 2015 Aug 26. No abstract available.

17.

Monitoring microbial metabolites using an inductively coupled resonance circuit.

Karnaushenko D, Baraban L, Ye D, Uguz I, Mendes RG, Rümmeli MH, de Visser JA, Schmidt OG, Cuniberti G, Makarov D.

Sci Rep. 2015 Aug 12;5:12878. doi: 10.1038/srep12878.

18.

Negative Epistasis and Evolvability in TEM-1 β-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder.

Dellus-Gur E, Elias M, Caselli E, Prati F, Salverda ML, de Visser JA, Fraser JS, Tawfik DS.

J Mol Biol. 2015 Jul 17;427(14):2396-409. doi: 10.1016/j.jmb.2015.05.011. Epub 2015 May 22.

19.

Role of pleiotropy during adaptation of TEM-1 β-lactamase to two novel antibiotics.

Schenk MF, Witte S, Salverda ML, Koopmanschap B, Krug J, de Visser JA.

Evol Appl. 2015 Mar;8(3):248-60. doi: 10.1111/eva.12200. Epub 2014 Sep 18.

20.

Empirical fitness landscapes and the predictability of evolution.

de Visser JA, Krug J.

Nat Rev Genet. 2014 Jul;15(7):480-90. doi: 10.1038/nrg3744. Epub 2014 Jun 10. Review.

PMID:
24913663
21.

Heterosis is prevalent among domesticated but not wild strains of Saccharomyces cerevisiae.

Plech M, de Visser JA, Korona R.

G3 (Bethesda). 2014 Feb 19;4(2):315-23. doi: 10.1534/g3.113.009381.

22.

Incidence of symbiotic dsRNA 'killer' viruses in wild and domesticated yeast.

Pieczynska MD, de Visser JA, Korona R.

FEMS Yeast Res. 2013 Dec;13(8):856-9. doi: 10.1111/1567-1364.12086. Epub 2013 Oct 7.

23.

Patterns of Epistasis between beneficial mutations in an antibiotic resistance gene.

Schenk MF, Szendro IG, Salverda ML, Krug J, de Visser JA.

Mol Biol Evol. 2013 Aug;30(8):1779-87. doi: 10.1093/molbev/mst096. Epub 2013 May 15.

24.

Predicting the evolution of antibiotic resistance.

Schenk MF, de Visser JA.

BMC Biol. 2013 Feb 22;11:14. doi: 10.1186/1741-7007-11-14.

25.

Predictability of evolution depends nonmonotonically on population size.

Szendro IG, Franke J, de Visser JA, Krug J.

Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):571-6. doi: 10.1073/pnas.1213613110. Epub 2012 Dec 24.

26.

Quantifying the adaptive potential of an antibiotic resistance enzyme.

Schenk MF, Szendro IG, Krug J, de Visser JA.

PLoS Genet. 2012 Jun;8(6):e1002783. doi: 10.1371/journal.pgen.1002783. Epub 2012 Jun 28.

27.

Model and test in a fungus of the probability that beneficial mutations survive drift.

Gifford DR, de Visser JA, Wahl LM.

Biol Lett. 2013 Feb 23;9(1):20120310. doi: 10.1098/rsbl.2012.0310. Epub 2012 Jun 27.

28.

Millifluidic droplet analyser for microbiology.

Baraban L, Bertholle F, Salverda ML, Bremond N, Panizza P, Baudry J, de Visser JA, Bibette J.

Lab Chip. 2011 Dec 7;11(23):4057-62. doi: 10.1039/c1lc20545e. Epub 2011 Oct 20.

PMID:
22012599
29.

The causes of epistasis.

de Visser JA, Cooper TF, Elena SF.

Proc Biol Sci. 2011 Dec 22;278(1725):3617-24. doi: 10.1098/rspb.2011.1537. Epub 2011 Oct 5. Review.

30.

Evolutionary accessibility of mutational pathways.

Franke J, Klözer A, de Visser JA, Krug J.

PLoS Comput Biol. 2011 Aug;7(8):e1002134. doi: 10.1371/journal.pcbi.1002134. Epub 2011 Aug 18.

31.

Evolutionary genetics: evolution with foresight.

Salverda ML, de Visser JA.

Curr Biol. 2011 May 24;21(10):R398-400. doi: 10.1016/j.cub.2011.04.023.

32.

Initial mutations direct alternative pathways of protein evolution.

Salverda ML, Dellus E, Gorter FA, Debets AJ, van der Oost J, Hoekstra RF, Tawfik DS, de Visser JA.

PLoS Genet. 2011 Mar;7(3):e1001321. doi: 10.1371/journal.pgen.1001321. Epub 2011 Mar 3.

33.

Natural evolution of TEM-1 β-lactamase: experimental reconstruction and clinical relevance.

Salverda ML, De Visser JA, Barlow M.

FEMS Microbiol Rev. 2010 Nov;34(6):1015-36. doi: 10.1111/j.1574-6976.2010.00222.x. Review.

34.

Exploring the effect of sex on empirical fitness landscapes.

de Visser JA, Park SC, Krug J.

Am Nat. 2009 Jul;174 Suppl 1:S15-30. doi: 10.1086/599081.

PMID:
19456267
35.

Mixed infections and the competitive fitness of faster-acting genetically modified viruses.

Zwart MP, Van Der Werf W, Van Oers MM, Hemerik L, Van Lent JM, De Visser JA, Vlak JM, Cory JS.

Evol Appl. 2009 May;2(2):209-21. doi: 10.1111/j.1752-4571.2008.00058.x. Epub 2009 Feb 2.

36.

An experimental test of the independent action hypothesis in virus-insect pathosystems.

Zwart MP, Hemerik L, Cory JS, de Visser JA, Bianchi FJ, Van Oers MM, Vlak JM, Hoekstra RF, Van der Werf W.

Proc Biol Sci. 2009 Jun 22;276(1665):2233-42. doi: 10.1098/rspb.2009.0064. Epub 2009 Mar 11.

37.

The social evolution of somatic fusion.

Aanen DK, Debets AJ, de Visser JA, Hoekstra RF.

Bioessays. 2008 Nov;30(11-12):1193-203. doi: 10.1002/bies.20840.

PMID:
18937373
38.

Low multiplicity of infection in vivo results in purifying selection against baculovirus deletion mutants.

Zwart MP, Erro E, van Oers MM, de Visser JAGM, Vlak JM.

J Gen Virol. 2008 May;89(Pt 5):1220-1224. doi: 10.1099/vir.0.83645-0.

PMID:
18420800
39.

Heterogeneous adaptive trajectories of small populations on complex fitness landscapes.

Rozen DE, Habets MG, Handel A, de Visser JA.

PLoS One. 2008 Mar 5;3(3):e1715. doi: 10.1371/journal.pone.0001715.

40.

Effect of dispersal and nutrient availability on the competitive ability of toxin-producing yeast.

Wloch-Salamon DM, Gerla D, Hoekstra RF, de Visser JA.

Proc Biol Sci. 2008 Mar 7;275(1634):535-41. doi: 10.1098/rspb.2007.1461.

41.

Bacterial solutions to the problem of sex.

de Visser JA.

PLoS Biol. 2007 Sep;5(9):e245. No abstract available.

42.

Spatial structure inhibits the rate of invasion of beneficial mutations in asexual populations.

Habets MG, Czárán T, Hoekstra RF, de Visser JA.

Proc Biol Sci. 2007 Sep 7;274(1622):2139-43.

43.

The evolution of sex: empirical insights into the roles of epistasis and drift.

de Visser JA, Elena SF.

Nat Rev Genet. 2007 Feb;8(2):139-49. Review.

PMID:
17230200
44.
45.

Clonal interference and the periodic selection of new beneficial mutations in Escherichia coli.

de Visser JA, Rozen DE.

Genetics. 2006 Apr;172(4):2093-100. Epub 2006 Feb 19.

46.

Limits to adaptation in asexual populations.

de Visser JA, Rozen DE.

J Evol Biol. 2005 Jul;18(4):779-88. Review.

47.

Insertion-sequence-mediated mutations isolated during adaptation to growth and starvation in Lactococcus lactis.

de Visser JA, Akkermans AD, Hoekstra RF, de Vos WM.

Genetics. 2004 Nov;168(3):1145-57.

48.

Comment on "High deleterious genomic mutation rate in stationary phase of Escherichia coli".

de Visser JA, Rozen DE.

Science. 2004 Apr 23;304(5670):518; author reply 518. No abstract available.

49.

Perspective: Evolution and detection of genetic robustness.

de Visser JA, Hermisson J, Wagner GP, Ancel Meyers L, Bagheri-Chaichian H, Blanchard JL, Chao L, Cheverud JM, Elena SF, Fontana W, Gibson G, Hansen TF, Krakauer D, Lewontin RC, Ofria C, Rice SH, von Dassow G, Wagner A, Whitlock MC.

Evolution. 2003 Sep;57(9):1959-72. Review.

PMID:
14575319
50.

Environmental stress and the effects of mutation.

Elena SF, de Visser JA.

J Biol. 2003;2(2):12. Epub 2003 Jun 26. Review.

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