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Items: 30

1.

Inferring bacterial recombination rates from large-scale sequencing datasets.

Lin M, Kussell E.

Nat Methods. 2019 Feb;16(2):199-204. doi: 10.1038/s41592-018-0293-7. Epub 2019 Jan 21.

PMID:
30664775
2.

The impact of bottlenecks on microbial survival, adaptation, and phenotypic switching in host-pathogen interactions.

Moxon R, Kussell E.

Evolution. 2017 Dec;71(12):2803-2816. doi: 10.1111/evo.13370. Epub 2017 Oct 30.

3.

Inferring fitness landscapes and selection on phenotypic states from single-cell genealogical data.

Nozoe T, Kussell E, Wakamoto Y.

PLoS Genet. 2017 Mar 7;13(3):e1006653. doi: 10.1371/journal.pgen.1006653. eCollection 2017 Mar.

4.

Correlated Mutations and Homologous Recombination Within Bacterial Populations.

Lin M, Kussell E.

Genetics. 2017 Feb;205(2):891-917. doi: 10.1534/genetics.116.189621. Epub 2016 Dec 22.

5.

Evolutionary Phase Transitions in Random Environments.

Skanata A, Kussell E.

Phys Rev Lett. 2016 Jul 15;117(3):038104. doi: 10.1103/PhysRevLett.117.038104. Epub 2016 Jul 15.

6.

Complex Interplay of Physiology and Selection in the Emergence of Antibiotic Resistance.

Lin WH, Kussell E.

Curr Biol. 2016 Jun 6;26(11):1486-93. doi: 10.1016/j.cub.2016.04.015. Epub 2016 May 19.

7.

Noise-driven growth rate gain in clonal cellular populations.

Hashimoto M, Nozoe T, Nakaoka H, Okura R, Akiyoshi S, Kaneko K, Kussell E, Wakamoto Y.

Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):3251-6. doi: 10.1073/pnas.1519412113. Epub 2016 Mar 7.

8.

Bacterial Autoimmunity Due to a Restriction-Modification System.

PleŇ°ka M, Qian L, Okura R, Bergmiller T, Wakamoto Y, Kussell E, Guet CC.

Curr Biol. 2016 Feb 8;26(3):404-9. doi: 10.1016/j.cub.2015.12.041. Epub 2016 Jan 21.

9.

Quantifying selective pressures driving bacterial evolution using lineage analysis.

Lambert G, Kussell E.

Phys Rev X. 2015 Jan-Mar;5(1). pii: 011016.

10.

Populations adapt to fluctuating selection using derived and ancestral allelic diversity.

Lin WH, Rocco MJ, Bertozzi-Villa A, Kussell E.

Evolution. 2015 Jun;69(6):1448-1460. doi: 10.1111/evo.12665. Epub 2015 May 27.

11.

Non-equilibrium physics and evolution--adaptation, extinction, and ecology: a key issues review.

Kussell E, Vucelja M.

Rep Prog Phys. 2014 Oct;77(10):102602. doi: 10.1088/0034-4885/77/10/102602. Epub 2014 Oct 10. Review.

PMID:
25303141
12.

Memory and fitness optimization of bacteria under fluctuating environments.

Lambert G, Kussell E.

PLoS Genet. 2014 Sep 25;10(9):e1004556. doi: 10.1371/journal.pgen.1004556. eCollection 2014 Sep. Erratum in: PLoS Genet. 2014 Oct;10(10):e1004793. Kussel, Edo [corrected to Kussell, Edo].

13.

Evolution in microbes.

Kussell E.

Annu Rev Biophys. 2013;42:493-514. doi: 10.1146/annurev-biophys-083012-130320.

PMID:
23654305
14.

Evolutionary dynamics of restriction site avoidance.

Qian L, Kussell E.

Phys Rev Lett. 2012 Apr 13;108(15):158105. Epub 2012 Apr 13.

PMID:
22587291
15.

Stochastic de-repression of Rhodopsins in single photoreceptors of the fly retina.

Sood P, Johnston RJ Jr, Kussell E.

PLoS Comput Biol. 2012 Feb;8(2):e1002357. doi: 10.1371/journal.pcbi.1002357. Epub 2012 Feb 2.

16.

Optimal lineage principle for age-structured populations.

Wakamoto Y, Grosberg AY, Kussell E.

Evolution. 2012 Jan;66(1):115-34. doi: 10.1111/j.1558-5646.2011.01418.x. Epub 2011 Sep 13.

PMID:
22220869
17.

Evolutionary pressures on simple sequence repeats in prokaryotic coding regions.

Lin WH, Kussell E.

Nucleic Acids Res. 2012 Mar;40(6):2399-413. doi: 10.1093/nar/gkr1078. Epub 2011 Nov 28.

18.

Measuring cell identity in noisy biological systems.

Birnbaum KD, Kussell E.

Nucleic Acids Res. 2011 Nov;39(21):9093-107. doi: 10.1093/nar/gkr591. Epub 2011 Jul 29.

19.

Interlocked feedforward loops control cell-type-specific Rhodopsin expression in the Drosophila eye.

Johnston RJ Jr, Otake Y, Sood P, Vogt N, Behnia R, Vasiliauskas D, McDonald E, Xie B, Koenig S, Wolf R, Cook T, Gebelein B, Kussell E, Nakagoshi H, Desplan C.

Cell. 2011 Jun 10;145(6):956-68. doi: 10.1016/j.cell.2011.05.003.

20.

Individual histories and selection in heterogeneous populations.

Leibler S, Kussell E.

Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):13183-8. doi: 10.1073/pnas.0912538107. Epub 2010 Jul 2.

21.

Polymer-population mapping and localization in the space of phenotypes.

Kussell E, Leibler S, Grosberg A.

Phys Rev Lett. 2006 Aug 11;97(6):068101. Epub 2006 Aug 7.

PMID:
17026205
22.

Phenotypic diversity, population growth, and information in fluctuating environments.

Kussell E, Leibler S.

Science. 2005 Sep 23;309(5743):2075-8. Epub 2005 Aug 25.

23.

The designability hypothesis and protein evolution.

Kussell E.

Protein Pept Lett. 2005 Feb;12(2):111-6. Review.

PMID:
15723636
24.

Bacterial persistence: a model of survival in changing environments.

Kussell E, Kishony R, Balaban NQ, Leibler S.

Genetics. 2005 Apr;169(4):1807-14. Epub 2005 Jan 31.

25.

Side-chain dynamics and protein folding.

Kussell E, Shimada J, Shakhnovich EI.

Proteins. 2003 Aug 1;52(2):303-21.

PMID:
12833553
26.

Glassy dynamics of side-chain ordering in a simple model of protein folding.

Kussell E, Shakhnovich EI.

Phys Rev Lett. 2002 Oct 14;89(16):168101. Epub 2002 Sep 25.

PMID:
12398757
27.

A structure-based method for derivation of all-atom potentials for protein folding.

Kussell E, Shimada J, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5343-8. Epub 2002 Apr 9.

28.

Excluded volume in protein side-chain packing.

Kussell E, Shimada J, Shakhnovich EI.

J Mol Biol. 2001 Aug 3;311(1):183-93.

PMID:
11469867
29.

The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation.

Shimada J, Kussell EL, Shakhnovich EI.

J Mol Biol. 2001 Apr 20;308(1):79-95.

PMID:
11302709
30.

Recovery of protein structure from contact maps.

Vendruscolo M, Kussell E, Domany E.

Fold Des. 1997;2(5):295-306.

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