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Items: 32

1.

A Gene Regulatory Network for Cellular Reprogramming in Plant Regeneration.

Ikeuchi M, Shibata M, Rymen B, Iwase A, Bågman AM, Watt L, Coleman D, Favero DS, Takahashi T, Ahnert SE, Brady SM, Sugimoto K.

Plant Cell Physiol. 2018 Apr 1;59(4):765-777. doi: 10.1093/pcp/pcy013.

PMID:
29462363
2.

Phenotypes can be robust and evolvable if mutations have non-local effects on sequence constraints.

Weiß M, Ahnert SE.

J R Soc Interface. 2018 Jan;15(138). pii: 20170618. doi: 10.1098/rsif.2017.0618.

PMID:
29321270
3.

Social network fragmentation and community health.

Chami GF, Ahnert SE, Kabatereine NB, Tukahebwa EM.

Proc Natl Acad Sci U S A. 2017 Sep 5;114(36):E7425-E7431. doi: 10.1073/pnas.1700166114. Epub 2017 Jul 24.

4.

Structural properties of genotype-phenotype maps.

Ahnert SE.

J R Soc Interface. 2017 Jul;14(132). pii: 20170275. doi: 10.1098/rsif.2017.0275. Review.

5.

Corrigendum: Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis.

Fokas AS, Cole DJ, Ahnert SE, Chin AW.

Sci Rep. 2017 Feb 27;7:42654. doi: 10.1038/srep42654. No abstract available.

6.

Nondeterministic self-assembly with asymmetric interactions.

Tesoro S, Göpfrich K, Kartanas T, Keyser UF, Ahnert SE.

Phys Rev E. 2016 Aug;94(2-1):022404. doi: 10.1103/PhysRevE.94.022404. Epub 2016 Aug 8.

PMID:
27627332
7.

Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis.

Fokas AS, Cole DJ, Ahnert SE, Chin AW.

Sci Rep. 2016 Sep 14;6:33213. doi: 10.1038/srep33213.

8.
9.

Nondeterministic self-assembly of two tile types on a lattice.

Tesoro S, Ahnert SE.

Phys Rev E. 2016 Apr;93:042412. doi: 10.1103/PhysRevE.93.042412. Epub 2016 Apr 18.

PMID:
27176334
10.

Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability.

Greenbury SF, Schaper S, Ahnert SE, Louis AA.

PLoS Comput Biol. 2016 Mar 3;12(3):e1004773. doi: 10.1371/journal.pcbi.1004773. eCollection 2016 Mar.

11.

Principles of assembly reveal a periodic table of protein complexes.

Ahnert SE, Marsh JA, Hernández H, Robinson CV, Teichmann SA.

Science. 2015 Dec 11;350(6266):aaa2245. doi: 10.1126/science.aaa2245.

12.
13.

Structural and evolutionary versatility in protein complexes with uneven stoichiometry.

Marsh JA, Rees HA, Ahnert SE, Teichmann SA.

Nat Commun. 2015 Mar 16;6:6394. doi: 10.1038/ncomms7394.

PMID:
25775164
14.

An Arabidopsis gene regulatory network for secondary cell wall synthesis.

Taylor-Teeples M, Lin L, de Lucas M, Turco G, Toal TW, Gaudinier A, Young NF, Trabucco GM, Veling MT, Lamothe R, Handakumbura PP, Xiong G, Wang C, Corwin J, Tsoukalas A, Zhang L, Ware D, Pauly M, Kliebenstein DJ, Dehesh K, Tagkopoulos I, Breton G, Pruneda-Paz JL, Ahnert SE, Kay SA, Hazen SP, Brady SM.

Nature. 2015 Jan 29;517(7536):571-5. doi: 10.1038/nature14099. Epub 2014 Dec 24.

15.

Ranking competitors using degree-neutralized random walks.

Shin S, Ahnert SE, Park J.

PLoS One. 2014 Dec 17;9(12):e113685. doi: 10.1371/journal.pone.0113685. eCollection 2014.

16.

Social network analysis predicts health behaviours and self-reported health in African villages.

Chami GF, Ahnert SE, Voors MJ, Kontoleon AA.

PLoS One. 2014 Jul 29;9(7):e103500. doi: 10.1371/journal.pone.0103500. eCollection 2014.

17.

A tractable genotype-phenotype map modelling the self-assembly of protein quaternary structure.

Greenbury SF, Johnston IG, Louis AA, Ahnert SE.

J R Soc Interface. 2014 Apr 9;11(95):20140249. doi: 10.1098/rsif.2014.0249. Print 2014 Jun 6.

18.
19.

Power graph compression reveals dominant relationships in genetic transcription networks.

Ahnert SE.

Mol Biosyst. 2013 Nov;9(11):2681-5. doi: 10.1039/c3mb70236g. Review.

PMID:
23963601
20.

Protein complexes are under evolutionary selection to assemble via ordered pathways.

Marsh JA, Hernández H, Hall Z, Ahnert SE, Perica T, Robinson CV, Teichmann SA.

Cell. 2013 Apr 11;153(2):461-70. doi: 10.1016/j.cell.2013.02.044.

21.

The rich club of the C. elegans neuronal connectome.

Towlson EK, Vértes PE, Ahnert SE, Schafer WR, Bullmore ET.

J Neurosci. 2013 Apr 10;33(15):6380-7. doi: 10.1523/JNEUROSCI.3784-12.2013.

22.

The emergence of protein complexes: quaternary structure, dynamics and allostery. Colworth Medal Lecture.

Perica T, Marsh JA, Sousa FL, Natan E, Colwell LJ, Ahnert SE, Teichmann SA.

Biochem Soc Trans. 2012 Jun 1;40(3):475-91. doi: 10.1042/BST20120056.

PMID:
22616857
23.

Flavor network and the principles of food pairing.

Ahn YY, Ahnert SE, Bagrow JP, Barabási AL.

Sci Rep. 2011;1:196. doi: 10.1038/srep00196. Epub 2011 Dec 15.

24.

Evolutionary dynamics in a simple model of self-assembly.

Johnston IG, Ahnert SE, Doye JP, Louis AA.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Jun;83(6 Pt 2):066105. Epub 2011 Jun 13.

PMID:
21797439
25.

Self-assembly, modularity, and physical complexity.

Ahnert SE, Johnston IG, Fink TM, Doye JP, Louis AA.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Aug;82(2 Pt 2):026117. Epub 2010 Aug 27.

PMID:
20866886
26.

Oscillating gene expression determines competence for periodic Arabidopsis root branching.

Moreno-Risueno MA, Van Norman JM, Moreno A, Zhang J, Ahnert SE, Benfey PN.

Science. 2010 Sep 10;329(5997):1306-11. doi: 10.1126/science.1191937.

27.

Detecting separate time scales in genetic expression data.

Orlando DA, Brady SM, Fink TM, Benfey PN, Ahnert SE.

BMC Genomics. 2010 Jun 16;11:381. doi: 10.1186/1471-2164-11-381.

28.

Networks for all.

Ahnert SE, Teichmann SA.

Genome Biol. 2008 Oct 27;9(10):324. doi: 10.1186/gb-2008-9-10-324.

29.

Clustering signatures classify directed networks.

Ahnert SE, Fink TM.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Sep;78(3 Pt 2):036112. Epub 2008 Sep 18.

PMID:
18851110
30.

How much non-coding DNA do eukaryotes require?

Ahnert SE, Fink TM, Zinovyev A.

J Theor Biol. 2008 Jun 21;252(4):587-92. doi: 10.1016/j.jtbi.2008.02.005. Epub 2008 Feb 14.

PMID:
18384817
31.

Ensemble approach to the analysis of weighted networks.

Ahnert SE, Garlaschelli D, Fink TM, Caldarelli G.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Jul;76(1 Pt 2):016101. Epub 2007 Jul 2.

PMID:
17677527
32.

Unbiased pattern detection in microarray data series.

Ahnert SE, Willbrand K, Brown FC, Fink TM.

Bioinformatics. 2006 Jun 15;22(12):1471-6. Epub 2006 Apr 3.

PMID:
16766565

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