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1.

Evolution of Gene Duplication in Plants.

Panchy N, Lehti-Shiu M, Shiu SH.

Plant Physiol. 2016 Aug;171(4):2294-316. doi: 10.1104/pp.16.00523. Epub 2016 Jun 10. Review.

2.

Cycling Transcriptional Networks Optimize Energy Utilization on a Genome Scale.

Wang GZ, Hickey SL, Shi L, Huang HC, Nakashe P, Koike N, Tu BP, Takahashi JS, Konopka G.

Cell Rep. 2015 Dec 1;13(9):1868-80. doi: 10.1016/j.celrep.2015.10.043. Epub 2015 Nov 19.

3.

Adaptation to High Ethanol Reveals Complex Evolutionary Pathways.

Voordeckers K, Kominek J, Das A, Espinosa-Cantú A, De Maeyer D, Arslan A, Van Pee M, van der Zande E, Meert W, Yang Y, Zhu B, Marchal K, DeLuna A, Van Noort V, Jelier R, Verstrepen KJ.

PLoS Genet. 2015 Nov 6;11(11):e1005635. doi: 10.1371/journal.pgen.1005635. eCollection 2015 Nov.

4.

Gene duplication and the evolution of moonlighting proteins.

Espinosa-Cantú A, Ascencio D, Barona-Gómez F, DeLuna A.

Front Genet. 2015 Jul 7;6:227. doi: 10.3389/fgene.2015.00227. eCollection 2015. Review.

5.

Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts.

Morel G, Sterck L, Swennen D, Marcet-Houben M, Onesime D, Levasseur A, Jacques N, Mallet S, Couloux A, Labadie K, Amselem J, Beckerich JM, Henrissat B, Van de Peer Y, Wincker P, Souciet JL, Gabaldón T, Tinsley CR, Casaregola S.

Sci Rep. 2015 Jun 25;5:11571. doi: 10.1038/srep11571. Erratum in: Sci Rep. 2015;5:12596.

6.

A Minimal Set of Glycolytic Genes Reveals Strong Redundancies in Saccharomyces cerevisiae Central Metabolism.

Solis-Escalante D, Kuijpers NG, Barrajon-Simancas N, van den Broek M, Pronk JT, Daran JM, Daran-Lapujade P.

Eukaryot Cell. 2015 Aug;14(8):804-16. doi: 10.1128/EC.00064-15. Epub 2015 Jun 12.

7.

Predicting functional and regulatory divergence of a drug resistance transporter gene in the human malaria parasite.

Siwo GH, Tan A, Button-Simons KA, Samarakoon U, Checkley LA, Pinapati RS, Ferdig MT.

BMC Genomics. 2015 Feb 22;16:115. doi: 10.1186/s12864-015-1261-6.

8.

Mechanistic links between cellular trade-offs, gene expression, and growth.

Weiße AY, Oyarzún DA, Danos V, Swain PS.

Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):E1038-47. doi: 10.1073/pnas.1416533112. Epub 2015 Feb 18.

9.

Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences.

Nguyen Ba AN, Strome B, Hua JJ, Desmond J, Gagnon-Arsenault I, Weiss EL, Landry CR, Moses AM.

PLoS Comput Biol. 2014 Dec 4;10(12):e1003977. doi: 10.1371/journal.pcbi.1003977. eCollection 2014 Dec.

10.

In silico prediction of synthetic lethality by meta-analysis of genetic interactions, functions, and pathways in yeast and human cancer.

Wu M, Li X, Zhang F, Li X, Kwoh CK, Zheng J.

Cancer Inform. 2014 Nov 5;13(Suppl 3):71-80. doi: 10.4137/CIN.S14026. eCollection 2014.

11.

Gene duplication of type-B ARR transcription factors systematically extends transcriptional regulatory structures in Arabidopsis.

Choi SH, Hyeon do Y, Lee LH, Park SJ, Han S, Lee IC, Hwang D, Nam HG.

Sci Rep. 2014 Nov 26;4:7197. doi: 10.1038/srep07197.

12.

Genomic evidence for adaptation by gene duplication.

Qian W, Zhang J.

Genome Res. 2014 Aug;24(8):1356-62. doi: 10.1101/gr.172098.114. Epub 2014 Jun 5.

13.

Expression evolution facilitated the convergent neofunctionalization of a sodium channel gene.

Thompson A, Vo D, Comfort C, Zakon HH.

Mol Biol Evol. 2014 Aug;31(8):1941-55. doi: 10.1093/molbev/msu145. Epub 2014 Apr 29.

14.

High-resolution profiling of stationary-phase survival reveals yeast longevity factors and their genetic interactions.

Garay E, Campos SE, González de la Cruz J, Gaspar AP, Jinich A, Deluna A.

PLoS Genet. 2014 Feb 27;10(2):e1004168. doi: 10.1371/journal.pgen.1004168. eCollection 2014 Feb.

15.

Genetic robustness and functional evolution of gene duplicates.

Plata G, Vitkup D.

Nucleic Acids Res. 2014 Feb;42(4):2405-14. doi: 10.1093/nar/gkt1200. Epub 2013 Nov 27.

16.
17.

Duplication and retention biases of essential and non-essential genes revealed by systematic knockdown analyses.

Woods S, Coghlan A, Rivers D, Warnecke T, Jeffries SJ, Kwon T, Rogers A, Hurst LD, Ahringer J.

PLoS Genet. 2013 May;9(5):e1003330. doi: 10.1371/journal.pgen.1003330. Epub 2013 May 9.

18.

Circuit-level input integration in bacterial gene regulation.

Espinar L, Dies M, Cagatay T, Süel GM, Garcia-Ojalvo J.

Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):7091-6. doi: 10.1073/pnas.1216091110. Epub 2013 Apr 9.

19.

Robustness of Helicobacter pylori infection conferred by context-variable redundancy among cysteine-rich paralogs.

Putty K, Marcus SA, Mittl PR, Bogadi LE, Hunter AM, Arur S, Berg DE, Sethu P, Kalia A.

PLoS One. 2013;8(3):e59560. doi: 10.1371/journal.pone.0059560. Epub 2013 Mar 26.

20.

The pattern of Phosphate transporter 1 genes evolutionary divergence in Glycine max L.

Fan C, Wang X, Hu R, Wang Y, Xiao C, Jiang Y, Zhang X, Zheng C, Fu YF.

BMC Plant Biol. 2013 Mar 20;13:48. doi: 10.1186/1471-2229-13-48.

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