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Items: 35

1.

The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation.

Rendón-Anaya M, Ibarra-Laclette E, Méndez-Bravo A, Lan T, Zheng C, Carretero-Paulet L, Perez-Torres CA, Chacón-López A, Hernandez-Guzmán G, Chang TH, Farr KM, Barbazuk WB, Chamala S, Mutwil M, Shivhare D, Alvarez-Ponce D, Mitter N, Hayward A, Fletcher S, Rozas J, Sánchez Gracia A, Kuhn D, Barrientos-Priego AF, Salojärvi J, Librado P, Sankoff D, Herrera-Estrella A, Albert VA, Herrera-Estrella L.

Proc Natl Acad Sci U S A. 2019 Aug 20;116(34):17081-17089. doi: 10.1073/pnas.1822129116. Epub 2019 Aug 6.

2.

Molecular chaperones accelerate the evolution of their protein clients in yeast.

Alvarez-Ponce D, Aguilar-Rodríguez J, Fares MA.

Genome Biol Evol. 2019 Jul 11. pii: evz147. doi: 10.1093/gbe/evz147. [Epub ahead of print]

PMID:
31297528
3.

What lies beneath? Molecular evolution during the radiation of caecilian amphibians.

Torres-Sánchez M, Gower DJ, Alvarez-Ponce D, Creevey CJ, Wilkinson M, San Mauro D.

BMC Genomics. 2019 May 9;20(1):354. doi: 10.1186/s12864-019-5694-1.

4.

Codon Usage Differences among Genes Expressed in Different Tissues of Drosophila melanogaster.

Payne BL, Alvarez-Ponce D.

Genome Biol Evol. 2019 Apr 1;11(4):1054-1065. doi: 10.1093/gbe/evz051.

5.

N-glycoproteins exhibit a positive expression level-evolutionary rate correlation.

Feyertag F, Berninsone PM, Alvarez-Ponce D.

J Evol Biol. 2019 Apr;32(4):390-394. doi: 10.1111/jeb.13420. Epub 2019 Mar 5.

PMID:
30697857
6.

Proteins of generalist and specialist pathogens differ in their amino acid composition.

Blanco LP, Payne BL, Feyertag F, Alvarez-Ponce D.

Life Sci Alliance. 2018 Jul 17;1(4):e201800017. doi: 10.26508/lsa.201800017. eCollection 2018 Aug.

7.

Arabidopsis Heat Stress-Induced Proteins Are Enriched in Electrostatically Charged Amino Acids and Intrinsically Disordered Regions.

Alvarez-Ponce D, Ruiz-González MX, Vera-Sirera F, Feyertag F, Perez-Amador MA, Fares MA.

Int J Mol Sci. 2018 Aug 3;19(8). pii: E2276. doi: 10.3390/ijms19082276.

8.

High quality draft genome sequences of Mycoplasma agassizii strains PS6T and 723 isolated from Gopherus tortoises with upper respiratory tract disease.

Alvarez-Ponce D, Weitzman CL, Tillett RL, Sandmeier FC, Tracy CR.

Stand Genomic Sci. 2018 Apr 27;13:12. doi: 10.1186/s40793-018-0315-1. eCollection 2018.

9.

High quality draft genome sequence of Mycoplasma testudineum strain BH29T, isolated from the respiratory tract of a desert tortoise.

Weitzman CL, Tillett RL, Sandmeier FC, Tracy CR, Alvarez-Ponce D.

Stand Genomic Sci. 2018 Apr 11;13:9. doi: 10.1186/s40793-018-0309-z. eCollection 2018.

10.

Molecular evolution of DNMT1 in vertebrates: Duplications in marsupials followed by positive selection.

Alvarez-Ponce D, Torres-Sánchez M, Feyertag F, Kulkarni A, Nappi T.

PLoS One. 2018 Apr 5;13(4):e0195162. doi: 10.1371/journal.pone.0195162. eCollection 2018.

11.
12.

Phylogenetic Distribution of CMP-Neu5Ac Hydroxylase (CMAH), the Enzyme Synthetizing the Proinflammatory Human Xenoantigen Neu5Gc.

Peri S, Kulkarni A, Feyertag F, Berninsone PM, Alvarez-Ponce D.

Genome Biol Evol. 2018 Jan 1;10(1):207-219. doi: 10.1093/gbe/evx251.

13.

Position Matters: Network Centrality Considerably Impacts Rates of Protein Evolution in the Human Protein-Protein Interaction Network.

Alvarez-Ponce D, Feyertag F, Chakraborty S.

Genome Biol Evol. 2017 Jun 1;9(6):1742-1756. doi: 10.1093/gbe/evx117.

14.

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory.

Fukushima K, Fang X, Alvarez-Ponce D, Cai H, Carretero-Paulet L, Chen C, Chang TH, Farr KM, Fujita T, Hiwatashi Y, Hoshi Y, Imai T, Kasahara M, Librado P, Mao L, Mori H, Nishiyama T, Nozawa M, Pálfalvi G, Pollard ST, Rozas J, Sánchez-Gracia A, Sankoff D, Shibata TF, Shigenobu S, Sumikawa N, Uzawa T, Xie M, Zheng C, Pollock DD, Albert VA, Li S, Hasebe M.

Nat Ecol Evol. 2017 Feb 6;1(3):59. doi: 10.1038/s41559-016-0059.

PMID:
28812732
15.

Disulfide Bonds Enable Accelerated Protein Evolution.

Feyertag F, Alvarez-Ponce D.

Mol Biol Evol. 2017 Aug 1;34(8):1833-1837. doi: 10.1093/molbev/msx135.

PMID:
28431018
16.

Intrinsic protein disorder reduces small-scale gene duplicability.

Banerjee S, Feyertag F, Alvarez-Ponce D.

DNA Res. 2017 Aug 1;24(4):435-444. doi: 10.1093/dnares/dsx015.

17.

Chance and necessity in the genome evolution of endosymbiotic bacteria of insects.

Sabater-Muñoz B, Toft C, Alvarez-Ponce D, Fares MA.

ISME J. 2017 Jun;11(6):1291-1304. doi: 10.1038/ismej.2017.18. Epub 2017 Mar 21.

18.

Secreted Proteins Defy the Expression Level-Evolutionary Rate Anticorrelation.

Feyertag F, Berninsone PM, Alvarez-Ponce D.

Mol Biol Evol. 2017 Mar 1;34(3):692-706. doi: 10.1093/molbev/msw268.

19.

Essentiality Is a Strong Determinant of Protein Rates of Evolution during Mutation Accumulation Experiments in Escherichia coli.

Alvarez-Ponce D, Sabater-Muñoz B, Toft C, Ruiz-González MX, Fares MA.

Genome Biol Evol. 2016 Sep 26;8(9):2914-2927.

20.
21.

The Molecular Chaperone DnaK Is a Source of Mutational Robustness.

Aguilar-Rodríguez J, Sabater-Muñoz B, Montagud-Martínez R, Berlanga V, Alvarez-Ponce D, Wagner A, Fares MA.

Genome Biol Evol. 2016 Oct 5;8(9):2979-2991.

22.

Positive Selection and Centrality in the Yeast and Fly Protein-Protein Interaction Networks.

Chakraborty S, Alvarez-Ponce D.

Biomed Res Int. 2016;2016:4658506. doi: 10.1155/2016/4658506. Epub 2016 Mar 28.

23.

Recent positive selection has acted on genes encoding proteins with more interactions within the whole human interactome.

Luisi P, Alvarez-Ponce D, Pybus M, Fares MA, Bertranpetit J, Laayouni H.

Genome Biol Evol. 2015 Apr 2;7(4):1141-54. doi: 10.1093/gbe/evv055.

24.

Integration of two ancestral chaperone systems into one: the evolution of eukaryotic molecular chaperones in light of eukaryogenesis.

Bogumil D, Alvarez-Ponce D, Landan G, McInerney JO, Dagan T.

Mol Biol Evol. 2014 Feb;31(2):410-8. doi: 10.1093/molbev/mst212. Epub 2013 Nov 4.

25.

Comment on "The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway".

Alvarez-Ponce D, Aguadé M, Rozas J.

Evol Bioinform Online. 2013 Jun 10;9:229-34. doi: 10.4137/EBO.S11915. Print 2013.

26.

Gene similarity networks provide tools for understanding eukaryote origins and evolution.

Alvarez-Ponce D, Lopez P, Bapteste E, McInerney JO.

Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):E1594-603. doi: 10.1073/pnas.1211371110. Epub 2013 Apr 1.

27.

Evolutionary rate and duplicability in the Arabidopsis thaliana protein-protein interaction network.

Alvarez-Ponce D, Fares MA.

Genome Biol Evol. 2012;4(12):1263-74. doi: 10.1093/gbe/evs101.

28.
29.

Increased genome sampling reveals a dynamic relationship between gene duplicability and the structure of the primate protein-protein interaction network.

Doherty A, Alvarez-Ponce D, McInerney JO.

Mol Biol Evol. 2012 Nov;29(11):3563-73. doi: 10.1093/molbev/mss165. Epub 2012 Jun 21.

PMID:
22723304
30.

Network-level and population genetics analysis of the insulin/TOR signal transduction pathway across human populations.

Luisi P, Alvarez-Ponce D, Dall'Olio GM, Sikora M, Bertranpetit J, Laayouni H.

Mol Biol Evol. 2012 May;29(5):1379-92. doi: 10.1093/molbev/msr298. Epub 2011 Dec 1.

PMID:
22135191
31.

The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences.

Alvarez-Ponce D, McInerney JO.

Genome Biol Evol. 2011;3:782-90. doi: 10.1093/gbe/evr073. Epub 2011 Jul 27.

32.

Molecular population genetics of the insulin/TOR signal transduction pathway: a network-level analysis in Drosophila melanogaster.

Alvarez-Ponce D, Guirao-Rico S, Orengo DJ, Segarra C, Rozas J, Aguadé M.

Mol Biol Evol. 2012 Jan;29(1):123-32. doi: 10.1093/molbev/msr160. Epub 2011 Jun 16.

PMID:
21680868
33.

Comparative genomics of the vertebrate insulin/TOR signal transduction pathway: a network-level analysis of selective pressures.

Alvarez-Ponce D, Aguadé M, Rozas J.

Genome Biol Evol. 2011;3:87-101. doi: 10.1093/gbe/evq084. Epub 2010 Dec 13.

34.

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle.

Kirkness EF, Haas BJ, Sun W, Braig HR, Perotti MA, Clark JM, Lee SH, Robertson HM, Kennedy RC, Elhaik E, Gerlach D, Kriventseva EV, Elsik CG, Graur D, Hill CA, Veenstra JA, Walenz B, Tubío JM, Ribeiro JM, Rozas J, Johnston JS, Reese JT, Popadic A, Tojo M, Raoult D, Reed DL, Tomoyasu Y, Kraus E, Mittapalli O, Margam VM, Li HM, Meyer JM, Johnson RM, Romero-Severson J, Vanzee JP, Alvarez-Ponce D, Vieira FG, Aguadé M, Guirao-Rico S, Anzola JM, Yoon KS, Strycharz JP, Unger MF, Christley S, Lobo NF, Seufferheld MJ, Wang N, Dasch GA, Struchiner CJ, Madey G, Hannick LI, Bidwell S, Joardar V, Caler E, Shao R, Barker SC, Cameron S, Bruggner RV, Regier A, Johnson J, Viswanathan L, Utterback TR, Sutton GG, Lawson D, Waterhouse RM, Venter JC, Strausberg RL, Berenbaum MR, Collins FH, Zdobnov EM, Pittendrigh BR.

Proc Natl Acad Sci U S A. 2010 Jul 6;107(27):12168-73. doi: 10.1073/pnas.1003379107. Epub 2010 Jun 21. Erratum in: Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6335. Krause, Emily [corrected to Kraus, Emily].

35.

Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes.

Alvarez-Ponce D, Aguadé M, Rozas J.

Genome Res. 2009 Feb;19(2):234-42. doi: 10.1101/gr.084038.108. Epub 2009 Jan 13.

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