Publications

See our Google Scholar profile here.

Members of the Alvarez-Ponce lab are highlighted.

2017

24. David Alvarez-Ponce, Felix Feyertag, Sandip Chakraborty. 2017. Position matters: Network centrality considerably impacts rates of protein evolution in the human protein–protein interaction network. Genome Biology and Evolution 9(6):1742-1756 [link].

23. Felix Feyertag, David Alvarez-Ponce. 2017. Disulfide bonds enable accelerated protein evolution. Molecular Biology and Evolution 34(8):1833–1837 [link].

22. Sanghita Banerjee, Felix Feyertag, David Alvarez-Ponce. 2017. Intrinsic protein disorder reduces small-scale gene duplicability. DNA Research 24(4):435–444 [link].

21. Beatriz Sabater-Muñoz, Christina Toft, David Alvarez-Ponce, Mario Fares. 2017. Chance and Necessity in the Genome Evolution of Endosymbiotic Bacteria of Insects. The ISME Journal 11:1291–1304 [link].

20. K Fukushima, X Fang, D Alvarez-Ponce, H Cai, L Carretero-Paulet, C Chen, T-H Chang, K Farr, T Fujita, Y Hiwatashi, Y Hoshi, T Imai, M Kasahara, P Librado, L Mao, H Mori, T Nishiyama, M Nozawa, G Pálfalvi, S Pollard, J Rozas, A Sánchez-Gracia, D Sankoff, T Shibata, S Shigenobu, N Sumikawa, T Uzawa, M Xie, C Zheng, D Pollock, V Albert, S Li, M Hasebe. 2017. The pitcher plant Cephalotus genome reveals genetic changes associated with carnivory. Nature Ecology and Evolution 1:0059 [link].

  • Paper highlighted by Nature [link] and Nature Plants [link].
  • Media coverage: Scientific American [link], ScienceDaily [link], NPR [link], Science 2.0 [link], New Scientist [link], NCBC [link], Discover Magazine [link], ABC [link], International Business Times UK [link], Laboratory Equipment [link], BT.com [link], KLCC [link], The Sun [link], and a long etc. [link].
  • Cover of Nevada Weekly [link].
  • Paper highlighted by the Faculty of 1000. [link]. f1000

19. Felix Feyertag, Patricia Berninsone, David Alvarez-Ponce. 2017. Secreted proteins defy the expression level–evolutionary rate anticorrelation. Molecular Biology and Evolution 34(3):692–706 [link].

18. David Alvarez-Ponce. 2017. Recording negative results of protein–protein interaction assays: an easy way to deal with the biases and errors of interactomic datasets. Briefings in Bioinformatics [link].

2016

17. David Alvarez-Ponce, Beatriz Sabater-Muñoz, Christina Toft, Mario X. Ruiz-González, Mario A. Fares. 2016. Essentiality is a strong determinant of protein rates of evolution during mutation accumulation experiments in Escherichia coli. Genome Biology and Evolution 8(9):2914–2927 [link].

16. José Aguilar-Rodríguez, Beatriz Sabater-Muñoz, Roser Montagud-Martínez, Víctor Berlanga, David Alvarez-Ponce, Andreas Wagner, Mario A. Fares. 2016. The molecular chaperone DnaK is a source of mutational robustness. Genome Biology and Evolution 8(9):2979–299 [link].

  • Paper highlighted by Genome Biology and Evolution: [link].

15. Sandip Chakraborty, David Alvarez-Ponce. 2016. Positive selection and centrality in the yeast and fly protein–protein interaction networks. BioMed Research International 2016:4658506 [link].

2015

14. Pierre Luisi*, David Alvarez-Ponce*, Marc Pybus, Mario A. Fares, Jaume Bertranpetit, Hafid Laayouni (*Co-first authors). 2015. Recent positive selection has acted on genes encoding proteins with more interactions within the whole human interactome. Genome Biology and Evolution 7(4):1141–1154 [link].

2014

13. David Alvarez-Ponce. 2014. Why proteins evolve at different rates: The determinants of proteins’ rates of evolution. In M. Fares (editor): Natural Selection: Methods and Applications. Pages 126–178. CRC Press (Taylor & Francis) [link] [pdf].

12. David Bogumil, David Alvarez-Ponce, Giddy Landan, James McInerney, Tal Dagan. 2014. Integration of two ancestral chaperone systems into one: the evolution of eukaryotic molecular chaperones in light of eukaryogenesis. Molecular Biology and Evolution 31(2):410–418 [link].

2013

11. David Alvarez-Ponce, Philippe Lopez, Eric Bapteste, James McInerney. 2013. Gene similarity networks provide tools for understanding eukaryote origins and evolution. Proceedings of the National Academy of Sciences USA 110(17):E1594–E1603 [link].

10. David Alvarez-Ponce, Montserrat Aguadé, Julio Rozas. 2013. Comment on “The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway”. Evolutionary Bioinformatics 9:229–234 [link].

2012

9. David Alvarez-Ponce, Mario A. Fares. 2012. Evolutionary rate and duplicability in the Arabidopsis thaliana protein–protein interaction network. Genome Biology and Evolution 4:1263–1274 [link].

8. David Alvarez-Ponce. 2012. The relationship between the hierarchical position of proteins in the human signal transduction network and their rate of evolution. BMC Evolutionary Biology 12:192 [link].

  • Paper classified as “highly accessed” by BMC. highlyaccessed-large

7. Aoife Doherty*, David Alvarez-Ponce*, James McInerney (*Co-first authors). 2012. Increased genome sampling reveals a dynamic relationship between gene duplicability and the structure of the primate protein-protein interaction network. Molecular Biology and Evolution 29:3563–3573. [link].

6. Pierre Luisi, David Alvarez-Ponce, Giovanni Marco Dall’Olio, Martin Sikora, Jaume Bertranpetit, Hafid Laayouni. 2012. Network-level and population genetics analysis of the insulin/TOR signal transduction pathway across human populations. Molecular Biology and Evolution 29:1379–1392. [link].

5. David Alvarez-Ponce*, Sara Guirao-Rico*, Dorcas Orengo*, Carmen Segarra, Julio Rozas, Montserrat Aguadé (*Co-first authors). 2012. Molecular population genetics of the insulin/TOR signal transduction pathway: A network-level analysis in Drosophila melanogaster. Molecular Biology and Evolution 29:123–132. [link].

2011

4. David Alvarez-Ponce, James McInerney. 2011. The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences. Genome Biology and Evolution 3:782–790. [link].

  • Paper highlighted by WIRED. [link]. wired
  • Paper highlighted by Nautilus. [link].   nautilus

3. David Alvarez-Ponce, Montserrat Aguadé, Julio Rozas. 2011. Comparative genomics of the vertebrate insulin/TOR signal transduction pathway genes: A network-level analysis of selective pressures along the pathway. Genome Biology and Evolution 3:87–101. [link].

2010

2. 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, Krause 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. 2010. Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle. Proceedings of the National Academy of Sciences USA 107(27): 12168–73. [link].

  • Paper highlighted by the Faculty of 1000. [link]. f1000
  • Paper highlighted by dozens of websites and newspapers. [link].

2009

1. David Alvarez-Ponce, Montserrat Aguadé, Julio Rozas. 2009. Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes. Genome Research 19(2): 234–42. [link].

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