David Alvarez-Ponce, Ph.D - Publications

2014- Biology University of Nevada, Reno, Reno, NV, United States 
Molecular evolution, Bioinformatics, Network evolution

29 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 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, et al. The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation. Proceedings of the National Academy of Sciences of the United States of America. PMID 31387975 DOI: 10.1073/Pnas.1822129116  0.96
2019 Alvarez-Ponce D, Aguilar-Rodríguez J, Fares MA. Molecular chaperones accelerate the evolution of their protein clients in yeast. Genome Biology and Evolution. PMID 31297528 DOI: 10.1093/Gbe/Evz147  0.96
2019 Torres-Sánchez M, Gower DJ, Alvarez-Ponce D, Creevey CJ, Wilkinson M, San Mauro D. What lies beneath? Molecular evolution during the radiation of caecilian amphibians. Bmc Genomics. 20: 354. PMID 31072350 DOI: 10.1186/S12864-019-5694-1  0.32
2019 Feyertag F, Berninsone PM, Alvarez-Ponce D. N-glycoproteins exhibit a positive expression level-evolutionary rate correlation. Journal of Evolutionary Biology. PMID 30697857 DOI: 10.1111/jeb.13420  0.32
2018 Blanco LP, Payne BL, Feyertag F, Alvarez-Ponce D. Proteins of generalist and specialist pathogens differ in their amino acid composition. Life Science Alliance. 1: e201800017. PMID 30456362 DOI: 10.26508/lsa.201800017  0.32
2018 Alvarez-Ponce D, Ruiz-González MX, Vera-Sirera F, Feyertag F, Perez-Amador MA, Fares MA. Arabidopsis Heat Stress-Induced Proteins Are Enriched in Electrostatically Charged Amino Acids and Intrinsically Disordered Regions. International Journal of Molecular Sciences. 19. PMID 30081447 DOI: 10.3390/Ijms19082276  0.96
2018 Alvarez-Ponce D, Torres-Sánchez M, Feyertag F, Kulkarni A, Nappi T. Molecular evolution of DNMT1 in vertebrates: Duplications in marsupials followed by positive selection. Plos One. 13: e0195162. PMID 29621315 DOI: 10.1371/Journal.Pone.0195162  0.32
2017 Peri S, Kulkarni A, Feyertag F, Berninsone PM, Alvarez-Ponce D. Phylogenetic distribution of CMP-Neu5Ac hydroxylase (CMAH), the enzyme synthetizing the pro-inflammatory human xeno-antigen Neu5Gc. Genome Biology and Evolution. PMID 29206915 DOI: 10.1093/Gbe/Evx251  0.32
2017 Alvarez-Ponce D, Feyertag F, Chakraborty S. Position Matters: Network Centrality Considerably Impacts Rates of Protein Evolution in the Human Protein-Protein Interaction Network. Genome Biology and Evolution. 9: 1742-1756. PMID 28854629 DOI: 10.1093/Gbe/Evx117  0.32
2017 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, et al. Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory. Nature Ecology & Evolution. 1: 59. PMID 28812732 DOI: 10.1038/S41559-016-0059  0.96
2017 Feyertag F, Alvarez-Ponce D. Disulfide bonds enable accelerated protein evolution. Molecular Biology and Evolution. PMID 28431018 DOI: 10.1093/Molbev/Msx135  0.32
2017 Banerjee S, Feyertag F, Alvarez-Ponce D. Intrinsic protein disorder reduces small-scale gene duplicability. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 28430886 DOI: 10.1093/Dnares/Dsx015  0.32
2017 Sabater-Muñoz B, Toft C, Alvarez-Ponce D, Fares MA. Chance and necessity in the genome evolution of endosymbiotic bacteria of insects. The Isme Journal. PMID 28323281 DOI: 10.1038/Ismej.2017.18  0.96
2016 Feyertag F, Berninsone PM, Alvarez-Ponce D. Secreted proteins defy the expression level-evolutionary rate anticorrelation. Molecular Biology and Evolution. PMID 28007979 DOI: 10.1093/Molbev/Msw268  0.32
2016 Alvarez-Ponce D, Sabater-Muñoz B, Toft C, Ruiz-González MX, Fares MA. Essentiality Is a Strong Determinant of Protein Rates of Evolution during Mutation Accumulation Experiments in Escherichia coli. Genome Biology and Evolution. PMID 27566759 DOI: 10.1093/Gbe/Evw205  0.96
2016 Aguilar-Rodríguez J, Sabater-Muñoz B, Montagud-Martínez R, Berlanga V, Alvarez-Ponce D, Wagner A, Fares MA. The molecular chaperone DnaK is a source of mutational robustness. Genome Biology and Evolution. PMID 27497316 DOI: 10.1093/Gbe/Evw176  0.96
2015 Luisi P, Alvarez-Ponce D, Pybus M, Fares MA, Bertranpetit J, Laayouni H. Recent positive selection has acted on genes encoding proteins with more interactions within the whole human interactome. Genome Biology and Evolution. 7: 1141-54. PMID 25840415 DOI: 10.1093/Gbe/Evv055  0.96
2014 Bogumil D, Alvarez-Ponce D, Landan G, McInerney JO, Dagan T. Integration of two ancestral chaperone systems into one: the evolution of eukaryotic molecular chaperones in light of eukaryogenesis. Molecular Biology and Evolution. 31: 410-8. PMID 24188869 DOI: 10.1093/Molbev/Mst212  0.96
2013 Alvarez-Ponce D, Aguadé M, Rozas J. Comment on "The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway". Evolutionary Bioinformatics Online. 9: 229-34. PMID 23818748 DOI: 10.4137/Ebo.S11915  0.96
2013 Alvarez-Ponce D, Lopez P, Bapteste E, McInerney JO. Gene similarity networks provide tools for understanding eukaryote origins and evolution. Proceedings of the National Academy of Sciences of the United States of America. 110: E1594-603. PMID 23576716 DOI: 10.1073/Pnas.1211371110  0.96
2012 Alvarez-Ponce D, Fares MA. Evolutionary rate and duplicability in the Arabidopsis thaliana protein-protein interaction network. Genome Biology and Evolution. 4: 1263-74. PMID 23160177 DOI: 10.1093/Gbe/Evs101  0.96
2012 Alvarez-Ponce D. The relationship between the hierarchical position of proteins in the human signal transduction network and their rate of evolution. Bmc Evolutionary Biology. 12: 192. PMID 23020283 DOI: 10.1186/1471-2148-12-192  0.96
2012 Doherty A, Alvarez-Ponce D, McInerney JO. 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: 3563-73. PMID 22723304 DOI: 10.1093/Molbev/Mss165  0.96
2012 Luisi P, Alvarez-Ponce D, Dall'Olio GM, Sikora M, Bertranpetit J, Laayouni H. Network-level and population genetics analysis of the insulin/TOR signal transduction pathway across human populations. Molecular Biology and Evolution. 29: 1379-92. PMID 22135191 DOI: 10.1093/Molbev/Msr298  0.96
2012 Alvarez-Ponce D, Guirao-Rico S, Orengo DJ, Segarra C, Rozas J, Aguadé M. Molecular population genetics of the insulin/TOR signal transduction pathway: a network-level analysis in Drosophila melanogaster. Molecular Biology and Evolution. 29: 123-32. PMID 21680868 DOI: 10.1093/Molbev/Msr160  0.96
2011 Alvarez-Ponce D, McInerney JO. The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences. Genome Biology and Evolution. 3: 782-90. PMID 21795752 DOI: 10.1093/Gbe/Evr073  0.96
2011 Alvarez-Ponce D, Aguadé M, Rozas J. Comparative genomics of the vertebrate insulin/TOR signal transduction pathway: a network-level analysis of selective pressures. Genome Biology and Evolution. 3: 87-101. PMID 21149867 DOI: 10.1093/Gbe/Evq084  0.96
2010 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, ... ... Alvarez-Ponce D, et al. 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 of the United States of America. 107: 12168-73. PMID 20566863 DOI: 10.1073/Pnas.1003379107  0.96
2009 Alvarez-Ponce D, Aguadé M, Rozas J. Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes. Genome Research. 19: 234-42. PMID 19141596 DOI: 10.1101/Gr.084038.108  0.96
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