| Year |
Citation |
Score |
| 2022 |
Yim WC, Swain ML, Ma D, An H, Bird KA, Curdie DD, Wang S, Ham HD, Luzuriaga-Neira A, Kirkwood JS, Hur M, Solomon JKQ, Harper JF, Kosma DK, Alvarez-Ponce D, et al. The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome. The Plant Cell. PMID 35961044 DOI: 10.1093/plcell/koac249 |
0.324 |
|
| 2022 |
Subramanian K, Payne B, Feyertag F, Alvarez-Ponce D. The Codon Statistics Database: a Database of Codon Usage Bias. Molecular Biology and Evolution. PMID 35859338 DOI: 10.1093/molbev/msac157 |
0.3 |
|
| 2020 |
Kyger R, Luzuriaga-Neira A, Layman T, Sandberg TOM, Singh D, Huchon D, Peri S, Atkinson SD, Bartholomew JL, Yi SV, Alvarez-Ponce D. Myxosporea (Myxozoa, Cnidaria) lack DNA cytosine methylation. Molecular Biology and Evolution. PMID 32898240 DOI: 10.1093/Molbev/Msaa214 |
0.358 |
|
| 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 |
0.789 |
|
| 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 |
0.678 |
|
| 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 |
0.642 |
|
| 2019 |
Payne BL, Alvarez-Ponce D. Codon usage differences among genes expressed in different tissues of Drosophila melanogaster. Genome Biology and Evolution. PMID 30859203 DOI: 10.1093/Gbe/Evz051 |
0.407 |
|
| 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 |
0.614 |
|
| 2018 |
Alvarez-Ponce D, Weitzman CL, Tillett RL, Sandmeier FC, Tracy CR. High quality draft genome sequences of strains PS6 and 723 isolated from tortoises with upper respiratory tract disease. Standards in Genomic Sciences. 13: 12. PMID 29725499 DOI: 10.1186/S40793-018-0315-1 |
0.461 |
|
| 2018 |
Weitzman CL, Tillett RL, Sandmeier FC, Tracy CR, Alvarez-Ponce D. High quality draft genome sequence of strain BH29, isolated from the respiratory tract of a desert tortoise. Standards in Genomic Sciences. 13: 9. PMID 29682170 DOI: 10.1186/S40793-018-0309-Z |
0.42 |
|
| 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 |
0.493 |
|
| 2018 |
Payne BL, Alvarez-Ponce D. Higher Rates of Protein Evolution in the Self-Fertilizing Plant Arabidopsis thaliana than in the Out-Crossers Arabidopsis lyrata and Arabidopsis halleri. Genome Biology and Evolution. 10: 895-900. PMID 29608724 DOI: 10.1093/Gbe/Evy053 |
0.403 |
|
| 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 |
0.433 |
|
| 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 |
0.456 |
|
| 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 |
0.741 |
|
| 2017 |
Feyertag F, Alvarez-Ponce D. Disulfide bonds enable accelerated protein evolution. Molecular Biology and Evolution. PMID 28431018 DOI: 10.1093/Molbev/Msx135 |
0.357 |
|
| 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 |
0.486 |
|
| 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 |
0.805 |
|
| 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 |
0.381 |
|
| 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 |
0.788 |
|
| 2016 |
Alvarez-Ponce D. Recording negative results of protein-protein interaction assays: an easy way to deal with the biases and errors of interactomic data sets. Briefings in Bioinformatics. PMID 27542401 DOI: 10.1093/Bib/Bbw075 |
0.33 |
|
| 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 |
0.646 |
|
| 2016 |
Chakraborty S, Alvarez-Ponce D. Positive Selection and Centrality in the Yeast and Fly Protein-Protein Interaction Networks. Biomed Research International. 2016: 4658506. PMID 27119079 DOI: 10.1155/2016/4658506 |
0.507 |
|
| 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 |
0.73 |
|
| 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 |
0.693 |
|
| 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 |
0.743 |
|
| 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 |
0.684 |
|
| 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 |
0.73 |
|
| 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 |
0.533 |
|
| 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 |
0.77 |
|
| 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 |
0.524 |
|
| 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 |
0.72 |
|
| 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 |
0.693 |
|
| 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 |
0.803 |
|
| 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 |
0.746 |
|
| 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 |
0.804 |
|
| Low-probability matches (unlikely to be authored by this person) |
| 2023 |
Bauschlicher SN, Weitzman CL, Martinez V, Tracy CR, Alvarez-Ponce D, Sandmeier FC. Assessing spatial distribution, genetic variants, and virulence of pathogen in threatened Mojave desert tortoises. Ecology and Evolution. 13: e10173. PMID 37284665 DOI: 10.1002/ece3.10173 |
0.282 |
|
| 2020 |
Alvarez-Ponce D. Richard Dickerson, Molecular Clocks, and Rates of Protein Evolution. Journal of Molecular Evolution. PMID 33205299 DOI: 10.1007/s00239-020-09973-x |
0.274 |
|
| 2020 |
Cullen CM, Aneja KK, Beyhan S, Cho CE, Woloszynek S, Convertino M, McCoy SJ, Zhang Y, Anderson MZ, Alvarez-Ponce D, Smirnova E, Karstens L, Dorrestein PC, Li H, Sen Gupta A, et al. Emerging Priorities for Microbiome Research. Frontiers in Microbiology. 11: 136. PMID 32140140 DOI: 10.3389/Fmicb.2020.00136 |
0.273 |
|
| 2022 |
Luzuriaga-Neira A, Subramanian K, Alvarez-Ponce D. Functional compensation of mouse duplicates by their paralogs expressed in the same tissues. Genome Biology and Evolution. PMID 35945673 DOI: 10.1093/gbe/evac126 |
0.265 |
|
| 2021 |
Roddy AB, Alvarez-Ponce D, Roy SW. Mammals with small populations do not exhibit larger genomes. Molecular Biology and Evolution. PMID 33956142 DOI: 10.1093/molbev/msab142 |
0.245 |
|
| 2023 |
Luzuriaga-Neira AR, Ritchie AM, Payne BL, Carrillo-Parramon O, Liberles DA, Alvarez-Ponce D. Highly Abundant Proteins Are Highly Thermostable. Genome Biology and Evolution. 15. PMID 37399326 DOI: 10.1093/gbe/evad112 |
0.242 |
|
| 2022 |
Luzuriaga-Neira AR, Alvarez-Ponce D. Rates of Protein Evolution across the Marsupial Phylogeny: Heterogeneity and Link to Life-History Traits. Genome Biology and Evolution. 14. PMID 34894228 DOI: 10.1093/gbe/evab277 |
0.228 |
|
| 2021 |
Luzuriaga-Neira A, Sandmeier FC, Weitzman CL, Tracy CR, Bauschlicher SN, Tillett RL, Alvarez-Ponce D. Mycoplasma agassizii, an opportunistic pathogen of tortoises, shows very little genetic variation across the Mojave and Sonoran Deserts. Plos One. 16: e0245895. PMID 33534823 DOI: 10.1371/journal.pone.0245895 |
0.225 |
|
| 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 |
0.219 |
|
| 2021 |
Sarkar C, Alvarez-Ponce D. Extracellular domains of transmembrane proteins defy the expression level-evolutionary rate anticorrelation. Genome Biology and Evolution. PMID 34665250 DOI: 10.1093/gbe/evab235 |
0.194 |
|
| 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 |
0.184 |
|
| 2021 |
Singh D, Sun D, King AG, Alquezar-Planas DE, Johnson RN, Alvarez-Ponce D, Yi SV. Koala methylomes reveal divergent and conserved DNA methylation signatures of X chromosome regulation. Proceedings. Biological Sciences. 288: 20202244. PMID 33622136 DOI: 10.1098/rspb.2020.2244 |
0.172 |
|
| 2023 |
Liberles DA, Alvarez-Ponce D, Meyer MM, Minh BQ, Silva JC. 2022 Zuckerkandl Prize. Journal of Molecular Evolution. 91: 1. PMID 36609706 DOI: 10.1007/s00239-022-10089-7 |
0.04 |
|
| Hide low-probability matches. |