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Items: 1 to 50 of 127

1.

ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models.

Darriba D, Posada D, Kozlov AM, Stamatakis A, Morel B, Flouri T.

Mol Biol Evol. 2019 Aug 20. pii: msz189. doi: 10.1093/molbev/msz189. [Epub ahead of print]

PMID:
31432070
2.

Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution.

Ren M, Feng X, Huang Y, Wang H, Hu Z, Clingenpeel S, Swan BK, Fonseca MM, Posada D, Stepanauskas R, Hollibaugh JT, Foster PG, Woyke T, Luo H.

ISME J. 2019 Sep;13(9):2150-2161. doi: 10.1038/s41396-019-0418-8. Epub 2019 Apr 25.

PMID:
31024152
3.

Selective Pressures on Human Cancer Genes along the Evolution of Mammals.

Vicens A, Posada D.

Genes (Basel). 2018 Nov 28;9(12). pii: E582. doi: 10.3390/genes9120582.

4.

Author Correction: A comparison of tools for the simulation of genomic next-generation sequencing data.

Escalona M, Rocha S, Posada D.

Nat Rev Genet. 2018 Nov;19(11):733. doi: 10.1038/s41576-018-0058-2.

PMID:
30283054
5.

RecPhyloXML: a format for reconciled gene trees.

Duchemin W, Gence G, Arigon Chifolleau AM, Arvestad L, Bansal MS, Berry V, Boussau B, Chevenet F, Comte N, Davín AA, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, Posada D, Scornavacca C, Szöllosi G, Zhang L, Tannier É, Daubin V.

Bioinformatics. 2018 Nov 1;34(21):3646-3652. doi: 10.1093/bioinformatics/bty389.

6.

Sensitivity to sequencing depth in single-cell cancer genomics.

Alves JM, Posada D.

Genome Med. 2018 Apr 16;10(1):29. doi: 10.1186/s13073-018-0537-2.

7.

NGSphy: phylogenomic simulation of next-generation sequencing data.

Escalona M, Rocha S, Posada D.

Bioinformatics. 2018 Jul 15;34(14):2506-2507. doi: 10.1093/bioinformatics/bty146.

PMID:
29534152
8.

Classifying the evolutionary and ecological features of neoplasms.

Maley CC, Aktipis A, Graham TA, Sottoriva A, Boddy AM, Janiszewska M, Silva AS, Gerlinger M, Yuan Y, Pienta KJ, Anderson KS, Gatenby R, Swanton C, Posada D, Wu CI, Schiffman JD, Hwang ES, Polyak K, Anderson ARA, Brown JS, Greaves M, Shibata D.

Nat Rev Cancer. 2017 Oct;17(10):605-619. doi: 10.1038/nrc.2017.69. Epub 2017 Sep 15. Review.

9.

Multiregional Tumor Trees Are Not Phylogenies.

Alves JM, Prieto T, Posada D.

Trends Cancer. 2017 Aug;3(8):546-550. doi: 10.1016/j.trecan.2017.06.004. Epub 2017 Jul 17.

10.

Species Tree Estimation from Genome-Wide Data with guenomu.

de Oliveira Martins L, Posada D.

Methods Mol Biol. 2017;1525:461-478.

PMID:
27896732
11.

Multilocus inference of species trees and DNA barcoding.

Mallo D, Posada D.

Philos Trans R Soc Lond B Biol Sci. 2016 Sep 5;371(1702). pii: 20150335. doi: 10.1098/rstb.2015.0335. Review.

12.

Correction: A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis.

Murgarella M, Puiu D, Novoa B, Figueras A, Posada D, Canchaya C.

PLoS One. 2016 Jul 21;11(7):e0160081. doi: 10.1371/journal.pone.0160081. eCollection 2016.

13.

A comparison of tools for the simulation of genomic next-generation sequencing data.

Escalona M, Rocha S, Posada D.

Nat Rev Genet. 2016 Aug;17(8):459-69. doi: 10.1038/nrg.2016.57. Epub 2016 Jun 20. Review. Erratum in: Nat Rev Genet. 2018 Nov;19(11):733.

14.

Phylogenomics for Systematic Biology.

Posada D.

Syst Biol. 2016 May;65(3):353-6. doi: 10.1093/sysbio/syw027. No abstract available.

PMID:
27129844
15.

Infinitely long branches and an informal test of common ancestry.

de Oliveira Martins L, Posada D.

Biol Direct. 2016 Apr 7;11(1):19. doi: 10.1186/s13062-016-0120-y.

16.

A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis.

Murgarella M, Puiu D, Novoa B, Figueras A, Posada D, Canchaya C.

PLoS One. 2016 Mar 15;11(3):e0151561. doi: 10.1371/journal.pone.0151561. eCollection 2016. Erratum in: PLoS One. 2016;11(7):e0160081.

17.

High-Frame-Rate Echocardiography Using Coherent Compounding With Doppler-Based Motion-Compensation.

Poree J, Posada D, Hodzic A, Tournoux F, Cloutier G, Garcia D.

IEEE Trans Med Imaging. 2016 Jul;35(7):1647-57. doi: 10.1109/TMI.2016.2523346. Epub 2016 Feb 3.

PMID:
26863650
18.

Staggered Multiple-PRF Ultrafast Color Doppler.

Posada D, Poree J, Pellissier A, Chayer B, Tournoux F, Cloutier G, Garcia D.

IEEE Trans Med Imaging. 2016 Jun;35(6):1510-21. doi: 10.1109/TMI.2016.2518638. Epub 2016 Jan 18.

PMID:
26780789
19.

SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees.

Mallo D, De Oliveira Martins L, Posada D.

Syst Biol. 2016 Mar;65(2):334-44. doi: 10.1093/sysbio/syv082. Epub 2015 Nov 1.

20.

RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues.

Moreira R, Pereiro P, Canchaya C, Posada D, Figueras A, Novoa B.

BMC Genomics. 2015 Sep 24;16:728. doi: 10.1186/s12864-015-1817-5.

21.

Cancer Molecular Evolution.

Posada D.

J Mol Evol. 2015 Oct;81(3-4):81-3. doi: 10.1007/s00239-015-9695-7. Epub 2015 Aug 20. No abstract available.

22.

Flow-induced 2D protein crystallization: characterization of the coupled interfacial and bulk flows.

Young JE, Posada D, Lopez JM, Hirsa AH.

Soft Matter. 2015 May 14;11(18):3618-28. doi: 10.1039/c5sm00429b.

PMID:
25805062
23.

CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation.

Arenas M, Lopes JS, Beaumont MA, Posada D.

Mol Biol Evol. 2015 Apr;32(4):1109-12. doi: 10.1093/molbev/msu411. Epub 2015 Jan 9.

24.

A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction.

De Oliveira Martins L, Mallo D, Posada D.

Syst Biol. 2016 May;65(3):397-416. doi: 10.1093/sysbio/syu082. Epub 2014 Oct 3.

25.

HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations.

Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, Tatem AJ, Sousa JD, Arinaminpathy N, Pépin J, Posada D, Peeters M, Pybus OG, Lemey P.

Science. 2014 Oct 3;346(6205):56-61. doi: 10.1126/science.1256739. Epub 2014 Oct 2.

26.

The inversion of the Control Region in three mitogenomes provides further evidence for an asymmetric model of vertebrate mtDNA replication.

Fonseca MM, Harris DJ, Posada D.

PLoS One. 2014 Sep 30;9(9):e106654. doi: 10.1371/journal.pone.0106654. eCollection 2014.

27.

Unsorted homology within locus and species trees.

Mallo D, De Oliveira Martins L, Posada D.

Syst Biol. 2014 Nov;63(6):988-92. doi: 10.1093/sysbio/syu050. Epub 2014 Jul 30. No abstract available.

28.

Testing for universal common ancestry.

de Oliveira Martins L, Posada D.

Syst Biol. 2014 Sep;63(5):838-42. doi: 10.1093/sysbio/syu041. Epub 2014 Jun 23. No abstract available.

29.

The evolution and appearance of C3 duplications in fish originate an exclusive teleost c3 gene form with anti-inflammatory activity.

Forn-Cuní G, Reis ES, Dios S, Posada D, Lambris JD, Figueras A, Novoa B.

PLoS One. 2014 Jun 13;9(6):e99673. doi: 10.1371/journal.pone.0099673. eCollection 2014.

30.

Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories.

Arenas M, Posada D.

Mol Biol Evol. 2014 May;31(5):1295-301. doi: 10.1093/molbev/msu078. Epub 2014 Feb 19.

31.

jmodeltest.org: selection of nucleotide substitution models on the cloud.

Santorum JM, Darriba D, Taboada GL, Posada D.

Bioinformatics. 2014 May 1;30(9):1310-1. doi: 10.1093/bioinformatics/btu032. Epub 2014 Jan 21.

32.

Origin and length distribution of unidirectional prokaryotic overlapping genes.

Fonseca MM, Harris DJ, Posada D.

G3 (Bethesda). 2014 Jan 10;4(1):19-27. doi: 10.1534/g3.113.005652.

33.

Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation.

Lopes JS, Arenas M, Posada D, Beaumont MA.

Heredity (Edinb). 2014 Mar;112(3):255-64. doi: 10.1038/hdy.2013.101. Epub 2013 Oct 23.

34.

Protein evolution along phylogenetic histories under structurally constrained substitution models.

Arenas M, Dos Santos HG, Posada D, Bastolla U.

Bioinformatics. 2013 Dec 1;29(23):3020-8. doi: 10.1093/bioinformatics/btt530. Epub 2013 Sep 12.

35.

Phylogenetic models of molecular evolution: next-generation data, fit, and performance.

Posada D.

J Mol Evol. 2013 Jun;76(6):351-2. doi: 10.1007/s00239-013-9566-z. Epub 2013 May 22. No abstract available.

36.

Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands.

Rocha S, Posada D, Harris DJ.

BMC Evol Biol. 2013 Jan 5;13:3. doi: 10.1186/1471-2148-13-3.

37.

Insights into origins of Human T-cell Lymphotropic Virus Type 1 based on new strains from aboriginal people of Canada.

Andonov A, Coulthart MB, Pérez-Losada M, Crandall KA, Posada D, Padmore R, Giulivi A, Oger JJ, Peters AA, Dekaban GA.

Infect Genet Evol. 2012 Dec;12(8):1822-30. doi: 10.1016/j.meegid.2012.07.015. Epub 2012 Aug 13.

PMID:
22921499
38.

jModelTest 2: more models, new heuristics and parallel computing.

Darriba D, Taboada GL, Doallo R, Posada D.

Nat Methods. 2012 Jul 30;9(8):772. doi: 10.1038/nmeth.2109. No abstract available.

39.

Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes.

Fonseca MM, Rocha S, Posada D.

PLoS One. 2012;7(5):e36605. doi: 10.1371/journal.pone.0036605. Epub 2012 May 9.

40.

Proving universal common ancestry with similar sequences.

Martins LD, Posada D.

Trends Evol Biol. 2012 May 9;4(1). pii: e5.

41.

The evolution of the mitochondrial genetic code in arthropods revisited.

Abascal F, Posada D, Zardoya R.

Mitochondrial DNA. 2012 Apr;23(2):84-91. doi: 10.3109/19401736.2011.653801. Epub 2012 Mar 7.

PMID:
22397376
42.

Removal versus fragmentation of amyloid-forming precursors via membrane filtration.

Posada D, Tessier PM, Hirsa AH.

Biotechnol Bioeng. 2012 Mar;109(3):840-5. doi: 10.1002/bit.24341. Epub 2011 Nov 6.

PMID:
22012557
43.

Genome-wide heterogeneity of nucleotide substitution model fit.

Arbiza L, Patricio M, Dopazo H, Posada D.

Genome Biol Evol. 2011;3:896-908. doi: 10.1093/gbe/evr080. Epub 2011 Aug 7.

44.

Gene expression analysis of clams Ruditapes philippinarum and Ruditapes decussatus following bacterial infection yields molecular insights into pathogen resistance and immunity.

Moreira R, Balseiro P, Romero A, Dios S, Posada D, Novoa B, Figueras A.

Dev Comp Immunol. 2012 Jan;36(1):140-9. doi: 10.1016/j.dci.2011.06.012. Epub 2011 Jul 3.

PMID:
21756933
45.

Analysing recombination in nucleotide sequences.

Martin DP, Lemey P, Posada D.

Mol Ecol Resour. 2011 Nov;11(6):943-55. doi: 10.1111/j.1755-0998.2011.03026.x. Epub 2011 May 19. Review.

PMID:
21592314
46.

Hemoptysis in a patient with testicular microlithiasis and a germ cell tumor: a rare combination.

Télles AC, Luna Jde J, Posada DM, Bouscoulet LT.

J Bras Pneumol. 2011 Mar-Apr;37(2):277-80. English, Portuguese. No abstract available.

47.

Phylodynamics of HIV-1 from a phase III AIDS vaccine trial in Bangkok, Thailand.

Pérez-Losada M, Jobes DV, Sinangil F, Crandall KA, Arenas M, Posada D, Berman PW.

PLoS One. 2011 Mar 10;6(3):e16902. doi: 10.1371/journal.pone.0016902.

48.

HIV-1 infected monozygotic twins: a tale of two outcomes.

Tazi L, Imamichi H, Hirschfeld S, Metcalf JA, Orsega S, Pérez-Losada M, Posada D, Lane HC, Crandall KA.

BMC Evol Biol. 2011 Mar 8;11:62. doi: 10.1186/1471-2148-11-62.

49.

ProtTest 3: fast selection of best-fit models of protein evolution.

Darriba D, Taboada GL, Doallo R, Posada D.

Bioinformatics. 2011 Apr 15;27(8):1164-5. doi: 10.1093/bioinformatics/btr088. Epub 2011 Feb 17.

50.

Computational design of centralized HIV-1 genes.

Arenas M, Posada D.

Curr HIV Res. 2010 Dec;8(8):613-21. Review.

PMID:
21054255

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