Genómica del Cáncer

Brea-Iglesias J, Gallardo-Gomez M, Oitaben A, Lazaro-Quintela ME, Leon L,Alves JM, Pino-Gonzalez M, Juaneda-Magdalena L, Garcia-Benito C, Abdulkader I,Muinelo L, Paramio JM, Martinez-Fernandez M. Genomics guiding personalizedfirst-line immunotherapy response in lung and bladder tumors. J Transl Med. 2025Apr 5;23(1):404. doi: 10.1186/s12967-025-06323-7. PubMed PMID: 40188131; PubMedCentral PMCID: PMC11972471.

Estevez-Gomez N, Prieto T, Tomas L, Alvarino P, Guillaumet-Adkins A, Heyn H,Prado-Lopez S, Posada D. Differential performance of strategies for single-cellwhole-genome amplification. Cell Rep Methods. 2025 Apr 21;5(4):101025. doi:10.1016/j.crmeth.2025.101025. PubMed PMID: 40262527; PubMed Central PMCID:PMC12256942.

Gallardo-Gomez M, Costas-Rios L, Garcia-Prieto CA, Alvarez-Rodriguez L,Bujanda L, Barrero M, Castells A, Balaguer F, Jover R, Esteller M, Tardio BaigesA, Gonzalez-Carrero Fojon J, Cubiella J, De Chiara L. Serum DNA methylome of thecolorectal cancer serrated pathway enables non-invasive detection. Mol Oncol.2024 Nov;18(11):2696-2713. doi: 10.1002/1878-0261.13573. Epub 2024 Jan 10. PubMedPMID: 38129291; PubMed Central PMCID: PMC11547225.

Gallego-Garcia P, Estevez-Gomez N, De Chiara L, Alvarino P, Juiz-Gonzalez PM,Torres-Beceiro I, Poza M, Vallejo JA, Rumbo-Feal S, Conde-Perez K, Aja-Macaya P,Ladra S, Moreno-Flores A, Gude-Gonzalez MJ, Coira A, Aguilera A, Costa-AlcaldeJJ, Trastoy R, Barbeito-Castineiras G, Garcia-Souto D, Tubio JMC, Trigo-DaportaM, Camacho-Zamora P, Costa JG, Gonzalez-Dominguez M, Canoura-Fernandez L,Glez-Pena D, Perez-Castro S, Cabrera JJ, Davina-Nunez C, Godoy-Diz M,Treinta-Alvarez AB, Veiga MI, Sousa JC, Osorio NS, Comas I, Gonzalez-Candelas F,Hong SL, Bollen N, Dellicour S, Baele G, Suchard MA, Lemey P, Agulla A, Bou G,Alonso-Garcia P, Perez-Del-Molino ML, Garcia-Campello M, Paz-Vidal I, Regueiro B,Posada D. Dispersal history of SARS-CoV-2 in Galicia, Spain. J Med Virol. 2024Jul;96(7):e29773. doi: 10.1002/jmv.29773. PubMed PMID: 38940448; PubMed CentralPMCID: PMC11742125.

Liu Y, Sapoval N, Gallego-Garcia P, Tomas L, Posada D, Treangen TJ, StadlerLB. Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater.Nat Commun. 2024 May 28;15(1):4545. doi: 10.1038/s41467-024-48334-w. PubMed PMID:38806450; PubMed Central PMCID: PMC11133379.

Borgsmuller N, Valecha M, Kuipers J, Beerenwinkel N, Posada D. Single-cellphylogenies reveal changes in the evolutionary rate within cancer and healthytissues. Cell Genom. 2023 Aug 17;3(9):100380. doi: 10.1016/j.xgen.2023.100380.eCollection 2023 Sep 13. PubMed PMID: 37719146; PubMed Central PMCID:PMC10504633.

Bruzos AL, Santamarina M, Garcia-Souto D, Diaz S, Rocha S, Zamora J, Lee Y,Vina-Feas A, Quail MA, Otero I, Pequeno-Valtierra A, Temes J, Rodriguez-Castro J,Aramburu L, Vidal-Capon A, Villanueva A, Costas D, Rodriguez R, Prieto T, TomasL, Alvarino P, Alonso J, Cao A, Iglesias D, Carballal MJ, Amaral AM, Balseiro P,Calado R, El Khalfi B, Izagirre U, de Montaudouin X, Pade NG, Probert I, RicardoF, Ruiz P, Skazina M, Smolarz K, Pasantes JJ, Villalba A, Ning Z, Ju YS, PosadaD, Demeulemeester J, Baez-Ortega A, Tubio JMC. Somatic evolution of marinetransmissible leukemias in the common cockle, Cerastoderma edule. Nat Cancer.2023 Nov;4(11):1575-1591. doi: 10.1038/s43018-023-00641-9. Epub 2023 Oct 2.PubMed PMID: 37783803.

Gallardo-Gomez M, Rodriguez-Girondo M, Planell N, Moran S, Bujanda L, EtxartA, Castells A, Balaguer F, Jover R, Esteller M, Cubiella J, Gomez-Cabrero D, DeChiara L. Serum methylation of GALNT9, UPF3A, WARS, and LDB2 as noninvasivebiomarkers for the early detection of colorectal cancer and advanced adenomas.Clin Epigenetics. 2023 Oct 4;15(1):157. doi: 10.1186/s13148-023-01570-1. PubMedPMID: 37794510; PubMed Central PMCID: PMC10552320.

Trigo-Tasende N, Vallejo JA, Rumbo-Feal S, Conde-Perez K, Vaamonde M,Lopez-Oriona A, Barbeito I, Nasser-Ali M, Reif R, Rodino-Janeiro BK,Fernandez-Alvarez E, Iglesias-Corras I, Freire B, Tarrio-Saavedra J, Tomas L,Gallego-Garcia P, Posada D, Bou G, Lopez-de-Ullibarri I, Cao R, Ladra S, Poza M.Wastewater early warning system for SARS-CoV-2 outbreaks and variants in aCoruna, Spain. Environ Sci Pollut Res Int. 2023 Jul;30(32):79315-79334. doi:10.1007/s11356-023-27877-3. Epub 2023 Jun 7. PubMed PMID: 37286834; PubMedCentral PMCID: PMC10247271.

Trovao NS, Pan V, Goel C, Gallego-Garcia P, Liu Y, Barbara C, Borg R, BriffaM, Cilia C, Grech L, Vassallo M, Treangen TJ, Posada D, Beheshti A, Borg J, ZahraG. Evolutionary and spatiotemporal analyses reveal multiple introductions andcryptic transmission of SARS-CoV-2 VOC/VOI in Malta. Microbiol Spectr. 2023 Dec12;11(6):e0153923. doi: 10.1128/spectrum.01539-23. Epub 2023 Oct 6. PubMed PMID:37800925; PubMed Central PMCID: PMC10714767.

Almeida J, Perez-Figueroa A, Alves JM, Valecha M, Prado-Lopez S, Alvarino P,Cameselle-Teijeiro JM, Chantada D, Fonseca MM, Posada D. Single-cell mtDNAheteroplasmy in colorectal cancer. Genomics. 2022 Mar;114(2):110315. doi:10.1016/j.ygeno.2022.110315. Epub 2022 Feb 16. PubMed PMID: 35181467.
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Alvarez H, Ruiz-Mateos E, Juiz-Gonzalez PM, Vitalle J, Vieitez I,Vazquez-Friol MDC, Torres-Beceiro I, Perez-Gomez A, Gallego-Garcia P,Estevez-Gomez N, De Chiara L, Poveda E, Posada D, Llibre JM. SARS-CoV-2 Evolutionand Spike-Specific CD4+ T-Cell Response in Persistent COVID-19 with Severe HIVImmune Suppression. Microorganisms. 2022 Jan 11;10(1):143. doi:10.3390/microorganisms10010143. PubMed PMID: 35056592; PubMed Central PMCID:PMC8780218.
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Alves JM, Estevez-Gomez N, Valecha M, Prado-Lopez S, Tomas L, Alvarino P,Pineiro R, Muinelo-Romay L, Mondelo-Macia P, Salgado M, Iglesias-Gomez A,Codesido-Prada L, Cubiella J, Posada D. Comparative analysis of capture methodsfor genomic profiling of circulating tumor cells in colorectal cancer. Genomics.2022 Nov;114(6):110500. doi: 10.1016/j.ygeno.2022.110500. Epub 2022 Oct 4. PubMedPMID: 36202322.

Alves JM, Prado-Lopez S, Tomas L, Valecha M, Estevez-Gomez N, Alvarino P,Geisel D, Modest DP, Sauer IM, Pratschke J, Raschzok N, Sers C, Mamlouk S, PosadaD. Clonality and timing of relapsing colorectal cancer metastasis revealedthrough whole-genome single-cell sequencing. Cancer Lett. 2022 Sep 1;543:215767.doi: 10.1016/j.canlet.2022.215767. Epub 2022 Jun 7. PubMed PMID: 35688262.

De Chiara L, Barcia-Castro L, Gallardo-Gomez M, Paez de la Cadena M,Martinez-Zorzano VS, Rodriguez-Berrocal FJ, Bujanda L, Etxart A, Castells A,Balaguer F, Jover R, Cubiella J, Cordero OJ. Evaluation of Blood Soluble CD26 asa Complementary Biomarker for Colorectal Cancer Screening Programs. Cancers(Basel). 2022 Sep 20;14(19):4563. doi: 10.3390/cancers14194563. PubMed PMID:36230486; PubMed Central PMCID: PMC9559671.

Edrisi M, Valecha MV, Chowdary SBV, Robledo S, Ogilvie HA, Posada D, Zafar H,Nakhleh L. Phylovar: toward scalable phylogeny-aware inference ofsingle-nucleotide variations from single-cell DNA sequencing data.Bioinformatics. 2022 Jun 24;38(Suppl 1):i195-i202. doi:10.1093/bioinformatics/btac254. Erratum In: Bioinformatics. 2023 May 4;39(5):PubMed PMID: 35758771; PubMed Central PMCID: PMC9235480.

Gallego-Garcia P, Varela N, Estevez-Gomez N, De Chiara L, Fernandez-Silva I,Valverde D, Sapoval N, Treangen TJ, Regueiro B, Cabrera-Alvargonzalez JJ, DelCampo V, Perez S, Posada D. Limited genomic reconstruction of SARS-CoV-2transmission history within local epidemiological clusters. Virus Evol. 2022 Feb4;8(1):veac008. doi: 10.1093/ve/veac008. eCollection 2022. PubMed PMID: 35242361;PubMed Central PMCID: PMC8889950.

Garcia-Souto D, Bruzos AL, Diaz S, Rocha S, Pequeño-Valtierra A, Roman-Lewis CF, Alonso J, Rodriguez R, Costas D, Rodriguez-Castro J, Villanueva A, Silva L, Valencia JM, Annona G, Tarallo A, Ricardo F, Bratoš Cetini? A, Posada D, Pasantes JJ, Tubio JM. Mitochondrial genome sequencing of marine leukaemias reveals cancer contagion between clam species in the Seas of Southern Europe. Elife. 2022;11:e66946. PMID: 35040778. DOI: 10.7554/eLife.66946. http://www.ncbi.nlm.nih.gov/pubmed/35040778
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Kang S, Borgsmuller N, Valecha M, Kuipers J, Alves JM, Prado-Lopez S, ChantadaD, Beerenwinkel N, Posada D, Szczurek E. SIEVE: joint inference ofsingle-nucleotide variants and cell phylogeny from single-cell DNA sequencingdata. Genome Biol. 2022 Nov 30;23(1):248. doi: 10.1186/s13059-022-02813-9. PubMedPMID: 36451239; PubMed Central PMCID: PMC9714196.

Kozlov A, Alves JM, Stamatakis A, Posada D. CellPhy: accurate and fastprobabilistic inference of single-cell phylogenies from scDNA-seq data. GenomeBiol. 2022 Jan 26;23(1):37. doi: 10.1186/s13059-021-02583-w. PubMed PMID:35081992; PubMed Central PMCID: PMC8790911.
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Moyano A, Blanch-Lombarte O, Tarancon-Diez L, Pedreno-Lopez N, Arenas M,Alvaro T, Casado C, Olivares I, Vera M, Rodriguez C, Del Romero J, Lopez-GalindezC, Ruiz-Mateos E, Prado JG, Pernas M. Immunoescape of HIV-1 in Env-EL9 CD8 + Tcell response restricted by HLA-B*14:02 in a Non progressor who lost twenty-sevenyears of HIV-1 control. Retrovirology. 2022 Mar 26;19(1):6. doi:10.1186/s12977-022-00591-7. PubMed PMID: 35346235; PubMed Central PMCID:PMC8962528.
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Valecha M, Posada D. Somatic variant calling from single-cell DNA sequencingdata. Comput Struct Biotechnol J. 2022 Jun 14;20:2978-2985. doi:10.1016/j.csbj.2022.06.013. eCollection 2022. PubMed PMID: 35782734; PubMedCentral PMCID: PMC9218383.

Álvarez EG, Demeulemeester J, Otero P, Jolly C, García-Souto D, Pequeño-Valtierra A, Zamora J, Tojo M, Temes J, Baez-Ortega A, Rodriguez-Martin B, Oitaben A, Bruzos AL, Martínez-Fernández M, Haase K, Zumalave S, Abal R, Rodríguez-Castro J, Rodriguez-Casanova A, Diaz-Lagares A, Li Y, Raine KM, Butler AP, Otero I, Ono A, Aikata H, Chayama K, Ueno M, Hayami S, Yamaue H, Maejima K, Blanco MG, Forns X, Rivas C, Ruiz-Bañobre J, Pérez-Del-Pulgar S, Torres-Ruiz R, Rodriguez-Perales S, Garaigorta U, Campbell PJ, Nakagawa H, Van Loo P, Tubio JMC. Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture. Nat Commun. 2021;12(1):6910. PMID: 34824211. DOI: 10.1038/s41467-021-26805-8. http://www.ncbi.nlm.nih.gov/pubmed/34824211
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Carvalho-Correia E, Calçada C, Branca F, Estévez-Gómez N, De Chiara L, Varela N, Gallego-García P, Posada D, Sousa H, Sousa J, Veiga MI, Osório NS. OmniSARS2: A Highly Sensitive and Specific RT-qPCR-Based COVID-19 Diagnostic Method Designed to Withstand SARS-CoV-2 Lineage Evolution. Biomedicines. 2021 Sep;9(10):1314. PMID: 34680431. DOI: 10.3390/biomedicines9101314. http://www.ncbi.nlm.nih.gov/pubmed/34680431
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Crespo FF, Posada D, Wiuf C. Coalescent models derived from birth-death processes. Theor Popul Biol. 2021 Dec;142:1–11. PMID: 34563554. DOI: 10.1016/j.tpb.2021.09.003. http://www.ncbi.nlm.nih.gov/pubmed/34563554
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Gallardo-Gómez M, De Chiara L, Álvarez-Chaver P, Cubiella J. Colorectal cancer screening and diagnosis: omics-based technologies for development of a non-invasive blood-based method. Expert Rev Anticancer Ther. 2021 Jul;21(7):723–38. PMID: 33507120. DOI: 10.1080/14737140.2021.1882858. http://www.ncbi.nlm.nih.gov/pubmed/33507120
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González-Ballesteros N, Diego-González L, Lastra-Valdor M, Grimaldi M, Cavazza A, Bigi F, Rodríguez-Argüelles MC, Simón-Vázquez R. Saccorhiza polyschides used to synthesize gold and silver nanoparticles with enhanced antiproliferative and immunostimulant activity. Mater Sci Eng C Mater Biol Appl. 2021 Apr;123:111960. PMID: 33812588. DOI: 10.1016/j.msec.2021.111960. http://www.ncbi.nlm.nih.gov/pubmed/33812588
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Hodcroft EB, Zuber M, Nadeau S, Vaughan TG, Crawford KHD, Althaus CL, Reichmuth ML, Bowen JE, Walls AC, Corti D, Bloom JD, Veesler D, Mateo D, Hernando A, Comas I, González-Candelas F, SeqCOVID-SPAIN consortium (David Posada; Diana Valverde; Nuria Estévez; Loretta de Chiara; Pilar Gallego-García; Nair Varela), Stadler T, Neher RA. Spread of a SARS-CoV-2 variant through Europe in the summer of 2020. Nature. 2021;595(7869):707–12. PMID: 34098568. DOI: 10.1038/s41586-021-03677-y. http://www.ncbi.nlm.nih.gov/pubmed/34098568
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López MG, Chiner-Oms Á, García de Viedma D, Ruiz-Rodriguez P, Bracho MA, Cancino-Muñoz I, D’Auria G, de Marco G, García-González N, Goig GA, Gómez-Navarro I, Jiménez-Serrano S, Martinez-Priego L, Ruiz-Hueso P, Ruiz-Roldán L, Torres-Puente M, Alberola J, Albert E, Aranzamendi Zaldumbide M, Bea-Escudero MP, Boga JA, Bordoy AE, Canut-Blasco A, Carvajal A, Cilla Eguiluz G, Cordón Rodríguez ML, Costa-Alcalde JJ, de Toro M, de Toro Peinado I, Del Pozo JL, Duchêne S, Fernández-Pinero J, Fuster Escrivá B, Gimeno Cardona C, González Galán V, Gonzalo Jiménez N, Hernáez Crespo S, Herranz M, Lepe JA, López-Causapé C, López-Hontangas JL, Martín V, Martró E, Milagro Beamonte A, Montes Ros M, Moreno-Muñoz R, Navarro D, Navarro-Marí JM, Not A, Oliver A, Palop-Borrás B, Parra Grande M, Pedrosa-Corral I, Pérez González MC, Pérez-Lago L, Pérez-Ruiz M, Piñeiro Vázquez L, Rabella N, Rezusta A, Robles Fonseca L, Rodríguez-Villodres Á, Sanbonmatsu-Gámez S, Sicilia J, Soriano A, Tirado Balaguer MD, Torres I, Tristancho A, Marimón JM
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Posada D, Crandall KA. Felsenstein Phylogenetic Likelihood. J Mol Evol. 2021;89(3):134–45. PMID: 33438113. DOI: 10.1007/s00239-020-09982-w. http://www.ncbi.nlm.nih.gov/pubmed/33438113
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Ruiz-Rodriguez P, Francés-Gómez C, Chiner-Oms Á, López MG, Jiménez-Serrano S, Cancino-Muñoz I, Ruiz-Hueso P, Torres-Puente M, Bracho MA, D’Auria G, Martinez-Priego L, Guerreiro M, Montero-Alonso M, Gómez MD, Piñana JL, SeqCOVID-Spain consortium (David Posada; Diana Valverde; Nuria Estévez; Loretta de Chiara; Pilar Gallego-García; Nair Varela), González-Candelas F, Comas I, Marina A, Geller R, Coscolla M. Evolutionary and Phenotypic Characterization of Two Spike Mutations in European Lineage 20E of SARS-CoV-2. MBio. 2021;12(6):e0231521. PMID: 34781748. DOI: 10.1128/mBio.02315-21. http://www.ncbi.nlm.nih.gov/pubmed/34781748
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Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RAL, Wang Q, Albin D, Ogilvie HA, Lee MD, Villapol S, Hernandez KM, Maljkovic Berry I, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck FJ, Treangen TJ. SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission. Genome Res. 2021;31(4):635–44. PMID: 33602693. DOI: 10.1101/gr.268961.120. http://www.ncbi.nlm.nih.gov/pubmed/33602693
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Arenas M, Bastolla U. ProtASR2: Ancestral reconstruction of protein sequences accounting for folding stability. Paradis E (ed.). Methods Ecol Evol. 2020 Feb;11(2):248–57. DOI: 10.1111/2041-210X.13341. https://doi.org/10.1111/2041-210X.13341
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Arenas M. Protein Evolution in the Flaviviruses. J Mol Evol. 2020;88(6):473–6. PMID: 32451560. DOI: 10.1007/s00239-020-09953-1. http://www.ncbi.nlm.nih.gov/pubmed/32451560
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Darriba D, Posada D, Kozlov AM, Stamatakis A, Morel B, Flouri T. ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models. Mol Biol Evol. 2020 Jan;37(1):291–4. PMID: 31432070. DOI: 10.1093/molbev/msz189. http://www.ncbi.nlm.nih.gov/pubmed/31432070
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De Chiara L, Leiro-Fernandez V, Rodríguez-Girondo M, Valverde D, Botana-Rial MI, Fernández-Villar A. Comparison of Bisulfite Pyrosequencing and Methylation-Specific qPCR for Methylation Assessment. Int J Mol Sci. 2020 Dec;21(23):1–13. PMID: 33287451. DOI: 10.3390/ijms21239242. http://www.ncbi.nlm.nih.gov/pubmed/33287451
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De Chiara L, Páez de la Cadena M, Rodríguez-Berrocal J, Alvarez-Pardiñas MC, Pardiñas-Añón MC, Varela-Calviño R, Cordero OJ. CD26-Related Serum Biomarkers: sCD26 Protein, DPP4 Activity, and Anti-CD26 Isotype Levels in a Colorectal Cancer-Screening Context. Dis Markers. 2020;2020:4347936. PMID: 32051696. DOI: 10.1155/2020/4347936. http://www.ncbi.nlm.nih.gov/pubmed/32051696
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Del Amparo R, Vicens A, Arenas M. The influence of heterogeneous codon frequencies along sequences on the estimation of molecular adaptation. Bioinformatics. 2020;36(2):430–6. PMID: 31304972. DOI: 10.1093/bioinformatics/btz558. http://www.ncbi.nlm.nih.gov/pubmed/31304972
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González-Ballesteros N, Rodríguez-Argüelles MC, Lastra-Valdor M, González-Mediero G, Rey-Cao S, Grimaldi M, Cavazza A, Bigi F. Synthesis of silver and gold nanoparticles by Sargassum muticum biomolecules and evaluation of their antioxidant activity and antibacterial properties. J Nanostructure Chem. 2020 Dec;10(4):317–30. DOI: 10.1007/s40097-020-00352-y. https://doi.org/10.1007/s40097-020-00352-y
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Lago-Docampo M, Tenorio J, Hernández-González I, Pérez-Olivares C, Escribano-Subías P, Pousada G, Baloira A, Arenas M, Lapunzina P, Valverde D. Characterization of rare ABCC8 variants identified in Spanish pulmonary arterial hypertension patients. Sci Rep. 2020;10(1):15135. PMID: 32934261. DOI: 10.1038/s41598-020-72089-1. http://www.ncbi.nlm.nih.gov/pubmed/32934261
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Liberles DA, Chang B, Geiler-Samerotte K, Goldman A, Hey J, Kaçar B, Meyer M, Murphy W, Posada D, Storfer A. Emerging Frontiers in the Study of Molecular Evolution. J Mol Evol. 2020;88(3):211–26. PMID: 32060574. DOI: 10.1007/s00239-020-09932-6. http://www.ncbi.nlm.nih.gov/pubmed/32060574
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Mamlouk S, Simon T, Tomás L, Wedge DC, Arnold A, Menne A, Horst D, Capper D, Morkel M, Posada D, Sers C, Bläker H. Malignant transformation and genetic alterations are uncoupled in early colorectal cancer progression. BMC Biol. 2020;18(1):116. PMID: 32895052. DOI: 10.1186/s12915-020-00844-x. http://www.ncbi.nlm.nih.gov/pubmed/32895052
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Otero-Estévez O, Gallardo-Gomez M, Cadena MP de la, Rodríguez-Berrocal FJ, Cubiella J, Ramirez VH, García-Nimo L, Chiara L De. Value of Serum NEUROG1 Methylation for the Detection of Advanced Adenomas and Colorectal Cancer. Diagnostics (Basel, Switzerland). 2020 Jun;10(7) PMID: 32605302. DOI: 10.3390/diagnostics10070437. http://www.ncbi.nlm.nih.gov/pubmed/32605302
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Pérez-Losada M, Arenas M, Galán JC, Bracho MA, Hillung J, García-González N, González-Candelas F. High-throughput sequencing (HTS) for the analysis of viral populations. Infect Genet Evol. 2020;80:104208. PMID: 32001386. DOI: 10.1016/j.meegid.2020.104208. http://www.ncbi.nlm.nih.gov/pubmed/32001386
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Posada D. CellCoal: Coalescent Simulation of Single-Cell Sequencing Samples. Mol Biol Evol. 2020;37(5):1535–42. PMID: 32027371. DOI: 10.1093/molbev/msaa025. http://www.ncbi.nlm.nih.gov/pubmed/32027371
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Rebelo MÂ, Gómez C, Gomes I, Poza J, Martins S, Maturana-Candelas A, Ruiz-Gómez SJ, Durães L, Sousa P, Figueruelo M, Rodríguez M, Pita C, Arenas M, Álvarez L, Hornero R, Pinto N, Lopes AM. Genome-Wide Scan for Five Brain Oscillatory Phenotypes Identifies a New QTL Associated with Theta EEG Band. Brain Sci. 2020 Nov;10(11):870. PMID: 33218114. DOI: 10.3390/brainsci10110870. http://www.ncbi.nlm.nih.gov/pubmed/33218114
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Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PAW, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine K, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH, PCAWG Structural Variation Working Group, Campbell PJ, Tubio JMC, PCAWG Consortium. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet. 2020;52(3):306–19. PMID: 32024998. DOI: 10.1038/s41588-019-0562-0. http://www.ncbi.nlm.nih.gov/pubmed/32024998
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Alves JM, Prado-López S, Cameselle-Teijeiro JM, Posada D. Rapid evolution and biogeographic spread in a colorectal cancer. Nat Commun. Springer US; 2019;10(1):5139. PMID: 31723138. DOI: 10.1038/s41467-019-12926-8. http://www.ncbi.nlm.nih.gov/pubmed/31723138
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Chávez JC, Vicens A, Wrighton DC, Andrade-López K, Beltrán C, Gutiérrez RM, Lippiat JD, Treviño CL. A cytoplasmic Slo3 isoform is expressed in somatic tissues. Mol Biol Rep. 2019 Oct;46(5):5561–7. PMID: 31270758. DOI: 10.1007/s11033-019-04943-z. http://www.ncbi.nlm.nih.gov/pubmed/31270758
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Currat M, Arenas M, Quilodràn CS, Excoffier L, Ray N. SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal. Bioinformatics. 2019;35(21):4480–3. PMID: 31077292. DOI: 10.1093/bioinformatics/btz311. http://www.ncbi.nlm.nih.gov/pubmed/31077292
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Dueñas M, Pérez-Figueroa A, Oliveira C, Suárez-Cabrera C, Sousa A, Oliveira P, Villacampa F, Paramio JM, Martínez-Fernández M. Gene Expression Analyses in Non Muscle Invasive Bladder Cancer Reveals a Role for Alternative Splicing and Tp53 Status. Sci Rep. 2019;9(1):10362. PMID: 31316092. DOI: 10.1038/s41598-019-46652-4. http://www.ncbi.nlm.nih.gov/pubmed/31316092
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González-Ballesteros N, Diego-González L, Lastra-Valdor M, Rodríguez-Argüelles MC, Grimaldi M, Cavazza A, Bigi F, Simón-Vázquez R. Immunostimulant and biocompatible gold and silver nanoparticles synthesized using the Ulva intestinalis L. aqueous extract. J Mater Chem B. 2019;7(30):4677–91. PMID: 31364682. DOI: 10.1039/c9tb00215d. http://www.ncbi.nlm.nih.gov/pubmed/31364682
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González-Ballesteros N, Rodríguez-Argüelles MC, Prado-López S, Lastra M, Grimaldi M, Cavazza A, Nasi L, Salviati G, Bigi F. Macroalgae to nanoparticles: Study of Ulva lactuca L. role in biosynthesis of gold and silver nanoparticles and of their cytotoxicity on colon cancer cell lines. Mater Sci Eng C Mater Biol Appl. 2019 Apr;97:498–509. PMID: 30678937. DOI: 10.1016/j.msec.2018.12.066. http://www.ncbi.nlm.nih.gov/pubmed/30678937
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Illera JC, Arenas M, López-Sánchez CA, Obeso JR, Laiolo P. Gradual Distance Dispersal Shapes the Genetic Structure in an Alpine Grasshopper. Genes (Basel). 2019;10(8) PMID: 31387238. DOI: 10.3390/genes10080590. http://www.ncbi.nlm.nih.gov/pubmed/31387238
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Lázaro S, Pérez-Crespo M, Lorz C, Bernardini A, Oteo M, Enguita AB, Romero E, Hernández P, Tomás L, Morcillo MÁ, Paramio JM, Santos M. Differential development of large-cell neuroendocrine or small-cell lung carcinoma upon inactivation of 4 tumor suppressor genes. Proc Natl Acad Sci U S A. 2019;116(44):22300–6. PMID: 31611390. DOI: 10.1073/pnas.1821745116. http://www.ncbi.nlm.nih.gov/pubmed/31611390
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Leiro V, De Chiara L, Rodríguez-Girondo M, Botana-Rial M, Valverde D, Núñez-Delgado M, Fernández-Villar A. Methylation Assessment for the Prediction of Malignancy in Mediastinal Adenopathies Obtained by Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration in Patients with Lung Cancer. Cancers (Basel). 2019 Sep;11(10):1–13. PMID: 31547177. DOI: 10.3390/cancers11101408. http://www.ncbi.nlm.nih.gov/pubmed/31547177
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López-Cortegano E, Pérez-Figueroa A, Caballero A. metapop2: Re-implementation of software for the analysis and management of subdivided populations using gene and allelic diversity. Mol Ecol Resour. 2019 Jul;19(4):1095–100. PMID: 30938911. DOI: 10.1111/1755-0998.13015. http://www.ncbi.nlm.nih.gov/pubmed/30938911
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López-Cortegano E, Pouso R, Labrador A, Pérez-Figueroa A, Fernández J, Caballero A. Optimal Management of Genetic Diversity in Subdivided Populations. Front Genet. 2019;10(September):843. PMID: 31572448. DOI: 10.3389/fgene.2019.00843. http://www.ncbi.nlm.nih.gov/pubmed/31572448
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Mann DK, Xu J, Mordvinova NE, Yannello V, Ziouani Y, González-Ballesteros N, Sousa JPS, Lebedev OI, Kolen’ko Y V., Shatruk M. Electrocatalytic water oxidation over AlFe2B2. Chem Sci. 2019 Mar;10(9):2796–804. PMID: 30997000. DOI: 10.1039/c8sc04106g. http://www.ncbi.nlm.nih.gov/pubmed/30997000
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Negredo A, Habela MÁ, Ramírez de Arellano E, Diez F, Lasala F, López P, Sarriá A, Labiod N, Calero-Bernal R, Arenas M, Tenorio A, Estrada-Peña A, Sánchez-Seco MP. Survey of Crimean-Congo Hemorrhagic Fever Enzootic Focus, Spain, 2011-2015. Emerg Infect Dis. 2019;25(6):1177–84. PMID: 31107219. DOI: 10.3201/eid2506.180877. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6537724/pdf/18-0877.pdf
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Owens-Baird B, Xu J, Petrovykh DY, Bondarchuk O, Ziouani Y, González-Ballesteros N, Yox P, Sapountzi FM, Niemantsverdriet H, Kolen’ko Y V., Kovnir K. NiP 2?: A Story of Two Divergent Polymorphic Multifunctional Materials. Chem Mater. 2019 May;31(9):3407–18. DOI: 10.1021/acs.chemmater.9b00565. https://pubs.acs.org/doi/10.1021/acs.chemmater.9b00565
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Pascual-García A, Arenas M, Bastolla U. The Molecular Clock in the Evolution of Protein Structures. Mueller R (ed.). Syst Biol. 2019 Nov;68(6):987–1002. PMID: 31111152. DOI: 10.1093/sysbio/syz022. http://www.ncbi.nlm.nih.gov/pubmed/31111152
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Pimenta J, Lopes AM, Carracedo A, Arenas M, Amorim A, Comas D. Spatially explicit analysis reveals complex human genetic gradients in the Iberian Peninsula. Sci Rep. 2019;9(1):7825. PMID: 31127131. DOI: 10.1038/s41598-019-44121-6. http://www.ncbi.nlm.nih.gov/pubmed/31127131
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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. Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution. ISME J. 2019;13(9):2150–61. PMID: 31024152. DOI: 10.1038/s41396-019-0418-8. http://www.ncbi.nlm.nih.gov/pubmed/31024152
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Sousa V, Gonçalves BF, Franco M, Ziouani Y, González-Ballesteros N, Fátima Cerqueira M, Yannello V, Kovnir K, Lebedev OI, Kolen’ko Y V. Superstructural Ordering in Hexagonal CuInSe 2 Nanoparticles. Chem Mater. 2019 Jan;31(1):260–7. DOI: 10.1021/acs.chemmater.8b04368. https://pubs.acs.org/doi/10.1021/acs.chemmater.8b04368
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Vicens A, Vinuesa P, Arenas M, Treviño CL. Analyzing the functional divergence of Slo1 and Slo3 channel subfamilies. Mol Phylogenet Evol. 2019;133:33–41. PMID: 30586650. DOI: 10.1016/j.ympev.2018.12.026. http://www.ncbi.nlm.nih.gov/pubmed/30586650
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Arenas M. Applications of the Coalescent for the Evolutionary Analysis of Genetic Data. Encyclopedia of Bioinformatics and Computational Biology. Elsevier; 2019. p. 746–58. ISBN: 9780128114322. https://linkinghub.elsevier.com/retrieve/pii/B9780128096338202604
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Bastolla U, Arenas M. The Influence of Protein Stability on Sequence Evolution: Applications to Phylogenetic Inference. In: Sikosek T (ed.). Computational Methods in Protein Evolution Methods in Molecular Biology, vol 1851. New York, NY: Humana Press; 2019. p. 215–31. ISBN: 978-1-4939-8736-8. https://doi.org/10.1007/978-1-4939-8736-8_11
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Oliveira M, Arenas M, Pinto N, Amorim A. Genética forense no humana. In: Crespillo M, Barrio P (eds.). Genética Forense Del laboratorio a los tribunales. Ediciones Díaz de Santos; 2019. p. 291–317. Depósito Legal: M-37475-2018. ISBN: 9788490522134. https://doi.org/10.5377/rcfh.v5i1.8720
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Alves JM, Posada D. Sensitivity to sequencing depth in single-cell cancer genomics. Genome Med. Genome Medicine; 2018;10(1):29. PMID: 29661213. DOI: 10.1186/s13073-018-0537-2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5901877/pdf/13073_2018_Article_537.pdf
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Arenas M, Araujo NM, Branco C, Castelhano N, Castro-Nallar E, Pérez-Losada M. Mutation and recombination in pathogen evolution: Relevance, methods and controversies. Infect Genet Evol. 2018;63:295–306. PMID: 28951202. DOI: 10.1016/j.meegid.2017.09.029. http://www.ncbi.nlm.nih.gov/pubmed/28951202
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Duchemin W, Gence G, Arigon Chifolleau A-M, 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. RecPhyloXML: a format for reconciled gene trees. Bioinformatics. 2018;34(21):3646–52. PMID: 29762653. DOI: 10.1093/bioinformatics/bty389. http://www.ncbi.nlm.nih.gov/pubmed/29762653
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Escalona M, Rocha S, Posada D. NGSphy: phylogenomic simulation of next-generation sequencing data. Bioinformatics. 2018;34(14):2506–7. PMID: 29534152. DOI: 10.1093/bioinformatics/bty146. http://www.ncbi.nlm.nih.gov/pubmed/29534152
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Jimenez MJ, Arenas M, Bastolla U. Substitution Rates Predicted by Stability-Constrained Models of Protein Evolution Are Not Consistent with Empirical Data. Mol Biol Evol. 2018 Mar;35(3):743–55. PMID: 29294047. DOI: 10.1093/molbev/msx327. http://www.ncbi.nlm.nih.gov/pubmed/29294047
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Jiménez-Santos MJ, Arenas M, Bastolla U. Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution. PeerJ. 2018;6(10):e5549. PMID: 30310736. DOI: 10.7717/peerj.5549. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6174885/pdf/peerj-06-5549.pdf
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Oliveira M, Arenas M, Amorim A. New Trends in Microbial Epidemiology?: Can An Old Dog Learn New Tricks?? Ann Microbiol Immunol. 2018;1(1):Ref. 1004. http://www.remedypublications.com/annals-of-microbiology-and-immunology/articles/pdfs_folder/ami-v1-id1004.pdf
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Pérez-Losada M, Arenas M, Castro-Nallar E. Microbial sequence typing in the genomic era. Infect Genet Evol. 2018;63:346–59. PMID: 28943406. DOI: 10.1016/j.meegid.2017.09.022. http://www.ncbi.nlm.nih.gov/pubmed/28943406
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Pousada G, Lago-Docampo M, Prado S, Varela-Calviño R, Mantiñán B, Valverde D. Functional assessment of the BMPR2 gene in lymphoblastoid cell lines from Graves’ disease patients. J Cell Mol Med. 2018 Mar;22(3):1538–47. PMID: 29266775. DOI: 10.1111/jcmm.13425. http://www.ncbi.nlm.nih.gov/pubmed/29266775
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Vicens A, Posada D. Selective Pressures on Human Cancer Genes along the Evolution of Mammals. Genes (Basel). 2018 Nov;9(12) PMID: 30487452. DOI: 10.3390/genes9120582. http://www.ncbi.nlm.nih.gov/pubmed/30487452
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Vicens A, Treviño CL. Positive Selection in the Evolution of Mammalian CRISPs. J Mol Evol. 2018;86(9):635–45. PMID: 30370448. DOI: 10.1007/s00239-018-9872-6. http://www.ncbi.nlm.nih.gov/pubmed/30370448
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Prado-López S, González-Ballesteros N, Rodríguez-Argüelles M. Nanometals in Cancer diagnosis and therapy. Biomaterials in clinical practice Advances in Clinical Research and Medical Devices. 2018. ISBN: 978-3-319-68025-5. http://www.springer.com/gp/book/9783319680248#aboutBook
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Alves JM, Prieto T, Posada D. Multiregional Tumor Trees Are Not Phylogenies. Trends in cancer. Elsevier; 2017 Aug;3(8):546–50. PMID: 28780931. DOI: 10.1016/j.trecan.2017.06.004. IF2017: 7.038; Q1. http://www.ncbi.nlm.nih.gov/pubmed/28780931
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Arenas M, Pereira F, Oliveira M, Pinto N, Lopes AM, Gomes V, Carracedo A, Amorim A. Forensic genetics and genomics: Much more than just a human affair. Crandall KA (ed.). PLOS Genet. 2017 Sep;13(9):e1006960. PMID: 28934201. DOI: 10.1371/journal.pgen.1006960. IF2017: 5.540; Q1. http://www.ncbi.nlm.nih.gov/pubmed/28934201
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Arenas M, Weber CC, Liberles DA, Bastolla U. ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability. Syst Biol. 2017 Nov;66(6):1054–64. PMID: 28057858. DOI: 10.1093/sysbio/syw121. IF2017: 8.523; D1. http://www.ncbi.nlm.nih.gov/pubmed/28057858
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Castelhano N, Araujo NM, Arenas M. Heterogeneous recombination among Hepatitis B virus genotypes. Infect Genet Evol. 2017 Oct;54:486–90. PMID: 28827173. DOI: 10.1016/j.meegid.2017.08.015. IF2017: 2.545; Q3. http://www.ncbi.nlm.nih.gov/pubmed/28827173
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González-Ballesteros N, Prado-López S, Rodríguez-González JB, Lastra M, Rodríguez-Argüelles MC. Green synthesis of gold nanoparticles using brown algae Cystoseira baccata: Its activity in colon cancer cells. Colloids Surf B Biointerfaces. 2017 May;153:190–8. PMID: 28242372. DOI: 10.1016/j.colsurfb.2017.02.020. IF2017: 3.997; Q1. http://www.ncbi.nlm.nih.gov/pubmed/28242372
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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 C-I, Schiffman JD, Hwang ES, Polyak K, Anderson ARA, Brown JS, Greaves M, Shibata D. Classifying the evolutionary and ecological features of neoplasms. Nat Rev Cancer. 2017 Oct;17(10):605–19. PMID: 28912577. DOI: 10.1038/nrc.2017.69. IF2017: 42.784; D1. http://www.ncbi.nlm.nih.gov/pubmed/28912577
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de Oliveira Martins L, Posada D. Species Tree Estimation from Genome-Wide Data with guenomu. In: Keith J (ed.). Methods in molecular biology (Clifton, NJ). New York, NY: Humana Press; 2017. p. 461–78. ISBN: 978-1-4939-6622-6. http://link.springer.com/10.1007/978-1-4939-6622-6_18
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De Oliveira Martins L, Mallo D, Posada D. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction. Syst Biol. 2016 May;65(3):397–416. PMID: 25281847. DOI: 10.1093/sysbio/syu082. IF2016: 8.917; D1. http://www.ncbi.nlm.nih.gov/pubmed/25281847
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de Oliveira Martins L, Posada D. Infinitely long branches and an informal test of common ancestry. Biol Direct. 2016 Apr;11(1):19. PMID: 27055810. DOI: 10.1186/s13062-016-0120-y. IF2016: 2.856; Q1. http://www.ncbi.nlm.nih.gov/pubmed/27055810
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Escalona M, Rocha S, Posada D. A comparison of tools for the simulation of genomic next-generation sequencing data. Nat Rev Genet. 2016 Aug;17(8):459–69. PMID: 27320129. DOI: 10.1038/nrg.2016.57. IF2016: 40.282; D1. http://www.ncbi.nlm.nih.gov/pubmed/27320129
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González-Ballesteros N, Pérez-Álvarez D, Rodríguez-Argüelles MC, Henriques MSC, Paixão JA, Prado-López S. Synthesis, spectral characterization and X-ray crystallographic study of new copper(I) complexes. Antitumor activity in colon cancer. Polyhedron. 2016 Nov;119:112–9. DOI: 10.1016/j.poly.2016.08.023. IF2016: 1.926; Q2. http://linkinghub.elsevier.com/retrieve/pii/S0277538716303825
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Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J, Ribeiro JM, Megy K, Thimmapuram J, Miller JR, Walenz BP, Koren S, Hostetler JB, Thiagarajan M, Joardar VS, Hannick LI, Bidwell S, Hammond MP, Young S, Zeng Q, Abrudan JL, Almeida FC, Ayllón N, Bhide K, Bissinger BW, Bonzon-Kulichenko E, Buckingham SD, Caffrey DR, Caimano MJ, Croset V, Driscoll T, Gilbert D, Gillespie JJ, Giraldo-Calderón GI, Grabowski JM, Jiang D, Khalil SMS, Kim D, Kocan KM, Ko?i J, Kuhn RJ, Kurtti TJ, Lees K, Lang EG, Kennedy RC, Kwon H, Perera R, Qi Y, Radolf JD, Sakamoto JM, Sánchez-Gracia A, Severo MS, Silverman N, Šimo L, Tojo M, Tornador C, Van Zee JP, Vázquez J, Vieira FG, Villar M, Wespiser AR, Yang Y, Zhu J, Arensburger P, Pietrantonio P V, Barker SC, Shao R, Zdobnov EM, Hauser F, Grimmelikhuijzen CJP, Park Y, Rozas J, Benton R, Pedra JHF, Nelson DR, Unger MF, Tubio JM, Tu Z, Robertson HM, Shumway M, Sutton G, Wortman JR, Lawson D, Wikel SK, Nene VM, Fraser CM, Collins FH, Birren B, N
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Mallo D, De Oliveira Martins L, Posada D. SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees. Syst Biol. 2016 Mar;65(2):334–44. PMID: 26526427. DOI: 10.1093/sysbio/syv082. IF2016: 8.917; D1. http://www.ncbi.nlm.nih.gov/pubmed/26526427
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Mallo D, Posada D. Multilocus inference of species trees and DNA barcoding. Philos Trans R Soc Lond B Biol Sci. 2016 Sep;371(1702):20150335. PMID: 27481787. DOI: 10.1098/rstb.2015.0335. IF2016: 5.846; D1. http://www.ncbi.nlm.nih.gov/pubmed/27481787
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Murgarella M, Puiu D, Novoa B, Figueras A, Posada D, Canchaya C. A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis. Craft JA (ed.). PLoS One. 2016 Mar;11(3):e0151561. PMID: 26977809. DOI: 10.1371/journal.pone.0151561. IF2016: 2.806; Q1. http://www.ncbi.nlm.nih.gov/pubmed/26977809
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Posada D. Phylogenomics for Systematic Biology. Syst Biol. 2016 May;65(3):353–6. PMID: 27129844. DOI: 10.1093/sysbio/syw027. IF2016: 8.917; D1. http://www.ncbi.nlm.nih.gov/pubmed/27129844
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Prieto T, Alves JM, Posada D. NGS Analysis of Somatic Mutations in Cancer Genomes. In: Wong K-C (ed.). Big Data Analytics in Genomics. Springer International Publishing; 2016. p. 357–72. ISBN: 978-3-319-41279-5. http://link.springer.com/10.1007/978-3-319-41279-5_11
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Arenas M, Lopes JS, Beaumont MA, Posada D. CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation. Mol Biol Evol. Oxford University Press; 2015 Apr;32(4):1109–12. PMID: 25577191. DOI: 10.1093/molbev/msu411. IF2015: 13.649; D1. http://www.ncbi.nlm.nih.gov/pubmed/25577191
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Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JMC, Papaemmanuil E, Brewer DS, Kallio HML, Högnäs G, Annala M, Kivinummi K, Goody V, Latimer C, O’Meara S, Dawson KJ, Isaacs W, Emmert-Buck MR, Nykter M, Foster C, Kote-Jarai Z, Easton D, Whitaker HC, ICGC Prostate Group, Neal DE, Cooper CS, Eeles RA, Visakorpi T, Campbell PJ, McDermott U, Wedge DC, Bova GS, ICGC Prostate UK Grp. The evolutionary history of lethal metastatic prostate cancer. Nature. 2015 Apr;520(7547):353–7. PMID: 25830880. DOI: 10.1038/nature14347. IF2015: 38.138; D1. http://www.ncbi.nlm.nih.gov/pubmed/25830880
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Ju YS, Tubio JMC, Mifsud W, Fu B, Davies HR, Ramakrishna M, Li Y, Yates L, Gundem G, Tarpey PS, Behjati S, Papaemmanuil E, Martin S, Fullam A, Gerstung M, ICGC Prostate Cancer Working Group, ICGC Bone Cancer Working Group, ICGC Breast Cancer Working Group, Nangalia J, Green AR, Caldas C, Borg Å, Tutt A, Lee MTM, van’t Veer LJ, Tan BKT, Aparicio S, Span PN, Martens JWM, Knappskog S, Vincent-Salomon A, Børresen-Dale A-L, Eyfjörd JE, Myklebost O, Flanagan AM, Foster C, Neal DE, Cooper C, Eeles R, Bova SG, Lakhani SR, Desmedt C, Thomas G, Richardson AL, Purdie CA, Thompson AM, McDermott U, Yang F, Nik-Zainal S, Campbell PJ, Stratton MR, Grp IPCW, Grp IBCW, Grp IBCW. Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells. Genome Res. 2015 Jun;25(6):814–24. PMID: 25963125. DOI: 10.1101/gr.190470.115. IF2015: 11.351; D1. http://www.ncbi.nlm.nih.gov/pubmed/25963125
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Martincorena I, Roshan A, Gerstung M, Ellis P, Van Loo P, McLaren S, Wedge DC, Fullam A, Alexandrov LB, Tubio JM, Stebbings L, Menzies A, Widaa S, Stratton MR, Jones PH, Campbell PJ. Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin. Science. 2015 May;348(6237):880–6. PMID: 25999502. DOI: 10.1126/science.aaa6806. IF2015: 34.661; D1. http://www.ncbi.nlm.nih.gov/pubmed/25999502
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Moreira R, Pereiro P, Canchaya C, Posada D, Figueras A, Novoa B. RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues. BMC Genomics. BioMed Central Ltd.; 2015 Sep;16(1):728. PMID: 26400066. DOI: 10.1186/s12864-015-1817-5. IF2015: 3.86; Q1. http://www.ncbi.nlm.nih.gov/pubmed/26400066
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Posada D. Cancer Molecular Evolution. J Mol Evol. Springer New York LLC; 2015 Oct;81(3–4):81–3. PMID: 26289731. DOI: 10.1007/s00239-015-9695-7. IF2015: 1.847; Q3. http://www.ncbi.nlm.nih.gov/pubmed/26289731
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Tubio JMC. Somatic structural variation and cancer. Brief Funct Genomics. 2015 Sep;14(5):339–51. PMID: 25903743. DOI: 10.1093/bfgp/elv016. IF2015: 3.124; Q2. http://www.ncbi.nlm.nih.gov/pubmed/25903743
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Buhay JE, Crandall KA, Posada D. Nested clade phylogeographic analysis for conservation genetics. In: Bertorelle G, Bruford MW, Hauffe HC, Rizzoli A, Vernesi C (eds.). Population Genetics for Animal Conservation. Cambridge: Cambridge University Press; 2015. p. 80–103. (online publication). ISBN: 9780511626920. http://ebooks.cambridge.org/ref/id/CBO9780511626920
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Arenas M, Posada D. Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories. Mol Biol Evol. Oxford University Press; 2014 May;31(5):1295–301. PMID: 24557445. DOI: 10.1093/molbev/msu078. IF2014: 9.105; Q1. http://www.ncbi.nlm.nih.gov/pubmed/24557445
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Bolli N, Avet-Loiseau H, Wedge DC, Van Loo P, Alexandrov LB, Martincorena I, Dawson KJ, Iorio F, Nik-Zainal S, Bignell GR, Hinton JW, Li Y, Tubio JMC, McLaren S, O’ Meara S, Butler AP, Teague JW, Mudie L, Anderson E, Rashid N, Tai Y-T, Shammas MA, Sperling AS, Fulciniti M, Richardson PG, Parmigiani G, Magrangeas F, Minvielle S, Moreau P, Attal M, Facon T, Futreal PA, Anderson KC, Campbell PJ, Munshi NC. Heterogeneity of genomic evolution and mutational profiles in multiple myeloma. Nat Commun. 2014 Jan;5:2997. PMID: 24429703. DOI: 10.1038/ncomms3997. IF2014: 11.470; D1. http://www.ncbi.nlm.nih.gov/pubmed/24429703
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Cooke SL, Shlien A, Marshall J, Pipinikas CP, Martincorena I, Tubio JMC, Li Y, Menzies A, Mudie L, Ramakrishna M, Yates L, Davies H, Bolli N, Bignell GR, Tarpey PS, Behjati S, Nik-Zainal S, Papaemmanuil E, Teixeira VH, Raine K, O’Meara S, Dodoran MS, Teague JW, Butler AP, Iacobuzio-Donahue C, Santarius T, Grundy RG, Malkin D, Greaves M, Munshi N, Flanagan AM, Bowtell D, Martin S, Larsimont D, Reis-Filho JS, Boussioutas A, Taylor JA, Hayes ND, Janes SM, Futreal PA, Stratton MR, McDermott U, Campbell PJ, ICGC Breast Cancer Group. Processed pseudogenes acquired somatically during cancer development. Nat Commun. 2014 Apr;5:3644. PMID: 24714652. DOI: 10.1038/ncomms4644. IF2014: 11.470; D1. http://www.ncbi.nlm.nih.gov/pubmed/24714652
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Darriba D, Taboada GL, Doallo R, Posada D. High-performance computing selection of models of DNA substitution for multicore clusters. Int J High Perform Comput Appl. 2014 Feb;28(1):112–25. DOI: 10.1177/1094342013495095. IF2014: 1.477; Q2. http://hpc.sagepub.com/cgi/doi/10.1177/1094342013495095
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de Oliveira Martins L, Posada D. Testing for universal common ancestry. Syst Biol. Oxford University Press; 2014 Sep;63(5):838–42. PMID: 24958930. DOI: 10.1093/sysbio/syu041. IF2014: 14.387; Q1. http://www.ncbi.nlm.nih.gov/pubmed/24958930
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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. HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations. Science. American Association for the Advancement of Science; 2014 Oct;346(6205):56–61. PMID: 25278604. DOI: 10.1126/science.1256739. IF2014: 33.611; Q1. http://www.ncbi.nlm.nih.gov/pubmed/25278604
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Fonseca MM, Harris DJ, Posada D. Origin and length distribution of unidirectional prokaryotic overlapping genes. G3 (Bethesda). Genetics Society of America; 2014 Jan;4(1):19–27. PMID: 24192837. DOI: 10.1534/g3.113.005652. IF2014: 2.511; Q3. http://www.ncbi.nlm.nih.gov/pubmed/24192837
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Fonseca MM, Harris DJ, Posada D. The inversion of the Control Region in three mitogenomes provides further evidence for an asymmetric model of vertebrate mtDNA replication. PLoS One. Public Library of Science; 2014 Sep;9(9):e106654. PMID: 25268704. DOI: 10.1371/journal.pone.0106654. IF2014: 3.234; Q1. http://www.ncbi.nlm.nih.gov/pubmed/25268704
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Forn-Cuní G, Reis ES, Dios S, Posada D, Lambris JD, Figueras A, Novoa B. The evolution and appearance of C3 duplications in fish originate an exclusive teleost c3 gene form with anti-inflammatory activity. PLoS One. Public Library of Science; 2014 Jun;9(6):e99673. PMID: 24926798. DOI: 10.1371/journal.pone.0099673. IF2014: 3.234; Q1. http://www.ncbi.nlm.nih.gov/pubmed/24926798
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Lopes JS, Arenas M, Posada D, Beaumont MA. Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation. Heredity (Edinb). 2014 Mar;112(3):255–64. PMID: 24149652. DOI: 10.1038/hdy.2013.101. IF2014: 3.805; Q2. http://www.ncbi.nlm.nih.gov/pubmed/24149652
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Mallo D, De Oliveira Martins L, Posada D. Unsorted homology within locus and species trees. Syst Biol. Oxford University Press; 2014 Nov;63(6):988–92. PMID: 25077514. DOI: 10.1093/sysbio/syu050. IF2014: 14.387; Q1. http://www.ncbi.nlm.nih.gov/pubmed/25077514
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Murchison EP, Wedge DC, Alexandrov LB, Fu B, Martincorena I, Ning Z, Tubio JMC, Werner EI, Allen J, De Nardi AB, Donelan EM, Marino G, Fassati A, Campbell PJ, Yang F, Burt A, Weiss RA, Stratton MR. Transmissible [corrected] dog cancer genome reveals the origin and history of an ancient cell lineage. Science. 2014 Jan;343(6169):437–40. PMID: 24458646. DOI: 10.1126/science.1247167. IF2014: 33.611; D1. http://www.ncbi.nlm.nih.gov/pubmed/24458646
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Papaemmanuil E, Rapado I, Li Y, Potter NE, Wedge DC, Tubio J, Alexandrov LB, Van Loo P, Cooke SL, Marshall J, Martincorena I, Hinton J, Gundem G, van Delft FW, Nik-Zainal S, Jones DR, Ramakrishna M, Titley I, Stebbings L, Leroy C, Menzies A, Gamble J, Robinson B, Mudie L, Raine K, O’Meara S, Teague JW, Butler AP, Cazzaniga G, Biondi A, Zuna J, Kempski H, Muschen M, Ford AM, Stratton MR, Greaves M, Campbell PJ. RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia. Nat Genet. 2014 Feb;46(2):116–25. PMID: 24413735. DOI: 10.1038/ng.2874. IF2014: 29.352; D1. http://www.ncbi.nlm.nih.gov/pubmed/24413735
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Prado-Lòpez S, Duffy MM, Baustian C, Alagesan S, Hanley SA, Stocca A, Griffin MD, Ceredig R. The influence of hypoxia on the differentiation capacities and immunosuppressive properties of clonal mouse mesenchymal stromal cell lines. Immunol Cell Biol. 2014 Aug;92(7):612–23. PMID: 24777310. DOI: 10.1038/icb.2014.30. IF2014: 4.147; Q1. http://www.ncbi.nlm.nih.gov/pubmed/24777310
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Santorum JM, Darriba D, Taboada GL, Posada D. jmodeltest.org: selection of nucleotide substitution models on the cloud. Bioinformatics. Oxford University Press; 2014 May;30(9):1310–1. PMID: 24451621. DOI: 10.1093/bioinformatics/btu032. IF2014: 4.981; Q1. http://www.ncbi.nlm.nih.gov/pubmed/24451621
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Arenas M, Posada D. The Influence of Recombination on the Estimation of Selection from Coding Sequence Alignments. In: Fares MA (ed.). Natural Selection: Methods and Applications. CRC Press; 2014. p. 112–25. DOI: 10.1201/b17795-7. ISBN: 978-1-4822-6372-5. http://www.crcnetbase.com/doi/abs/10.1201/b17795-7
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Mallo D, de Oliveira Martins L, Posada D. Estimation of Species Trees. Encyclopedia of Life Sciences 2014. Chichester, UK: John Wiley & Sons, Ltd; 2014. DOI: 10.1002/9780470015902.a0025781. http://doi.wiley.com/10.1002/9780470015902.a0025781
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