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Items: 1 to 50 of 59

1.

Transcriptomics data of 11 species of yeast identically grown in rich media and oxidative stress conditions.

Blevins WR, Carey LB, Albà MM.

BMC Res Notes. 2019 May 3;12(1):250. doi: 10.1186/s13104-019-4286-0.

2.

Translation of Small Open Reading Frames: Roles in Regulation and Evolutionary Innovation.

Ruiz-Orera J, Albà MM.

Trends Genet. 2019 Mar;35(3):186-198. doi: 10.1016/j.tig.2018.12.003. Epub 2018 Dec 31. Review.

PMID:
30606460
3.

Identification, characterization and application of a new peptide against anterior gradient homolog 2 (AGR2).

Garri C, Howell S, Tiemann K, Tiffany A, Jalali-Yazdi F, Alba MM, Katz JE, Takahashi TT, Landgraf R, Gross ME, Roberts RW, Kani K.

Oncotarget. 2018 Jun 8;9(44):27363-27379. doi: 10.18632/oncotarget.25221. eCollection 2018 Jun 8.

4.

Translation of neutrally evolving peptides provides a basis for de novo gene evolution.

Ruiz-Orera J, Verdaguer-Grau P, Villanueva-Cañas JL, Messeguer X, Albà MM.

Nat Ecol Evol. 2018 May;2(5):890-896. doi: 10.1038/s41559-018-0506-6. Epub 2018 Mar 19.

PMID:
29556078
5.

Transcriptomics in the wild: Hibernation physiology in free-ranging dwarf lemurs.

Faherty SL, Villanueva-Cañas JL, Blanco MB, Albà MM, Yoder AD.

Mol Ecol. 2018 Feb;27(3):709-722. doi: 10.1111/mec.14483. Epub 2018 Jan 29.

PMID:
29319912
6.

Zinc-finger domains in metazoans: evolution gone wild.

Albà MM.

Genome Biol. 2017 Sep 6;18(1):168. doi: 10.1186/s13059-017-1307-y. No abstract available.

7.

New Genes and Functional Innovation in Mammals.

Luis Villanueva-Cañas J, Ruiz-Orera J, Agea MI, Gallo M, Andreu D, Albà MM.

Genome Biol Evol. 2017 Jul 1;9(7):1886-1900. doi: 10.1093/gbe/evx136.

8.

No Evidence for Phylostratigraphic Bias Impacting Inferences on Patterns of Gene Emergence and Evolution.

Domazet-Lošo T, Carvunis AR, Albà MM, Šestak MS, Bakaric R, Neme R, Tautz D.

Mol Biol Evol. 2017 Apr 1;34(4):843-856. doi: 10.1093/molbev/msw284.

9.

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.

Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A, Marcet-Houben M, Martínez-Cruz B, Cheng JY, Prieto P, Quesada V, Quilez J, Li G, García F, Rubio-Camarillo M, Frias L, Ribeca P, Capella-Gutiérrez S, Rodríguez JM, Câmara F, Lowy E, Cozzuto L, Erb I, Tress ML, Rodriguez-Ales JL, Ruiz-Orera J, Reverter F, Casas-Marce M, Soriano L, Arango JR, Derdak S, Galán B, Blanc J, Gut M, Lorente-Galdos B, Andrés-Nieto M, López-Otín C, Valencia A, Gut I, García JL, Guigó R, Murphy WJ, Ruiz-Herrera A, Marques-Bonet T, Roma G, Notredame C, Mailund T, Albà MM, Gabaldón T, Alioto T, Godoy JA.

Genome Biol. 2016 Dec 14;17(1):251.

10.

Gene Expression Profiling in the Hibernating Primate, Cheirogaleus Medius.

Faherty SL, Villanueva-Cañas JL, Klopfer PH, Albà MM, Yoder AD.

Genome Biol Evol. 2016 Aug 25;8(8):2413-26. doi: 10.1093/gbe/evw163.

11.

Origins of De Novo Genes in Human and Chimpanzee.

Ruiz-Orera J, Hernandez-Rodriguez J, Chiva C, Sabidó E, Kondova I, Bontrop R, Marqués-Bonet T, Albà MM.

PLoS Genet. 2015 Dec 31;11(12):e1005721. doi: 10.1371/journal.pgen.1005721. eCollection 2015 Dec.

12.

High evolutionary turnover of satellite families in Caenorhabditis.

Subirana JA, Albà MM, Messeguer X.

BMC Evol Biol. 2015 Oct 5;15:218. doi: 10.1186/s12862-015-0495-x.

13.

Tobacco and end stage renal disease: a multicenter, cross-sectional study in Argentinian Northern Patagonia.

Alba MM, Citarelli AN, Menni F, Agricola M, Braicovich A, De Horta E, De Rosa F, Filanino G, Gaggiotti R, Junqueras N, Martinelli S, Milan A, Morales ME, Setti S, Villalba DO.

Tob Induc Dis. 2015 Sep 1;13(1):28. doi: 10.1186/s12971-015-0051-x. eCollection 2015.

14.

Gut Microbiota Dynamics during Dietary Shift in Eastern African Cichlid Fishes.

Baldo L, Riera JL, Tooming-Klunderud A, Albà MM, Salzburger W.

PLoS One. 2015 May 15;10(5):e0127462. doi: 10.1371/journal.pone.0127462. eCollection 2015.

15.

Key Role of Amino Acid Repeat Expansions in the Functional Diversification of Duplicated Transcription Factors.

Radó-Trilla N, Arató K, Pegueroles C, Raya A, de la Luna S, Albà MM.

Mol Biol Evol. 2015 Sep;32(9):2263-72. doi: 10.1093/molbev/msv103. Epub 2015 Apr 29.

16.

Long non-coding RNAs as a source of new peptides.

Ruiz-Orera J, Messeguer X, Subirana JA, Alba MM.

Elife. 2014 Sep 16;3:e03523. doi: 10.7554/eLife.03523.

17.

Uncovering adaptive evolution in the human lineage.

Gayà-Vidal M, Albà MM.

BMC Genomics. 2014 Jul 16;15:599. doi: 10.1186/1471-2164-15-599.

18.

Comparative genomics of mammalian hibernators using gene networks.

Villanueva-Cañas JL, Faherty SL, Yoder AD, Albà MM.

Integr Comp Biol. 2014 Sep;54(3):452-62. doi: 10.1093/icb/icu048. Epub 2014 May 31.

PMID:
24881044
19.

Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis.

Trilling M, Bellora N, Rutkowski AJ, de Graaf M, Dickinson P, Robertson K, Prazeres da Costa O, Ghazal P, Friedel CC, Albà MM, Dölken L.

Nucleic Acids Res. 2013 Sep;41(17):8107-25. doi: 10.1093/nar/gkt589. Epub 2013 Jul 5.

20.

Accelerated evolution after gene duplication: a time-dependent process affecting just one copy.

Pegueroles C, Laurie S, Albà MM.

Mol Biol Evol. 2013 Aug;30(8):1830-42. doi: 10.1093/molbev/mst083. Epub 2013 Apr 26.

PMID:
23625888
21.

Dynamics and adaptive benefits of modular protein evolution.

Bornberg-Bauer E, Albà MM.

Curr Opin Struct Biol. 2013 Jun;23(3):459-66. doi: 10.1016/j.sbi.2013.02.012. Epub 2013 Apr 3. Review.

PMID:
23562500
22.

Emergence of novel domains in proteins.

Toll-Riera M, Albà MM.

BMC Evol Biol. 2013 Feb 20;13:47. doi: 10.1186/1471-2148-13-47.

23.

Improving genome-wide scans of positive selection by using protein isoforms of similar length.

Villanueva-Cañas JL, Laurie S, Albà MM.

Genome Biol Evol. 2013;5(2):457-67. doi: 10.1093/gbe/evt017.

24.

Structure and age jointly influence rates of protein evolution.

Toll-Riera M, Bostick D, Albà MM, Plotkin JB.

PLoS Comput Biol. 2012 May;8(5):e1002542. doi: 10.1371/journal.pcbi.1002542. Epub 2012 May 31.

25.

The human cytomegalovirus-specific UL1 gene encodes a late-phase glycoprotein incorporated in the virion envelope.

Shikhagaie M, Mercé-Maldonado E, Isern E, Muntasell A, Albà MM, López-Botet M, Hengel H, Angulo A.

J Virol. 2012 Apr;86(8):4091-101. doi: 10.1128/JVI.06291-11. Epub 2012 Feb 15.

26.

Sequence shortening in the rodent ancestor.

Laurie S, Toll-Riera M, Radó-Trilla N, Albà MM.

Genome Res. 2012 Mar;22(3):478-85. doi: 10.1101/gr.121897.111. Epub 2011 Nov 29.

27.

Role of low-complexity sequences in the formation of novel protein coding sequences.

Toll-Riera M, Radó-Trilla N, Martys F, Albà MM.

Mol Biol Evol. 2012 Mar;29(3):883-6. doi: 10.1093/molbev/msr263. Epub 2011 Oct 31.

PMID:
22045997
28.

Human cytomegalovirus UL7, a homologue of the SLAM-family receptor CD229, impairs cytokine production.

Engel P, Pérez-Carmona N, Albà MM, Robertson K, Ghazal P, Angulo A.

Immunol Cell Biol. 2011 Oct;89(7):753-66. doi: 10.1038/icb.2011.55. Epub 2011 Jun 14.

PMID:
21670740
29.

Lineage-specific variation in intensity of natural selection in mammals.

Toll-Riera M, Laurie S, Albà MM.

Mol Biol Evol. 2011 Jan;28(1):383-98. doi: 10.1093/molbev/msq206. Epub 2010 Aug 5.

PMID:
20688808
30.

Natural selection drives the accumulation of amino acid tandem repeats in human proteins.

Mularoni L, Ledda A, Toll-Riera M, Albà MM.

Genome Res. 2010 Jun;20(6):745-54. doi: 10.1101/gr.101261.109. Epub 2010 Mar 24.

31.

Heterogeneous patterns of gene-expression diversification in mammalian gene duplicates.

Farré D, Albà MM.

Mol Biol Evol. 2010 Feb;27(2):325-35. doi: 10.1093/molbev/msp242. Epub 2009 Oct 12.

PMID:
19822635
32.

Evolution of primate orphan proteins.

Toll-Riera M, Castelo R, Bellora N, Albà MM.

Biochem Soc Trans. 2009 Aug;37(Pt 4):778-82. doi: 10.1042/BST0370778. Review.

PMID:
19614593
33.

Jagged1 is the pathological link between Wnt and Notch pathways in colorectal cancer.

Rodilla V, Villanueva A, Obrador-Hevia A, Robert-Moreno A, Fernández-Majada V, Grilli A, López-Bigas N, Bellora N, Albà MM, Torres F, Duñach M, Sanjuan X, Gonzalez S, Gridley T, Capella G, Bigas A, Espinosa L.

Proc Natl Acad Sci U S A. 2009 Apr 14;106(15):6315-20. doi: 10.1073/pnas.0813221106. Epub 2009 Mar 26.

34.

Genome-wide analysis of histidine repeats reveals their role in the localization of human proteins to the nuclear speckles compartment.

Salichs E, Ledda A, Mularoni L, Albà MM, de la Luna S.

PLoS Genet. 2009 Mar;5(3):e1000397. doi: 10.1371/journal.pgen.1000397. Epub 2009 Mar 6.

35.

Origin of primate orphan genes: a comparative genomics approach.

Toll-Riera M, Bosch N, Bellora N, Castelo R, Armengol L, Estivill X, Albà MM.

Mol Biol Evol. 2009 Mar;26(3):603-12. doi: 10.1093/molbev/msn281. Epub 2008 Dec 8.

PMID:
19064677
36.

Amino acid repeats and the structure and evolution of proteins.

Albà MM, Tompa P, Veitia RA.

Genome Dyn. 2007;3:119-30. doi: 10.1159/000107607. Review.

PMID:
18753788
37.
38.

Housekeeping genes tend to show reduced upstream sequence conservation.

Farré D, Bellora N, Mularoni L, Messeguer X, Albà MM.

Genome Biol. 2007;8(7):R140.

39.
40.

Highly constrained proteins contain an unexpectedly large number of amino acid tandem repeats.

Mularoni L, Veitia RA, Albà MM.

Genomics. 2007 Mar;89(3):316-25. Epub 2006 Dec 28.

41.
42.

Mutation patterns of amino acid tandem repeats in the human proteome.

Mularoni L, Guigó R, Albà MM.

Genome Biol. 2006;7(4):R33. Epub 2006 Apr 26.

43.

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

Blanco E, Farré D, Albà MM, Messeguer X, Guigó R.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D63-7.

44.

Inverse relationship between evolutionary rate and age of mammalian genes.

Albà MM, Castresana J.

Mol Biol Evol. 2005 Mar;22(3):598-606. Epub 2004 Nov 10. Erratum in: Mol Biol Evol. 2005 Apr;22(4):1159.

PMID:
15537804
45.
46.

Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes.

Huang H, Winter EE, Wang H, Weinstock KG, Xing H, Goodstadt L, Stenson PD, Cooper DN, Smith D, Albà MM, Ponting CP, Fechtel K.

Genome Biol. 2004;5(7):R47. Epub 2004 Jun 28.

47.
48.

Virus bioinformatics: databases and recent applications.

Kellam P, Albà MM.

Appl Bioinformatics. 2002;1(1):37-42. Review.

PMID:
15130855
49.

Comparative analysis of amino acid repeats in rodents and humans.

Albà MM, Guigó R.

Genome Res. 2004 Apr;14(4):549-54.

50.

Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN.

Farré D, Roset R, Huerta M, Adsuara JE, Roselló L, Albà MM, Messeguer X.

Nucleic Acids Res. 2003 Jul 1;31(13):3651-3.

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