Datasets

  • Mularoni, L., Veitia, R.A., Albà, M.M. (2007). Highly constrained proteins contain an unexpectedly large number of amino acid tandem repeats. Genomics 89:316-325.

    Supplementary files: Mularoni_etal.xls

  • Farre, D., Bellora, N., Mularoni, L., Messeguer, X., Albà, M.M. (2007). Housekeeping genes tend to show reduced upstream sequence conservation. Genome Biology, 8:R140.

    Supplementary file 1: Supplementary tables
    Supplementary file 2: Supplementary figures
    Supplementary file 3: Orthologous pairs (RefSeq IDs) with sequence divergence and expression classification [595KB]
    Supplementary file 4: Human 2kb upstream sequences (FASTA) [14.1MB]
    Supplementary file 5: Mouse 2kb upstream sequences (FASTA) [14.1MB]

  • Toll-Riera, M., Bosch, N., Bellora, N., Castelo, R., Armengol,Ll., Estivill, X., Albà, M.M. (2009). Origin of primate orphan genes: a comparative genomics approach. Molecular Biology and Evolution, 26:603-612.

    Supplementary file 1: Supplementary file 1
    Supplementary file 2: Supplementary file 2

  • Farre, D., Albà, M.M. (2010). Heterogeneous patterns of gene expression diversification in mammalian gene duplicates. Molecular Biology and Evolution, 27:325-335.

    Supplementary file 1: Supplementary file 1
    Supplementary file 2: Supplementary file 2

  • Mularoni, L., Ledda, A., Toll-Riera, M., Albà, M.M. (2010) Natural selection drives the accumulation of amino acid tandem repeats in human proteins. Genome Research, 20: 745-754

    Supplementary file 1: Supplementary file 1
    Supplementary file 2: Supplementary file 2
    Supplementary file 3: Supplementary file 3

  • Toll-Riera, M., Laurie, S., Albà, M.M. (2011) Lineage-specific Variation in Intensity of Natural Selection in Mammals. Molecular Biology and Evolution, 28: 383-398

    Supplementary file 1: Supplementary file 1 (data in excel format)
    Supplementary file 2: Supplementary file 2 (data in excel format)
    Supplementary file 3: Supplementary file 3 (data in excel format)
    Supplementary file 4: Supplementary S1-S9 (doc file)

  • Laurie, S., Toll-Riera, M., Radó-Trilla, N., Albà, M.M. (2012) Sequence shortening in the rodent ancestor. Genome research, 22: 478-85
    Supplementary file 1: README file
    Supplementary file 2: coding insertions
    Supplementary file 3: coding deletions
    Supplementary file 4: compressed Prank+F alignments

  • Toll-Riera, M., Radó-Trilla, N., Martys, F., Albà, M.M. (2012) Role of low-complexity sequences in the formation of novel protein coding sequences. Mol Biol Evol. 2012 Mar;29(3):883-6.
    Supplementary file 1: supplementary file 1 (excel file)
    Supplementary file 2: supplementary file 2 (pdf)

  • Radó-Trilla, N., Albà, M.M. (2012) Dissecting the role of low-complexity regions in the evolution of vertebrate proteins. BMC Evol. Biol., Aug 24;12:155.
    Supplementary file 1: sup1 (excel file)
    Supplementary file 2: sup2 (pdf)

  • Villanueva-Cañas, J.L., Laurie, S., Albà, M.M. (2013) Improving genome-wide scans of positive selection by using protein isoforms of similar length.Genome Biol Evol. 2013 Jan;5(2):457-67
    Supplementary file 1: sup1 (excel file)
    Supplementary file 2: sup2 (pdf)

  • Toll-Riera, M., Albà, M.M. (2013) Emergence of novel domains in proteins. BMC Evol. Biol., 20;13(1):47.
    Supplementary file 1: sup1 (excel file)
    Supplementary file 2: sup2 (pdf)
    Supplementary file 3: sup3 (excel file)

  • Pegueroles, C., Laurie, S., Albà, M.M. (2013) Accelerated Evolution after Gene Duplication: A Time-Dependent Process Affecting Just One Copy. Mol Biol Evol., Aug; 30: 1830-1842.
    Supplementary file 1: sup (excel file)

  • Villanueva-Cañas, J.L., Faherty, S.L., Yoder, A.D., Albà, M.M. (2014) A network level approach into mammalian hibernation identifies key common molecular pathways in diverse species. Integr. Comp. Biol. 54:452-462.
    Excel supplementary file: suppl
    cytoscape files: Cytoscape networks (.cys)

  • Ruiz-Orera, J., Messeguer, X., Subirana, J.A., Albà, M.M. (2014). Long non-coding RNAs as a source of new peptides. arXiv preprint arXiv:1405.4174
    Supplementary file 1 (suppl results): pdf
    Supplementary file 2 (datasets): xls

  • Ruiz-Orera, J., Messeguer, X., Subirana, J.A., Albà, M.M. (2014). Long non-coding RNAs as a source of new peptides. eLife, 16 Sep, e03523.
    Supplementary data file 1: docx
    Supplementary data file 2: xls
    Transcript genomic coordinates (GTF files) and sequences with significant coding scores at p<0.05 (FASTA files) at figshare

  • Radó-Trilla, N., Arató, K., Pegueroles, C., Raya, A., de la Luna, S., Albà, M.M. (2015). Key role of amino acid repeat expansions in the functional diversification of duplicated transcription factors. bioRxiv.
    Supplementary file: xls file.
    Supplementary file: xlsx file(old).

  • Ruiz-Orera, J.,Hernandez-Rodriguez, J.,Chiva, C., Sabidó, E., Kondova, I., Bontrop, R., Marqués-Bonet, M., Albà, M.M. (2015). Origins of de novo genes in human and chimpanzee.
    supplementary file 1:Ruiz-Orera_sup1.pdf.
    supplementary file 2:Ruiz-Orera_sup2.xls.
    gene annotation file (gtf) de novo genes in human:hsa_denovo.gtf.
    gene annotation file (gtf) de novo genes in chimpanzee: ptr_denovo.gtf.