Publications

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2013
Gabaldón T, Koonin EV.  2013.  Functional and evolutionary implications of gene orthology.. Nat. Rev. Genet.. 14:360–366. Abstract
application/pdf iconGabaldon_Koonin_orthology_persp_NRG_2013.pdf
Bava FA, Eliscovich C, Ferreira PG, Miñana B, Ben-Dov C, Guigó R, Valcárcel J, Méndez R.  2013.  CPEB1 coordinates alternative 3'-UTR formation with translational regulation. Nature. 495:121–125. Abstract
Collén J, Porcel B, Carré W, Ball SG, Chaparro C, Tonon T, Barbeyron T, Michel G, Noel B, Valentin K et al..  2013.  Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida.. Proc. Natl. Acad. Sci. U.S.A.. 110:5247–5252. Abstract
application/pdf iconChondrus_genome_PNAS-2013_1221259110.pdf
Lavín JL, Marcet-Houben M, Gutiérrez-Vázquez RL, Ramírez L, Pisabarro AG, Gabaldón T, Oguiza JA.  2013.  FUNGALOXPHOS: An integrated database for oxidative phosphorylation in fungi.. Mitochondrion. 13:357–359. Abstract
application/pdf iconLavin_FUNGALOXPHOS_Mitochondrion_2013.pdf
Knowles D, Röder M, Merkel A, Guigó R.  2013.  Grape RNA-Seq analysis pipeline environment. Bioinformatics. 10.1093/bioinformatics/btt016 Abstract
Ferreira PG, Patalano S, Chauhan R, Ffrench-Constant R, Gabaldon T, Guigo R, Sumner S.  2013.  Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes. Genome Biol. 14:R20. Abstract
Ferreira PG, Patalano S, Chauhan R, Ffrench-Constant R, Gabaldón T, Guigó R, Sumner S.  2013.  Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes.. Genome Biol.. 14:R20. Abstract
application/pdf iconFerreira_WAspTRanscript_provisional_GEnomeBiology.pdf
Capella-Gutiérrez S, Gabaldón T.  2013.  Measuring guide-tree dependency of inferred gaps in progressive aligners.. Bioinformatics. 29:1011–1017. Abstract
application/pdf iconCapella_Gabaldon_GAPS_bioinformatics_2013.pdf
Mohd-Padil H, Mohd-Adnan A, Gabaldón T.  2013.  Phylogenetic analyses uncover a novel clade of transferrin in nonmammalian vertebrates.. Mol. Biol. Evol.. 30:894–905. Abstract
application/pdf iconMohdPadil_Transferrin_VErtebrates_MBE_2013.pdf
Jiménez-Guri E, Huerta-Cepas J, Cozzuto L, Wotton KR, Kang H, Himmelbauer H, Roma G, Gabaldón T, Jaeger J.  2013.  Comparative transcriptomics of early dipteran development.. BMC Genomics. 14:123. Abstract
application/pdf iconJimenez_guri_dipteran_transcriptomics_BMC_Genomics_2013.pdf
Cirillo D, Agostini F, Klus P, Marchese D, Rodriguez S, Bolognesi B, Tartaglia GG.  2013.  Neurodegenerative diseases: Quantitative predictions of protein-RNA interactions. RNA.
Agostini F, Cirillo D, Bolognesi B, Tartaglia GG.  2013.  X-inactivation: quantitative predictions of protein interactions in the Xist network. Nucleic Acids Res..
2012
Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T et al..  2012.  Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res.. 22:1698–1710.
Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigo R.  2012.  Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res.. 22:1616–1625.
Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG et al..  2012.  The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res.. 22:1775–1789.
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S et al..  2012.  GENCODE: The reference human genome annotation for The ENCODE Project. Genome Res.. 22:1760–1774.
Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M, Dunham I, Kundaje A, Aldred SF, Collins PJ et al..  2012.  An integrated encyclopedia of DNA elements in the human genome. Nature. 489:57–74.
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F et al..  2012.  Landscape of transcription in human cells. Nature. 489:101–108.
Valach M, Pryszcz LP, Tomaska L, Gacser A, Gabaldón T, Nosek J.  2012.  Mitochondrial genome variability within the Candida parapsilosis species complex.. Mitochondrion. 12:514–519. Abstract
application/pdf iconValack_parapsilosis_mtGenomes_Mitochondrion_2012.pdf
Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E et al..  2012.  Modeling gene expression using chromatin features in various cellular contexts.. Genome Biol.. 13:R53. Abstract
Povolotskaya IS, Kondrashov FA, Lleda A, Vlasov PK.  2012.  Stop codons in bacteria are not selectively equivalent. Biol. Direct. 7:30.
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Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y et al..  2012.  Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res.. 22:1658–1667.
Breen MS, Kemena C, Vlasov PK, Notredame C, Kondrashov FA.  2012.  Epistasis as the primary factor in molecular evolution. Nature. 490:535–538.
application/pdf iconMain text
application/pdf iconSupplementary
Pervouchine DD, Knowles DG, Guigó R.  2012.  Intron-Centric Estimation of Alternative Splicing from RNA-seq data. Bioinformatics. 29(2):273-274. Abstract
Griebel T, Zacher B, Ribeca P, Raineri E, Lacroix V, Guigó R, Sammeth M.  2012.  Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic Acids Res.. 40:10073–10083. Abstract