Publications

Publications of the whole Bioinformatics and Genomics programme

2012

Ng, SY., Johnson R, Stanton LW..  2012.  Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors.. EMBO J.. 31:522–533. Abstract
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Derrien, T, Estell, Marco Sola S, Knowles DG., Raineri E, Guigo R, Ribeca P.  2012.  Fast computation and applications of genome mappability.. PLoS ONE. 7:e30377. Abstract
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Djebali, S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM., Howald C, Foissac S, Ucla C, Chrast J et al..  2012.  Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells. PLoS ONE. 7:e28213. Abstract
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2011

Silva, LL., Marcet-Houben M, Zerlotini A, Gabaldón T, Oliveira G, Nahum LA..  2011.  Evolutionary histories of expanded peptidase families in Schistosoma mansoni.. Mem. Inst. Oswaldo Cruz. 106:864–877. Abstract
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Agostini, F, Vendruscolo M, Tartaglia GG.  2011.  Sequence-based prediction of protein solubility. Journal of Molecular Biology.
Murakami, T, Yang SP, Xie L, Kawano T, Fu D, Mukai A, Bohm C, Chen F, Robertson J, Suzuki H et al..  2011.  ALS mutations in FUS cause neuronal dysfunction and death in Caenorhabditis elegans by a dominant gain-of-function mechanism. Hum Mol Genet. Abstract
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Maxwell, CA., Benítez J, Gómez-Baldó L, Osorio A, Bonifaci N, Fernández-Ramires R, Costes SV., Guinó E, Chen H, Evans GJ. et al..  2011.  Interplay between BRCA1 and RHAMM Regulates Epithelial Apicobasal Polarization and May Influence Risk of Breast Cancer. PLoS Biol.. 9:e1001199. Abstract
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Gonzalez-Porta, M, Calvo M, Sammeth M, Guigo R.  2011.  Estimation of alternative splicing variability in human populations. Genome research. Abstract
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Kedzierska, AM., Drton M, Guigo R, Casanellas M.  2011.  SPIn: model selection for phylogenetic mixtures via linear invariants.. Molecular biology and evolution. Abstract
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Baldwin, AJ., Knowles TP., Tartaglia G, Fitzpatrick A, Devlin G, Shammas S, Waudby CA., Mossuto MF., Gras SL., Christodoulou J et al..  2011.  Metastability of Native Proteins and the Phenomenon of Amyloid Formation.. Journal of the American Chemical Society. Abstract
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Huerta-Cepas, J, Dopazo J, Huynen MA., Gabaldón T.  2011.  Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.. Briefings in bioinformatics. Abstract
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Sánchez, R, Serra F, Tárraga J, Medina I, Carbonell J, Pulido L, de María A, Capella-Gutiérrez S, Huerta-Cepas J, Gabaldón T et al..  2011.  Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.. Nucleic Acids Res.. 39 Suppl 2:W470–W474. Abstract
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Vellozo, AF., Véron AS., Baa-Puyoulet P, Huerta-Cepas J, Cottret L, Febvay G, Calevro F, Rahbé Y, Douglas AE., Gabaldón T et al..  2011.  CycADS: an annotation database system to ease the development and update of BioCyc databases.. Database (Oxford). 2011:bar008. Abstract
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Neurohr, G, Naegeli A, Titos I, Theler D, Greber B, Díez J, Gabaldón T, Mendoza M, Barral Y.  2011.  A midzone-based ruler adjusts chromosome compaction to anaphase spindle length.. Science. 332:465–468. Abstract
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Consortium, ENCODE P, Myers RM., Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC., Bernstein BE., Gingeras TR., Kent WJ., Birney E et al..  2011.  A user's guide to the encyclopedia of DNA elements (ENCODE).. PLoS Biol.. 9:e1001046. Abstract
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Martin, D, Pantoja C, Miñán AF., Valdes-Quezada C, Moltó E, Matesanz F, Bogdanović O, de la Calle-Mustienes E, Domínguez O, Taher L et al..  2011.  Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes. Nat. Struct. Mol. Biol.. 18:708–714. Abstract
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Puente, XS., Pinyol M, Quesada V, Conde L, Ordonez GR., Villamor N, Escaramis G, Jares P, Bea S, González-Díaz M et al..  2011.  Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature. Abstract
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Bellucci, M, Agostini F, Masin M, Tartaglia GG.  2011.  Predicting protein associations with long noncoding RNAs. Nat. Methods. 8:444–445.
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Mossuto, MF, Bolognesi B, Guixer B, Dhulesia A, Agostini F, Janet R, Kumita JR, Tartaglia GG, Dumoulin M, Dobson CM et al..  2011.  Disulfide bonds reduce the toxicity of the amyloid fibrils formed by an extracellular protein. Angew Chem Intl Ed.
Mudge, JM., Frankish A, Fernandez-Banet J, Alioto T, Derrien T, Howald C, Reymond A, Guigo R, Hubbard T, Harrow J.  2011.  The origins, evolution and functional potential of alternative splicing in vertebrates. Molecular biology and evolution. Abstract
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Orom, UA., Derrien T, Guigo R, Shiekhattar R.  2011.  Long Noncoding RNAs as Enhancers of Gene Expression. Cold Spring Harbor symposia on quantitative biology. Abstract
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Derrien, T, Guigó R.  2011.  [Long non-coding RNAs with enhancerlike function in human cells.]. Medecine sciences : M/S. 27:359–361.
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Huerta-Cepas, J, Gabaldón T.  2011.  Assigning duplication events to relative temporal scales in genome-wide studies.. Bioinformatics. 27:38–45. Abstract
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Huerta-Cepas, J, Capella-Gutiérrez S, Pryszcz LP., Denisov I, Kormes D, Marcet-Houben M, Gabaldón T.  2011.  PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions.. Nucleic Acids Res.. 39:D556–D560. Abstract
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Roetzer, A, Klopf E, Gratz N, Marcet-Houben M, Hiller E, Rupp S, Gabaldón T, Kovarik P, Schüller C.  2011.  Regulation of Candida glabrata oxidative stress resistance is adapted to host environment.. FEBS Lett.. 585:319–327. Abstract
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Pryszcz, LP., Huerta-Cepas J, Gabaldón T.  2011.  MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score.. Nucleic Acids Res.. 39:e32. Abstract
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Marcet-Houben, M, Gabaldón T.  2011.  TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees.. Nucleic acids research. Abstract
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Raimondi, S, Guglielmi F, Giorgetti S, Di Gaetano S, Arciello A, Monti M, Relini A, Nichino D, Doglia AM., Natalello A et al..  2011.  Effects of the known pathogenic mutations on the aggregation pathway of the amyloidogenic peptide of Apolipoprotein A-I. J. Mol. Biol..
Jahn, TR., Kohloff KJ., Scott M, Tartaglia GG., Lomas DA., Dobson CM., Vendruscolo M, Crowther DC..  2011.  Detection of Early Locomotor Abnormalities in a Drosophila Model of Alzheimer's Disease.. Journal of Neuroscience Methods.
Olzscha, H, Schermann SM., Woerner AC., Pinkert S, Hecht MH., Tartaglia GG., Vendruscolo M, Hayer-Hartl M, Hartl FU., Vabulas RM..  2011.  Amyloid-like Aggregates Sequester Numerous Metastable Proteins with Essential Cellular Functions.. Cell. Abstract
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2010

Brorsson, AC., Bolognesi B, Tartaglia GG., Shammas SL., Favrin G, Watson I, Lomas DA., Chiti F, Vendruscolo M, Dobson CM. et al..  2010.  Intrinsic determinants of neurotoxic aggregate formation by the amyloid beta peptide.. Biophys. J.. 98:1677–1684. Abstract
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Tartaglia, GG., Dobson CM., Hartl FU., Vendruscolo M.  2010.  Physicochemical determinants of chaperone requirements.. J. Mol. Biol.. 400:579–588. Abstract
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Tartaglia, GG., Vendruscolo M.  2010.  Proteome-level interplay between folding and aggregation propensities of proteins.. J. Mol. Biol.. 402:919–928. Abstract
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Szczepankiewicz, O, Cabaleiro-Lago C, Tartaglia GG., Vendruscolo M, Hunter T, Hunter GJ., Nilsson H, Thulin E, Linse S.  2010.  Interactions in the native state of monellin, which play a protective role against aggregation.. Molecular bioSystems. Abstract
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Lee, Y, Zhou T, Tartaglia GG., Vendruscolo M, Wilke CO..  2010.  Translationally optimal codons associate with aggregation-prone sites in proteins.. Proteomics. Abstract
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Meer, MV, Kondrashov AS, Artzy-Randrup Y, Kondrashov FA.  2010.  Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature. 464:279–282.
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Kondrashov, FA, Kondrashov AS.  2010.  Measurements of spontaneous rates of mutations in the recent past and the near future. Philos. Trans. R. Soc. Lond., B, Biol. Sci.. 365:1169–1176.
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Povolotskaya, IS, Kondrashov FA.  2010.  Sequence space and the ongoing expansion of the protein universe. Nature. 465:922–926.
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Nikolaou, C, Althammer S, Beato M, Guigo R.  2010.  Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae. Epigenetics & chromatin. 3:20. Abstract
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Arensburger, P, Megy K, Waterhouse RM., Abrudan J, Amedeo P, Antelo B, Bartholomay L, Bidwell S, Caler E, Câmara F et al..  2010.  Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.. Science. 330:86–88. Abstract
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Gil Borlado, MC., Moreno Lastres D, Gonzalez Hoyuela M, Moran M, Blazquez A, Pello R, Marin Buera L, Gabaldón T, Garcia Peñas JJ., Martín MA. et al..  2010.  Impact of the mitochondrial genetic background in complex III deficiency.. PLoS ONE. 5 Abstract
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Lingner, T, Muhlhausen S, Gabaldón T, Notredame C, Meinicke P.  2010.  Predicting phenotypic traits of prokaryotes from protein domain frequencies.. BMC bioinformatics. 11:481. Abstract
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Benítez-Páez, A, Villarroya M, Douthwaite S, Gabaldón T, Armengod ME..  2010.  YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNALeu isoacceptors.. RNA (New York, N.Y.). Abstract
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Roetzer, A, Gabaldón T, Schüller C.  2010.  From Saccharomyces cerevisiae to Candida glabrata in a few easy steps: important adaptations for an opportunistic pathogen.. FEMS microbiology letters. Abstract
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Orom, UA., Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q et al..  2010.  Long Noncoding RNAs with Enhancer-like Function in Human Cells. Cell. 143:46–58. Abstract
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Mariotti, M, Guigó R.  2010.  Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes. Bioinformatics (Oxford, England). Abstract
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Manichanh, C, Reeder J, Gibert P, Varela E, Llopis M, Antolin M, Guigo R, Knight R, Guarner F.  2010.  Reshaping the gut microbiome with bacterial transplantation and antibiotic intake.. Genome research. Abstract
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Gabaldón, T, Capella-Gutiérrez S.  2010.  Lack of phylogenetic support for a supposed actinobacterial origin of peroxisomes.. Gene. Abstract
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Montgomery, SB., Sammeth M, Gutierrez-Arcelus M, Lach RP., Ingle C, Nisbett J, Guigo R, Dermitzakis ET..  2010.  Transcriptome genetics using second generation sequencing in a Caucasian population. Nature. 464:773–777. Abstract
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Stajich, JE., Wilke SK., Ahrén D, Au CH., Birren BW., Borodovsky M, Burns C, Canbäck B, Casselton LA., Cheng CK. et al..  2010.  Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proceedings of the National Academy of Sciences of the United States of America. 10.1073:1003391107. Abstract
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Huerta-Cepas, J, Marcet-Houben M, Pignatelli M, Moya A, Gabaldón T.  2010.  The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes.. Insect Mol. Biol.. 19 Suppl 2:13–21. Abstract
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Novoa, I, Gallego J, Ferreira PG., Mendez R.  2010.  Mitotic cell-cycle progression is regulated by CPEB1 and CPEB4-dependent translational control. Nature cell biology. 12(5):447-456. Abstract
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Gómez-Baldó, L, Schmidt S, Maxwell CA., Bonifaci N, Gabaldón T, Vidalain PO., Senapedis W, Kletke A, Rosing M, Barnekow A et al..  2010.  TACC3-TSC2 maintains nuclear envelope structure and controls cell division.. Cell cycle . 9 Abstract
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Díez, J, Walter D, Muñoz-Pinedo C, Gabaldón T.  2010.  DeathBase: a database on structure, evolution and function of proteins involved in apoptosis and other forms of cell death.. Cell Death Differ.. 17:735–736.
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Consortium, I C G.  2010.  International network of cancer genome projects. Nature. 464:993–998. Abstract
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Tilgner, H, Guigó R.  2010.  From chromatin to splicing: RNA-processing as a total artwork. Epigenetics : official journal of the DNA Methylation Society. 5(3):180-184. Abstract
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Horner, DS., Pavesi G, Castrignanò T, De Meo PD., Liuni S, Sammeth M, Picardi E, Pesole G.  2010.  Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Brief. Bioinformatics. 11:181–197. Abstract
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Peña, A, Teeling H, Huerta-Cepas J, Santos F, Yarza P, Brito-Echeverría J, Lucio M, Schmitt-Kopplin P, Meseguer I, Schenowitz C et al..  2010.  Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains.. The ISME journal. Abstract
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Ahmadinejad, N, Dagan T, Gruenheit N, Martin W, Gabaldón T.  2010.  Evolution of spliceosomal introns following endosymbiotic gene transfer.. BMC evolutionary biology. 10:57. Abstract
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Consortium, T I A G.  2010.  Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS biology. 8:e1000313. Abstract
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Gerardo, NM., Altincicek B, Anselme C, Atamian H, Barribeau SM., de Vos M, Duncan E, Evans JD., Gabaldón T, Ghanim M et al..  2010.  Immunity and other defenses in pea aphids, Acyrthosiphon pisum.. Genome biology. 11:R21. Abstract
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Milinkovitch, MC., Helaers R, Depiereux E, Tzika AC., Gabaldon T.  2010.  2X genomes - depth does matter.. Genome biology. 11:R16. Abstract
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Gabaldón, T.  2010.  Peroxisome diversity and evolution.. Philos. Trans. R. Soc. Lond., B, Biol. Sci.. 365:765–773. Abstract
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Mihailovich, M, Militti C, Gabaldón T, Gebauer F.  2010.  Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression.. BioEssays. 32:109–118. Abstract
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Huerta-Cepas, J, Dopazo J, Gabaldón T.  2010.  ETE: a python Environment for Tree Exploration.. BMC bioinformatics. 11:24. Abstract
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Innan, H, Kondrashov FA.  2010.  The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet. 11(2):108.
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Kondrashov, AS, Povolotskaya IS, Ivankov DN, Kondrashov FA.  2010.  Rate of sequence divergence under constant selection. Biology Direct. 5(1) Abstract
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Kondrashov, FA.  2010.  Gene Dosage and Duplication. Evolution after Gene Duplication. Abstract
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2009

Calamai, M, Tartaglia GG., Vendruscolo M, Chiti F, Dobson CM..  2009.  Mutational analysis of the aggregation-prone and disaggregation-prone regions of acylphosphatase.. J. Mol. Biol.. 387:965–974. Abstract
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Hamada, D, Tanaka T, Tartaglia GG., Pawar A, Vendruscolo M, Kawamura M, Tamura A, Tanaka N, Dobson CM..  2009.  Competition between folding, native-state dimerisation and amyloid aggregation in beta-lactoglobulin.. J. Mol. Biol.. 386:878–890. Abstract
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Yanamandra, K, Alexeyev O, Zamotin V, Srivastava V, Shchukarev A, Brorsson AC., Tartaglia GG., Vogl T, Kayed R, Wingsle G et al..  2009.  Amyloid formation by the pro-inflammatory S100A8/A9 proteins in the ageing prostate.. PLoS ONE. 4:e5562. Abstract
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Pechmann, S, Levy ED., Tartaglia GG., Vendruscolo M.  2009.  Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins.. Proc. Natl. Acad. Sci. U.S.A.. 106:10159–10164. Abstract
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Tartaglia, GG., Vendruscolo M.  2009.  Correlation between mRNA expression levels and protein aggregation propensities in subcellular localisations.. Mol Biosyst. 5:1873–1876. Abstract
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Routledge, KE., Tartaglia GG., Platt GW., Vendruscolo M, Radford SE..  2009.  Competition between intramolecular and intermolecular interactions in an amyloid-forming protein.. J. Mol. Biol.. 389:776–786. Abstract
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Tartaglia, GG., Pechmann S, Dobson CM., Vendruscolo M.  2009.  A relationship between mRNA expression levels and protein solubility in E. coli.. J. Mol. Biol.. 388:381–389. Abstract
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Buell, AK., Tartaglia GG., Birkett NR., Waudby CA., Vendruscolo M, Salvatella X, Welland ME., Dobson CM., Knowles TP..  2009.  Position-dependent electrostatic protection against protein aggregation.. Chembiochem. 10:1309–1312. Abstract
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Ferreira, P G, Silva CG, Azevedo PJ, Brito RM.  2009.  Spatial Clustering of Molecular Dynamics Trajectories in Protein Unfolding Simulations. :156–166.
Sammeth, M.  2009.  Complete alternative splicing events are bubbles in splicing graphs. J. Comput. Biol.. 16:1117–1140. Abstract
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Thornton, J, including Guigó BS NR.  2009.  Annotations for all by all - the BioSapiens network.. Genome Biol.. 10:401. Abstract
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Makrythanasis, P, Kapranov P, Bartoloni L, Reymond A, Deutsch S, Guigó R, Denoeud F, Drenkow J, Rossier C, Ariani F et al..  2009.  Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls.. Hum. Mutat.. 30:E866–E879. Abstract
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Tilgner, H, Nikolaou C, Althammer S, Sammeth M, Beato M, Valcárcel J, Guigó R.  2009.  Nucleosome positioning as a determinant of exon recognition. Nat. Struct. Mol. Biol.. 16:996–1001. Abstract
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Marcet-Houben, M, Marceddu G, Gabaldón T.  2009.  Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence.. BMC Evol. Biol.. 9:295. Abstract
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Gabaldón, T, Dessimoz C, Huxley-Jones J, Vilella AJ, Sonnhammer EL, Lewis S.  2009.  Joining forces in the quest for orthologs. Genome Biol.. 10:403.
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Marcet-Houben, M, Gabaldón T.  2009.  Acquisition of prokaryotic genes by fungal genomes. Trends Genet..
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Schlüter, A, Real-Chicharro A, Gabaldón T, Sánchez-Jiménez F, Pujol A.  2009.  PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome. Nucleic Acids Res..
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Takeuchi, A, Schmitt D, Chapple C, Babaylova E, Karpova G, Guigo R, Krol A, Allmang C.  2009.  A short motif in Drosophila SECIS Binding Protein 2 provides differential binding affinity to SECIS RNA hairpins.. Nucleic Acids Res.. 37:2126–2141. Abstract
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Marcet-Houben, M, Gabaldón T.  2009.  The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome.. PLoS ONE. 4:e4357. Abstract
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Chapple, CE., Guigó R, Krol A.  2009.  SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements.. Bioinformatics. 25:674–675. Abstract
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Harrow, J, Nagy A, Reymond A, Alioto T, Patthy L, Antonarakis SE., Guigó R.  2009.  Identifying protein-coding genes in genomic sequences.. Genome Biol.. 10:201. Abstract
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Koscielny, G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ., Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M et al..  2009.  ASTD: The Alternative Splicing and Transcript Diversity database.. Genomics. 93:213–220. Abstract
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Boj, SF., Servitja JM., Martin D, Rios M, Talianidis I, Guigo R, Ferrer J.  2009.  Functional targets of the monogenic diabetes transcription factors HNF-1alpha and HNF-4alpha are highly conserved between mice and humans.. Diabetes. 58:1245–1253. Abstract
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Sequencing, B G, Consortium A, Elsik CG., Tellam RL., Worley KC., Gibbs RA., Muzny DM., Weinstock GM., Adelson DL., Eichler EE. et al..  2009.  The genome sequence of taurine cattle: a window to ruminant biology and evolution.. Science. 324:522–528. Abstract
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Servitja, JM., Pignatelli M, Maestro MA., Cardalda C, Boj SF., Lozano J, Blanco E, Lafuente A, McCarthy MI., Sumoy L et al..  2009.  Hnf1alpha (MODY3) controls tissue-specific transcriptional programs and exerts opposed effects on cell growth in pancreatic islets and liver.. Mol. Cell. Biol.. 29:2945–2959. Abstract
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Arman, M, Aguilera-Montilla N, Mas V, Puig-Kröger A, Pignatelli M, Guigó R, Corbí AL., Lozano F.  2009.  The human CD6 gene is transcriptionally regulated by RUNX and Ets transcription factors in T cells.. Mol. Immunol.. 46:2226–2235. Abstract
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Castellano, S, Andrés AM., Bosch E, Bayes M, Guigó R, Clark AG..  2009.  Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins.. Mol. Biol. Evol.. 26:2031–2040. Abstract
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Pignatelli, M, Serras F, Moya A, Guigó R, Corominas M.  2009.  CROC: finding chromosomal clusters in eukaryotic genomes.. Bioinformatics. 25:1552–1553. Abstract
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Capella-Gutiérrez, S, Silla-Martínez JM., Gabaldón T.  2009.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.. Bioinformatics. 25:1972–1973. Abstract
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Gil-Borlado, MC., González-Hoyuela M, Blázquez A, García-Silva MT., Gabaldón T, Manzanares J, Vara J, Martín MA., Seneca S, Arenas J et al..  2009.  Pathogenic mutations in the 5' untranslated region of BCS1L mRNA in mitochondrial complex III deficiency.. Mitochondrion. 9:299–305. Abstract
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Kemena, C, Notredame C.  2009.  Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics. 25:2455-65. Abstract
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Gauthier, JA, Widmer E, Bucher P, Notredame C.  2009.  How much does it cost? Optimization of costs in sequence analysis of social science data Sociological Methods and Research. Volume 38:Pages197-231.
Varas, F, Stadtfeld M, de Andres-Aguayo L, Maherali N, di Tullio A, Pantano L, Notredame C, Hochedlinger K, Graf T.  2009.  Fibroblast-derived induced pluripotent stem cells show no common retroviral vector insertions. Stem Cells. 27:300-6. Abstract
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Buschbeck, M, Uribesalgo I, Wibowo I, Rué P, Martin D, Gutierrez A, Morey L, Guigó R, López-Schier H, Di Croce L.  2009.  The histone variant macroH2A is an epigenetic regulator of key developmental genes.. Nat. Struct. Mol. Biol.. 16:1074–1079. Abstract
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Alkalaeva, E, Eliseev B, Ambrogelly A, Vlasov P, Kondrashov FA, Gundllapalli S, Frolova L, Söll D, Kisselev L.  2009.  Translation termination in pyrrolysine-utilizing archaea.. FEBS Lett.. 583(21):3460. Abstract
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2008

Tartaglia, GG., Vendruscolo M.  2008.  The Zyggregator method for predicting protein aggregation propensities.. Chem Soc Rev. 37:1395–1401. Abstract
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Rivers, RC., Kumita JR., Tartaglia GG., Dedmon MM., Pawar A, Vendruscolo M, Dobson CM., Christodoulou J.  2008.  Molecular determinants of the aggregation behavior of alpha- and beta-synuclein.. Protein Sci.. 17:887–898. Abstract
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Vendruscolo, M, Tartaglia GG..  2008.  Towards quantitative predictions in cell biology using chemical properties of proteins.. Mol Biosyst. 4:1170–1175. Abstract
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Weng, Z, Guigó R.  2008.  In silico meets in vivo.. Genome Biol.. 9:302. Abstract
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Castellano, S, Gladyshev VN., Guigó R, Berry MJ..  2008.  SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.. Nucleic Acids Res.. 36:D332–D338. Abstract
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Consortium, STAR, Saar K, Beck A, Bihoreau MT., Birney E, Brocklebank D, Chen Y, Cuppen E, Demonchy S, Dopazo J et al..  2008.  SNP and haplotype mapping for genetic analysis in the rat.. Nat. Genet.. 40:560–566. Abstract
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Consortium, BM, Wilkinson MD., Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D et al..  2008.  Interoperability with Moby 1.0–it's better than sharing your toothbrush!. Brief. Bioinformatics. 9:220–231. Abstract
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Manichanh, C, Chapple CE., Frangeul L, Gloux K, Guigo R, Dore J.  2008.  A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.. Nucleic Acids Res.. 36:5180–5188. Abstract
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Gabaldón, T.  2008.  Large-scale assignment of orthology: back to phylogenetics? Genome Biol.. 9:235. Abstract
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Djebali, S, Kapranov P, Foissac S, Lagarde J, Reymond A, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR. et al..  2008.  Efficient targeted transcript discovery via array-based normalization of RACE libraries.. Nat. Methods. 5:629–635. Abstract
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Chapple, CE., Guigó R.  2008.  Relaxation of selective constraints causes independent selenoprotein extinction in insect genomes.. PLoS ONE. 3:e2968. Abstract
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Blanco, E, Pignatelli M, Beltran S, Punset A, Pérez-Lluch S, Serras F, Guigó R, Corominas M.  2008.  Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila.. Genome Biol.. 9:R134. Abstract
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Sammeth, M, Foissac S, Guigó R.  2008.  A general definition and nomenclature for alternative splicing events.. PLoS Comput. Biol.. 4:e1000147. Abstract
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Piqué, M, López JM., Foissac S, Guigó R, Méndez R.  2008.  A combinatorial code for CPE-mediated translational control.. Cell. 132:434–448. Abstract
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Huerta-Cepas, J, Bueno A, Dopazo J, Gabaldón T.  2008.  PhylomeDB: a database for genome-wide collections of gene phylogenies.. Nucleic Acids Res.. 36:D491–D496. Abstract
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Rausch, T, Emde AK, Weese D, Doring A, Notredame C, Reinert K.  2008.  Segment-based multiple sequence alignment. Bioinformatics. 24:i187-92. Abstract
Moretti, S, Wilm A, Higgins DG, Xenarios I, Notredame C.  2008.  R-Coffee: a web server for accurately aligning noncoding RNA sequences. Nucleic Acids Res. 36:W10-3. Abstract
Wilm, A, Higgins DG, Notredame C.  2008.  R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res. 36:e52. Abstract
Donaldson, ZR., Kondrashov FA, Putnam A, Bai Y, Stoinski TL., Hammock EA., Young LJ..  2008.  Evolution of a behavior-linked microsatellite-containing element in the 5' flanking region of the primate AVPR1A gene.. BMC Evol. Biol.. 8:180. Abstract
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Schmidt, S, Gerasimova A, Kondrashov FA, Adzhubei IA., Adzuhbei IA., Kondrashov AS., Sunyaev S.  2008.  Hypermutable non-synonymous sites are under stronger negative selection.. PLoS Genet.. 4:e1000281. Abstract
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Assis, R, Kondrashov AS., Koonin EV., Kondrashov FA.  2008.  Nested genes and increasing organizational complexity of metazoan genomes.. Trends Genet.. 24:475–478. Abstract
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Arkhipov, VY, Koblik EA, Redkin YA, Kondrashov FA.  2008.  Birds of the Krasnoye Lake area (South Chukotka). Arch Zool Mus MGU. 49:159-183. Abstract
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2007

Tartaglia, GG., Cavalli A, Vendruscolo M.  2007.  Prediction of local structural stabilities of proteins from their amino acid sequences.. Structure. 15:139–143. Abstract
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Tartaglia, GG., Caflisch A.  2007.  Computational analysis of the S. cerevisiae proteome reveals the function and cellular localization of the least and most amyloidogenic proteins.. Proteins. 68:273–278. Abstract
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Meinhardt, J, Tartaglia GG., Pawar A, Christopeit T, Hortschansky P, Schroeckh V, Dobson CM., Vendruscolo M, F√§ndrich M.  2007.  Similarities in the thermodynamics and kinetics of aggregation of disease-related Abeta(1-40) peptides.. Protein Sci.. 16:1214–1222. Abstract
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Monsellier, E, Ramazzotti M, de Laureto PP., Tartaglia GG., Taddei N, Fontana A, Vendruscolo M, Chiti F.  2007.  The distribution of residues in a polypeptide sequence is a determinant of aggregation optimized by evolution.. Biophys. J.. 93:4382–4391. Abstract
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Tartaglia, GG., Pechmann S, Dobson CM., Vendruscolo M.  2007.  Life on the edge: a link between gene expression levels and aggregation rates of human proteins.. Trends Biochem. Sci.. 32:204–206.
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Meehan, S, Knowles TP., Baldwin AJ., Smith JF., Squires AM., Clements P, Treweek TM., Ecroyd H, Tartaglia GG., Vendruscolo M et al..  2007.  Characterisation of amyloid fibril formation by small heat-shock chaperone proteins human alphaA-, alphaB- and R120G alphaB-crystallins.. J. Mol. Biol.. 372:470–484. Abstract
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Luheshi, LM., Tartaglia GG., Brorsson AC., Pawar AP., Watson IE., Chiti F, Vendruscolo M, Lomas DA., Dobson CM., Crowther DC..  2007.  Systematic in vivo analysis of the intrinsic determinants of amyloid Beta pathogenicity.. PLoS Biol.. 5:e290. Abstract
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Schlüter, A, Fourcade S, Domènech-Estévez E, Gabaldón T, Huerta-Cepas J, Berthommier G, Ripp R, Wanders RJ., Poch O, Pujol A.  2007.  PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.. Nucleic Acids Res.. 35:D815–D822. Abstract
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Gabaldón, T, Peretó J, Montero F, Gil R, Latorre A, Moya A.  2007.  Structural analyses of a hypothetical minimal metabolism.. Philos. Trans. R. Soc. Lond., B, Biol. Sci.. 362:1751–1762. Abstract
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Blanco, E, Parra G, Guigó R.  2007.  Using geneid to identify genes.. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. Chapter 4:Unit4.3. Abstract
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Tanner, S, Shen Z, Ng J, Florea L, Guigó R, Briggs SP., Bafna V.  2007.  Improving gene annotation using peptide mass spectrometry.. Genome Res.. 17:231–239. Abstract
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Blanco, E, Guigó R, Messeguer X.  2007.  Multiple non-collinear TF-map alignments of promoter regions.. BMC Bioinformatics. 8:138. Abstract
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Zheng, D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW., Lu Y, Denoeud F, Antonarakis SE., Snyder M et al..  2007.  Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.. Genome Res.. 17:839–851. Abstract
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Tress, ML., Martelli PL., Frankish A, Reeves GA., Wesselink JJ., Yeats C, Olason PI., Albrecht M, Hegyi H, Giorgetti A et al..  2007.  The implications of alternative splicing in the ENCODE protein complement.. Proc. Natl. Acad. Sci. U.S.A.. 104:5495–5500. Abstract
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Kerhornou, A, Guigó R.  2007.  BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations.. Bioinformatics. 23:1831–1833. Abstract
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Washietl, S, Pedersen JS., Korbel JO., Stocsits C, Gruber AR., Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A et al..  2007.  Structured RNAs in the ENCODE selected regions of the human genome.. Genome Res.. 17:852–864. Abstract
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Rozowsky, JS., Newburger D, Sayward F, Wu J, Jordan G, Korbel JO., Nagalakshmi U, Yang J, Zheng D, Guigó R et al..  2007.  The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.. Genome Res.. 17:732–745. Abstract
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Denoeud, F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J et al..  2007.  Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.. Genome Res.. 17:746–759. Abstract
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Consortium, D G12, Clark AG., Eisen MB., Smith DR., Bergman CM., Oliver B, Markow TA., Kaufman TC., Kellis M, Gelbart W et al..  2007.  Evolution of genes and genomes on the Drosophila phylogeny.. Nature. 450:203–218. Abstract
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Lyle, R, Prandini P, Osoegawa K, ten Hallers B, Humphray S, Zhu B, Eyras E, Castelo R, Bird CP., Gagos S et al..  2007.  Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21.. Genome Res.. 17:1690–1696. Abstract
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Huerta-Cepas, J, Dopazo H, Dopazo J, Gabaldón T.  2007.  The human phylome.. Genome Biol.. 8:R109. Abstract
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Consortium, ENCODE P, Birney E, Stamatoyannopoulos JA., Dutta A, Guigó R, Gingeras TR., Margulies EH., Weng Z, Snyder M, Dermitzakis ET. et al..  2007.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.. Nature. 447:799–816. Abstract
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Retelska, D, Beaudoing E, Notredame C, Jongeneel CV, Bucher P.  2007.  Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time. BMC Genomics. 8:398. Abstract
Moretti, S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C.  2007.  The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Nucleic Acids Res. 35:W645-8. Abstract
Notredame, C.  2007.  Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol. 3:e123.
Tárraga, J, Medina I, Arbiza L, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H.  2007.  Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. Nucleic Acids Res.. 35:38–42.
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Plotnikova, OV, Kondrashov FA, Vlasov PK, Grigorenko AP, Ginter EK, Rogaev EI.  2007.  Conversion and Compensatory Evolution of the Gamma-crystallin Genes and Identification of a Cataractogenic Mutation that Reverses the Sequence of the Human CRYGD gene to an Ancestral State. Am J Hum Genet. 81:32-43. Abstract
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Kondrashov, FA, Gurbich TA, Vlasov PK.  2007.  Selection for Functional Uniformity of tuf Duplicates in Gamma-proteobacteria. Trends Genet. 23:215-218. Abstract
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Bazykin, GA, Kondrashov FA, Brudno M, Poliakov A, Dubchak I, Kondrashov AS.  2007.  Extensive Parallelism in Protein Evolution. Biol Direct. 2:20-20. Abstract
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Popadin, K Y, Mamirova LA, Kondrashov FA.  2007.  A Manually Curated Database of Tetrapod Mitochondrially Encoded tRNA Sequences and Secondary Structures. BMC Bioinformatics. 8:441-441. Abstract
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2006

Gabaldón, T, Snel B, van Zimmeren F, Hemrika W, Tabak H, Huynen MA..  2006.  Origin and evolution of the peroxisomal proteome.. Biol. Direct. 1:8. Abstract
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Parra, G, Reymond A, Dabbouseh N, Dermitzakis ET., Castelo R, Thomson TM., Antonarakis SE., Guigó R.  2006.  Tandem chimerism as a means to increase protein complexity in the human genome.. Genome Res.. 16:37–44. Abstract
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Mularoni, L, Guigó R, Albà MM..  2006.  Mutation patterns of amino acid tandem repeats in the human proteome.. Genome Biol.. 7:R33. Abstract
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Blanco, E, Farré D, Albà MM., Messeguer X, Guigó R.  2006.  ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.. Nucleic Acids Res.. 34:D63–D67. Abstract
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Reese, MG., Guigó R.  2006.  EGASP: Introduction.. Genome Biol.. 7 Suppl 1:S1.1–S1.3.
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Guigó, R, Valcárcel J.  2006.  Unweaving the meanings of messenger RNA sequences.. Mol. Cell. 23:150–151. Abstract
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Blanco, E, Messeguer X, Smith TF., Guigó R.  2006.  Transcription factor map alignment of promoter regions.. PLoS Comput. Biol.. 2:e49. Abstract
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Harrow, J, Denoeud F, Frankish A, Reymond A, Chen CK., Chrast J, Lagarde J, Gilbert JG., Storey R, Swarbreck D et al..  2006.  GENCODE: producing a reference annotation for ENCODE.. Genome Biol.. 7 Suppl 1:S4.1–S4.9. Abstract
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Guigó, R, Flicek P, Abril JF., Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB., Birney E et al..  2006.  EGASP: the human ENCODE Genome Annotation Assessment Project.. Genome Biol.. 7 Suppl 1:S2.1–S231. Abstract
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Aury, JM., Jaillon O, Duret L, Noel B, Jubin C, Porcel BM., Ségurens B, Daubin V, Anthouard V, Aiach N et al..  2006.  Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.. Nature. 444:171–178. Abstract
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Armougom, F, Moretti S, Keduas V, Notredame C.  2006.  The iRMSD: a local measure of sequence alignment accuracy using structural information. Bioinformatics. 22:e35-9. Abstract
Armougom, F, Poirot O, Moretti S, Higgins DG, Bucher P, Keduas V, Notredame C.  2006.  APDB: a web server to evaluate the accuracy of sequence alignments using structural information. Bioinformatics. 22:2439-40. Abstract
Moretti, S, Reinier F, Poirot O, Armougom F, Audic S, Keduas V, Notredame C.  2006.  PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments. Nucleic Acids Res. 34:W600-3. Abstract
Armougom, F, Moretti S, Poirot O, Audic S, Dumas P, Schaeli B, Keduas V, Notredame C.  2006.  Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res. 34:W604-8. Abstract
Wallace, IM, O'Sullivan O, Higgins DG, Notredame C.  2006.  M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 34:1692-9. Abstract
Kondrashov, FA, Ogurtsov AY, Kondrashov AS.  2006.  Selection in Favor of Nucleotides G and C Diversifies Evolution Rates and Levels of Polymorphism at Mammalian Synonymous Sites. J Theor Biol. 240:616-626. Abstract
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Rogaev, EI, Moliaka YK, Malyarchuk BA, Kondrashov FA, Derenko MV, Chumakov I, Grigorenko AP.  2006.  Complete Mitochondrial Genome and Phylogeny of Pleistocene Mammoth Mammuthus Primigenius. PLoS Biol. 4:e73-e73. Abstract
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Kondrashov, FA, Kondrashov AS.  2006.  Role of Selection in Fixation of gene Duplications. J Theor Biol. 239:141-151. Abstract
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Kondrashov, FA, Koonin EV, Morgunov IG, Finogenova TV, Kondrashova MN.  2006.  Evolution of Glyoxylate Cycle Enzymes in Metazoa: Evidence of Multiple Horizontal Transfer Events and Pseudogene Formation. Biol Direct. 1:31-31. Abstract
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Babenko, VN, Basu MK, Kondrashov FA, Rogozin IB, Koonin EV.  2006.  Signs of Positive Selection of Somatic Mutations in Human Cancers Detected by EST Sequence Analysis. BMC Cancer. 6:36-36. Abstract
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2005

Tartaglia, GG., Pellarin R, Cavalli A, Caflisch A.  2005.  Organism complexity anti-correlates with proteomic beta-aggregation propensity.. Protein Sci.. 14:2735–2740. Abstract
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Tartaglia, GG., Cavalli A, Pellarin R, Caflisch A.  2005.  Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences.. Protein Sci.. 14:2723–2734. Abstract
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Gabaldón, T, Rainey D, Huynen MA..  2005.  Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I).. J. Mol. Biol.. 348:857–870. Abstract
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Gabaldón, T, Huynen MA..  2005.  Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes.. Bioinformatics. 21 Suppl 2:ii144–ii150. Abstract
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Abril, JF., Castelo R, Guigó R.  2005.  Comparison of splice sites in mammals and chicken.. Genome Res.. 15:111–119. Abstract
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Szafranski, K, Lehmann R, Parra G, Guigo R, Glöckner G.  2005.  Gene organization features in A/T-rich organisms.. J. Mol. Evol.. 60:90–98. Abstract
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Castelo, R, Reymond A, Wyss C, Câmara F, Parra G, Antonarakis SE., Guigó R, Eyras E.  2005.  Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.. Nucleic Acids Res.. 33:1935–1939. Abstract
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López-Bigas, N, Audit B, Ouzounis C, Parra G, Guigó R.  2005.  Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett.. 579:1900–1903. Abstract
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Taskov, K, Chapple C, Kryukov GV., Castellano S, Lobanov AV., Korotkov KV., Guigó R, Gladyshev VN..  2005.  Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome? Nucleic Acids Res.. 33:2227–2238. Abstract
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Eyras, E, Reymond A, Castelo R, Bye JM., Câmara F, Flicek P, Huckle EJ., Parra G, Shteynberg DD., Wyss C et al..  2005.  Gene finding in the chicken genome.. BMC Bioinformatics. 6:131. Abstract
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Guigó, R, Reese MG..  2005.  EGASP: collaboration through competition to find human genes.. Nat. Methods. 2:575–577. Abstract
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Castellano, S, Lobanov AV., Chapple C, Novoselov SV., Albrecht M, Hua D, Lescure A, Lengauer T, Krol A, Gladyshev VN. et al..  2005.  Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family.. Proc. Natl. Acad. Sci. U.S.A.. 102:16188–16193. Abstract
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Izquierdo, JM., Majós N, Bonnal S, Martínez C, Castelo R, Guigó R, Bilbao D, Valcárcel J.  2005.  Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition.. Mol. Cell. 19:475–484. Abstract
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Boxma, B, de Graaf RM., van der Staay GW., van Alen TA., Ricard G, Gabaldón T, van Hoek AH., Moon-van der Staay SY., Koopman WJ., van Hellemond JJ. et al..  2005.  An anaerobic mitochondrion that produces hydrogen.. Nature. 434:74–79. Abstract
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Kondrashov, FA.  2005.  In Search of the Limits of Evolution. Nat Genet. 37:9-10.
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Yampolsky, LY, Kondrashov FA, Kondrashov AS.  2005.  Distribution of the Strength of Selection Against Amino acid Replacements in Human Proteins. Hum Mol Genet. 14:3191-3201. Abstract
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Jordan, KI, Kondrashov FA, Adzhubei IA, Wolf YI, Koonin EV, Kondrashov AS, Sunyaev S.  2005.  A Universal Trend of Amino acid gain and loss in Protein Evolution. Nature. 433:633-638. Abstract
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Kondrashov, FA.  2005.  [The Convergent Evolution of the Secondary Structure of Mitochondrial Cysteine tRNA in the Nine-banded Armadillo Dasypus Novemcinctus]. Biofizika. 50:396-403. Abstract
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Kondrashov, FA.  2005.  Prediction of Pathogenic Mutations in Mitochondrially Encoded Human tRNAs. Hum Mol Genet. 14:2415-2419. Abstract
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Kondrashov, FA.  2005.  [The Analysis of Monomer Sequences in Protein and tRNA and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution]. Biofizika. 50:389-395. Abstract
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2004

Feng, J, Tartaglia GG., Tirozzi B.  2004.  A note on minimum variance theory and beyond.. J. Phys. A Mat.. :4685-4700. Abstract
Tartaglia, GG., Cavalli A, Pellarin R, Caflisch A.  2004.  The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates.. Protein Sci.. 13:1939–1941. Abstract
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Gibbs, RA., Weinstock GM., Metzker ML., Muzny DM., Sodergren EJ., Scherer S, Scott G, Steffen D, Worley KC., Burch PE. et al..  2004.  Genome sequence of the Brown Norway rat yields insights into mammalian evolution.. Nature. 428:493–521. Abstract
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Castresana, J, Guigó R, Albà MM..  2004.  Clustering of genes coding for DNA binding proteins in a region of atypical evolution of the human genome.. J. Mol. Evol.. 59:72–79. Abstract
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Brent, MR., Guigó R.  2004.  Recent advances in gene structure prediction.. Curr. Opin. Struct. Biol.. 14:264–272. Abstract
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Consortium, ENCODE P.  2004.  The ENCODE (ENCyclopedia Of DNA Elements) Project.. Science. 306:636–640. Abstract
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Jaillon, O, Aury JM., Brunet F, Petit JL., Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A et al..  2004.  Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.. Nature. 431:946–957. Abstract
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Castelo, R, Guigó R.  2004.  Splice site identification by idlBNs.. Bioinformatics. 20 Suppl 1:i69–i76. Abstract
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Consortium, I C G S.  2004.  Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.. Nature. 432:695–716. Abstract
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Notredame, C, Suhre K.  2004.  Computing multiple sequence/structure alignments with the T-coffee package. Curr Protoc Bioinformatics. Chapter 3:Unit38. Abstract
Poirot, O, Suhre K, Abergel C, O'Toole E, Notredame C.  2004.  3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. Nucleic Acids Res. 32:W37-40. Abstract
Claude, JB, Suhre K, Notredame C, Claverie JM, Abergel C.  2004.  CaspR: a web server for automated molecular replacement using homology modelling. Nucleic Acids Res. 32:W606-9. Abstract
O'Sullivan, O, Suhre K, Abergel C, Higgins DG, Notredame C.  2004.  3DCoffee: combining protein sequences and structures within multiple sequence alignments. J Mol Biol. 340:385-95. Abstract
Vella, F, Mietchen D, Gabaldón T.  2004.  Perceptions about postdocs. EMBO Rep.. 5:1104.
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Castillo-Davis, CI, Kondrashov FA, Hartl DL, Kulathinal RJ.  2004.  The Functional Genomic Distribution of Protein Divergence in two Animal Phyla: Coevolution, Genomic Conflict, and Constraint. Genome Res. 14:802-811. Abstract
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Kondrashov, FA, Koonin EV.  2004.  A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of gene Duplications. Trends Genet. 20:287-290.
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Kondrashov, FA, Ogurtsov AY, Kondrashov AS.  2004.  Bioinformatical Assay of Human gene Morbidity. Nucleic Acids Res. 32:1731-1737. Abstract
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Panchenko, AR, Kondrashov FA, Bryant S.  2004.  Prediction of Functional Sites by Analysis of Sequence and Structure Conservation. Protein Sci. 13:884-892. Abstract
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Kern, AD, Kondrashov FA.  2004.  Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial tRNAs. Nat Genet. 36:1207-1212. Abstract
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Bazykin, GA, Kondrashov FA, Ogurtsov AY, Sunyaev S, Kondrashov AS.  2004.  Positive Selection at Sites of Multiple Amino acid Replacements Since Rat-mouse Divergence. Nature. 429:558-562. Abstract
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2003

Beltran, S, Blanco E, Serras F, Pérez-Villamil B, Guigó R, Artavanis-Tsakonas S, Corominas M.  2003.  Transcriptional network controlled by the trithorax-group gene ash2 in Drosophila melanogaster.. Proc. Natl. Acad. Sci. U.S.A.. 100:3293–3298. Abstract
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Parra, G, Agarwal P, Abril JF., Wiehe T, Fickett JW., Guigó R.  2003.  Comparative gene prediction in human and mouse.. Genome Res.. 13:108–117. Abstract
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Abril, JF., Guigó R, Wiehe T.  2003.  gff2aplot: Plotting sequence comparisons.. Bioinformatics. 19:2477–2479. Abstract
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Kryukov, GV., Castellano S, Novoselov SV., Lobanov AV., Zehtab O, Guigó R, Gladyshev VN..  2003.  Characterization of mammalian selenoproteomes.. Science. 300:1439–1443. Abstract
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Gabaldón, T, Huynen MA..  2003.  Reconstruction of the proto-mitochondrial metabolism.. Science. 301:609.
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Guigo, R, Dermitzakis ET., Agarwal P, Ponting CP., Parra G, Reymond A, Abril JF., Keibler E, Lyle R, Ucla C et al..  2003.  Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes.. Proc. Natl. Acad. Sci. U.S.A.. 100:1140–1145. Abstract
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Abergel, C, Coutard B, Byrne D, Chenivesse S, Claude JB, Deregnaucourt C, Fricaux T, Gianesini-Boutreux C, Jeudy S, Lebrun R et al..  2003.  Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. J Struct Funct Genomics. 4:141-57. Abstract
O'Sullivan, O, Zehnder M, Higgins D, Bucher P, Grosdidier A, Notredame C.  2003.  APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. Bioinformatics. 19 Suppl 1:i215-21. Abstract
Poirot, O, O'Toole E, Notredame C.  2003.  Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res. 31:3503-6. Abstract
Sunyaev, S, Kondrashov FA, Bork P, Ramensky V.  2003.  Impact of Selection, Mutation rate and Genetic Drift on Human Genetic Variation. Hum Mol Genet. 12:3325-3330. Abstract
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Kondrashov, FA, Koonin EV.  2003.  Evolution of Alternative Splicing: Deletions, Insertions and Origin of Functional Parts of Proteins from Intron Sequences. Trends Genet. 19:115-119. Abstract
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2002

Holt, RA., Subramanian GM., Halpern A, Sutton GG., Charlab R, Nusskern DR., Wincker P, Clark AG., Ribeiro JM., Wides R et al..  2002.  The genome sequence of the malaria mosquito Anopheles gambiae.. Science. 298:129–149. Abstract
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Glöckner, G, Eichinger L, Szafranski K, Pachebat JA., Bankier AT., Dear PH., Lehmann R, Baumgart C, Parra G, Abril JF. et al..  2002.  Sequence and analysis of chromosome 2 of Dictyostelium discoideum.. Nature. 418:79–85. Abstract
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Consortium, M G S, Waterston RH., Lindblad-Toh K, Birney E, Rogers J, Abril JF., Agarwal P, Agarwala R, Ainscough R, Alexandersson M et al..  2002.  Initial sequencing and comparative analysis of the mouse genome.. Nature. 420:520–562. Abstract
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Notredame, C.  2002.  Recent progress in multiple sequence alignment: a survey. Pharmacogenomics. 3:131-44. Abstract
Perelygin, AA, Kondrashov FA, Rogozin IB, Brinton MA.  2002.  Evolution of the Mouse polyubiquitin-C gene. J Mol Evol. 55:202-210. Abstract
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Castillo-Davis, CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA.  2002.  Selection for Short Introns in Highly Expressed Genes. Nat Genet. 31:415-418. Abstract
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Kondrashov, FA, Rogozin IB, Wolf YI, Koonin EV.  2002.  Selection in the Evolution of gene Duplications. Genome Biol. 3:RESEARCH0008-RESEARCH0008. Abstract
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Kondrashov, AS, Sunyaev S, Kondrashov FA.  2002.  Dobzhansky-Muller Incompatibilities in Protein Evolution. Proc Natl Acad Sci U S A. 99:14878-14883. Abstract
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2001

Venter, JC., Adams MD., Myers EW., Li PW., Mural RJ., Sutton GG., Smith HO., Yandell M, Evans CA., Holt RA. et al..  2001.  The sequence of the human genome.. Science. 291:1304–1351. Abstract
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Notredame, C.  2001.  Mocca: semi-automatic method for domain hunting. Bioinformatics. 17:373-4. Abstract
Dietmann, S, Park J, Notredame C, Heger A, Lappe M, Holm L.  2001.  A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucleic Acids Res. 29:55-7. Abstract
Jordan, IK., Kondrashov FA, Rogozin IB., Tatusov RL., Wolf YI., Koonin EV..  2001.  Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins.. Genome Biol.. 2:RESEARCH0053. Abstract
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Rogozin, I, Kondrashov FA, Glazko G.  2001.  Use of Mutation Spectra Analysis Software. Hum Mutat. 17:83-8102. Abstract
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Kondrashov, FA, Kondrashov AS.  2001.  Multidimensional Epistasis and the Disadvantage of sex. Proc Natl Acad Sci U S A. 98:12089-12092. Abstract
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Rogozin, IB, Kochetov AV, Kondrashov FA, Koonin EV, Milanesi L.  2001.  Presence of ATG Triplets in 5' Untranslated Regions of Eukaryotic cDNAs Correlates with a 'weak' Context of the Start Codon. Bioinformatics. 17:890-900. Abstract
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Kondrashov, FA, Koonin EV.  2001.  Origin of Alternative Splicing by Tandem exon Duplication. Hum Mol Genet. 10:2661-2669. Abstract
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Wolf, YI, Kondrashov FA, Koonin EV.  2001.  Footprints of Primordial Introns on the Eukaryotic Genome: Still no Clear Traces. Trends Genet. 17:499-501.
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2000

Guigó, R, Agarwal P, Abril JF., Burset M, Fickett JW..  2000.  An assessment of gene prediction accuracy in large DNA sequences.. Genome Res.. 10:1631–1642. Abstract
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Notredame, C, Higgins DG, Heringa J.  2000.  T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 302:205-17. Abstract
Wolf, YI, Kondrashov FA, Koonin EV.  2000.  No Footprints of Primordial Introns in a Eukaryotic Genome. Trends Genet. 16:333-334.
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1999

Kondrashov, AS, Kondrashov FA.  1999.  Interactions Among Quantitative Traits in the Course of Sympatric Speciation. Nature. 400:351-354. Abstract
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1998

O'Brien, EA, Notredame C, Higgins DG.  1998.  Optimization of ribosomal RNA profile alignments. Bioinformatics. 14:332-41. Abstract
Notredame, C, Holm L, Higgins DG.  1998.  COFFEE: an objective function for multiple sequence alignments. Bioinformatics. 14:407-22. Abstract

1997

Notredame, C, O'Brien EA, Higgins DG.  1997.  RAGA: RNA sequence alignment by genetic algorithm. Nucleic Acids Res. 25:4570-80. Abstract

1996

Burset, M, Guigó R.  1996.  Evaluation of gene structure prediction programs.. Genomics. 34:353–367. Abstract
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Notredame, C, Higgins DG.  1996.  SAGA: sequence alignment by genetic algorithm. Nucleic Acids Res. 24:1515-24. Abstract

1992

Guigó, R, Knudsen S, Drake N, Smith T.  1992.  Prediction of gene structure.. J. Mol. Biol.. 226:141–157. Abstract
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