Publications

Publications of the whole Bioinformatics and Genomics programme

2013

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
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
Knowles D, Röder M, Merkel A, Guigó R.  2013.  Grape RNA-Seq analysis pipeline environment. Bioinformatics. 10.1093/bioinformatics/btt016 Abstract
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

Johnson R.  2012.  Long non-coding RNAs in Huntington's disease neurodegeneration.. Neurobiol. Dis.. 46:245–254. Abstract
Johnson R, Noble W, Tartaglia GG, Buckley NJ.  2012.  Neurodegeneration as an RNA disorder. Prog Neurobiol..
Cirillo D, Agostini F, Tartaglia GG.  2012.  Predictions of protein–RNA interactions. WIREs Comput Mol Sci..
Roodveldt C, Andersson A, De Genst EJ, Labrador-Garrido A, Buell AK, Dobson CM, Tartaglia GG, M. V.  2012.  A rationally designed six-residue swap generates comparability in the aggregation behavior of α-synuclein and β-synuclein. Biochemistry.
Marcet-Houben M, Ballester AR, de la Fuente B, Harries E, Marcos JF, González-Candelas L, Gabaldón T.  2012.  Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus.. BMC Genomics. 13:646. Abstract
Pubmed
Silva LL, Marcet-Houben M, Nahum LA, Zerlotini A, Gabaldón T, Oliveira G.  2012.  The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite's biology.. BMC Genomics. 13:617. Abstract
application/pdf iconSilva_et_al_Schistosoma_phylome_BMCGenomics_2012.pdf
 Pubmed
application/pdf iconSilva_et_al_Schistosoma_phylome_BMCGenomics_2012.pdf
Pervouchine DD, Knowles DG, Guigó R.  2012.  Intron-Centric Estimation of Alternative Splicing from RNA-seq data. Bioinformatics. 29(2):273-274. Abstract
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
 Pubmed
application/pdf iconMain text
application/pdf iconSupplementary
Kondrashov FA.  2012.  Gene duplication as a mechanism of genomic adaptation to a changing environment. Proc. Biol. Sci.. 279:5048–5057.
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Povolotskaya IS, Kondrashov FA, Lleda A, Vlasov PK.  2012.  Stop codons in bacteria are not selectively equivalent. Biol. Direct. 7:30.
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, Del Pozo A, Tress M, Johnson R, Guigo R et al..  2012.  Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.. Genome Res.. 22:1231–1242. 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
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
Marco-Sola S, Sammeth M, Guigó R, Ribeca P.  2012.  The GEM mapper: fast, accurate and versatile alignment by filtration. Nat. Methods. 9:1185–1188. Abstract
Miranda-Saavedra D, Gabaldón T, Barton GJ, Langsley G, Doerig C.  2012.  The kinomes of apicomplexan parasites.. Microbes Infect.. 14:796–810. Abstract
application/pdf iconMiranda_Saavedra_apicomplexan_kinomes_MI_2012.pdf
application/pdf iconMiranda_Saavedra_apicomplexan_kinomes_MI_2012.pdf
Piškur J, Ling Z, Marcet-Houben M, Ishchuk OP, Aerts A, LaButti K, Copeland A, Lindquist E, Barry K, Compagno C et al..  2012.  The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties.. Int. J. Food Microbiol.. 157:202–209. Abstract
application/pdf iconPiskur_Dekkera_Genome_paper_IJFM_2012.pdf
application/pdf iconPiskur_Dekkera_Genome_paper_IJFM_2012.pdf
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
application/pdf iconValack_parapsilosis_mtGenomes_Mitochondrion_2012.pdf
Capella-Gutiérrez S, Marcet-Houben M, Gabaldón T.  2012.  Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi.. BMC Biol.. 10:47. Abstract
application/pdf iconCapella_microsporidia_BMCBiol_2012.pdf
application/pdf iconCapella_microsporidia_BMCBiol_2012.pdf
Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, González VM, Hénaff E, Câmara F, Cozzuto L, Lowy E et al..  2012.  The genome of melon (Cucumis melo L.).. Proc. Natl. Acad. Sci. U.S.A.. 109:11872–11877. Abstract
Pubmed
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.
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.
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.
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.
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.
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.
Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T et al..  2012.  An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol.. 13:418.
Johnson R, Richter N, Bogu GK, Bhinge A, Teng SW, Choo SH, Andrieux LO, de Benedictis C, Jauch R, Stanton LW.  2012.  A genome-wide screen for genetic variants that modify the recruitment of REST to its target genes. PLoS Genet.. 8:e1002624. Abstract
Pubmed
Consortium TTG, Institute KDNAR, Sato S, Tabata S, Hirakawa H, Asamizu E, Shirasawa K, Isobe S, Kaneko T, Nakamura Y et al..  2012.  The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 485:635–641. Abstract
Pubmed
Arnold P, Erb I, Pachkov M, Molina N, van Nimwegen E.  2012.  MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. Bioinformatics. 28:487–494.
Torrent M, Di Tommaso P, Pulido D, Nogués MV, Notredame C, Boix E, Andreu D.  2012.  AMPA: an automated web server for prediction of protein antimicrobial regions.. Bioinformatics. 28:130–131. Abstract
Pubmed
Chang JM, Di Tommaso P, Taly JF, Notredame C.  2012.  Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee.. BMC Bioinformatics. 13 Suppl 4:S1. Abstract
Pubmed
Erb I, González-Vallinas JR, Bussotti G, Blanco E, Eyras E, Notredame C.  2012.  Use of ChIP-Seq data for the design of a multiple promoter-alignment method.. Nucleic Acids Res.. 40:e52. Abstract
Pubmed
Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL, Herrero J, the for Consortium QO.  2012.  Toward community standards in the quest for orthologs.. Bioinformatics (Oxford, England). 28:900–904. Abstract
application/pdf iconDessimoz_and_QfO_Bioinformatics_2012.pdf
 Pubmed
application/pdf iconDessimoz_and_QfO_Bioinformatics_2012.pdf
Bohle HM, Gabaldón T.  2012.  Selection of marker genes using whole-genome DNA polymorphism analysis.. Evol. Bioinform. Online. 8:161–169. Abstract
application/pdf iconBohle_Gabaldon_EvolBioinf_2012_MarkerGenes.pdf
 Pubmed
application/pdf iconBohle_Gabaldon_EvolBioinf_2012_MarkerGenes.pdf
Mariotti M, Ridge PG, Zhang Y, Lobanov AV, Pringle TH, Guigo R, Hatfield DL, Gladyshev VN.  2012.  Composition and evolution of the vertebrate and Mammalian selenoproteomes. PLoS ONE. 7:e33066.
Pubmed
Speretta E, Jahn TR, Tartaglia GG, Favrin G, Barros TP, Imarisio S, Lomas DA, Luheshi LM, Crowther DC, Dobson CM.  2012.  Expression in Drosophila of Tandem Aβ Peptides Provides Insights Into the Link Between Aggregation and Neurotoxicity. J Biol Chem.
Pubmed
Calloni G, Chen T, Schermann SM, Chang H, Genevaux P, Agostini F, Tartaglia GG, Hayer-Hartl M, Hartl FU.  2012.  DnaK Functions as a Central Hub in the E. coli Chaperone Network. Cell Reports.
Lee JH., Wan KL., Mohd-Adnan A., Gabaldón T.  2012.  Evolution of the ferritin family in vertebrates. Trends in Evol Biol. 4:e3. Abstract
application/pdf iconLee_et_al_Ferritin_TEB.pdf
application/pdf iconLee_et_al_Ferritin_TEB.pdf
Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, Bock C, Boehm B, Campo E, Caricasole A et al..  2012.  BLUEPRINT to decode the epigenetic signature written in blood. Nat. Biotechnol.. 30:224–226.
Pubmed
Ollivier M, Gabaldón T, Poulain J, Gavory F, Leterme N, Gauthier JP, Legeai F, Tagu D, Simon JC, Rispe C.  2012.  Comparison of gene repertoires and patterns of evolutionary rates in eight aphid species that differ by reproductive mode.. Genome Biol Evol. 4:155–167. Abstract
application/pdf iconOllivier_GBE_2012_eight_aphids.pdf
 Pubmed
application/pdf iconOllivier_GBE_2012_eight_aphids.pdf
Derrien T, Guigo R, Johnson R.  2012.  The Long Non-Coding RNAs: A New (P)layer in the "Dark Matter". Front Genet.. 2(107):1–6. Abstract
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed

2011

Koblik EA, Red'kin YA, Meer MS, Derelle R, Golenkina SA, Kondrashov FA, Arkhipov VY.  2011.  Acrocephalus orinus: a case of mistaken identity. PLoS ONE. 6:e17716.
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Erb I, van Nimwegen E.  2011.  Transcription Factor Binding Site Positioning in Yeast: Proximal Promoter Motifs Characterize TATA-Less Promoters. PloS one. 6:e24279.
Taly JF, Magis C, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Kemena C, Notredame C.  2011.  Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures.. Nat Protoc. 6:1669–1682. Abstract
Pubmed
Bussotti G, Raineri E, Erb I, Zytnicki M, Wilm A, Beaudoing E, Bucher P, Notredame C.  2011.  BlastR–fast and accurate database searches for non-coding RNAs.. Nucleic Acids Res.. 39:6886–6895. Abstract
Pubmed
Kemena C, Taly JF, Kleinjung J, Notredame C.  2011.  STRIKE: evaluation of protein MSAs using a single 3D structure.. Bioinformatics. 27:3385–3391. Abstract
Pubmed
Merhej V, Notredame C, Royer-Carenzi M, Pontarotti P, Raoult D.  2011.  The rhizome of life: the sympatric Rickettsia felis paradigm demonstrates the random transfer of DNA sequences.. Mol. Biol. Evol.. 28:3213–3223. Abstract
Pubmed
Lin HN, Notredame C, Chang JM, Sung TY, Hsu WL.  2011.  Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words.. PLoS ONE. 6:e27872. Abstract
Pubmed
Esteve-Codina A, Kofler R, Palmieri N, Bussotti G, Notredame C, Pérez-Enciso M.  2011.  Exploring the gonad transcriptome of two extreme male pigs with RNA-seq.. BMC Genomics. 12:552. Abstract
Pubmed
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
application/pdf iconLopezSilva_Schistosoma_Peptidases_MIOC_2011.pdf
 Pubmed
application/pdf iconLopezSilva_Schistosoma_Peptidases_MIOC_2011.pdf
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
Pubmed
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
Pubmed
Gonzalez-Porta M, Calvo M, Sammeth M, Guigo R.  2011.  Estimation of alternative splicing variability in human populations. Genome research. 22:528-538. Abstract
Pubmed
Kedzierska AM, Drton M, Guigo R, Casanellas M.  2011.  SPIn: model selection for phylogenetic mixtures via linear invariants.. Molecular biology and evolution. Abstract
Pubmed
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
Pubmed
Rius J, Cores F, Solsona F, van Hemert JI, Koetsier J, Notredame C.  2011.  A user-friendly web portal for T-Coffee on supercomputers.. BMC Bioinformatics. 12:150. Abstract
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Consortium ENCODEP, 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
Pubmed
Di Tommaso P, Moretti S, Xenarios I, Orobitg M, Montanyola A, Chang JM, Taly JF, Notredame C.  2011.  T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.. Nucleic acids research. Abstract
Pubmed
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
Pubmed
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
Pubmed
Bellucci M, Agostini F, Masin M, Tartaglia GG.  2011.  Predicting protein associations with long noncoding RNAs. Nat. Methods. 8:444–445.
Pubmed
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
Pubmed
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
Pubmed
Derrien T, Guigó R.  2011.  [Long non-coding RNAs with enhancerlike function in human cells.]. Medecine sciences : M/S. 27:359–361.
Pubmed
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
Pubmed
Huerta-Cepas J, Gabaldón T.  2011.  Assigning duplication events to relative temporal scales in genome-wide studies.. Bioinformatics. 27:38–45. Abstract
application/pdf iconHuerta-cepas_Gabaldon_Bioinformatics_2010.pdf
 Pubmed
application/pdf iconHuerta-cepas_Gabaldon_Bioinformatics_2010.pdf
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
Pubmed
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
Pubmed
Marcet-Houben M, Gabaldón T.  2011.  TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees.. Nucleic acids research. Abstract
Pubmed
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
Pubmed
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..

2010

Notredame C.  2010.  Computing multiple sequence/structure alignments with the T-coffee package.. Curr Protoc Bioinformatics. Chapter 3:Unit3.8.1–Unit3.825. Abstract
Pubmed
Di Tommaso P, Orobitg M, Guirado F, Cores F, Espinosa T, Notredame C.  2010.  Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud.. Bioinformatics. 26:1903–1904. Abstract
Pubmed
Coll O, Villalba A, Bussotti G, Notredame C, Gebauer F.  2010.  A novel, noncanonical mechanism of cytoplasmic polyadenylation operates in Drosophila embryogenesis.. Genes Dev.. 24:129–134. Abstract
Pubmed
Magis C, Stricher F, van der Sloot AM, Serrano L, Notredame C.  2010.  T-RMSD: a fine-grained, structure-based classification method and its application to the functional characterization of TNF receptors.. J. Mol. Biol.. 400:605–617. Abstract
Pubmed
Yau WL, Blisnick T, Taly JF, Helmer-Citterich M, Schiene-Fischer C, Leclercq O, Li J, Schmidt-Arras D, Morales MA, Notredame C et al..  2010.  Cyclosporin A treatment of Leishmania donovani reveals stage-specific functions of cyclophilins in parasite proliferation and viability.. PLoS Negl Trop Dis. 4:e729. Abstract
Pubmed
Lingner T, Mühlhausen S, Gabaldón T, Notredame C, Meinicke P.  2010.  Predicting phenotypic traits of prokaryotes from protein domain frequencies.. BMC Bioinformatics. 11:481. Abstract
Pubmed
Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg LA, Bouffard P, Burt DW, Crasta O, Crooijmans RP et al..  2010.  Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.. PLoS Biol.. 8 Abstract
Pubmed
Tartaglia GG, Dobson CM, Hartl FU, Vendruscolo M.  2010.  Physicochemical determinants of chaperone requirements.. J. Mol. Biol.. 400:579–588. Abstract
Pubmed
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
Pubmed
Tartaglia GG, Vendruscolo M.  2010.  Proteome-level interplay between folding and aggregation propensities of proteins.. J. Mol. Biol.. 402:919–928. Abstract
Pubmed
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
Pubmed
Lee Y, Zhou T, Tartaglia GG, Vendruscolo M, Wilke CO.  2010.  Translationally optimal codons associate with aggregation-prone sites in proteins.. Proteomics. Abstract
Pubmed
Meer MV, Kondrashov AS, Artzy-Randrup Y, Kondrashov FA.  2010.  Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature. 464:279–282.
application/pdf iconMain text
application/pdf iconSupplementary Information
 Pubmed
application/pdf iconMain text
application/pdf iconSupplementary Information
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.
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Povolotskaya IS, Kondrashov FA.  2010.  Sequence space and the ongoing expansion of the protein universe. Nature. 465:922–926.
application/pdf iconMain text
application/pdf iconSupplementary Information
application/pdf iconSupplementary Table
 Pubmed
application/pdf iconMain text
application/pdf iconSupplementary Information
application/pdf iconSupplementary Table
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Mariotti M, Guigó R.  2010.  Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes. Bioinformatics (Oxford, England). Abstract
application/pdf iconbioinformatics.btq516.full_.pdf
 Pubmed
application/pdf iconbioinformatics.btq516.full_.pdf
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
Pubmed
Gabaldón T, Capella-Gutiérrez S.  2010.  Lack of phylogenetic support for a supposed actinobacterial origin of peroxisomes.. Gene. Abstract
Pubmed
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
Pubmed
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
Pubmed
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
application/pdf iconpdf
 Pubmed
application/pdf iconpdf
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
Pubmed
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
Pubmed
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.
application/pdf iconDiez_DeathBase_CDD_2010.pdf
 Pubmed
application/pdf iconDiez_DeathBase_CDD_2010.pdf
Consortium ICG.  2010.  International network of cancer genome projects. Nature. 464:993–998. Abstract
Pubmed
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
Pubmed
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
Pubmed
Consortium TIAG.  2010.  Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS biology. 8:e1000313. Abstract
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Milinkovitch MC, Helaers R, Depiereux E, Tzika AC, Gabaldon T.  2010.  2X genomes - depth does matter.. Genome biology. 11:R16. Abstract
Pubmed
Gabaldón T.  2010.  Peroxisome diversity and evolution.. Philos. Trans. R. Soc. Lond., B, Biol. Sci.. 365:765–773. Abstract
Pubmed
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
application/pdf iconMihailovich_et_al_BioEssays_2009_coldShok.pdf
 Pubmed
application/pdf iconMihailovich_et_al_BioEssays_2009_coldShok.pdf
Huerta-Cepas J, Dopazo J, Gabaldón T.  2010.  ETE: a python Environment for Tree Exploration.. BMC bioinformatics. 11:24. Abstract
application/pdf iconHuerta_cepas_et_al_2010_ETE.pdf
 Pubmed
application/pdf iconHuerta_cepas_et_al_2010_ETE.pdf
Innan H, Kondrashov FA.  2010.  The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet. 11(2):108.
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Kondrashov AS, Povolotskaya IS, Ivankov DN, Kondrashov FA.  2010.  Rate of sequence divergence under constant selection. Biology Direct. 5(1) Abstract
application/msword iconMain text
application/msword iconMain text
Kondrashov FA.  2010.  Gene Dosage and Duplication. Evolution after Gene Duplication. Abstract
application/msword iconMain text
image/jpeg iconFigure 1
image/jpeg iconFigure 2
application/msword iconMain text
image/jpeg iconFigure 1
image/jpeg iconFigure 2

2009

Taddei A, Van Houwe G, Nagai S, Erb I, van Nimwegen E, Gasser SM.  2009.  The functional importance of telomere clustering: Global changes in gene expression result from SIR factor dispersion. Genome research. 19:611–625.
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. 27:300–306. Abstract
Pubmed
Kemena C, Notredame C.  2009.  Upcoming challenges for multiple sequence alignment methods in the high-throughput era.. Bioinformatics. 25:2455–2465. Abstract
Pubmed
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
Pubmed
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
Pubmed
Tartaglia GG, Vendruscolo M.  2009.  Correlation between mRNA expression levels and protein aggregation propensities in subcellular localisations.. Mol Biosyst. 5:1873–1876. Abstract
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Ferreira PG, 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
Pubmed
Thornton J, including Guigó BSNR.  2009.  Annotations for all by all - the BioSapiens network.. Genome Biol.. 10:401. Abstract
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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.
Pubmed
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..
Pubmed
Marcet-Houben M, Gabaldón T.  2009.  Acquisition of prokaryotic genes by fungal genomes. Trends Genet..
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Sequencing BG, 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
Pubmed
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
Pubmed
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
Pubmed
Pignatelli M, Serras F, Moya A, Guigó R, Corominas M.  2009.  CROC: finding chromosomal clusters in eukaryotic genomes.. Bioinformatics. 25:1552–1553. Abstract
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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.
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
Pubmed
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
application/pdf iconMain text
 Pubmed
application/pdf iconMain text

2008

Schlecht U, Erb I, Demougin P, Robine N, Borde V, van Nimwegen E, Nicolas A, Primig M.  2008.  Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast. Molecular Biology of the Cell. 19:2193–2207.
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
Pubmed
Tartaglia GG, Vendruscolo M.  2008.  The Zyggregator method for predicting protein aggregation propensities.. Chem Soc Rev. 37:1395–1401. Abstract
Pubmed
Vendruscolo M, Tartaglia GG.  2008.  Towards quantitative predictions in cell biology using chemical properties of proteins.. Mol Biosyst. 4:1170–1175. Abstract
Pubmed
Weng Z, Guigó R.  2008.  In silico meets in vivo.. Genome Biol.. 9:302. Abstract
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Chapple CE, Guigó R.  2008.  Relaxation of selective constraints causes independent selenoprotein extinction in insect genomes.. PLoS ONE. 3:e2968. Abstract
Pubmed
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
Pubmed
Sammeth M, Foissac S, Guigó R.  2008.  A general definition and nomenclature for alternative splicing events.. PLoS Comput. Biol.. 4:e1000147. Abstract
Pubmed
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
Pubmed
Gabaldón T.  2008.  Large-scale assignment of orthology: back to phylogenetics? Genome Biol.. 9:235. Abstract
Pubmed
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
Pubmed
Piqué M, López JM, Foissac S, Guigó R, Méndez R.  2008.  A combinatorial code for CPE-mediated translational control.. Cell. 132:434–448. Abstract
Pubmed
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
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Schmidt S, Gerasimova A, Kondrashov FA, Adzhubei IA, Kondrashov AS, Sunyaev S.  2008.  Hypermutable non-synonymous sites are under stronger negative selection.. PLoS Genet.. 4:e1000281. Abstract
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Assis R, Kondrashov AS, Koonin EV, Kondrashov FA.  2008.  Nested genes and increasing organizational complexity of metazoan genomes.. Trends Genet.. 24:475–478. Abstract
application/pdf iconMain text
application/pdf iconSupplementary Information
 Pubmed
application/pdf iconMain text
application/pdf iconSupplementary Information
Arkhipov VY, Koblik EA, Red'kin YA, Kondrashov FA.  2008.  Birds of the Krasnoye Lake area (South Chukotka). Arch Zool Mus MGU. 49:159-183. Abstract
application/pdf iconMain text
application/pdf iconMain text

2007

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
Pubmed
Tartaglia GG, Cavalli A, Vendruscolo M.  2007.  Prediction of local structural stabilities of proteins from their amino acid sequences.. Structure. 15:139–143. Abstract
Pubmed
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.
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Blanco E, Guigó R, Messeguer X.  2007.  Multiple non-collinear TF-map alignments of promoter regions.. BMC Bioinformatics. 8:138. Abstract
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Consortium DG12, 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
Pubmed
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
Pubmed
Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldón T.  2007.  The human phylome.. Genome Biol.. 8:R109. Abstract
Pubmed
Consortium ENCODEP, 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
Pubmed
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.
Pubmed
Kondrashov FA, Gurbich TA, Vlasov PK.  2007.  Selection for Functional Uniformity of tuf Duplicates in Gamma-proteobacteria. Trends Genet. 23:215-218. Abstract
application/pdf iconMain text
application/pdf iconSupplementary Information
 Pubmed
application/pdf iconMain text
application/pdf iconSupplementary Information
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
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Popadin KY, Mamirova LA, Kondrashov FA.  2007.  A Manually Curated Database of Tetrapod Mitochondrially Encoded tRNA Sequences and Secondary Structures. BMC Bioinformatics. 8:441-441. Abstract
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Bazykin GA, Kondrashov FA, Brudno M, Poliakov A, Dubchak I, Kondrashov AS.  2007.  Extensive Parallelism in Protein Evolution. Biol Direct. 2:20-20. Abstract
application/pdf iconMain text
 Pubmed
application/pdf iconMain text

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
Pubmed
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
Pubmed
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
Pubmed
Mularoni L, Guigó R, Albà MM.  2006.  Mutation patterns of amino acid tandem repeats in the human proteome.. Genome Biol.. 7:R33. Abstract
Pubmed
Guigó R, Valcárcel J.  2006.  Unweaving the meanings of messenger RNA sequences.. Mol. Cell. 23:150–151. Abstract
Pubmed
Blanco E, Messeguer X, Smith TF, Guigó R.  2006.  Transcription factor map alignment of promoter regions.. PLoS Comput. Biol.. 2:e49. Abstract
Pubmed
Reese MG, Guigó R.  2006.  EGASP: Introduction.. Genome Biol.. 7 Suppl 1:S1.1–S1.3.
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
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, 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
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
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
application/pdf iconMain text
application/pdf iconMain text
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
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Kondrashov FA, Kondrashov AS.  2006.  Role of Selection in Fixation of gene Duplications. J Theor Biol. 239:141-151. Abstract
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
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
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
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
application/pdf iconMain text
application/msword iconSupplementary Information
 Pubmed
application/pdf iconMain text
application/msword iconSupplementary Information

2005

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
Pubmed
Tartaglia GG, Pellarin R, Cavalli A, Caflisch A.  2005.  Organism complexity anti-correlates with proteomic beta-aggregation propensity.. Protein Sci.. 14:2735–2740. Abstract
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Abril JF, Castelo R, Guigó R.  2005.  Comparison of splice sites in mammals and chicken.. Genome Res.. 15:111–119. Abstract
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Guigó R, Reese MG.  2005.  EGASP: collaboration through competition to find human genes.. Nat. Methods. 2:575–577. Abstract
Pubmed
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
Pubmed
Kondrashov FA.  2005.  In Search of the Limits of Evolution. Nat Genet. 37:9-10.
application/pdf iconMain text
application/pdf iconMain text
Jordan IK, 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
application/pdf iconShort correction
application/msword iconSupplementary Tables
application/msword iconSupplementary Methods
 Pubmed
application/pdf iconShort correction
application/msword iconSupplementary Tables
application/msword iconSupplementary Methods
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
application/msword iconMain text
application/msword iconMain text [In Russian]
application/zip iconFigures [In Russian]
 Pubmed
application/msword iconMain text
application/msword iconMain text [In Russian]
application/zip iconFigures [In Russian]
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
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
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
application/msword iconMain text
application/msword iconMain text [In Russian]
application/vnd.ms-powerpoint iconFigures [In Russian]
application/vnd.ms-powerpoint iconFigures
 Pubmed
application/msword iconMain text
application/msword iconMain text [In Russian]
application/vnd.ms-powerpoint iconFigures [In Russian]
application/vnd.ms-powerpoint iconFigures
Kondrashov FA.  2005.  Prediction of Pathogenic Mutations in Mitochondrially Encoded Human tRNAs. Hum Mol Genet. 14:2415-2419. Abstract
application/pdf iconMain text
application/vnd.ms-excel iconSupplementary Information
 Pubmed
application/pdf iconMain text
application/vnd.ms-excel iconSupplementary Information

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
Pubmed
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
Pubmed
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
Pubmed
Brent MR, Guigó R.  2004.  Recent advances in gene structure prediction.. Curr. Opin. Struct. Biol.. 14:264–272. Abstract
Pubmed
Castelo R, Guigó R.  2004.  Splice site identification by idlBNs.. Bioinformatics. 20 Suppl 1:i69–i76. Abstract
Pubmed
Consortium ENCODEP.  2004.  The ENCODE (ENCyclopedia Of DNA Elements) Project.. Science. 306:636–640. Abstract
Pubmed
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
Pubmed
Consortium ICGS.  2004.  Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.. Nature. 432:695–716. Abstract
Pubmed
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
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
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.
Pubmed
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
application/pdf iconMain text
application/pdf iconMain text
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.
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Panchenko AR, Kondrashov FA, Bryant S.  2004.  Prediction of Functional Sites by Analysis of Sequence and Structure Conservation. Protein Sci. 13:884-892. Abstract
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
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
application/pdf iconMain text
application/msword iconSupplementary Information
 Pubmed
application/pdf iconMain text
application/msword iconSupplementary Information
Kondrashov FA, Ogurtsov AY, Kondrashov AS.  2004.  Bioinformatical Assay of Human gene Morbidity. Nucleic Acids Res. 32:1731-1737. Abstract
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Kern AD, Kondrashov FA.  2004.  Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial tRNAs. Nat Genet. 36:1207-1212. Abstract
application/pdf iconMain text
application/pdf iconSupplementary Figure1
application/pdf iconSupplementary Table
application/pdf iconSupplementary Note
application/pdf iconSupplementary Methods
 Pubmed
application/pdf iconMain text
application/pdf iconSupplementary Figure1
application/pdf iconSupplementary Table
application/pdf iconSupplementary Note
application/pdf iconSupplementary Methods

2003

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
Pubmed
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
Pubmed
Kryukov GV, Castellano S, Novoselov SV, Lobanov AV, Zehtab O, Guigó R, Gladyshev VN.  2003.  Characterization of mammalian selenoproteomes.. Science. 300:1439–1443. Abstract
Pubmed
Abril JF, Guigó R, Wiehe T.  2003.  gff2aplot: Plotting sequence comparisons.. Bioinformatics. 19:2477–2479. Abstract
Pubmed
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
Pubmed
Gabaldón T, Huynen MA.  2003.  Reconstruction of the proto-mitochondrial metabolism.. Science. 301:609.
Pubmed
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
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
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
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
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
application/pdf iconMain text
 Pubmed
application/pdf iconMain text

2002

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
Pubmed
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
Pubmed
Consortium MGS, 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
Pubmed
Notredame C.  2002.  Recent progress in multiple sequence alignment: a survey. Pharmacogenomics. 3:131-44. Abstract
Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV.  2002.  Selection in the Evolution of gene Duplications. Genome Biol. 3:RESEARCH0008-RESEARCH0008. Abstract
application/pdf iconMain text
application/pdf iconMain text
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
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Perelygin AA, Kondrashov FA, Rogozin IB, Brinton MA.  2002.  Evolution of the Mouse polyubiquitin-C gene. J Mol Evol. 55:202-210. Abstract
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Kondrashov AS, Sunyaev S, Kondrashov FA.  2002.  Dobzhansky-Muller Incompatibilities in Protein Evolution. Proc Natl Acad Sci U S A. 99:14878-14883. Abstract
application/pdf iconMain text
application/pdf iconSupplementary Table2
application/pdf iconSupplementary Table3
text/plain iconSupplementary Information
 Pubmed
application/pdf iconMain text
application/pdf iconSupplementary Table2
application/pdf iconSupplementary Table3
text/plain iconSupplementary Information

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
Pubmed
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
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Rogozin IB, Kondrashov FA, Glazko G.  2001.  Use of Mutation Spectra Analysis Software. Hum Mutat. 17:83-8102. Abstract
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
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
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Kondrashov FA, Kondrashov AS.  2001.  Multidimensional Epistasis and the Disadvantage of sex. Proc Natl Acad Sci U S A. 98:12089-12092. Abstract
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Kondrashov FA, Koonin EV.  2001.  Origin of Alternative Splicing by Tandem exon Duplication. Hum Mol Genet. 10:2661-2669. Abstract
application/pdf iconMain text
 Pubmed
application/pdf iconMain text
Wolf YI, Kondrashov FA, Koonin EV.  2001.  Footprints of Primordial Introns on the Eukaryotic Genome: Still no Clear Traces. Trends Genet. 17:499-501.
application/pdf iconMain text
 Pubmed
application/pdf iconMain text

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
Pubmed
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.
application/pdf iconMain text
application/pdf iconErratum Table
 Pubmed
application/pdf iconMain text
application/pdf iconErratum Table

1999

Kondrashov AS, Kondrashov FA.  1999.  Interactions Among Quantitative Traits in the Course of Sympatric Speciation. Nature. 400:351-354. Abstract
application/pdf iconMain text
 Pubmed
application/pdf iconMain text

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
Pubmed
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
Pubmed
Syndicate content