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Scientific Publications

Laia Navarro-Martín, Jordi Viñas, Laia Ribas, Noelia Díaz, Arantxa Gutiérrez, Luciano Di Croce.
DNA Methylation of the Gonadal Aromatase (cyp19a) Promoter Is Involved in Temperature-Dependent SexRatio Shifts in the European Sea Bass/ 7(12):e1002447
PLoS Genetics 7(12):e1002447 (2011).
Mancuso FM, Montfort M, Carreras A, Alibes A, Roma G..
"HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data".
BMC Res Notes. 4(1):546. [Epub ahead of print] (2011). abstract
Kemena C, Taly JF, Kleinjung J, Notredame C..
STRIKE: evaluation of protein MSAs using a single 3D structure.
Bioinformatics 2011 Dec 15;27(24):3385-91. Epub 2011 Oct 28. (2011). abstract
Bruns C, McCaffery JM, Curwin AJ, Duran JM, Malhotra V..
Biogenesis of a novel compartment for autophagosome-mediated unconventional protein secretion
Journal of Cell Biology 195(6):979-92. Epub 2011 Dec 5 (2011). abstract
Burga A, Casanueva MO, Lehner B..
Predicting mutation outcome from early stochastic variation in genetic interaction partners
Nature 480(7376):250-3. doi: 10.1038/nature10665 (2011).
Graf T.
Historical origins of transdifferentiation and reprogramming.
Cell Stem Cell. 9(6):504-16. (2011).
Lin HN, Notredame C, Chang JM, Sung TY, Hsu WL..
Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words.
PLoS One. 2011;6(12):e27872. Epub 2011 Dec 2. (2011). abstract
Blanco S, Kurowski A, Nichols J, Watt FM, Benitah SA, Frye M.
The RNA-Methyltransferase Misu (NSun2) Poises Epidermal Stem Cells to Differentiate
PLoS Genetics 7(12):e1002403. (2011).
Schroeder I.S., Sulzbacher S., Nolden T., Fuchs J., Czarnota J., Meisterfeld R., Himmelbauer H., Wobus A.M..
Induction and selection of Sox17 expressing endoderm cells generated from murine embryonic stem cells"
Cells Tissues Organs 195(6):507-23. doi: 10.1159/000329864 (2011). abstract
Christina Kiel, Andreas Vogt, Anne Campagna, Andrew Chatr-aryamontri, Monika BeerMonika Beer Magdalena Swiatek-de Lange et al.
Structural and functional protein network analyses predict novel signaling functions for rhodopsin
Molecular Systems Biology 7: Article number 551 (2011). abstract
Nascimento EM, Cox CL, Macarthur S, Hussain S, Trotter M, Blanco S, Suraj M, Nichols J, Kübler B, Benitah SA, Hendrich B, Odom DT, Frye M..
The opposing transcriptional functions of Sin3a and c-Myc are required to maintain tissue homeostasis.
Nature Cell Biology 13(12):1395-405. doi: 10.1038/ncb2385 (2011).
Pantano L, Estivill X, Marti E..
"A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome."
Bioinformatics 27(22):3202-3 (2011).
Simboeck E, Ribeiro JD, Teichmann S, Di Croce L..
Epigenetics and senescence: Learning from the INK4-ARF locus.
Biochemical Pharmacology 82(10):1361-70 (2011).
Jelier R, Semple JI, Garcia-Verdugo R, Lehner B..
Predicting phenotypic variation in yeast from individual genome sequences
Nat Genet 43(12):1270-4. doi: 10.1038/ng.1007 (2011). abstract
Meunier S, Vernos I..
K-fibre minus ends are stabilized by a RanGTP-dependent mechanism essential/ for functional spindle assembly
Nature Cell Biology 13(12):1406-14. doi: 10.1038/ncb2372 (2011). abstract
Vrijheid M, Martinez D, Aguilera I, Bustamante M, Ballester F, Estarlich M, Fernandez-Somoano A, Guxens M, Lertxundi N, et al.
"Indoor Air Pollution From Gas Cooking and Infant Neurodevelopment."
Epidemiology [Epub ahead of print] (2011).
Janich P, Pascual G, Merlos-Suárez A, Batlle E, Ripperger J, Albrecht U, Obrietan K, Di Croce L, Benitah SA..
The circadian molecular clock creates epidermal stem cell heterogeneity
Nature doi: 10.1038/nature10649. (2011).
Maxwell CA, Benítez J, Gómez-Baldó L, Osorio A, et al. (including Curado J, Tilgner H, Guigó R.).
Interplay between BRCA1 and RHAMM Regulates Epithelial Apicobasal Polarization and May Influence Risk of Breast Cancer.
PLoS Biology 2011 Nov;9(11):e1001199. Epub 2011 Nov 15. (2011). abstract
Esteve-Codina A, Kofler R, Palmieri N, Bussotti G, Notredame C, Pérez-Enciso M..
Exploring the gonad transcriptome of two extreme male pigs with RNA-seq.
BMC Genomics 2011 Nov 8;12:552. (2011). abstract
Minoche AE, Dohm JC, Himmelbauer H..
"Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems".
Genome Biology 12(11):R112. [Epub ahead of print] (2011). abstract
Taly JF, Magis C, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Kemena C, Notredame C..
Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures.
Nat Protoc. Nov;6(11):1669-82 (2011). abstract
Dobbernack G, Meinl W, Schade N, Florian S, Wend K, Voigt I, Himmelbauer H, Gross M, Liehr T, Glatt H. et al.
Altered tissue distribution of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine-DNA adducts in mice transgenic for human sulfotransferases 1A1 and 1A2"
Carcinogenesis 2011 Nov;32(11):1734-40. Epub 2011 Sep 7. (2011). abstract
Merhej V, Notredame C, Royer-Carenzi M, Pontarotti P, Raoult D..
The rhizome of life: the sympatric Rickettsia felis paradigm demonstrates the random transfer of DNA sequences.
Molecular Biology and Evolution 2011 Nov;28(11):3213-23. (2011). abstract
Rebordosa C, Kogevinas M, Guerra S, Castro-Giner F, Jarvis D, Cazzoletti L, Pin I, Siroux V, Wjst M, Antò JM, de Marco R, et al.
"ADRB2 Gly16Arg polymorphism, asthma control and lung function decline."
European Respiratory Journal 38(5):1029-35 (2011).
Silva LL, Marcet-Houben M, Zerlotini A, Gabaldón T, Oliveira G, Nahum LA..
Evolutionary histories of expanded peptidase families in Schistosoma mansoni.
Mem Inst Oswaldo Cruz. 2011 Nov;106(7):864-77. (2011). abstract
Teixeira CM, Martín ED, Sahún I, Masachs N, Pujadas Ll, Corvelo A, Bosch C, Rossi D, Martinez A, Maldonado R, Dierssen M Soriano E.
Over-expression of Reelin prevents the manifestation of behavioral phenotypes related to schizophrenia and bipolar disorder
Neuropsychopharmacology 36(12):2395-405 (2011).
Uribesalgo I, Buschbeck M, Gutiérrez A, Teichmann S, Demajo S, Kuebler B, Nomdedéu JF, Martín-Caballero J, Roma G, Benitah SA, Di Croce L.
E-box-independent regulation of transcription and differentiation by MYC.
Nature Cell Biology doi: 10.1038/ncb2355. (2011).
Salvador Aznar Benitah.
Tumour biology: Skin-cancer stem cells outwitted
Nature (2011). abstract
Abate-Daga D, Andreu N, Camacho-Sánchez J, Alemany R, Herance R, Millán O, Fillat C..
"Oncolytic Adenoviruses Armed with Thymidine Kinase Can Be Traced by PET Imaging and Show Potent Antitumoural Effects by Ganciclovir Dosing."
PLoS One 6(10):e26142 (2011).
Althammer S, González-Vallinas J, Ballaré C, Beato M, Eyras E..
Pyicos: A versatile toolkit for the analysis of high-throughput sequencing data.
Bioinformatics [Epub ahead of print] (2011). abstract
Di Tullio A, Manh TP, Schubert A, Månsson R, Graf T.
CCAAT/enhancer binding protein {alpha} (C/EBP{alpha})-induced transdifferentiation of pre-B/ cells into macrophages involves no overt retrodifferentiation.
Proceedings of the National Academy of Sciences of the United States of America 108(41):17016-21 (2011).
Schulz N, Himmelbauer H, Rath M, van Weeghel M, Houten S, Kulik W, Suhre K, Scherneck S, Vogel H, Kluge R, Wiedmer P, Joost HG, Schürmann A..
"Role of medium- and short-chain L-3-hydroxyacyl-CoA dehydrogenase in the regulation of body weight and thermogenesis".
Endocrinology 152(12):4641-51. Epub 2011 Oct 11. (2011). abstract
Lange M., Demajo S., Jain P., Di Croce L..
Combinatorial assembly and function of chromatin regulatory complexes
Epigenomics 3(5):567-80 (2011).
James Sharpe.
Two ways to use imaging: focusing directly on mechanism, or indirectly via behaviour?
Current Opinion in Genetics & Development 21(5):523-9. doi: 10.1016/j.gde.2011.08.012 (2011). abstract
R Sorek, L Serrano.
Bacterial genomes: from regulatory complexity to engineering
Current opinion in Microbiology 14:1–2 (2011). abstract
Szegezdi E, Reis CR, Van Der Sloot A, Natoni A, O'Reilly A, Reeve J, Cool RH, O'Dwyer M, Knapper S, Serrano L, Quax WJ, Samali A..
Targeting AML through DR4 with a novel variant of rhTRAIL.
J Cell Mol Med. 15(10):2216-31 (2011). abstract
Szegezdi E, Reis CR, van der Sloot AM, Natoni A, O'Reilly A, Reeve J, et al.
Targeting AML through DR4 with a novel variant of rhTRAIL.
J Cell Mol Med J Cell Mol Med. 2011 Oct;15(10):2216-31 (2011). abstract
Vanneste D, Ferreira V, Vernos I..
Chromokinesins: localization-dependent functions and regulation during cell division.
Biochem Soc Trans. 39(5):1154-60 (2011).
Oeschger FM, Wang WZ, Lee S, García-Moreno F, Goffinet AM, Arbonés ML, Rakic S, Molnár Z..
"Gene Expression Analysis of the Embryonic Subplate."
Cerebral Cortex [Epub ahead of print] (2011).
Azevedo D, Antunes M, Prag S, Ma X, Hacker U, Brodland GW, Hutson MS, Solon J, et al.
DRhoGEF2 Regulates Cellular Tension and Cell Pulsations in the Amnioserosa during/ Drosophila Dorsal Closure.
PLoS ONE 6(9):e23964. Epub 2011 Sep 16 (2011). abstract
Nicchia GP, Ficarella R, Rossi A, Giangreco I, Nicolotti O, Carotti A, Pisani F, Estivill X, Gasparini P, Svelto M, Frigeri A..
"D184E mutation in aquaporin-4 gene impairs water permeability and links to deafness."
Neuroscience 197:80-8 (2011).
Luis NM, Morey L, Mejetta S, Pascual G, Janich P, Kuebler B, Roma G, Nascimento E, Frye M, Di Croce L, Benitah SA..
Regulation of human epidermal stem cell proliferation and senescence requires polycomb- dependent and -independent functions of cbx4.
Cell Stem Cell. 9(3):233-46. (2011).
Bussotti G, Raineri E, Erb I, Zytnicki M, Wilm A, Beaudoing E, Bucher P, Notredame C..
BlastR--fast and accurate database searches for non-coding RNAs.
Nucleic Acids Research 2011 Sep 1;39(16):6886-6895. Epub 2011 May 30. (2011). abstract
Esteve-Codina A, Kofler R, Himmelbauer H, Ferretti L, Vivancos AP, Groenen MA, Folch JM, Rodríguez MC, Pérez-Enciso M..
"Partial short-read sequencing of a highly inbred Iberian pig and genomics inference thereof"
Heredity 107(3):256-64. doi: 10.1038/hdy.2011.13. (2011). abstract
Huerta-Cepas J, Dopazo J, Huynen MA, Gabaldón T..
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.
Briefings in Bioinformatics 2011 Sep;12(5):442-8. Epub 2011 Apr 22. (2011). abstract
Richly H, Aloia L, Di Croce L..
Roles of the Polycomb group proteins in stem cells and cancer
Cell Death Dis. 2:e204. doi: 10.1038/cddis.2011.84 (2011).
Jacquemont S, Reymond A, Zufferey F, Harewood L, Walters RG, Kutalik Z (...)Gratacòs M, (...)Villatoro Gomez S, , Estivill X, et al.
"Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus."
Nature 478(7367):97-102 (2011).
Malhotra V, Erlmann P..
Protein export at the ER: loading big collagens into COPII carriers.
EMBO Journal 30(17):3475-80 (2011).
Cao J, Schneeberger K, Ossowski S, Günther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C, Wang X, Ott F, Müller J, et al.
"Whole-genome sequencing of multiple Arabidopsis thaliana populations."
Nat Genet 43(10):956-63 (2011).
Baamonde C, Martínez-Cué C, Flórez J, Dierssen M..
"G protein-associated signal transduction processes are restored after post-weaning environmental enrichment in Ts65Dn, a Down syndrome mouse model"
Developmental Neuroscience 33(5):442-50. Epub 2011 Aug 25 (2011).
Constante M, Grünberg R, Isalan M..
A biobrick library for cloning custom eukaryotic plasmids
PLoS One 6(8):e23685. Epub 2011 Aug 25 (2011). abstract
Gomez-Marin A, Stephens GJ, Louis M..
Active sampling and decision making in Drosophila chemotaxis
Nature Communications 2:441. doi: 10.1038/ncomms1455 (2011). abstract
Di Croce L.
Regulating the shuttling of eukaryotic RNA polymerase II.
Molecular and Cellular Biology 31(19):3918-20. (2011).
Klein JD, Ossowski S, Schneeberger K, Weigel D, Huson DH..
"LOCAS - A Low Coverage Assembly Tool for Resequencing Projects."
PLoS One 6(8):e23455 (2011).
Marc Güell, Eva Yus, Maria Lluch-Senar, Luis Serrano.
Bacterial transcriptomics: what is beyond the RNA horiz-ome?
Nature Reviews Microbiology 9, 658-669 (2011). PubMed ID: transcriptomics: what is beyond the RNA horiz-ome?.abstract
Paronetto, MP, Miñana, B and Valcárcel, J.
The Ewing Sarcoma protein (EWS) regulates DNA damage-induced alternative splicing
Molecular Cell 43(3):353-68 (2011). abstract
Mejetta S, Morey L, Pascual G, Kuebler B, Mysliwiec MR, Lee Y, Shiekhattar R, Di Croce L, Benitah SA..
Jarid2 regulates mouse epidermal stem cell activation and differentiation.
EMBO Journal 30(17):3635-46. doi: 10.1038/emboj.2011.265. (2011).
B. Lehner.
Molecular mechanisms of epistasis within and between genes
Trends in Genetics 2011 Aug;27(8):323-31. Epub 2011 Jun 22 (2011). abstract
Beato M, Vicent GP..
"When every minute counts: the enzymatic complexity associated with the activation of hormone-dependent genes".
Cell Cycle 10(15):2407-9. Epub 2011 Aug 1. (2011). abstract
Miñones-Moyano E, Porta S, Escaramís G, Rabionet R, Iraola S, Kagerbauer B, Espinosa-Parrilla Y, Ferrer I, Estivill X, Martí E..
"MicroRNA profiling of Parkinson's disease brains identifies early downregulation of miR-34b/c which modulate mitochondrial function."
Human Molecular Genetics 20(15):3067-78 (2011). abstract
Villalba A, Coll O, Gebauer F. et al.
Cytoplasmic polyadenylation and translational control
Current Opinion in Genetics & Development 21(4):452-7. Epub 2011 Apr 30. (2011). abstract
Zakrzewski F, Weisshaar B, Fuchs J, Bannack E, Minoche AE, Dohm JC, Himmelbauer H, Schmidt T..
"Epigenetic profiling of heterochromatic satellite DNA"
Chromosoma 120(4):409-22. doi: 10.1007/s00412-011-0325-x. (2011). abstract
Mossuto MF, Bolognesi B, Guixer B, Dhulesia A, Agostini F, Kumita JR, Tartaglia GG, Dumoulin M, Dobson CM, Salvatella X..
Disulfide Bonds Reduce the Toxicity of the Amyloid Fibrils Formed by an Extracellular Protein./ 2011 Jul 25;50(31):7048-51. Epub 2011 Jun 10
Angew Chem Int Ed Engl. 2011 Jun 10. (2011). abstract
de Andrés-Aguayo L, Varas F, Kallin EM, Infante JF, Wurst W, Floss T, Graf T..
Musashi 2 is a regulator of the hematopoietic stem cell compartment identified by a retroviral insertion screen and knockout mice.
Blood 118(3):554-64. (2011).
Lluis F, Ombrato L, Pedone E, Pepe S, Merrill BJ, Cosma MP.
T-cell factor 3 (Tcf3) deletion increases somatic cell reprogramming by inducing epigenome modifications.
Proceedings of the National Academy of Sciences of the United States of America 108(29):11912-7 (2011).
Maier T, Schmidt A, Güell M, Kühner S, Gavin AC, Aebersold R, Serrano L..
Quantification of mRNA and protein and integration with protein turnover in a bacterium
Mol Syst Biol 7:511. doi: 10.1038/msb.2011.38 (2011). abstract
Mackereth CD, Madl T, Bonnal S, Simon B, Zanier K, Gasch A, Rybin V, Valcárcel J, Sattler M..
"Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF".
Nature 475(7356):408-11. doi: 10.1038/nature10171. (2011). abstract
Abrahams JP, Apweiler R, Balling R, Bertero MG, Bujnicki JM, Chayen NE, Chène P, Corthals GL, Dyl¿g T, Förster F, Heck AJ, Henderson PJ, Herwig R, et al.
4D Biology for health and disease" workshop report.
New Biotechnology 28(4):291-3. doi: 10.1016/j.nbt.2010.10.003 (2011). abstract
Di Tommaso P, Moretti S, Xenarios I, Orobitg M, Montanyola A, Chang JM, Taly JF, Notredame C..
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.
Nucleic Acids Research 2011 Jul;39(WS issue):W13-7. Epub 2011 May 9. (2011). abstract
Docampo E, Giardina E, Riveira-Muñoz E, de Cid R, Escaramís G, Perricone C, Fernández-Sueiro JL, Maymó J, González-Gay MA et al.
"Deletion of the LCE3C and LCE3B genes is a susceptibility factor for psoriatic arthritis: A/ study in Spanish and Italian populations and meta-analysis."
Arthritis Rheum. 63(7):1860-1865 (2011). abstract
Iraola-Guzmán S, Estivill X, Rabionet R..
"DNA methylation in neurodegenerative disorders: a missing link between genome and environment?"
Clinical Genetics 80(1):1-14 (2011). abstract
Peñas-Lledó EM, Dorado P, Agüera Z, Gratacós M, Estivill X, Fernández-Aranda F, Llerena A..
"High risk of lifetime history of suicide attempts among CYP2D6 ultrarapid metabolizers with eating disorders."
Molecular Psychiatry 16(7):691-2 (2011). abstract
Saito K, Yamashiro K, Ichikawa Y, Erlmann P, Kontani K, Malhotra V, Katada T..
cTAGE5 mediates collagen secretion through interaction with TANGO1 at endoplasmic reticulum exit sites.
Molecular Biology of the Cell 22(13):2301-8. Epub 2011 Apr 27 (2011).
Sánchez R, Serra F, Tárraga J, Medina I, Carbonell J, Pulido L, de María A, Capella-Gutíerrez S, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H..
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.
Nucleic Acids Research 2011 Jul;39 Suppl 2:W470-4. Epub 2011 Jun 6. (2011). abstract
Gauss R., Kanehara K., Carvalho, P., Nq DT., Aebi, M..
A complex of Pdi1p and the mannosidase Htm1p initiates clearance of unfolded/ glycoproteins from the endoplasmic reticulum.
Molecular and Cellular Biology 42(6):782-93 (2011). abstract
Llorens F, Hummel M, Pastor X, Ferrer A, Pluvinet R, Vivancos A, Castillo E, Iraola S, Mosquera AM, González E, Lozano J, Ingham M, Dohm JC, et al.
"Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis".
BMC Genomics 12:326. (2011). abstract
Verschueren E, Vanhee P, van der Sloot AM, Serrano L, Rousseau F, Schymkowitz J..
Protein design with fragment databases
Curr Opin Struct Biol (2011). abstract
Hyland EM, Molina H, Poorey K, Jie C, Xie Z, Dai J, Qian J, Bekiranov S, Auble DT, Pandey A, Boeke JD..
"An evolutionarily ‘young’ lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae".
Genes & Development 25(12):1306-19. doi: 10.1101/gad.2050311. (2011). abstract
J Van Durme, J Delgado, F Stricher, L Serrano, J Schymkowitz, F Rousseau.
A graphical interface for the FoldX forcefield
Bioinformatics 27(12):1711-2. doi: 10.1093/bioinformatics/btr254 (2011). abstract
Van Durme J, Delgado J, Stricher F, Serrano L, Schymkowitz J, Rousseau F..
A graphical interface for the FoldX forcefield.
Bioinformatics 27(12):1711-2 (2011). abstract
Herrmann F, Garriga-Canut M, Baumstark R, Fajardo-Sanchez E, Cotterell, J. et al.
p53 Gene Repair with Zinc Finger Nucleases Optimised by Yeast 1-Hybrid/ and Validated by Solexa Sequencing
PLoS One 6(6):e20913. doi: 10.1371/journal.pone.0020913 (2011).
García-Santamarina S, Boronat S, Espadas G, Ayté J, Molina H, Hidalgo E..
"The oxidized thiol proteome in fission yeast-Optimization of an ICAT-based method to identify H(2)O(2)-oxidized proteins".
Journal of Proteomics [Epub ahead of print] (2011). abstract
Schneeberger K, Ossowski S, Ott F, Klein JD, Wang X, Lanz C, Smith LM, Cao J, Fitz J, Warthmann N, Henz SR, Huson DH, Weigel D. Source..
"Reference-guided assembly of four diverse Arabidopsis thaliana genomes."
Proceedings of the National Academy of Sciences of the United States of America 108(25):10249-54 (2011).
Puente XS, Pinyol M, Quesada V, Conde L, Ordóñez GR, Villamor N, Escaramis G, Jares P, Beà S, González-Díaz M, Bassaganyas L, Baumann T et al.
"Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia."
Nature 475(7354):101-5 (2011). abstract
(...) M Gratacòs, P Cavalle, V Arija, A Gaviria, A Gutiérrez-Zotes, E Vilella..
"An association between plasma ferritin concentrations measured 48 hours after delivery and postpartum depression."
Journal of Affective Disorders 131(1-3):136-142 (2011). abstract
Bellucci M, Agostini F, Masin M, Tartaglia GG..
Predicting protein associations with long noncoding RNAs.
Nat Methods 8(6):444-5 (2011). abstract
De Masi F, Grove CA, Vedenko A, Alibés A, Gisselbrecht SS, Serrano L, et al.
Using a structural and logics systems approach to infer bHLH–DNA/ binding specificity determinants
Nucleic Acids Research 4553-4563. Epub 2011 Feb 18 (2011). abstract
Karwautz AF, Wagner G, Waldherr K, Nader IW, Fernandez-Aranda F, Estivill X, Holliday J, Collier DA, Treasure JL..
"Gene-environment interaction in anorexia nervosa: relevance of non-shared environment and the serotonin transporter gene."
Molecular Psychiatry 16(6):590-2 (2011). abstract
Laura Quintana & James Sharpe.
Optical projection tomography of vertebrate embryo development
Cold Spring Harbor Protocols 2011(6):586-94. doi: 10.1101/pdb.top116 (2011). abstract
M. Francesconi, R. Jelier, B. Lehner.
Integrated genome-scale prediction of detrimental mutations/ in transcription networks
PLoS Genetics 7(5):e1002077. doi: 10.1371/journal.pgen.1002077 (2011). abstract
Martin D, Pantoja C, Miñán AF, Valdes-Quezada C, Moltó E, Matesanz F, Bogdanovi¿ O, de la Calle-Mustienes E, Domínguez O et al.
Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes.
Nature Structural & Molecular Biology 2011 Jun;18(6):708-14. Epub 2011 May 22. (2011). abstract
von Blume J, Alleaume AM, Cantero-Recasens G, Curwin A, Carreras-Sureda A, et al.
ADF/Cofilin Regulates Secretory Cargo Sorting at the TGN via the Ca(2+) ATPase SPCA1.
Developmental Cell 20(5):652-62 (2011). abstract
Rius J, Cores F, Solsona F, van Hemert JI, Koetsier J, Notredame C..
A user-friendly web portal for T-Coffee on supercomputers.
BMC Bioinformatics 2011 May 12;12(1):150. [Epub ahead of print] (2011). abstract
Elena Domínguez-Frutos, Iris Lo´pez-Herna´ndez, Victor Vendrell, Joana Neves, Micaela Gallozzi,1 Katja Gutsche,1 et al.
N-myc controls proliferation, morphogenesis, and patterning of the inner ear
Journal of Neuroscience 31(19):7178-89 (2011). abstract
Ann Marie Stanley, Pedro Carvalho, Tom Rapoport..
Recognition of an ERAD-L substrate analyzed by site-specific in vivo photocrosslinking
FEBS LETT. 585(9):1281-6 (2011). abstract
Mudge JM, Frankish A, Fernandez-Banet J, Alioto T, Derrien T, Howald C, Reymond A, Guigo R, Hubbard T, Harrow J..
The origins, evolution and functional potential of alternative splicing in vertebrates.
Molecular Biology and Evolution 2011 Oct;28(10):2949-59. Epub 2011 May 6. (2011). abstract
Alonso P, Gratacòs M, Segalàs C, Escaramís G, Real E, Bayés M, Labad J, Pertusa A, Vallejo J, Estivill X, Menchón JM..
"Variants in estrogen receptor alpha gene are associated with phenotypical expression of obsessive-compulsive disorder"
Psychoneuroendocrinology 36(4):473-83 (2011). abstract
Calvo, V, Beato, M.
BRCA1 Counteracts Progesterone Action by Ubiquitination Leading to Progesterone Receptor Degradation and/ Epigenetic Silencing of Target Promoters
Cancer Research 71(9):3422-31. (2011). abstract
Capellini TD, Handschuh K, Quintana L, Ferretti E, Di Giacomo G, Fantini S, Vaccari G, Clarke SL et al.
Control of pelvic girdle development by genes of the Pbx family and Emx2
Developmental Dynamics (2011). abstract
Hopyan S, Sharpe J, Yang Y..
Budding behaviors: Growth of the limb as a model of morphogenesis
Developmental Dynamics (2011). abstract
Hummel M., Bonnin S., Lowy E., Roma G..
"TEQC: an R-package for quality control in target capture experiments"
Bioinformatics 27(9):1316-7. Epub 2011 Mar 12. (2011). abstract
Riveira-Munoz E, He SM, Escaramis G, (...) Ryan AW, Trembath RC, Reis A, Zhang XJ, Elder JT, Estivill X. et al.
"Meta-Analysis Confirms the LCE3C_LCE3B Deletion as a Risk Factor for Psoriasis in Several Ethnic Groups and Finds Interaction with HLA-Cw6."
Journal of Investigative Dermatology 131(5):1105-9 (2011).
Vanhee P, van der Sloot AM, Verschueren E, Serrano L, Rousseau F, Schymkowitz J..
Computational design of peptide ligands
Trends Biotechnol 29(5):231-9. Epub 2011 Feb 12 (2011). abstract
Hunziker L, Benitah SA, Braun KM, Jensen K, McNulty K, Butler C, Potton E, Nye E, Boyd R, Laurent G, Glogauer M, Wright NA, Watt FM, Janes SM..
Rac1 deletion causes thymic atrophy
PLoS One 6(4):e19292. (2011).
Derrien T, Guigó R..
[Long non-coding RNAs with enhancer-like function in human cells.]
Med Sci (Paris). 2011 Apr;27(4):359-361. Epub 2011 Apr 28. French. (2011). abstract
Mocholí E, Ballester-Lurbe B, Arqué G, Poch E, Peris B, Guerri C, Dierssen M, Guasch RM, Terrado J, Pérez-Roger I..
"RhoE Deficiency Produces Postnatal Lethality, Profound Motor Deficits and Neurodevelopmental Delay in Mice."
PLoS One 6(4):e19236 (2011).
Gfeller D, Butty F, Wierzbicka M, Verschueren E, Vanhee P, Huang H, et al.
The multiple-specificity landscape of modular peptide recognition domains
Molecular Systems Biology 7:484 (2011). abstract
Gabriel Neurohr, Andreas Naegeli, Iris Titos, Dominik Theler, Basil Greber, Javier Díez,Toni Gabaldón, Manuel Mendoza, and Yves Barral.
A Midzone-Based Ruler Adjusts Chromosome Compaction to Anaphase Spindle Length
Science 332(6028):465-8. Epub 2011 Mar 10 (2011). abstract
Koblik EA, Red'kin YA, Meer MS, Derelle R, Golenkina SA, Kondrashov FA, Arkhipov VY..
Acrocephalus orinus: A Case of Mistaken Identity.
PLoS One 2011 Apr 22;6(4):e17716. (2011). abstract
ENCODE Project Consortium (including Guigo R).
A user's guide to the encyclopedia of DNA elements (ENCODE).
PLoS Biology 2011 Apr;9(4):e1001046. Epub 2011 Apr 19. (2011). abstract
Orom UA, Derrien T, Guigo R, Shiekhattar R..
Long Noncoding RNAs as Enhancers of Gene Expression.
Cold Spring Harbor Symposia on Quantitative Biology 2011 Apr 18. [Epub ahead of print] (2011). abstract
Vicent GP, Nacht AS, Font-Mateu J, Castellano G, Gaveglia L, Ballaré C, Beato M.
Four enzymes cooperate to displace histone H1 during the first minute of hormonal gene activation.
Genes and Development 25(8):845-62. Epub 2011 Mar 29. (2011). abstract
Vavouri T, Lehner B..
Chromatin Organization in Sperm May Be the Major Functional Consequence/ of Base Composition Variation in the Human Genome
PLoS Genet. (4):e1002036. Epub 2011 Apr 7. (2011).
Vavouri T, Lehner B..
Chromatin organization in sperm may be the major functional consequence of base/ composition variation in the human genome
PLoS Genetics 7(4):e1002036. doi: 10.1371/journal.pgen.1002036 (2011). abstract
Vellozo AF, Véron AS, Baa-Puyoulet P, Huerta-Cepas J, Cottret L, Febvay G, Calevro F, Rahbé Y, Douglas AE, Gabaldón T, Sagot MF, Charles H, Colella S..
CycADS: an annotation database system to ease the development and update of BioCyc databases.
Database (Oxford). 2011 Apr 7;2011:bar008. Print 2011. (2011). abstract
Sanges D, Lluis F, Cosma MP.
Cell-fusion-mediated reprogramming: pluripotency or transdifferentiation? Implications for regenerative medicine.
Adv Exp Med Biol. 713:137-59 (2011).
Sun Y, Dierssen M, Toran N, Pollak DD, Chen WQ, Lubec G..
"A gel-based proteomic method reveals several protein pathway abnormalities in fetal Down syndrome brain."
Journal of Proteomics 74(4):547-57 (2011). abstract
Gilabert-Juan J, Ivorra JL, Tolosa A, Gratacòs M, Costas J, Sanjuán J, Moltó MD..
"Potential involvement of serotonin receptor genes with age of onset and gender in schizophrenia: a preliminary study in a Spanish sample."
Psychiatry Research 186(1):153-4 (2011). abstract
Muiños-Gimeno M, Espinosa-Parrilla Y, Guidi M, Kagerbauer B, Sipilä T, Maron E, Pettai K, et al.
"Human microRNAs miR-22, miR-138-2, miR-148a, and miR-488 Are Associated with Panic/ Disorder and Regulate Several Anxiety Candidate Genes and Related Pathways."
Biol Psychiatry. 69(6):526-33 (2011). abstract
Wibowo I, Pinto-Teixeira F, Satou C, Higashijima S, López-Schier H..
Compartmentalized Notch signaling sustains epithelial mirror symmetry
Development 138(6):1143-52 (2011).
Boehm B, Rautschka M, Quintana L, Raspopovic J, Jan Z, Sharpe J..
A landmark-free morphometric staging system for the mouse limb bud
Development 138(6):1227-34. Epub 2011 Feb 9 (2011). abstract
Corrionero A, Miñana B, Valcárcel J..
Reduced fidelity of branch point recognition and alternative splicing induced by the anti-tumor drug spliceostatin A
Genes and Development 25(5):445-59. (2011). abstract
Corrionero A, Raker VA, Izquierdo JM, Valcárcel J..
Strict 3' splice site sequence requirements for U2 snRNP recruitment after U2AF binding underlie a genetic defect leading to autoimmune disease
RNA 17(3):401-11 (2011). abstract
Garcia-Rodríguez L, Pérez-Torras S, Carrió M, Cascante A, García-Ribas I, Mazo A, Fillat C..
"Connexin-26 is a key factor mediating gemcitabine bystander effect."
Molecular Cancer Therapeutics 10(3):505-17 (2011).
Hartmann B, Castelo R, Miñana B, Peden E, Blanchette M, Rio DC, Singh R, Valcárcel J..
Distinct regulatory programs establish widespread sex-specific alternative splicing in Drosophila melanogaster.
RNA 17(3):453-68. Epub 2011 Jan 13. (2011). abstract
James Sharpe, Rachel Wong, Rafael Yuste.
Imaging in Developmental Biology: A Laboratory Manual
Cold Spring Harbor Laboratory Press (2011).
Lehner B, Kaneko K..
Fluctuation and response in biology
Cellular and Molecular Life Sciences 68(6):1005-10. Epub 2010 Nov 30 (2011). abstract
Pryszcz LP, Huerta-Cepas J, Gabaldón T..
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score.
Nucleic Acids Research 2011 Mar 1;39(5):e32. Epub 2010 Dec 11. (2011). abstract
Richly H, Di Croce L.
The flip side of the coin: Role of ZRF1 and histone H2A ubiquitination in transcriptional activation
Cell Cycle 10(5):745-50 (2011).
Dierssen M, Arqué G, McDonald J, Andreu N, Martínez-Cué C, Flórez J, Fillat C..
"Behavioral Characterization of a Mouse Model Overexpressing DSCR1/ RCAN1."
PLoS One 6(2):e17010 (2011).
Tubio JM, Estivill X..
"Cancer: When catastrophe strikes a cell."
Nature 470(7335):476-7 (2011). abstract
Morales E, Bustamante M, Gonzalez JR, Guxens M, Torrent M, Mendez M, Garcia-Esteban R, Julvez J, Forns J, Vrijheid M, , Molto-Puigmarti C, et al.
"Genetic Variants of the FADS Gene Cluster and ELOVL Gene Family, Colostrums LC-PUFA Levels, Breastfeeding, and Child Cognition."
PLoS One 6(2):e17181 (2011). abstract
Jahn TR, Kohlhoff KJ, Scott M, Tartaglia GG, Lomas DA, Dobson CM, Vendruscolo M, Crowther DC..
Detection of early locomotor abnormalities in a Drosophila model of Alzheimer's disease.
Journal of Neuroscience Methods 2011 Apr 15;197(1):186-9. Epub 2011 Feb 18. (2011). abstract
Marcet-Houben M, Gabaldón T..
TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees.
Nucleic Acids Research 2011 May;39(10):e66. Epub 2011 Feb 18. (2011). abstract
Papadopoulos C, Arato K, Lilienthal E, Zerweck J, Schutkowski M, Chatain N, Müller-Newen G, Becker W, de la Luna S..
"Splice variants of the dual-specificity tyrosine phosphorylation-regulated kinase 4/ (DYRK4) differ in their subcellular localization and catalytic activity."
Journal of Biological Chemistry 286(7):5494-505 (2011).
Graindorge A, Militti C and Gebauer F.
Post-transcriptional control of X-chromosome dosage compensation
WIREs RNA doi: 10.1002/jso.21957 (2011). abstract
Marcon L, Arqués CG, Torres MS, Sharpe J..
A computational clonal analysis of the developing mouse limb bud
PLoS Computational Biology 7(2):e1001071 (2011). abstract
Raimondi S, Guglielmi F, Giorgetti S, Gaetano SD, Arciello A, Monti DM, Relini A, Nichino D, Doglia SM, Natalello A, Pucci P, et al.
Effects of the known pathogenic mutations on the aggregation pathway of the amyloidogenic Peptide of apolipoprotein a-I.
Journal of Molecular Biology 2011 Apr 1;407(3):465-76. Epub 2011 Feb 4. (2011). abstract
Alló M, Schor IE, Muñoz MJ, de la Mata M, Agirre E, Valcárcel J, Eyras E, Kornblihtt AR..
Chromatin and Alternative Splicing
Cold Spring Harbor Symposia on Quantitative Biology 75:103-11. Epub 2011 Feb 2. (2011). abstract
Aranda S, Laguna A, de la Luna S..
"DYRK family of protein kinases: evolutionary relationships, biochemical properties, and functional roles"
FASEB Journal 25(2):449-62 (2011).
Keyes, W.M.*, Pecoraro, M, Aranda, V., Vernersson-Lindahl, E., Li, W.,Vogel, H., Garcia, E.L., Michurina, T., et al.
ANp63a is an oncogene that targets chromatin remodeler Lsh expression to drive skin stem cell proliferation and tumorigenesis
Cell Stem Cell 8(2) 164-176 (*Corresponding authors) (2011).
Morales E, Guerra S, García-Esteban R, Guxens M, Alvarez-Pedrerol M, Bustamante M, Estivill X, Antó JM, Sunyer J..
"Maternal C-reactive protein levels in pregnancy are associated with wheezing and lower respiratory tract infections in the offspring."
Am J Obstet Gynecol. 204(2):164.e1-9 (2011). abstract
Vivek Malhotra, Fèlix Campelo.
PKD regulates membrane fission to generate TGN to cell surface transport carriers.
Cold Spring Harbor Perspectives in Biology 3(2) (2011).
Faucherre A, López-Schier H..
Delaying Gal4-driven gene expression in the zebrafish with morpholinos and Gal80.
PLoS ONE 6(1):e16587 (2011).
JM C. Tubio, M Tojo, L Bassaganyas, G Escaramis, I V. Sharakhov4, M. V. Sharakhova, C Tornador, et al.
"Evolutionary dynamics of the Ty3/gypsy LTR retrotransposons in the genome of Anopheles gambiae."
PLoS ONE 6(1):e16328 (2011). abstract
Roetzer A, Klopf E, Gratz N, Marcet-Houben M, Hiller E, Rupp S, Gabaldón T, Kovarik P, Schüller C..
Regulation of Candida glabrata oxidative stress resistance is adapted to host environment.
FEBS Letters 2011 Jan 21;585(2):319-27. Epub 2010 Dec 13. (2011). abstract
Uribesalgo I, Di Croce L.
Dynamics of epigenetic modifications in leukemia.
Briefings in Functional Genomics 10(1):18-29 (2011).
E. P. Rakoczy, C. Kiel, R. McKeone, F. Stricher, L. Serrano.
Analysis of Disease-Linked Rhodopsin Mutations Based on Structure, Function,/ and Protein Stability Calculations
Journal of Molecular Biology 405(2):584-606. Epub 2010 Nov 19 (2011). abstract
Sanges D. and Cosma MP.
"Reprogramming cell fate to pluripotency: the decision-making signalling pathways"
International Journal of Developmental Biology 54(11-12):1575-87. (2011).
Andrea Duran, Hernan López-Schier.
El peix zebra com a sistema model per a l'estudi de malalties humanes
Treballs de la SCB 62 (2011) 141-153 (2011).
Fillat C, Jose A, Bofill-De Ros X, Mato-Berciano A, Maliandi MV, Sobrevals L.
"Pancreatic Cancer Gene Therapy: From Molecular Targets to Delivery Systems"
Cancers 3: 368-395 (2011).
Garcia-Rodríguez L, Abate-Daga D, Rojas A, González JR, Fillat C.
"E-cadherin contributes to the bystander effect of TK/GCV suicide therapy and enhances its antitumoral activity in pancreatic cancer models"
Gene Therapy 18(1):73-81 (2011).
Huerta-Cepas J, Capella-Gutierrez S, Pryszcz LP, Denisov I, Kormes D, Marcet-Houben M, Gabaldón T..
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions.
Nucleic Acids Research 2011 Jan;39(Database issue):D556-60. (2011). abstract
Huerta-Cepas J, Gabaldón T..
Assigning duplication events to relative temporal scales in genome-wide studies.
Bioinformatics 2011 Jan 1;27(1):38-45. Epub 2010 Nov 11. (2011). abstract
J. Jaeger.
The gap gene network
Cellular and Molecular Life Sciences 68(2):243-74; 2010 Oct 8. [Epub ahead of print] (2011). abstract
James Sharpe & Rachel O. Wong.
Imaging in Developmental Biology: A Laboratory Manual
Cols Spring Harbor Protocols 833pp (2011). abstract
Jim Swoger, Mariana Muzzopappa, Hernan Lopez-Schier, and James Sharpe.
4D retrospective lineage tracing using SPIM for zebrafish organogenesis studies
J Biophotonics 4(1-2):122-34. doi: 10.1002/jbio.201000087 (2011). abstract
Meunier D, Patra K, Smits R, Hägebarth A, Lüttges A, Jaussi R, Wieduwilt MJ, Quintanilla-Fend L, Himmelbauer H, Fodde R, Fundele RH..
"Expression analysis of proline rich 15 (Prr15) in mouse and human gastrointestinal tumors."
Molecular Carcinogenesis 50(1):8-15 (2011). abstract
Muñoz IG, Prieto J, Subramanian S, Coloma J, Redondo P, Villate M, Merino N, Marenchino M, D'Abramo M, Gervasio FL, Grizot S, Daboussi F, Smith J, et al.
Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus
Nucleic Acids Res 39(2):729-43. Epub 2010 Sep 16. (2011). abstract
P.Vanhee, E. Verschueren, L. Baeten, F. Stricher, Luis Serrano, F.Rousseau, J. Schymkowitz.
BriX: a database of protein building blocks for structural analysis, modeling and design
Nucleic Acids Research doi: 10.1093/nar/gkq972 (2011). abstract
Ziolkowska B, Gieryk A, Martin-Garcia E, Burokas A, Maldonado R, McDonald J, Dierssen M, Przewlocki R.
"Expression regulation of opioid propeptides and dopamine receptors in the mesostriatal system by chronic intake of palatable foods"
Pharmalogical Reports 63 (1): 259-259 (2011).