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Items: 36

1.

Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program.

Chagoyen M, Poyatos JF.

PLoS Comput Biol. 2019 Sep 17;15(9):e1007353. doi: 10.1371/journal.pcbi.1007353. eCollection 2019 Sep.

2.

The Opposing Roles of PIK3R1/p85α and PIK3R2/p85β in Cancer.

Vallejo-Díaz J, Chagoyen M, Olazabal-Morán M, González-García A, Carrera AC.

Trends Cancer. 2019 Apr;5(4):233-244. doi: 10.1016/j.trecan.2019.02.009. Epub 2019 Mar 16. Review.

PMID:
30961830
3.

Bacterial Feature Finder (BaFF)-a system for extracting features overrepresented in sets of prokaryotic organisms.

López-Ibáñez J, Martín LT, Chagoyen M, Pazos F.

Bioinformatics. 2019 Sep 15;35(18):3482-3483. doi: 10.1093/bioinformatics/btz099.

PMID:
30844057
4.

Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology.

Pazos F, Chagoyen M.

Brief Bioinform. 2019 Jul 19;20(4):1329-1336. doi: 10.1093/bib/bby001.

PMID:
29351590
5.

Factors affecting interactome-based prediction of human genes associated with clinical signs.

González-Pérez S, Pazos F, Chagoyen M.

BMC Bioinformatics. 2017 Jul 17;18(1):340. doi: 10.1186/s12859-017-1754-1.

6.

Functional Analysis of Metabolomics Data.

Chagoyen M, López-Ibáñez J, Pazos F.

Methods Mol Biol. 2016;1415:399-406. doi: 10.1007/978-1-4939-3572-7_20.

PMID:
27115644
7.

MBROLE 2.0-functional enrichment of chemical compounds.

López-Ibáñez J, Pazos F, Chagoyen M.

Nucleic Acids Res. 2016 Jul 8;44(W1):W201-4. doi: 10.1093/nar/gkw253. Epub 2016 Apr 15.

8.

Rare disease relations through common genes and protein interactions.

Fernandez-Novo S, Pazos F, Chagoyen M.

Mol Cell Probes. 2016 Jun;30(3):178-81. doi: 10.1016/j.mcp.2016.03.004. Epub 2016 Mar 16.

PMID:
26995712
9.

Characterization of clinical signs in the human interactome.

Chagoyen M, Pazos F.

Bioinformatics. 2016 Jun 15;32(12):1761-5. doi: 10.1093/bioinformatics/btw054. Epub 2016 Feb 9.

PMID:
26861820
10.

Clinical, genetics and bioinformatics characterization of a campomelic dysplasia case report.

Carvajal N, Martínez-García M, Chagoyen M, Morcillo N, Pino A, Lorda I, Trujillo-Tiebas MJ.

Gene. 2016 Feb 15;577(2):289-92. doi: 10.1016/j.gene.2015.11.039. Epub 2015 Nov 27.

PMID:
26631621
11.

Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases.

Buey RM, Ledesma-Amaro R, Velázquez-Campoy A, Balsera M, Chagoyen M, de Pereda JM, Revuelta JL.

Nat Commun. 2015 Nov 12;6:8923. doi: 10.1038/ncomms9923.

12.

Practical analysis of specificity-determining residues in protein families.

Chagoyen M, García-Martín JA, Pazos F.

Brief Bioinform. 2016 Mar;17(2):255-61. doi: 10.1093/bib/bbv045. Epub 2015 Jul 2. Review.

PMID:
26141829
13.

Strigolactone promotes degradation of DWARF14, an α/β hydrolase essential for strigolactone signaling in Arabidopsis.

Chevalier F, Nieminen K, Sánchez-Ferrero JC, Rodríguez ML, Chagoyen M, Hardtke CS, Cubas P.

Plant Cell. 2014 Mar;26(3):1134-50. doi: 10.1105/tpc.114.122903. Epub 2014 Mar 7.

14.

Functional signature for the recognition of specific target mRNAs by human Staufen1 protein.

de Lucas S, Oliveros JC, Chagoyen M, Ortín J.

Nucleic Acids Res. 2014 Apr;42(7):4516-26. doi: 10.1093/nar/gku073. Epub 2014 Jan 26.

15.

Molecular determinants of the ATP hydrolysis asymmetry of the CCT chaperonin complex.

Chagoyen M, Carrascosa JL, Pazos F, Valpuesta JM.

Proteins. 2014 May;82(5):703-7. doi: 10.1002/prot.24510. Epub 2014 Feb 12.

PMID:
24420718
16.

Structural characterization of the bacteriophage T7 tail machinery.

Cuervo A, Pulido-Cid M, Chagoyen M, Arranz R, González-García VA, Garcia-Doval C, Castón JR, Valpuesta JM, van Raaij MJ, Martín-Benito J, Carrascosa JL.

J Biol Chem. 2013 Sep 6;288(36):26290-9. doi: 10.1074/jbc.M113.491209. Epub 2013 Jul 24.

17.

Tools for the functional interpretation of metabolomic experiments.

Chagoyen M, Pazos F.

Brief Bioinform. 2013 Nov;14(6):737-44. doi: 10.1093/bib/bbs055. Epub 2012 Oct 14.

PMID:
23063930
18.

Nuclear but not cytosolic phosphoinositide 3-kinase beta has an essential function in cell survival.

Kumar A, Redondo-Muñoz J, Perez-García V, Cortes I, Chagoyen M, Carrera AC.

Mol Cell Biol. 2011 May;31(10):2122-33. doi: 10.1128/MCB.01313-10. Epub 2011 Mar 7.

19.

MBRole: enrichment analysis of metabolomic data.

Chagoyen M, Pazos F.

Bioinformatics. 2011 Mar 1;27(5):730-1. doi: 10.1093/bioinformatics/btr001. Epub 2011 Jan 5.

PMID:
21208985
20.

Genetic polymorphisms among C57BL/6 mouse inbred strains.

Zurita E, Chagoyen M, Cantero M, Alonso R, González-Neira A, López-Jiménez A, López-Moreno JA, Landel CP, Benítez J, Pazos F, Montoliu L.

Transgenic Res. 2011 Jun;20(3):481-9. doi: 10.1007/s11248-010-9403-8. Epub 2010 May 27.

PMID:
20506040
21.

Quantifying the biological significance of gene ontology biological processes--implications for the analysis of systems-wide data.

Chagoyen M, Pazos F.

Bioinformatics. 2010 Feb 1;26(3):378-84. doi: 10.1093/bioinformatics/btp663. Epub 2009 Dec 4.

PMID:
19965879
22.

SENT: semantic features in text.

Vazquez M, Carmona-Saez P, Nogales-Cadenas R, Chagoyen M, Tirado F, Carazo JM, Pascual-Montano A.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W153-9. doi: 10.1093/nar/gkp392. Epub 2009 May 20.

23.

Assessment of protein set coherence using functional annotations.

Chagoyen M, Carazo JM, Pascual-Montano A.

BMC Bioinformatics. 2008 Oct 20;9:444. doi: 10.1186/1471-2105-9-444.

24.

GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists.

Carmona-Saez P, Chagoyen M, Tirado F, Carazo JM, Pascual-Montano A.

Genome Biol. 2007;8(1):R3.

25.

bioNMF: a versatile tool for non-negative matrix factorization in biology.

Pascual-Montano A, Carmona-Saez P, Chagoyen M, Tirado F, Carazo JM, Pascual-Marqui RD.

BMC Bioinformatics. 2006 Jul 28;7:366.

26.

A literature-based similarity metric for biological processes.

Chagoyen M, Carmona-Saez P, Gil C, Carazo JM, Pascual-Montano A.

BMC Bioinformatics. 2006 Jul 26;7:363.

27.

Integrated analysis of gene expression by Association Rules Discovery.

Carmona-Saez P, Chagoyen M, Rodriguez A, Trelles O, Carazo JM, Pascual-Montano A.

BMC Bioinformatics. 2006 Feb 7;7:54.

28.

Discovering semantic features in the literature: a foundation for building functional associations.

Chagoyen M, Carmona-Saez P, Shatkay H, Carazo JM, Pascual-Montano A.

BMC Bioinformatics. 2006 Jan 26;7:41.

29.

Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology.

Heymann JB, Chagoyen M, Belnap DM.

J Struct Biol. 2005 Aug;151(2):196-207. Erratum in: J Struct Biol. 2006 Mar;153(3):312.

PMID:
16043364
30.

Designing and executing scientific workflows with a programmable integrator.

Chagoyen M, Kurul ME, De-Alarcón PA, Carazo JM, Gupta A.

Bioinformatics. 2004 Sep 1;20(13):2092-100. Epub 2004 Apr 1.

PMID:
15059834
31.

EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information.

Henrick K, Newman R, Tagari M, Chagoyen M.

J Struct Biol. 2003 Oct-Nov;144(1-2):228-37.

PMID:
14643225
32.

FEMME database: topologic and geometric information of macromolecules.

Jiménez-Lozano N, Chagoyen M, Cuenca-Alba J, Carazo JM.

J Struct Biol. 2003 Oct-Nov;144(1-2):104-13.

PMID:
14643213
33.

New electron microscopy database and deposition system.

Tagari M, Newman R, Chagoyen M, Carazo JM, Henrick K.

Trends Biochem Sci. 2002 Nov;27(11):589.

PMID:
12417136
34.

The need for a shared database infrastructure: combining X-ray crystallography and electron microscopy.

Kalko SG, Chagoyen M, Jiménez-Lozano N, Verdaguer N, Fita I, Carazo JM.

Eur Biophys J. 2000;29(6):457-62.

PMID:
11081407
35.

Design and realization of an on-line database for multidimensional microscopic images of biological specimens.

Lindek S, Fritsch R, Machtynger J, de Alarcón PA, Chagoyen M.

J Struct Biol. 1999 Apr-May;125(2-3):103-11.

PMID:
10222267
36.

Organising multi-dimensional biological image information: the BioImage Database.

Carazo JM, Stelzer EH, Engel A, Fita I, Henn C, Machtynger J, McNeil P, Shotton DM, Chagoyen M, de Alarcón PA, Fritsch R, Heymann JB, Kalko S, Pittet JJ, Rodriguez-Tomé P, Boudier T.

Nucleic Acids Res. 1999 Jan 1;27(1):280-3.

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