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Items: 49

1.

Estimating the predictability of cancer evolution.

Hosseini SR, Diaz-Uriarte R, Markowetz F, Beerenwinkel N.

Bioinformatics. 2019 Jul 15;35(14):i389-i397. doi: 10.1093/bioinformatics/btz332.

2.

Every which way? On predicting tumor evolution using cancer progression models.

Diaz-Uriarte R, Vasallo C.

PLoS Comput Biol. 2019 Aug 2;15(8):e1007246. doi: 10.1371/journal.pcbi.1007246. eCollection 2019 Aug.

3.

Cancer progression models and fitness landscapes: a many-to-many relationship.

Diaz-Uriarte R.

Bioinformatics. 2018 Mar 1;34(5):836-844. doi: 10.1093/bioinformatics/btx663.

4.

OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.

Diaz-Uriarte R.

Bioinformatics. 2017 Jun 15;33(12):1898-1899. doi: 10.1093/bioinformatics/btx077.

5.
6.

Genome wide association study identifies a novel putative mammographic density locus at 1q12-q21.

Fernandez-Navarro P, González-Neira A, Pita G, Díaz-Uriarte R, Tais Moreno L, Ederra M, Pedraz-Pingarrón C, Sánchez-Contador C, Vázquez-Carrete JA, Moreo P, Vidal C, Salas-Trejo D, Stone J, Southey MC, Hopper JL, Pérez-Gómez B, Benitez J, Pollan M.

Int J Cancer. 2015 May 15;136(10):2427-36. doi: 10.1002/ijc.29299. Epub 2014 Nov 10.

7.

Levels of active tyrosine kinase receptor determine the tumor response to Zalypsis.

Moneo V, Serelde BG, Blanco-Aparicio C, Diaz-Uriarte R, Avilés P, Santamaría G, Tercero JC, Cuevas C, Carnero A.

BMC Cancer. 2014 Apr 23;14:281. doi: 10.1186/1471-2407-14-281.

8.

ADaCGH2: parallelized analysis of (big) CNA data.

Diaz-Uriarte R.

Bioinformatics. 2014 Jun 15;30(12):1759-61. doi: 10.1093/bioinformatics/btu099. Epub 2014 Feb 14.

9.

An epistatic interaction between the PAX8 and STK17B genes in papillary thyroid cancer susceptibility.

Landa I, Boullosa C, Inglada-Pérez L, Sastre-Perona A, Pastor S, Velázquez A, Mancikova V, Ruiz-Llorente S, Schiavi F, Marcos R, Malats N, Opocher G, Diaz-Uriarte R, Santisteban P, Valencia A, Robledo M.

PLoS One. 2013 Sep 23;8(9):e74765. doi: 10.1371/journal.pone.0074765. eCollection 2013. Erratum in: PLoS One. 2013;8(10). doi:10.1371/annotation/cd94c3eb-70f2-4dfa-85be-b3fc41e495c3.

10.

Finding common regions of alteration in copy number data.

Rueda OM, Diaz-Uriarte R, Caldas C.

Methods Mol Biol. 2013;973:339-53. doi: 10.1007/978-1-62703-281-0_21. Review.

PMID:
23412800
11.

An optimized predictor panel for colorectal cancer diagnosis based on the combination of tumor-associated antigens obtained from protein and phage microarrays.

Barderas R, Babel I, Díaz-Uriarte R, Moreno V, Suárez A, Bonilla F, Villar-Vázquez R, Capellá G, Casal JI.

J Proteomics. 2012 Aug 3;75(15):4647-55. doi: 10.1016/j.jprot.2012.03.004. Epub 2012 Mar 18.

12.

miRNA expression in diffuse large B-cell lymphoma treated with chemoimmunotherapy.

Montes-Moreno S, Martinez N, Sanchez-Espiridión B, Díaz Uriarte R, Rodriguez ME, Saez A, Montalbán C, Gomez G, Pisano DG, García JF, Conde E, Gonzalez-Barca E, Lopez A, Mollejo M, Grande C, Martinez MA, Dunphy C, Hsi ED, Rocque GB, Chang J, Go RS, Visco C, Xu-Monette Z, Young KH, Piris MA.

Blood. 2011 Jul 28;118(4):1034-40. doi: 10.1182/blood-2010-11-321554. Epub 2011 Jun 1.

PMID:
21633089
13.

CNVassoc: Association analysis of CNV data using R.

Subirana I, Diaz-Uriarte R, Lucas G, Gonzalez JR.

BMC Med Genomics. 2011 May 24;4:47. doi: 10.1186/1755-8794-4-47.

14.

Identification of MST1/STK4 and SULF1 proteins as autoantibody targets for the diagnosis of colorectal cancer by using phage microarrays.

Babel I, Barderas R, Diaz-Uriarte R, Moreno V, Suarez A, Fernandez-Aceñero MJ, Salazar R, Capellá G, Casal JI.

Mol Cell Proteomics. 2011 Mar;10(3):M110.001784. doi: 10.1074/mcp.M110.001784. Epub 2011 Jan 12.

15.

waviCGH: a web application for the analysis and visualization of genomic copy number alterations.

Carro A, Rico D, Rueda OM, Díaz-Uriarte R, Pisano DG.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W182-7. doi: 10.1093/nar/gkq441. Epub 2010 May 27.

16.

Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously.

Rueda OM, Diaz-Uriarte R.

BMC Bioinformatics. 2009 Sep 23;10:308. doi: 10.1186/1471-2105-10-308.

17.

Identification of tumor-associated autoantigens for the diagnosis of colorectal cancer in serum using high density protein microarrays.

Babel I, Barderas R, Díaz-Uriarte R, Martínez-Torrecuadrada JL, Sánchez-Carbayo M, Casal JI.

Mol Cell Proteomics. 2009 Oct;8(10):2382-95. doi: 10.1074/mcp.M800596-MCP200. Epub 2009 Jul 28.

18.

Pomelo II: finding differentially expressed genes.

Morrissey ER, Diaz-Uriarte R.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W581-6. doi: 10.1093/nar/gkp366. Epub 2009 May 12.

19.

RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions.

Rueda OM, Diaz-Uriarte R.

Bioinformatics. 2009 Aug 1;25(15):1959-60. doi: 10.1093/bioinformatics/btp307. Epub 2009 May 6.

20.

Transcription initiation activity sets replication origin efficiency in mammalian cells.

Sequeira-Mendes J, Díaz-Uriarte R, Apedaile A, Huntley D, Brockdorff N, Gómez M.

PLoS Genet. 2009 Apr;5(4):e1000446. doi: 10.1371/journal.pgen.1000446. Epub 2009 Apr 10.

21.

E2F2 represses cell cycle regulators to maintain quiescence.

Infante A, Laresgoiti U, Fernández-Rueda J, Fullaondo A, Galán J, Díaz-Uriarte R, Malumbres M, Field SJ, Zubiaga AM.

Cell Cycle. 2008 Dec 15;7(24):3915-27. Epub 2008 Dec 10.

PMID:
19066456
22.

Mecp2-null mice provide new neuronal targets for Rett syndrome.

Urdinguio RG, Lopez-Serra L, Lopez-Nieva P, Alaminos M, Diaz-Uriarte R, Fernandez AF, Esteller M.

PLoS One. 2008;3(11):e3669. doi: 10.1371/journal.pone.0003669. Epub 2008 Nov 7.

23.

An approach to inferring transcriptional regulation among genes from large-scale expression data.

Herrero J, Díaz-Uriarte R, Dopazo J.

Comp Funct Genomics. 2003;4(1):148-54. doi: 10.1002/cfg.237.

24.

PaLS: filtering common literature, biological terms and pathway information.

Alibés A, Cañada A, Díaz-Uriarte R.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W364-7. doi: 10.1093/nar/gkn251. Epub 2008 May 8.

25.
28.

Genomic profiling of circulating plasma RNA for the analysis of cancer.

Collado M, Garcia V, Garcia JM, Alonso I, Lombardia L, Diaz-Uriarte R, Fernández LA, Zaballos A, Bonilla F, Serrano M.

Clin Chem. 2007 Oct;53(10):1860-3. Epub 2007 Aug 23.

29.
30.

Flexible and accurate detection of genomic copy-number changes from aCGH.

Rueda OM, Díaz-Uriarte R.

PLoS Comput Biol. 2007 Jun;3(6):e122. Epub 2007 May 16.

31.

Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite.

Díaz-Uriarte R, Alibés A, Morrissey ER, Cañada A, Rueda OM, Neves ML.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W75-80. Epub 2007 May 8.

32.

Levels of p27(kip1) determine Aplidin sensitivity.

Moneo V, Serelde BG, Leal JF, Blanco-Aparicio C, Diaz-Uriarte R, Aracil M, Tercero JC, Jimeno J, Carnero A.

Mol Cancer Ther. 2007 Apr;6(4):1310-6.

33.

IDconverter and IDClight: conversion and annotation of gene and protein IDs.

Alibés A, Yankilevich P, Cañada A, Díaz-Uriarte R.

BMC Bioinformatics. 2007 Jan 10;8:9.

34.

Asterias: a parallelized web-based suite for the analysis of expression and aCGH data.

Alibés A, Morrissey ER, Cañada A, Rueda OM, Casado D, Yankilevich P, Díaz-Uriarte R.

Cancer Inform. 2007 Feb 3;3:1-9.

35.

Gene selection and classification of microarray data using random forest.

Díaz-Uriarte R, Alvarez de Andrés S.

BMC Bioinformatics. 2006 Jan 6;7:3.

36.

GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data.

Vaquerizas JM, Conde L, Yankilevich P, Cabezón A, Minguez P, Díaz-Uriarte R, Al-Shahrour F, Herrero J, Dopazo J.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W616-20.

37.

Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information.

Al-Shahrour F, Díaz-Uriarte R, Dopazo J.

Bioinformatics. 2005 Jul 1;21(13):2988-93. Epub 2005 Apr 19.

PMID:
15840702
38.

A predictor based on the somatic genomic changes of the BRCA1/BRCA2 breast cancer tumors identifies the non-BRCA1/BRCA2 tumors with BRCA1 promoter hypermethylation.

Alvarez S, Diaz-Uriarte R, Osorio A, Barroso A, Melchor L, Paz MF, Honrado E, Rodríguez R, Urioste M, Valle L, Díez O, Cigudosa JC, Dopazo J, Esteller M, Benitez J.

Clin Cancer Res. 2005 Feb 1;11(3):1146-53.

39.

Identification of amplified and highly expressed genes in amplicons of the T-cell line huT78 detected by cDNA microarray CGH.

Meléndez B, Martínez-Delgado B, Cuadros M, Fernández V, Díaz-Uriarte R, Benítez J.

Mol Cancer. 2005 Jan 18;4(1):5.

40.

Gene expression analysis of chromosomal regions with gain or loss of genetic material detected by comparative genomic hybridization.

Meléndez B, Díaz-Uriarte R, Cuadros M, Martínez-Ramírez A, Fernández-Piqueras J, Dopazo A, Cigudosa JC, Rivas C, Dopazo J, Martínez-Delgado B, Benítez J.

Genes Chromosomes Cancer. 2004 Dec;41(4):353-65.

PMID:
15382261
41.

DNMAD: web-based diagnosis and normalization for microarray data.

Vaquerizas JM, Dopazo J, Díaz-Uriarte R.

Bioinformatics. 2004 Dec 12;20(18):3656-8. Epub 2004 Jul 9.

PMID:
15247094
42.

FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes.

Al-Shahrour F, Díaz-Uriarte R, Dopazo J.

Bioinformatics. 2004 Mar 1;20(4):578-80. Epub 2004 Jan 22.

PMID:
14990455
43.

Differential gene expression profile in endometrioid and nonendometrioid endometrial carcinoma: STK15 is frequently overexpressed and amplified in nonendometrioid carcinomas.

Moreno-Bueno G, Sánchez-Estévez C, Cassia R, Rodríguez-Perales S, Díaz-Uriarte R, Domínguez O, Hardisson D, Andujar M, Prat J, Matias-Guiu X, Cigudosa JC, Palacios J.

Cancer Res. 2003 Sep 15;63(18):5697-702.

44.

GEPAS: A web-based resource for microarray gene expression data analysis.

Herrero J, Al-Shahrour F, Díaz-Uriarte R, Mateos A, Vaquerizas JM, Santoyo J, Dopazo J.

Nucleic Acids Res. 2003 Jul 1;31(13):3461-7.

45.

Gene expression data preprocessing.

Herrero J, Díaz-Uriarte R, Dopazo J.

Bioinformatics. 2003 Mar 22;19(5):655-6.

PMID:
12651726
46.

Effects of branch length errors on the performance of phylogenetically independent contrasts.

Díaz-Uriarte R, Garland T Jr.

Syst Biol. 1998 Dec;47(4):654-72.

PMID:
12066309
47.
48.

Territorial intrusion risk and antipredator behaviour: a mathematical model.

Díaz-Uriarte R.

Proc Biol Sci. 2001 Jun 7;268(1472):1165-73.

49.

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