Publications by authors named "Ignacio Medina"

46Publications

VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy.

BMC Bioinformatics 2017 Sep 20;18(1):421. Epub 2017 Sep 20.

Clinical Bioinformatics Research Area, Fundación Progreso y Salud, Hospital Virgen del Rocío, 41013, Sevilla, Spain.

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http://dx.doi.org/10.1186/s12859-017-1837-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5607581PMC
September 2017

Web-based network analysis and visualization using CellMaps.

Bioinformatics 2016 10 13;32(19):3041-3. Epub 2016 Jun 13.

Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia 46012, Spain Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, Spain Functional Genomics Node, (INB, PRB2, ISCIII) at CIPF, Valencia 46012, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btw332DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5039919PMC
October 2016

Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models.

Nucleic Acids Res 2016 07 2;44(W1):W212-6. Epub 2016 May 2.

Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, 46012, Spain Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, 46012, Spain Functional Genomics Node, (INB, PRB2, ISCIII) at CIPF, Valencia 46012, Spain

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkw369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987920PMC
July 2016

HPG pore: an efficient and scalable framework for nanopore sequencing data.

BMC Bioinformatics 2016 Feb 27;17:107. Epub 2016 Feb 27.

Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, 46012, Spain.

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http://dx.doi.org/10.1186/s12859-016-0966-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4769497PMC
February 2016

Identification of epistatic interactions through genome-wide association studies in sporadic medullary and juvenile papillary thyroid carcinomas.

BMC Med Genomics 2015 Dec 21;8:83. Epub 2015 Dec 21.

Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.

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http://dx.doi.org/10.1186/s12920-015-0160-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4685628PMC
December 2015

A parallel and sensitive software tool for methylation analysis on multicore platforms.

Bioinformatics 2015 Oct 10;31(19):3130-8. Epub 2015 Jun 10.

Department of Computational Genomics, Centro de Investigación Príncipe Felipe.

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http://dx.doi.org/10.1093/bioinformatics/btv357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679392PMC
October 2015

Babelomics 5.0: functional interpretation for new generations of genomic data.

Nucleic Acids Res 2015 Jul 20;43(W1):W117-21. Epub 2015 Apr 20.

Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, 46012, Spain Computational Genomics Chair, Bull-CIPF, Valencia, 46012, Spain Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, 46012, Spain Functional Genomics Node, (INB) at CIPF, Valencia, 46012, Spain

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http://dx.doi.org/10.1093/nar/gkv384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489263PMC
July 2015

Assessing the impact of mutations found in next generation sequencing data over human signaling pathways.

Nucleic Acids Res 2015 Jul 16;43(W1):W270-5. Epub 2015 Apr 16.

Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, 46012, Spain Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, 46012, Spain Functional Genomics Node, (INB) at CIPF, Valencia, 45012, Spain

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http://dx.doi.org/10.1093/nar/gkv349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489259PMC
July 2015

Fast inexact mapping using advanced tree exploration on backward search methods.

BMC Bioinformatics 2015 Jan 28;16:18. Epub 2015 Jan 28.

GRyCAP department of I3M, Universitat Politècnica de València, Building 8B, Camino de vera s/n, Valencia, 46022, Spain.

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http://dx.doi.org/10.1186/s12859-014-0438-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384339PMC
January 2015

Acceleration of short and long DNA read mapping without loss of accuracy using suffix array.

Bioinformatics 2014 Dec 20;30(23):3396-8. Epub 2014 Aug 20.

Department of Computational Genomics, Centro de Investigación Príncipe Felipe (CIPF), Functional Genomics Node, (INB) at CIPF 46012, Departamento de Informática, Universidad de Valencia, 46100 Valencia, Departamento de Ingeniería y Ciencia de Computadores, Universitat Jaume I, 12071 Castellón de la Plana, Instituto de Investigación en Informática de Albacete, Universidad de Castilla-La Mancha, Campus Universitario, 02071 Albacete, Universitat Politècnica de València, Instituto de Instrumentación para Imagen Molecular, 46022 Valencia, Grupo de Investigación Biomédica de Imagen (GIBI 2^30), La Fe Polytechnic University Hospital, 46022 Valencia and Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btu553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4816028PMC
December 2014

A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications.

Nucleic Acids Res 2014 Jul 26;42(Web Server issue):W83-7. Epub 2014 May 26.

Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, 46012, Spain Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, 46012, Spain Functional Genomics Node, (INB) at CIPF, Valencia, 46012, Spain

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http://dx.doi.org/10.1093/nar/gku472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086136PMC
July 2014

A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies.

Nucleic Acids Res 2014 Jul 6;42(Web Server issue):W88-93. Epub 2014 May 6.

Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia 46012, Spain Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia 46010, Spain Functional Genomics Node, (INB) at CIPF, Valencia 46012, Spain

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http://academic.oup.com/nar/article/42/W1/W88/2437375/A-webb
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http://dx.doi.org/10.1093/nar/gku407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086071PMC
July 2014

Inferring the functional effect of gene expression changes in signaling pathways.

Nucleic Acids Res 2013 Jul 8;41(Web Server issue):W213-7. Epub 2013 Jun 8.

Department of Computational Genomics, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain.

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http://dx.doi.org/10.1093/nar/gkt451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692130PMC
July 2013

Genome Maps, a new generation genome browser.

Nucleic Acids Res 2013 Jul 8;41(Web Server issue):W41-6. Epub 2013 Jun 8.

Department of Computational Genomics, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain.

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http://dx.doi.org/10.1093/nar/gkt530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692043PMC
July 2013

Four new loci associations discovered by pathway-based and network analyses of the genome-wide variability profile of Hirschsprung's disease.

Orphanet J Rare Dis 2012 Dec 28;7:103. Epub 2012 Dec 28.

Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.

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http://dx.doi.org/10.1186/1750-1172-7-103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575329PMC
December 2012

A map of human microRNA variation uncovers unexpectedly high levels of variability.

Genome Med 2012 24;4(8):62. Epub 2012 Aug 24.

Institute of Computational Genomics, Centro de Investigación Príncipe Felipe (CIPF), C/ Eduardo Primo Yufera 3, Valencia, 46012, Spain ; Medical Genome Project, Andalusian Center for Human Genomic Sequencing, c/ Albert Einstein s/n. Plta. Baja, Sevilla, 41092, Spain ; BIER, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), CIPF, C/ Eduardo Primo Yufera 3, Valencia, 46012, Spain ; Functional Genomics Node (INB), CIPF, C/ Eduardo Primo Yufera 3, Valencia, 46012, Spain.

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http://link.springer.com/content/pdf/10.1186%2Fgm363.pdf
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http://genomemedicine.com/content/4/8/62
Publisher Site
http://dx.doi.org/10.1186/gm363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4064319PMC
August 2014

CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources.

Nucleic Acids Res 2012 Jul 12;40(Web Server issue):W609-14. Epub 2012 Jun 12.

Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe (CIPF), 46012 Valencia, Spain.

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http://dx.doi.org/10.1093/nar/gks575DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394301PMC
July 2012

VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing.

Nucleic Acids Res 2012 Jul 11;40(Web Server issue):W54-8. Epub 2012 Jun 11.

Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.

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http://dx.doi.org/10.1093/nar/gks572DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394276PMC
July 2012

Inferring the regulatory network behind a gene expression experiment.

Nucleic Acids Res 2012 Jul 11;40(Web Server issue):W168-72. Epub 2012 Jun 11.

Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.

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http://dx.doi.org/10.1093/nar/gks573DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394273PMC
July 2012

Whole-genome bisulfite DNA sequencing of a DNMT3B mutant patient.

Epigenetics 2012 Jun 1;7(6):542-50. Epub 2012 Jun 1.

Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.4161/epi.20523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398983PMC
June 2012

Determination of diffusion coefficients for supercritical fluids.

Authors:
Ignacio Medina

J Chromatogr A 2012 Aug 26;1250:124-40. Epub 2012 Apr 26.

Departamento de Ingeniería Química y T. M. A., Universidad de Oviedo, 33071 Oviedo, Spain.

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http://dx.doi.org/10.1016/j.chroma.2012.04.052DOI Listing
August 2012

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.

Nucleic Acids Res 2011 Jul 6;39(Web Server issue):W470-4. Epub 2011 Jun 6.

Evolutionary Genomics Lab, Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler, 16-3, 46013 Valencia, Spain.

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http://dx.doi.org/10.1093/nar/gkr408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125789PMC
July 2011

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.

Authors:
Leming Shi Gregory Campbell Wendell D Jones Fabien Campagne Zhining Wen Stephen J Walker Zhenqiang Su Tzu-Ming Chu Federico M Goodsaid Lajos Pusztai John D Shaughnessy André Oberthuer Russell S Thomas Richard S Paules Mark Fielden Bart Barlogie Weijie Chen Pan Du Matthias Fischer Cesare Furlanello Brandon D Gallas Xijin Ge Dalila B Megherbi W Fraser Symmans May D Wang John Zhang Hans Bitter Benedikt Brors Pierre R Bushel Max Bylesjo Minjun Chen Jie Cheng Jing Cheng Jeff Chou Timothy S Davison Mauro Delorenzi Youping Deng Viswanath Devanarayan David J Dix Joaquin Dopazo Kevin C Dorff Fathi Elloumi Jianqing Fan Shicai Fan Xiaohui Fan Hong Fang Nina Gonzaludo Kenneth R Hess Huixiao Hong Jun Huan Rafael A Irizarry Richard Judson Dilafruz Juraeva Samir Lababidi Christophe G Lambert Li Li Yanen Li Zhen Li Simon M Lin Guozhen Liu Edward K Lobenhofer Jun Luo Wen Luo Matthew N McCall Yuri Nikolsky Gene A Pennello Roger G Perkins Reena Philip Vlad Popovici Nathan D Price Feng Qian Andreas Scherer Tieliu Shi Weiwei Shi Jaeyun Sung Danielle Thierry-Mieg Jean Thierry-Mieg Venkata Thodima Johan Trygg Lakshmi Vishnuvajjala Sue Jane Wang Jianping Wu Yichao Wu Qian Xie Waleed A Yousef Liang Zhang Xuegong Zhang Sheng Zhong Yiming Zhou Sheng Zhu Dhivya Arasappan Wenjun Bao Anne Bergstrom Lucas Frank Berthold Richard J Brennan Andreas Buness Jennifer G Catalano Chang Chang Rong Chen Yiyu Cheng Jian Cui Wendy Czika Francesca Demichelis Xutao Deng Damir Dosymbekov Roland Eils Yang Feng Jennifer Fostel Stephanie Fulmer-Smentek James C Fuscoe Laurent Gatto Weigong Ge Darlene R Goldstein Li Guo Donald N Halbert Jing Han Stephen C Harris Christos Hatzis Damir Herman Jianping Huang Roderick V Jensen Rui Jiang Charles D Johnson Giuseppe Jurman Yvonne Kahlert Sadik A Khuder Matthias Kohl Jianying Li Li Li Menglong Li Quan-Zhen Li Shao Li Zhiguang Li Jie Liu Ying Liu Zhichao Liu Lu Meng Manuel Madera Francisco Martinez-Murillo Ignacio Medina Joseph Meehan Kelci Miclaus Richard A Moffitt David Montaner Piali Mukherjee George J Mulligan Padraic Neville Tatiana Nikolskaya Baitang Ning Grier P Page Joel Parker R Mitchell Parry Xuejun Peng Ron L Peterson John H Phan Brian Quanz Yi Ren Samantha Riccadonna Alan H Roter Frank W Samuelson Martin M Schumacher Joseph D Shambaugh Qiang Shi Richard Shippy Shengzhu Si Aaron Smalter Christos Sotiriou Mat Soukup Frank Staedtler Guido Steiner Todd H Stokes Qinglan Sun Pei-Yi Tan Rong Tang Zivana Tezak Brett Thorn Marina Tsyganova Yaron Turpaz Silvia C Vega Roberto Visintainer Juergen von Frese Charles Wang Eric Wang Junwei Wang Wei Wang Frank Westermann James C Willey Matthew Woods Shujian Wu Nianqing Xiao Joshua Xu Lei Xu Lun Yang Xiao Zeng Jialu Zhang Li Zhang Min Zhang Chen Zhao Raj K Puri Uwe Scherf Weida Tong Russell D Wolfinger

Nat Biotechnol 2010 Aug 30;28(8):827-38. Epub 2010 Jul 30.

National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA.

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http://dx.doi.org/10.1038/nbt.1665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315840PMC
August 2010

Serial Expression Analysis: a web tool for the analysis of serial gene expression data.

Nucleic Acids Res 2010 Jul 4;38(Web Server issue):W239-45. Epub 2010 Jun 4.

Statistics and Operation Research Department, University of Alicante, Spain.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkq488DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896172PMC
July 2010

Biological processes, properties and molecular wiring diagrams of candidate low-penetrance breast cancer susceptibility genes.

BMC Med Genomics 2008 Dec 18;1:62. Epub 2008 Dec 18.

Bioinformatics and Biostatistics Unit, and Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Spain.

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http://dx.doi.org/10.1186/1755-8794-1-62DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2628924PMC
December 2008

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

Nucleic Acids Res 2008 Jul 31;36(Web Server issue):W341-6. Epub 2008 May 31.

Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF), Autopista del Saler 16, E46013 Valencia, Spain.

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http://dx.doi.org/10.1093/nar/gkn318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447758PMC
July 2008

Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases.

Nucleic Acids Res 2008 Jan 17;36(Database issue):D825-9. Epub 2007 Dec 17.

Switch Laboratory, Department of Applied Biological Sciences, Vrije Universiteit Brussel, Switch Laboratory, VIB, Pleinlaan 2, 1050 Brussel, Belgium.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkm979DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238831PMC
January 2008

Using supercritical fluid chromatography to determine diffusion coefficients of 1,2-diethylbenzene, 1,4-diethylbenzene, 5-tert-butyl-m-xylene and phenylacetylene in supercritical carbon dioxide.

J Chromatogr A 2007 Oct 9;1167(2):202-9. Epub 2007 Aug 9.

Departamento de Ingeniería Química y T.M.A., Universidad de Oviedo, 33071 Oviedo, Spain.

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http://dx.doi.org/10.1016/j.chroma.2007.08.010DOI Listing
October 2007

ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling.

Nucleic Acids Res 2007 Jul 27;35(Web Server issue):W81-5. Epub 2007 Apr 27.

Bioinformatics Department, Centro de Investigación Príncipe Felipe, INB, CIPF, Valencia 46013, Spain.

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http://dx.doi.org/10.1093/nar/gkm257DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933149PMC
July 2007

Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics.

Nucleic Acids Res 2007 Jul 22;35(Web Server issue):W38-42. Epub 2007 Apr 22.

Bioinformatics Department, Centro de Investigación Príncipe Felipe, INB, CIPF, Valencia 46013, Spain.

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http://dx.doi.org/10.1093/nar/gkm224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933211PMC
July 2007

Prophet, a web-based tool for class prediction using microarray data.

Bioinformatics 2007 Feb 30;23(3):390-1. Epub 2006 Nov 30.

Department of Bioinformatics, Centro de Investigación Príncipe Felipe, Valencia, E46013, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btl602DOI Listing
February 2007

Inhibition of cancer growth by resveratrol is related to its low bioavailability.

Free Radic Biol Med 2002 Aug;33(3):387-98

Departamento de Fisiología, Universidad de Valencia, Valencia, Spain.

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http://dx.doi.org/10.1016/s0891-5849(02)00911-5DOI Listing
August 2002