00483nas a2200133 4500008004100000022002200041245005800063210005700121300001200178490000600190100002900196700002000225856010400245 2013 eng d a978-84-9858-872-900aDocencia en Estadística: Experiencias de Innovación0 aDocencia en Estadística Experiencias de Innovación a201-2100 v11 aGarcia-Garcia, Francisco1 aMontaner, David uhttps://www.clinbioinfosspa.es/content/docencia-en-estad%C3%ADstica-experiencias-de-innovaci%C3%B3n01411nas a2200157 4500008004100000245004400041210004300085260000900128300001100137490000800148520095000156100002101106700002301127700002401150856007901174 2010 eng d00aFunctional profiling methods in cancer.0 aFunctional profiling methods in cancer c2010 a363-740 v5763 a
The introduction of new high-throughput methodologies such as DNA microarrays constitutes a major breakthrough in cancer research. The unprecedented amount of data produced by such technologies has opened new avenues for interrogating living systems although, at the same time, it has demanded of the development of new data analytical methods as well as new strategies for testing hypotheses. A history of early successful applications in cancer boosted the use of microarrays and fostered further applications in other fields. Keeping the pace with these technologies, bioinformatics offers new solutions for data analysis and, what is more important, permits the formulation of a new class of hypotheses inspired in systems biology, more oriented to pathways or, in general, to modules of functionally related genes. Although these analytical methodologies are new, some options are already available and are discussed in this chapter.
1 aDopazo, Joaquín1 aGrützmann, Robert1 aPilarsky, Christian uhttps://www.clinbioinfosspa.es/content/functional-profiling-methods-cancer01750nas a2200181 4500008004100000022002200041245009600063210007100159260002600230300001000256520107600266100002101342700001501363700001501378700001501393700001601408856014401424 2009 eng d a978-84-92910-06-900aGenómica Comparativa y Selección Natural. Aplicaciones en el Genoma Humano. Capítulo 1.60 aGenómica Comparativa y Selección Natural Aplicaciones en el Geno aValenciabObrapropia. a51-593 aLa búsqueda de los eventos adaptativos a nivel molecular que ha diferenciado el genoma humano del de nuestro pariente vivo más cercano, el chimpancé, ha sido una de las áreas de mayor investigación en genómica comparativa. Paralelamente, la predicción funcional de variantes genéticas en nuestra especie ha sido un área de intenso desarrollo en bioinformática. En este trabajo discutiremos resultados previos y otros más recientes que dan cuenta de estos desarrollos. Veremos que en todos los casos la estimación de las presiones selectivas a nivel de los genes individuales o de los residuos de las proteínas son el denominador común para discutir ambos aspectos. Finalmente mostraremos cómo el análisis de estas presiones selectivas por grupos funcionales de genes resulta una alternativa viable y con suficiente poder estadístico para el análisis de la adaptación y de las restricciones evolutivas a nivel genómico.
1 aSerra, François1 aArbiza, L.1 aDopazo, H.1 aDopazo, H.1 aNavarro, A. uhttps://www.clinbioinfosspa.es/content/gen%C3%B3mica-comparativa-y-selecci%C3%B3n-natural-aplicaciones-en-el-genoma-humano-cap%C3%ADtulo-1600491nas a2200157 4500008004100000022002900041245004900070210004900119260003900168300001200207100001600219700001500235700001600250700001800266856004900284 2009 eng d a1605663980, 97816056639800aProtein Interactions for Functional Genomics0 aProtein Interactions for Functional Genomics aHershey, USAbIdea Group Inc (IGI) a223-2381 aMinguez, P.1 aDopazo, J.1 aLi, Xiao-Li1 aNg, See-Kiong uhttp://books.google.es/books?id=pNyCy5GsqtkC00479nas a2200157 4500008004100000245004000041210004000081250000800121260003700129653003000166100002400196700001800220700001900238700001500257856004900272 2009 eng d00aStructural Comparison and Alignment0 aStructural Comparison and Alignment a2nd aNew Jersey. USAbWiley-Blackwell10aStructural Bioinformatics1 aMarti-Renom, M., A.1 aCapriotti, E.1 aShindyalov, I.1 aBourne, P. uhttp://www.amazon.com/gp/product/0470181052/00387nas a2200109 4500008004100000245004800041210004800089260005700137100001800194700002400212856004100236 2008 eng d00aAssessment of protein structure predictions0 aAssessment of protein structure predictions aNew Jersey, USAbWorld Scientific Publishing Company1 aCapriotti, E.1 aMarti-Renom, M., A. uhttp://www.amazon.com/dp/9812778772/00426nas a2200109 4500008004100000245006200041210006100103260004700164490000800211100001800219856007900237 2008 eng d00aComparative genomics-based prediction of protein function0 aComparative genomicsbased prediction of protein function bM. Starkey and R. Elaswarapu, Humana press0 v4391 aGabaldón, T. uhttp://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-188-8_2600550nas a2200157 4500008004100000245007400041210006900115260002300184300001200207100001800219700001200237700001600249700001600265700001300281856009800294 2008 eng d00aThe core of a minimal gene set: insights from natural reduced genomes0 acore of a minimal gene set insights from natural reduced genomes aUSAbThe MIT Press a347-3661 aGabaldón, T.1 aGil, R.1 aPeretó, J.1 aLatorre, A.1 aMoya, A. uhttps://www.clinbioinfosspa.es/content/core-minimal-gene-set-insights-natural-reduced-genomes00479nas a2200097 4500008004100000245009300041210006900134260003200203100001500235856013100250 2008 eng d00aSelective Constraints and Human Disease Genes: Evolutionary and Bioinformatic Approaches0 aSelective Constraints and Human Disease Genes Evolutionary and B aUKbJohn Wiley & Sons, Ltd.1 aDopazo, H. uhttps://www.clinbioinfosspa.es/content/selective-constraints-and-human-disease-genes-evolutionary-and-bioinformatic-approaches00459nas a2200097 4500008004100000245007100041210006900112260007600181100001500257856008900272 2008 eng d00aSelective Constraints on Human Disease Mutations and Polymorphisms0 aSelective Constraints on Human Disease Mutations and Polymorphis aUKbHildegard Kehrer-Sawatzki & David N. Cooper. John Wiley & Sons, Ltd1 aDopazo, H. uhttp://eu.wiley.com/WileyCDA/WileyTitle/productCd-0470517468,descCd-description.html00428nas a2200097 4500008004100000245005700041210005400098260007600152100001500228856008700243 2007 eng d00aClustering - Class discovery in the post-genomic era0 aClustering Class discovery in the postgenomic era aNew York, USAbSpringer-Verlag, W. Dubitzky, M. Granzow and D.P. Berrar1 aDopazo, J. uhttps://www.clinbioinfosspa.es/content/clustering-class-discovery-post-genomic-era00524nas a2200121 4500008004100000245007600041210006900117260004900186100001600235700002300251700001500274856011300289 2007 eng d00af single nucleotide polymorphism arrays: Design, tools and applications0 af single nucleotide polymorphism arrays Design tools and applica aNew York, USAbTaylor & Francis, F. Falciani1 aRobledo, M.1 aGonzález-Neira, A1 aDopazo, J. uhttps://www.clinbioinfosspa.es/content/f-single-nucleotide-polymorphism-arrays-design-tools-and-applications00431nas a2200109 4500008004100000245005200041210005200093260004900145100001500194700002400209856008800233 2007 eng d00aFunctional annotation of microarray experiments0 aFunctional annotation of microarray experiments aNew York, USAbTaylor & Francis, F. Falciani1 aDopazo, J.1 aAl-Shahrour, Fatima uhttps://www.clinbioinfosspa.es/content/functional-annotation-microarray-experiments00560nas a2200169 4500008004100000022001800041245005100059210005100110260005300161300001200214653001500226100001500241700001600256700001400272700001700286856008700303 2007 eng d a0-4153-7853-200aMicroarray Technology in Agricultural Research0 aMicroarray Technology in Agricultural Research bF. Falciani. Publisher: Taylor and Francis Group a173-20910ababelomics1 aConesa, A.1 aForment, J.1 aGadea, J.1 avan Dijk, J. uhttps://www.clinbioinfosspa.es/content/microarray-technology-agricultural-research00491nas a2200157 4500008004100000022002200041245005800063210005800121260002100179300001200200490000700212100001700219700002400236700001500260856005800275 2007 eng d a978-3-540-71991-500aNew Trends in the Analysis of Functional Genomic Data0 aNew Trends in the Analysis of Functional Genomic Data aBerlinbSpringer a576-5800 v121 aMontaner, D.1 aAl-Shahrour, Fatima1 aDopazo, J. uhttp://www.springerlink.com/content/m62p07r8111004vr/00409nas a2200109 4500008004100000245004200041210004200083260002400125100001800149700001900167856011300186 2007 eng d00aReconstruction of ancestral proteomes0 aReconstruction of ancestral proteomes aOxfordbD. Liberles1 aGabaldón, T.1 aHuynen, M., A. uhttp://www.us.oup.com/us/catalog/general/subject/LifeSciences/EvolutionaryBiology/?view=usa&ci=978019929918800403nas a2200097 4500008004100000245004000041210004000081260008600121100001500207856008300222 2006 eng d00aLa clasificación de los organismos0 aLa clasificación de los organismos aBuenos AiresbCurtis, Barnes, Schnek & Flores. 2da, Editorial Medica Panamericana1 aDopazo, H. uhttps://www.clinbioinfosspa.es/content/la-clasificaci%C3%B3n-de-los-organismos00503nas a2200133 4500008004100000022001600041245010000057210006900157260003700226100001900263700001300282700001700295856005700312 2006 eng d a0-387-3452700aReliable and specific protein function prediction by combining homology with genomic(s) context0 aReliable and specific protein function prediction by combining h bF. Eisenhaber, Landes Bioscience1 aHuynen, M., A.1 aSnel, B.1 aT, Gabaldón uhttp://www.landesbioscience.com/iu/output.php?id=47900468nas a2200121 4500008004100000245006300041210006300104260003500167653001500202100001500217700001500232856009900247 2005 eng d00aData analysis and visualisation in genomics and proteomics0 aData analysis and visualisation in genomics and proteomics bWiley, F. Azuaje and J. Dopazo10ababelomics1 aAzuaje, F.1 aDopazo, J. uhttps://www.clinbioinfosspa.es/content/data-analysis-and-visualisation-genomics-and-proteomics00530nas a2200121 4500008004100000245009500041210006900136260003500205100001500240700001500255700001200270856012600282 2005 eng d00aData and Predictive Model Integration: an Overview of Key Concepts, Problems and Solutions0 aData and Predictive Model Integration an Overview of Key Concept bWiley, F. Azuaje and J. Dopazo1 aAzuaje, F.1 aDopazo, J.1 aWang, H uhttps://www.clinbioinfosspa.es/content/data-and-predictive-model-integration-overview-key-concepts-problems-and-solutions00538nas a2200121 4500008004100000245010500041210006900146260003500215300000800250100001500258700001500273856012800288 2005 eng d00aIntegrative Data Analysis and Visualization: Introduction to Critical Problems, Goals and Challenges0 aIntegrative Data Analysis and Visualization Introduction to Crit bWiley, F. Azuaje and J. Dopazo a3-91 aAzuaje, F.1 aDopazo, J. uhttps://www.clinbioinfosspa.es/content/integrative-data-analysis-and-visualization-introduction-critical-problems-goals-and00404nas a2200121 4500008004100000245003900041210003900080260003500119300001100154100002400165700001500189856007800204 2005 eng d00aOntologies and functional genomics0 aOntologies and functional genomics bWiley, F. Azuaje and J. Dopazo a99-1021 aAl-Shahrour, Fatima1 aDopazo, J. uhttps://www.clinbioinfosspa.es/content/ontologies-and-functional-genomics00738nas a2200229 4500008004100000245005000041210004900091260010900140300001200249490000600261100001400267700001300281700001400294700001400308700001900322700001300341700001500354700001600369700002200385700001300407856008800420 2005 eng d00aSalinibacter ruber: genomics and biogeography0 aSalinibacter ruber genomics and biogeography aDordrecht, NetherlandsbNina Gunde-Cimerman, Ana Plemenitas, and Aharon Oren. Kluwer Academic Publishers a257-2660 v91 aAntón, J1 aPeña, A1 aValens, M1 aSantos, F1 aGlöckner, F.O1 aBauer, M1 aDopazo, J.1 aHerrero, J.1 aRosselló-Mora, R1 aAmann, R uhttps://www.clinbioinfosspa.es/content/salinibacter-ruber-genomics-and-biogeography00556nas a2200133 4500008004100000245011100041210006900152300001000221100001200231700001500243700001900258700001500277856013000292 2004 eng d00aGene expression Correlation and Gene Ontology-Based Similarity: An Assessment of Quantitative Relationship0 aGene expression Correlation and Gene OntologyBased Similarity An a25-311 aWang, H1 aAzuaje, F.1 aBodenreider, O1 aDopazo, J. uhttps://www.clinbioinfosspa.es/content/gene-expression-correlation-and-gene-ontology-based-similarity-assessment-quantitative00611nas a2200133 4500008004100000245011000041210006900151260004900220300001200269100002100281700002400302700001500326856013600341 2003 eng d00aUse of GO Terms to Understand the Biological Significance of Microarray Differential Gene Expression Data0 aUse of GO Terms to Understand the Biological Significance of Mic bKluwer Academic, K. F. Johnson and S. M. Lin a233-2471 aDíaz-Uriarte, R1 aAl-Shahrour, Fatima1 aDopazo, J. uhttps://www.clinbioinfosspa.es/content/use-go-terms-understand-biological-significance-microarray-differential-gene-expression-data00720nas a2200181 4500008004100000245013000041210006900171260003000240300001000270653001500280100002400295700001600319700001500335700001600350700002100366700001500387856013600402 2003 eng d00aUsing Gene Ontology on genome-scale studies to find significant associations of biologically relevant terms to group of genes0 aUsing Gene Ontology on genomescale studies to find significant a aNew York, USAbIEEE Press a43-5210ababelomics1 aAl-Shahrour, Fatima1 aHerrero, J.1 aMateos, A.1 aSantoyo, J.1 aDíaz-Uriarte, R1 aDopazo, J. uhttps://www.clinbioinfosspa.es/content/using-gene-ontology-genome-scale-studies-find-significant-associations-biologically-relevant00367nas a2200109 4500008004100000245004400041210004400085260002000129300001000149100001500159856008300174 2002 eng d00aMicroarray Data Processing And Analysis0 aMicroarray Data Processing And Analysis bKluwer Academic a43-631 aDopazo, J. uhttps://www.clinbioinfosspa.es/content/microarray-data-processing-and-analysis00612nas a2200145 4500008004100000245013500041210006900176260002000245300001100265100001500276700001600291700001600307700001500323856012800338 2002 eng d00aSupervised Neural Networks For Clustering Conditions In DNA Array Data After Reducing Noise By Clustering Gene Expression Profiles0 aSupervised Neural Networks For Clustering Conditions In DNA Arra bKluwer Academic a91-1031 aMateos, A.1 aHerrero, J.1 aTamames, J.1 aDopazo, J. uhttps://www.clinbioinfosspa.es/content/supervised-neural-networks-clustering-conditions-dna-array-data-after-reducing-noise00621nas a2200133 4500008004100000245016500041210006900206260002000275300001200295100001500307700001600322700001500338856013400353 2002 eng d00aUsing perceptrons for supervised classification of DNA microarray samples: obtaining the optimal level of information and finding differentially expressed genes0 aUsing perceptrons for supervised classification of DNA microarra bJ.R. Dorronsoro a577-5821 aMateos, A.1 aHerrero, J.1 aDopazo, J. uhttps://www.clinbioinfosspa.es/content/using-perceptrons-supervised-classification-dna-microarray-samples-obtaining-optimal-level