|
|
Registro completo
|
Biblioteca (s) : |
INIA Las Brujas. |
Fecha : |
17/04/2024 |
Actualizado : |
17/04/2024 |
Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
Autor : |
JURBURG, S.D.; ÁLVAREZ BLANCO, M.J.; CHATZINOTAS, A.; KAZEM, A.; KÖNIG-RIES, B.; BABIN, D.; SMALLA, K.; CERECETTO, V.; FERNANDEZ-GNECCO, G.; COVACEVICH, F.; VIRUEL, E.; BERNASCHINA, Y.; LEONI, C.; GARAYCOCHEA, S.; TERRA, J.A.; FRESIA, P.; FIGUEROLA, E.L.M.; WALL, L.G.; COVELLI, J.M.; AGNELLO, A.C.; NIETO, E.E.; FESTA, S.; DOMINICI, L.E,; ALLEGRINI, M.; ZABALOY, M.C.; MORALES, M.E.; ERIJMAN, L.; CONIGLIO, A´.; CASSÁN, F.D.; NIEVAS, S.; ROLDÁN, D.M.; MENES, R.; VAZ JAURI, P.; MARRERO, C.S.; MASSA, A.M.; REVETRIA, M.A.M.; FERNÁNDEZ-SCAVINO, A.; PEREIRA-MORA, L.; MARTÍNEZ, S.; FRENE, J.P. |
Afiliación : |
STEPHANIE D. JURBURG, Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, 04318, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, 04103, Germany; MARÍA J. ÁLVAREZ BLANCO, Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, 04318, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, 04103, Germany; ANTONIS CHATZINOTAS, Dept. Applied Microbial Ecology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany; Institute Biology, Leipzig University, Leipzig, Germany; ANAHITA KAZEM, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany; Department of Mathematics and Computer Science, Friedrich Schiller University Jena Thüringen, Jena, Germany; BIRGITTA KÖNIG-RIES, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany; Department of Mathematics and Computer Science, Friedrich Schiller University Jena Thüringen, Jena, Germany; DOREEN BABIN, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, 38104, Germany; KORNELIA SMALLA, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, 38104, Germany; MARÍA VICTORIA CERECETTO GONZÁLEZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, 38104, Germany; GABRIELA FERNANDEZ-GNECCO, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, 38104, Germany; INBIOTEC-CONICET, Buenos Aires, Mar del Plata, Argentina; FERNANDA COVACEVICH, INBIOTEC-CONICET, Buenos Aires, Mar del Plata, Argentina; INTA, EEA Balcarce, Buenos Aires, Balcarce, Argentina; EMILCE VIRUEL, Instituto de Investigación Animal del Chaco Semiárido (IIACS), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Tucumán, Argentina; YESICA STEFANIA BERNASCHINA CORREA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; CAROLINA LEONI VELAZCO, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; SILVIA RAQUEL GARAYCOCHEA SOLSONA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; JOSÉ ALFREDO TERRA FERNÁNDEZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; PABLO FRESIA, Unidad Mixta UMPI, Institut Pasteur Montevideo + INIA, Montevideo, Uruguay; EVA LUCÍA MARGARITA FIGUEROLA, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina Instituto de Biociencias, Biotecnología y Biología Traslacional, Departamento de Fisiología y Biología Molecular y Celular, Facu; LUIS GABRIEL WALL, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina; Laboratorio de Bioquímica y Biología de Suelos, Centro de Bioquímica y Microbiología de Suelos, Universidad Nacional de Quilmes; JULIETA MARIANA COVELLI, Laboratorio de Bioquímica y Biología de Suelos, Centro de Bioquímica y Microbiología de Suelos, Universidad Nacional de Quilmes (UNQ), Buenos Aires, Bernal, Argentina; ANA CAROLINA AGNELLO, Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI, CONICET-UNLP), La Plata, Argentina; ESTEBAN EMANUEL NIETO, Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI, CONICET-UNLP), La Plata, Argentina; SABRINA FESTA, Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI, CONICET-UNLP), La Plata, Argentina; LINA EDITH DOMINICI, Centro de Investigación y Desarrollo en Tecnología de Pinturas y Recubrimientos (CIDEPINT, CICPBA-CONICET-UNLP), La Plata, A; MARCO ALLEGRINI, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS, CONICET-UNS), Buenos Aires, Bahía Blanca, Argentina; MARÍA CELINA ZABALOY, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS, CONICET-UNS), Buenos Aires, Bahía Blanca, Argentina; Departamento de Agronomía, Universidad Nacional del Sur (UNS); MARIANELA ESTEFANÍA MORALES, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS, CONICET-UNS), Buenos Aires, Bahía Blanca, Argentina; Departamento de Agronomía, Universidad Nacional del Sur (UNS); LEONARDO ERIJMAN, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Dr Héctor N Torres' (INGEBI-CONICET)T, Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular Dr Hé; ANAHI CONIGLIO, Laboratorio de Fisiología Vegetal y de la Interacción Planta Microorganismo (LFVIPM), Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Facultad de Ciencias Exactas Físico-Químicas y Naturales, Universidad Nacional de Río C; FABRICIO DARIO CASSÁN, Laboratorio de Fisiología Vegetal y de la Interacción Planta Microorganismo (LFVIPM), Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Facultad de Ciencias Exactas Físico-Químicas y Naturales, Universidad Nacional; SOFIA NIEVAS, Laboratorio de Fisiología Vegetal y de la Interacción Planta Microorganismo (LFVIPM), Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET), Facultad de Ciencias Exactas Físico-Químicas y Naturales, Universidad Nacional de Río Cua; DIEGO M. ROLDÁN, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Ministerio de Educación y Cultura, Montevideo, Uruguay; Laboratorio de Ecología Micr; RODOLFO MENES, Laboratorio de Ecología Microbiana Medioambiental, Facultad de Química, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay; Laboratorio de Microbiología, Unidad Asociada del; PATRICIA VAZ JAURI, Laboratorio de Microbiología de Suelos, Instituto de Ecología y Ciencias Ambientales, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay; Laboratorio de Interacción Plan; CARLA SILVA MARRERO, Laboratorio de Microbiología de Suelos, Instituto de Ecología y Ciencias Ambientales, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay; ADRIANA MONTAÑEZ MASSA, Laboratorio de Microbiología de Suelos, Instituto de Ecología y Ciencias Ambientales, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay; MARÍA ADELINA MOREL REVETRIA, Laboratorio de Microbiología de Suelos, Instituto de Ecología y Ciencias Ambientales, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay; ANA FERNÁNDEZ-SCAVINO, Laboratorio de Ecología Microbiana y Microbiología Ambiental, Departamento de Biociencias, Facultad de Química, Universidad de la República (UdelarR), Montevideo, Uruguay; LUCIANA PEREIRA-MORA, Laboratorio de Ecología Microbiana y Microbiología Ambiental, Departamento de Biociencias, Facultad de Química, Universidad de la República (UdelarR), Montevideo, Uruguay; SOLEDAD MARTÍNEZ, Laboratorio de Biotecnología, Departamento de Biociencias, Unidad de Análisis de Agua, Facultad de Química, Universidad de la República (UdelaR), Montevideo, Uruguay; JUAN PABLO FRENE, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, United Kingdom. |
Título : |
Datathons: fostering equitability in data reuse in ecology. |
Complemento del título : |
Science & Society. |
Fecha de publicación : |
2024 |
Fuente / Imprenta : |
Trends in Microbiology. 2024. https://doi.org/10.1016/j.tim.2024.02.010 -- OPEN ACCESS [Article in Press] |
ISSN : |
0966-842X |
DOI : |
10.1016/j.tim.2024.02.010 |
Idioma : |
Inglés |
Notas : |
Article history: Available online 21 March 2024. -- Correspondence: Jurburg, S.D.; Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany; email:s.d.jurburg@gmail.com -- LICENSE: Article under a Creative Commons license (http://creativecommons.org/licenses/by/4.0/ ) -- |
Contenido : |
ABSTRACT.- Approaches to rapidly collecting global biodiversity data are increasingly important, but biodiversity blind spots persist. We organized a three-day Datathon event to improve the openness of local biodiversity data and facilitate data reuse by local researchers. The first Datathon, organized among microbial ecologists in Uruguay and Argentina assembled the largest microbiome dataset in the region to date and formed collaborative consortia for microbiome data synthesis. © 2024 The Author(s) |
Palabras claves : |
ÁREA DE RECURSOS NATURALES, PRODUCCIÓN Y AMBIENTE - INIA; ÁREA MEJORAMIENTO GENÉTICO Y BIOTECNOLOGÍA VEGETAL - INIA; DATATHONS; SISTEMA ARROZ-GANADERÍA - INIA; SISTEMA VEGETAL INTENSIVO - INIA; The Datathon 2022 Consortium. |
Asunto categoría : |
-- |
URL : |
https://www.sciencedirect.com/science/article/pii/S0966842X24000507/pdf
|
Marc : |
LEADER 02820naa a2200697 a 4500 001 1064595 005 2024-04-17 008 2024 bl uuuu u00u1 u #d 022 $a0966-842X 024 7 $a10.1016/j.tim.2024.02.010$2DOI 100 1 $aJURBURG, S.D. 245 $aDatathons$bfostering equitability in data reuse in ecology.$h[electronic resource] 260 $c2024 500 $aArticle history: Available online 21 March 2024. -- Correspondence: Jurburg, S.D.; Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany; email:s.d.jurburg@gmail.com -- LICENSE: Article under a Creative Commons license (http://creativecommons.org/licenses/by/4.0/ ) -- 520 $aABSTRACT.- Approaches to rapidly collecting global biodiversity data are increasingly important, but biodiversity blind spots persist. We organized a three-day Datathon event to improve the openness of local biodiversity data and facilitate data reuse by local researchers. The first Datathon, organized among microbial ecologists in Uruguay and Argentina assembled the largest microbiome dataset in the region to date and formed collaborative consortia for microbiome data synthesis. © 2024 The Author(s) 653 $aÁREA DE RECURSOS NATURALES, PRODUCCIÓN Y AMBIENTE - INIA 653 $aÁREA MEJORAMIENTO GENÉTICO Y BIOTECNOLOGÍA VEGETAL - INIA 653 $aDATATHONS 653 $aSISTEMA ARROZ-GANADERÍA - INIA 653 $aSISTEMA VEGETAL INTENSIVO - INIA 653 $aThe Datathon 2022 Consortium 700 1 $aÁLVAREZ BLANCO, M.J. 700 1 $aCHATZINOTAS, A. 700 1 $aKAZEM, A. 700 1 $aKÖNIG-RIES, B. 700 1 $aBABIN, D. 700 1 $aSMALLA, K. 700 1 $aCERECETTO, V. 700 1 $aFERNANDEZ-GNECCO, G. 700 1 $aCOVACEVICH, F. 700 1 $aVIRUEL, E. 700 1 $aBERNASCHINA, Y. 700 1 $aLEONI, C. 700 1 $aGARAYCOCHEA, S. 700 1 $aTERRA, J.A. 700 1 $aFRESIA, P. 700 1 $aFIGUEROLA, E.L.M. 700 1 $aWALL, L.G. 700 1 $aCOVELLI, J.M. 700 1 $aAGNELLO, A.C. 700 1 $aNIETO, E.E. 700 1 $aFESTA, S. 700 1 $aDOMINICI, L.E, 700 1 $aALLEGRINI, M. 700 1 $aZABALOY, M.C. 700 1 $aMORALES, M.E. 700 1 $aERIJMAN, L. 700 1 $aCONIGLIO, A´. 700 1 $aCASSÁN, F.D. 700 1 $aNIEVAS, S. 700 1 $aROLDÁN, D.M. 700 1 $aMENES, R. 700 1 $aVAZ JAURI, P. 700 1 $aMARRERO, C.S. 700 1 $aMASSA, A.M. 700 1 $aREVETRIA, M.A.M. 700 1 $aFERNÁNDEZ-SCAVINO, A. 700 1 $aPEREIRA-MORA, L. 700 1 $aMARTÍNEZ, S. 700 1 $aFRENE, J.P. 773 $tTrends in Microbiology. 2024. https://doi.org/10.1016/j.tim.2024.02.010 -- OPEN ACCESS [Article in Press]
Descargar
Esconder MarcPresentar Marc Completo |
Registro original : |
INIA Las Brujas (LB) |
|
Biblioteca
|
Identificación
|
Origen
|
Tipo / Formato
|
Clasificación
|
Cutter
|
Registro
|
Volumen
|
Estado
|
Volver
|
|
Registro completo
|
Biblioteca (s) : |
INIA La Estanzuela. |
Fecha actual : |
21/02/2014 |
Actualizado : |
05/12/2018 |
Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
Circulación / Nivel : |
A - 1 |
Autor : |
BRANDARIZ , S.; GONZÁLEZ RAYMÚNDEZ, A.; LADO, B.; MALOSETTI, M.; FRANCO GARCIA, A.; QUINCKE, M.; VON ZITZEWITZ, J.; CASTRO, M.; MATUS,I.; DEL POZO, A.; CASTRO, A.J.; GUTIÉRREZ, L. |
Afiliación : |
SOFÍA P. BRANDARIZ, Universidad de la República (UdelaR); Facultad de Agronomía, Uruguay.; AGUSTÍN GONZÁLEZ REYMÚNDEZ; BETTINA LADO; MARCOS MALOSETTI; ANTONIO AUGUSTO FRANCO GARCIA; MARTIN CONRADO QUINCKE WALDEN, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; JARISLAV RAMON VON ZITZEWITZ VON SALVIATI, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; MARINA CASTRO DERENYI, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; IVÁN MATUS; ALEJANDRO DEL POZO; ARIEL J. CASTRO; LUCÍA GUTIÉRREZ. |
Título : |
Ascertainment bias from imputation methods evaluation in wheat. |
Fecha de publicación : |
2016 |
Fuente / Imprenta : |
BMC Genomics, 2016, v. 17, p.773. |
DOI : |
10.1186/s12864-016-3120-5 |
Idioma : |
Inglés |
Notas : |
OPEN ACCESS. Article history: Received 2016 Feb 24 // Accepted 2016 Sep 23. |
Contenido : |
Abstract
BACKGROUND:
Whole-genome genotyping techniques like Genotyping-by-sequencing (GBS) are being used for genetic studies such as Genome-Wide Association (GWAS) and Genomewide Selection (GS), where different strategies for imputation have been developed. Nevertheless, imputation error may lead to poor performance (i.e. smaller power or higher false positive rate) when complete data is not required as it is for GWAS, and each marker is taken at a time. The aim of this study was to compare the performance of GWAS analysis for Quantitative Trait Loci (QTL) of major and minor effect using different imputation methods when no reference panel is available in a wheat GBS panel.
RESULTS:
In this study, we compared the power and false positive rate of dissecting quantitative traits for imputed and not-imputed marker score matrices in: (1) a complete molecular marker barley panel array, and (2) a GBS wheat panel with missing data. We found that there is an ascertainment bias in imputation method comparisons. Simulating over a complete matrix and creating missing data at random proved that imputation methods have a poorer performance. Furthermore, we found that when QTL were simulated with imputed data, the imputation methods performed better than the not-imputed ones. On the other hand, when QTL were simulated with not-imputed data, the not-imputed method and one of the imputation methods performed better for dissecting quantitative traits. Moreover, larger differences between imputation methods were detected for QTL of major effect than QTL of minor effect. We also compared the different marker score matrices for GWAS analysis in a real wheat phenotype dataset, and we found minimal differences indicating that imputation did not improve the GWAS performance when a reference panel was not available.
CONCLUSIONS:
Poorer performance was found in GWAS analysis when an imputed marker score matrix was used, no reference panel is available, in a wheat GBS panel. MenosAbstract
BACKGROUND:
Whole-genome genotyping techniques like Genotyping-by-sequencing (GBS) are being used for genetic studies such as Genome-Wide Association (GWAS) and Genomewide Selection (GS), where different strategies for imputation have been developed. Nevertheless, imputation error may lead to poor performance (i.e. smaller power or higher false positive rate) when complete data is not required as it is for GWAS, and each marker is taken at a time. The aim of this study was to compare the performance of GWAS analysis for Quantitative Trait Loci (QTL) of major and minor effect using different imputation methods when no reference panel is available in a wheat GBS panel.
RESULTS:
In this study, we compared the power and false positive rate of dissecting quantitative traits for imputed and not-imputed marker score matrices in: (1) a complete molecular marker barley panel array, and (2) a GBS wheat panel with missing data. We found that there is an ascertainment bias in imputation method comparisons. Simulating over a complete matrix and creating missing data at random proved that imputation methods have a poorer performance. Furthermore, we found that when QTL were simulated with imputed data, the imputation methods performed better than the not-imputed ones. On the other hand, when QTL were simulated with not-imputed data, the not-imputed method and one of the imputation methods performed better for dissecting quantitative traits. Moreover, larger differences between ... Presentar Todo |
Palabras claves : |
FALSE POSITIVE; FALSO POSITIVO; GBS; GWAS; POWER; QTLs. |
Thesagro : |
MEJORAMIENTO DE TRIGO. |
Asunto categoría : |
F30 Genética vegetal y fitomejoramiento |
URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/12122/1/s12864-016-3120-5.pdf
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3120-5
|
Marc : |
LEADER 02972nam a2200349 a 4500 001 1047336 005 2018-12-05 008 2016 bl uuuu u0uu1 u #d 024 7 $a10.1186/s12864-016-3120-5$2DOI 100 1 $aBRANDARIZ , S. 245 $aAscertainment bias from imputation methods evaluation in wheat.$h[electronic resource] 260 $aBMC Genomics, 2016, v. 17, p.773.$c2016 500 $aOPEN ACCESS. Article history: Received 2016 Feb 24 // Accepted 2016 Sep 23. 520 $aAbstract BACKGROUND: Whole-genome genotyping techniques like Genotyping-by-sequencing (GBS) are being used for genetic studies such as Genome-Wide Association (GWAS) and Genomewide Selection (GS), where different strategies for imputation have been developed. Nevertheless, imputation error may lead to poor performance (i.e. smaller power or higher false positive rate) when complete data is not required as it is for GWAS, and each marker is taken at a time. The aim of this study was to compare the performance of GWAS analysis for Quantitative Trait Loci (QTL) of major and minor effect using different imputation methods when no reference panel is available in a wheat GBS panel. RESULTS: In this study, we compared the power and false positive rate of dissecting quantitative traits for imputed and not-imputed marker score matrices in: (1) a complete molecular marker barley panel array, and (2) a GBS wheat panel with missing data. We found that there is an ascertainment bias in imputation method comparisons. Simulating over a complete matrix and creating missing data at random proved that imputation methods have a poorer performance. Furthermore, we found that when QTL were simulated with imputed data, the imputation methods performed better than the not-imputed ones. On the other hand, when QTL were simulated with not-imputed data, the not-imputed method and one of the imputation methods performed better for dissecting quantitative traits. Moreover, larger differences between imputation methods were detected for QTL of major effect than QTL of minor effect. We also compared the different marker score matrices for GWAS analysis in a real wheat phenotype dataset, and we found minimal differences indicating that imputation did not improve the GWAS performance when a reference panel was not available. CONCLUSIONS: Poorer performance was found in GWAS analysis when an imputed marker score matrix was used, no reference panel is available, in a wheat GBS panel. 650 $aMEJORAMIENTO DE TRIGO 653 $aFALSE POSITIVE 653 $aFALSO POSITIVO 653 $aGBS 653 $aGWAS 653 $aPOWER 653 $aQTLs 700 1 $aGONZÁLEZ RAYMÚNDEZ, A. 700 1 $aLADO, B. 700 1 $aMALOSETTI, M. 700 1 $aFRANCO GARCIA, A. 700 1 $aQUINCKE, M. 700 1 $aVON ZITZEWITZ, J. 700 1 $aCASTRO, M. 700 1 $aMATUS,I. 700 1 $aDEL POZO, A. 700 1 $aCASTRO, A.J. 700 1 $aGUTIÉRREZ, L.
Descargar
Esconder MarcPresentar Marc Completo |
Registro original : |
INIA La Estanzuela (LE) |
|
Biblioteca
|
Identificación
|
Origen
|
Tipo / Formato
|
Clasificación
|
Cutter
|
Registro
|
Volumen
|
Estado
|
Volver
|
Expresión de búsqueda válido. Check! |
|
|