Next generation variety testing for improved cropping on European farmland

Deliverables

Researcher focussed website established - M30

LESP will develop a researcherfocused website that will allow researchers to query modify and update variety data and information Month 30

Road map reports detailing how new methods could be applied to each selected crop type

This report will provide a road map on how new methods could be applied to the crop subset Collaboration with INVITE is anticipated in the task relating to this report

Publications

Analysis of the chromosomal clustering of Fusarium-responsive wheat genes uncovers new players in the defence against head blight disease

Author(s): Alexandre Perochon, Harriet R. Benbow, Katarzyna Ślęczka-Brady, Keshav B. Malla, Fiona M. Doohan
Published in: Scientific Reports, Issue 11/1, 2021, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-86362-4

TrainSel: An R Package for Selection of Training Populations

Author(s): Deniz Akdemir, Simon Rio, Julio Isidro y Sánchez
Published in: Frontiers in Genetics, Issue 12, 2021, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2021.655287

Genotype by Environment Interaction Analysis of Agronomic Spring Barley Traits in Iceland Using AMMI, Factorial Regression Model and Linear Mixed Model

Author(s): Hrannar Smári Hilmarsson, Simon Rio, Julio Isidro y Sánchez
Published in: Agronomy, Issue 11/3, 2021, Page(s) 499, ISSN 2073-4395
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/agronomy11030499

Optimal age-specific vaccination control for COVID-19: An Irish case study

Author(s): Eleni Zavrakli, Andrew Parnell, David Malone, Ken Duffy, Subhrakanti Dey
Published in: PLOS ONE, Issue 18, 2023, Page(s) e0290974, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0290974

Modelling Excess Zeros in Count Data: A New Perspective on Modelling Approaches

Author(s): John Haslett; Andrew C. Parnell; John Hinde; Rafael de Andrade Moral
Published in: International Statistical Review, Issue 2, 2021, ISSN 0306-7734
Publisher: International Statistical Institute
DOI: 10.1111/insr.12479

Evaluation of the susceptibility of modern, wild, ancestral, and mutational wheat lines to Septoria tritici blotch disease

Author(s): Sobia Ajaz, Harriet R. Benbow, Thalia Christodoulou, Cristobal Uauy, Fiona M. Doohan
Published in: Plant Pathology, Issue 70/5, 2021, Page(s) 1123-1137, ISSN 0032-0862
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/ppa.13369

Comprehensive analysis of pathogen-responsive wheat NAC transcription factors: new candidates for crop improvement

Author(s): Monika Vranic, Alexandre Perochon, Harriet Benbow, Fiona M Doohan
Published in: G3 Genes|Genomes|Genetics, 2022, ISSN 2160-1836
Publisher: Genetics Society of America
DOI: 10.1093/g3journal/jkac247

Vector time series modelling of turbidity in Dublin Bay

Author(s): Amin Shoari Nejad, Gerard D. McCarthy, Brian Kelleher, Anthony Grey, Andrew Parnell
Published in: Journal of Applied Statistics, 2024, Page(s) 1-16, ISSN 0266-4763
Publisher: Routledge
DOI: 10.1080/02664763.2024.2315470

Bayesian multi-species N-mixture models for unmarked animal communities

Author(s): Niamh Mimnagh, Andrew Parnell, Estevão Prado, Rafael de Andrade Moral
Published in: Environmental and Ecological Statistics, Issue 29, 2022, Page(s) 755-778, ISSN 1352-8505
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10651-022-00542-7

Genomic prediction and training set optimization in a structured Mediterranean oat population.

Author(s): Simon Rio; Luis M. Gallego-Sánchez; Gracia Montilla-Bascón; Francisco José Canales; Julio Isidro y Sánchez; Elena Prats
Published in: Theoretical and Applied Genetics volume, Issue 134, 2021, ISSN 0040-5752
Publisher: Springer Verlag
DOI: 10.1007/s00122-021-03916-w

Transcriptional Profiling Reveals the Wheat Defences against Fusarium Head Blight Disease Regulated by a NAC Transcription Factor

Author(s): Monika Vranić; Alexandre Perochon; Fiona M. Doohan
Published in: Plants, Issue 12, 2023, ISSN 2223-7747
Publisher: MDPI
DOI: 10.3390/plants12142708

Training Set Optimization for Sparse Phenotyping in Genomic Selection: A Conceptual Overview

Author(s): Julio Isidro y Sánchez, Deniz Akdemir
Published in: Frontiers in Plant Science, Issue 12, 2021, ISSN 1664-462X
Publisher: Frontiers Media S. A.
DOI: 10.3389/fpls.2021.715910

GP-BART: A novel Bayesian additive regression trees approach using Gaussian processes

Author(s): Mateus Maia, Keefe Murphy, Andrew C. Parnell
Published in: Computational Statistics & Data Analysis, Issue 190, 2024, Page(s) 107858, ISSN 0167-9473
Publisher: Elsevier BV
DOI: 10.1016/j.csda.2023.107858

Accounting for shared covariates in semi-parametric Bayesian additive regression trees

Author(s): Batista Do Prado, Estevao; Parnell, Andrew; de Andrade Moral, Rafael; McJames, Nathan; O'Shea, Ann; Murphy, Keefe
Published in: Annals of Applied Statistics, Issue 1, 2024, ISSN 1932-6157
Publisher: Institute of Mathematical Statistics
DOI: 10.48550/arxiv.2108.07636

Assessment of genomic prediction reliability and optimization of experimental designs in multi-environment trials

Author(s): Simon Rio; Deniz Akdemir; Tiago Carvalho; Julio Isidro y Sánchez
Published in: Theoretical and Applied Genetics, Issue 2, 2022, ISSN 0040-5752
Publisher: Springer Verlag
DOI: 10.1007/s00122-021-03972-2

Revisiting superiority and stability metrics of cultivar performances using genomic data: derivations of new estimators

Author(s): Humberto Fanelli Carvalho, Simon Rio, Julian García-Abadillo, Julio Isidro y Sánchez
Published in: Plant Methods, Issue 20, 2024, ISSN 1746-4811
Publisher: BioMed Central
DOI: 10.1186/s13007-024-01207-1

Visualizing Variable Importance and Variable Interaction Effects in Machine Learning Models

Author(s): Alan Inglis; Andrew C. Parnell; Catherine B. Hurley
Published in: Journal of Computational and Graphical Statistics, Issue 2, 2021, ISSN 1061-8600
Publisher: American Statistical Association
DOI: 10.48550/arxiv.2108.04310

Bayesian additive regression trees for genotype by environment interaction models

Author(s): Danilo A. Sarti, Estevão B. Prado, Alan N. Inglis, Antônia A. L. dos Santos, Catherine B. Hurley, Rafael A. Moral, Andrew C. Parnell
Published in: The Annals of Applied Statistics, Issue 17, 2023, ISSN 1932-6157
Publisher: Institute of Mathematical Statistics
DOI: 10.1214/22-aoas1698

Changes in the Rhizosphere Biome Depending on the Variety of Wheat, Timing of Its Growing Season, and Agrochemical Components in the Soils of Italy

Author(s): Tommaso Bardelli, Flavio Fornasier, Elena Novarina, Antonella Donniacuo, Elio Romano, Pier Giacomo Bianchi, Anna Pia Maria Giulini
Published in: Agronomy, Issue 14, 2024, Page(s) 832, ISSN 2073-4395
Publisher: MDPI
DOI: 10.3390/agronomy14040832

Pollen Geochronology from the Atlantic Coast of the United States during the Last 500 Years

Author(s): Margaret Christie, Christopher Bernhardt, Andrew Parnell, Timothy Shaw, Nicole Khan, D. Corbett, Ane García-Artola, Jennifer Clear, Jennifer Walker, Jeffrey Donnelly, Tobias Hasse, Benjamin Horton
Published in: Water, Issue 13/3, 2021, Page(s) 362, ISSN 2073-4441
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/w13030362

A Bayesian time series model for reconstructing hydroclimate from multiple proxies

Author(s): Niamh Cahill, Jacky Croke, Micheline Campbell, Kate Hughes, John Vitkovsky, Jack Eaton Kilgallen, Andrew Parnell
Published in: Environmetrics, Issue 34, 2023, ISSN 1180-4009
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/env.2786

Dissecting the complex genetic basis of pre- and post-harvest traits in <i>Vitis vinifera L</i>. using genome-wide association studies

Author(s): Julian García-Abadillo, Paola Barba, Tiago Carvalho, Viviana Sosa-Zuñiga, Roberto Lozano, Humberto Fanelli Carvalho, Miguel Garcia-Rojas, Erika Salazar, Julio Isidro y Sánchez
Published in: Horticulture Research, Issue 11, 2024, ISSN 2052-7276
Publisher: Oxford University Press
DOI: 10.1093/hr/uhad283

Bayesian additive regression trees with model trees

Author(s): Estevão B. Prado, Rafael A. Moral, Andrew C. Parnell
Published in: Statistics and Computing, Issue 31, 2024, ISSN 0960-3174
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11222-021-09997-3

Towards a Digital Twin of the Earth System: Geo-Soft-CoRe, a Geoscientific Software & Code Repository

Author(s): Irene DeFelipe; Juan Alcalde; Eldar Baykiev; Isabel Bernal; Kittiphon Boonma; Ramon Carbonell; Stephanie Flude; Arnau Folch; Javier Fullea; Daniel García-Castellanos; Adelina Geyer; Santiago Giralt; Armand Hernández; Ivone Jiménez-Munt; Ajay Kumar; Maria-Gema Llorens; Joan Martí; Cecilia Molina; Andrés Olivar-Castaño; Andrew Parnell; Martin Schimmel; Montserrat Torné; Sergi Ventosa
Published in: Frontiers in Earth Science, Issue 10, 2022, ISSN 2296-6463
Publisher: Frontiers Media S.A.
DOI: 10.3389/feart.2022.828005

Visualisations for Bayesian Additive Regression Trees

Author(s): Alan Inglis, Andrew Parnell, Catherine Hurley
Published in: Journal of Data Science, Statistics, and Visualisation, Issue 4, 2024, ISSN 2773-0689
Publisher: IASC
DOI: 10.52933/jdssv.v4i1.79

AFBI Science Impacts 2021: InnoVar: Next generation variety testing for improved cropping on European farmland

Author(s): Gareth Burns, Lisa Black
Published in: AFBI Science Impacts, 2021
Publisher: AFBI

How InterTradeIreland helped InnoVar secure H2020 funding

Author(s): Lisa Black, Fiona Doohan, Elaine Groom, IntertradeIreland
Published in: 2020
Publisher: Intertrade Ireland

InnoVar Kicks Off!

Author(s): Lisa Black, Hazel Brown, Gerry Hoppe
Published in: 2019
Publisher: AFBI

Tystoftes deltagelse i EU projektet InnoVar

Author(s): Preben Klarskov Hansen
Published in: 2020
Publisher: Tystoftefonden

Fænotypiske forskelle mellem sorter EU projektet InnoVar

Author(s): Preben Klarskov Hansen
Published in: 2020
Publisher: Tystofte

Deliverables

Publications

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