Zobrazeno 1 - 10
of 32
pro vyhledávání: '"John M. Hickey"'
Publikováno v:
Crop Science
Gonen, S, Wimmer, V, Gaynor, C, Byrne, E, Gorjanc, G & Hickey, J 2021, ' Phasing and imputation of single nucleotide polymorphism data of missing parents of bi-parental plant populations ', Crop science, vol. 61, no. 4, pp. 2243-2253 . https://doi.org/10.1002/csc2.20409
Gonen, S, Wimmer, V, Gaynor, C, Byrne, E, Gorjanc, G & Hickey, J 2021, ' Phasing and imputation of single nucleotide polymorphism data of missing parents of bi-parental plant populations ', Crop science, vol. 61, no. 4, pp. 2243-2253 . https://doi.org/10.1002/csc2.20409
This paper presents an extension to a heuristic method for phasing and imputation of genotypes of descendants in biparental populations so that it can phase and impute genotypes of parents that are ungenotyped or partially genotyped. The imputed geno
Autor:
Sudam C. Patil, Diego Jarquin, John M. Hickey, T. Radhakrishnan, Subramaniam Sundravadana, Ramesh S. Bhat, Sunil Chaudhari, Dhirendra Khare, Rajeev K. Varshney, Manish K. Pandey, José Crossa, Pasupuleti Janila
Publikováno v:
TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik
Pandey, M K, Chaudhari, S, Jarquin, D, Janila, P, Crossa, J, Patil, S C, Sundravadana, S, Khare, D, Bhat, R S, Radhakrishnan, T, Hickey, J M & Varshney, R K 2020, ' Genome-based trait prediction in multi- environment breeding trials in groundnut ', TAG Theoretical and Applied Genetics . https://doi.org/10.1007/s00122-020-03658-1
Pandey, M K, Chaudhari, S, Jarquin, D, Janila, P, Crossa, J, Patil, S C, Sundravadana, S, Khare, D, Bhat, R S, Radhakrishnan, T, Hickey, J M & Varshney, R K 2020, ' Genome-based trait prediction in multi- environment breeding trials in groundnut ', TAG Theoretical and Applied Genetics . https://doi.org/10.1007/s00122-020-03658-1
Key message Comparative assessment identified naïve interaction model, and naïve and informed interaction GS models suitable for achieving higher prediction accuracy in groundnut keeping in mind the high genotype × environment interaction for comp
Publikováno v:
Bioinformatics
Whalen, A, Gorjanc, G & Hickey, J M 2020, ' AlphaFamImpute : high accuracy imputation in full-sib families from genotype-by-sequencing data ', Bioinformatics . https://doi.org/10.1093/bioinformatics/btaa499
Whalen, A, Gorjanc, G & Hickey, J M 2020, ' AlphaFamImpute : high accuracy imputation in full-sib families from genotype-by-sequencing data ', Bioinformatics . https://doi.org/10.1093/bioinformatics/btaa499
Summary AlphaFamImpute is an imputation package for calling, phasing and imputing genome-wide genotypes in outbred full-sib families from single nucleotide polymorphism (SNP) array and genotype-by-sequencing (GBS) data. GBS data are increasingly bein
Autor:
Martin Johnsson, Andrew Whalen, William O Herring, Ching-Yi Chen, Dirk-Jan de Koning, Roger Ros-Freixedes, Gregor Gorjanc, John M. Hickey
Publikováno v:
Repositorio Abierto de la UdL
Universitad de Lleida
Johnsson, M, Whalen, A, Ros-Freixedes, R, Gorjanc, G, Chen, C-Y, o Herring, W, De Koning, D & Hickey, J 2021, ' Genetic variation in recombination rate in the pig ', Genetics Selection Evolution, vol. 53, no. 1, pp. 54 . https://doi.org/10.1186/s12711-021-00643-0
Genetics, Selection, Evolution : GSE
Genetics Selection Evolution, Vol 53, Iss 1, Pp 1-19 (2021)
Universitad de Lleida
Johnsson, M, Whalen, A, Ros-Freixedes, R, Gorjanc, G, Chen, C-Y, o Herring, W, De Koning, D & Hickey, J 2021, ' Genetic variation in recombination rate in the pig ', Genetics Selection Evolution, vol. 53, no. 1, pp. 54 . https://doi.org/10.1186/s12711-021-00643-0
Genetics, Selection, Evolution : GSE
Genetics Selection Evolution, Vol 53, Iss 1, Pp 1-19 (2021)
Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assess
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::00ec16a086ab5ba51d90b544ed832b25
https://doi.org/10.1186/s12711-021-00643-0
https://doi.org/10.1186/s12711-021-00643-0
Publikováno v:
Genetics Selection Evolution
Genetics Selection Evolution, BioMed Central, 2020, 52 (1), pp.18. ⟨10.1186/s12711-020-00537-7⟩
Repositorio Abierto de la UdL
Universitad de Lleida
Ros-Freixedes, R, Whalen, A, Gorjanc, G, Mileham, A J & Hickey, J 2020, ' Evaluation of sequencing strategies for whole-genome imputation with hybrid peeling ', Genetics Selection Evolution . https://doi.org/10.1186/s12711-020-00537-7
Recercat: Dipósit de la Recerca de Catalunya
Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Genetics Selection Evolution, Vol 52, Iss 1, Pp 1-19 (2020)
Genetics, Selection, Evolution : GSE
Recercat. Dipósit de la Recerca de Catalunya
instname
Genetics Selection Evolution, BioMed Central, 2020, 52 (1), pp.18. ⟨10.1186/s12711-020-00537-7⟩
Repositorio Abierto de la UdL
Universitad de Lleida
Ros-Freixedes, R, Whalen, A, Gorjanc, G, Mileham, A J & Hickey, J 2020, ' Evaluation of sequencing strategies for whole-genome imputation with hybrid peeling ', Genetics Selection Evolution . https://doi.org/10.1186/s12711-020-00537-7
Recercat: Dipósit de la Recerca de Catalunya
Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Genetics Selection Evolution, Vol 52, Iss 1, Pp 1-19 (2020)
Genetics, Selection, Evolution : GSE
Recercat. Dipósit de la Recerca de Catalunya
instname
Background For assembling large whole-genome sequence datasets for routine use in research and breeding, the sequencing strategy should be adapted to the methods that will be used later for variant discovery and imputation. In this study, we used sim
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e7fb32fd0d117ad30651a8d53ca06a25
https://hal.archives-ouvertes.fr/hal-02541155/document
https://hal.archives-ouvertes.fr/hal-02541155/document
Autor:
Andrew Whalen, John M. Hickey
In this paper we present a new imputation algorithm, AlphaImpute2, which performs fast and accurate pedigree and population based imputation for livestock populations of hundreds of thousands of individuals. Genetic imputation is a tool used in genet
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::b0c181d6d3431bd83fa1cc9544cbb93d
https://doi.org/10.1101/2020.09.16.299677
https://doi.org/10.1101/2020.09.16.299677
For genomic selection in clonal breeding programs to be effective, crossing parents should be selected based on genomic predicted cross performance unless dominance is negligible. Genomic prediction of cross performance enables a balanced exploitatio
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d3badc8e7f19e40ac9ac6521eaee846a
https://doi.org/10.1101/2020.06.15.152017
https://doi.org/10.1101/2020.06.15.152017
Autor:
William O Herring, Roger Ros-Freixedes, Andrew Whalen, Alan J. Mileham, Gregor Gorjanc, John M. Hickey, Ching-Yi Chen
Publikováno v:
Ros-Freixedes, R, Whalen, A, Chen, C-Y, Gorjanc, G, Herring, WO, Mileham, A J & Hickey, J 2020, ' Accuracy of whole-genome sequence imputation using hybrid peeling in large pedigreed livestock populations ', Genetics Selection Evolution . https://doi.org/10.1186/s12711-020-00536-8
Repositorio Abierto de la UdL
Universitad de Lleida
Genetics Selection Evolution, Vol 52, Iss 1, Pp 1-15 (2020)
Genetics Selection Evolution
Genetics Selection Evolution, BioMed Central, 2020, 52 (1), pp.17. ⟨10.1186/s12711-020-00536-8⟩
Recercat: Dipósit de la Recerca de Catalunya
Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Genetics, Selection, Evolution : GSE
Recercat. Dipósit de la Recerca de Catalunya
instname
Repositorio Abierto de la UdL
Universitad de Lleida
Genetics Selection Evolution, Vol 52, Iss 1, Pp 1-15 (2020)
Genetics Selection Evolution
Genetics Selection Evolution, BioMed Central, 2020, 52 (1), pp.17. ⟨10.1186/s12711-020-00536-8⟩
Recercat: Dipósit de la Recerca de Catalunya
Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Genetics, Selection, Evolution : GSE
Recercat. Dipósit de la Recerca de Catalunya
instname
Background The coupling of appropriate sequencing strategies and imputation methods is critical for assembling large whole-genome sequence datasets from livestock populations for research and breeding. In this paper, we describe and validate the coup
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::23f27608c2414623039a4174c1c8e69c
https://www.pure.ed.ac.uk/ws/files/143097418/s12711_020_00536_8.pdf
https://www.pure.ed.ac.uk/ws/files/143097418/s12711_020_00536_8.pdf
SummaryAlphaFamImpute is an imputation package for calling, phasing, and imputing genome-wide genotypes in outbred full-sib families from single nucleotide polymorphism (SNP) array and genotype-by-sequencing (GBS) data. GBS data is increasingly being
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d1f07f95485ed18ff7c57a6dcc1ec194
Autor:
Martin Johnsson, John M. Hickey, Janez Jenko, Gregor Gorjanc, Dirk-Jan de Koning, R. Chris Gaynor
Publikováno v:
Genetics Selection Evolution
Genetics Selection Evolution, BioMed Central, 2019, 51 (1), pp.14. ⟨10.1186/s12711-019-0456-8⟩
Genetics, Selection, Evolution : GSE
Johnsson, M, Gaynor, R, Jenko, J, Gorjanc, G, De Koning, D-J & Hickey, J 2019, ' Removal of alleles by genome editing (RAGE) against deleterious load ', Genetics Selection Evolution . https://doi.org/10.1186/s12711-019-0456-8
Genetics Selection Evolution, Vol 51, Iss 1, Pp 1-18 (2019)
Genetics Selection Evolution, BioMed Central, 2019, 51 (1), pp.14. ⟨10.1186/s12711-019-0456-8⟩
Genetics, Selection, Evolution : GSE
Johnsson, M, Gaynor, R, Jenko, J, Gorjanc, G, De Koning, D-J & Hickey, J 2019, ' Removal of alleles by genome editing (RAGE) against deleterious load ', Genetics Selection Evolution . https://doi.org/10.1186/s12711-019-0456-8
Genetics Selection Evolution, Vol 51, Iss 1, Pp 1-18 (2019)
Background In this paper, we simulate deleterious load in an animal breeding program, and compare the efficiency of genome editing and selection for decreasing it. Deleterious variants can be identified by bioinformatics screening methods that use se
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::80f57ea7acb8fe1ea3f6fd06fc58f86d
https://hal.archives-ouvertes.fr/hal-02105889/file/12711_2019_456_MOESM1_ESM.pdf
https://hal.archives-ouvertes.fr/hal-02105889/file/12711_2019_456_MOESM1_ESM.pdf