Publications by authors named "Miguel Perez-Enciso"

67Publications

Estimating Conformational Traits in Dairy Cattle With DeepAPS: A Two-Step Deep Learning Automated Phenotyping and Segmentation Approach.

Front Genet 2020 21;11:513. Epub 2020 May 21.

Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Barcelona, Spain.

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http://dx.doi.org/10.3389/fgene.2020.00513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7253626PMC
May 2020

SeqBreed: a python tool to evaluate genomic prediction in complex scenarios.

Genet Sel Evol 2020 Feb 10;52(1). Epub 2020 Feb 10.

Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193, Bellaterra, Barcelona, Spain.

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http://dx.doi.org/10.1186/s12711-020-0530-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7008576PMC
February 2020

Special issue on livestock metagenomics.

J Anim Breed Genet 2020 Jan;137(1)

ICREA, Barcelona and Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Spain.

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http://dx.doi.org/10.1111/jbg.12460DOI Listing
January 2020

HIV drug resistance prediction with weighted categorical kernel functions.

BMC Bioinformatics 2019 Jul 30;20(1):410. Epub 2019 Jul 30.

Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Campus UAB, 08193 Bellaterra, Barcelona, Spain.

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http://dx.doi.org/10.1186/s12859-019-2991-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6668108PMC
July 2019

A Guide for Using Deep Learning for Complex Trait Genomic Prediction.

Genes (Basel) 2019 07 20;10(7). Epub 2019 Jul 20.

Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193 Bellaterra, Barcelona, Spain.

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http://dx.doi.org/10.3390/genes10070553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6678200PMC
July 2019

pSBVB: A Versatile Simulation Tool To Evaluate Genomic Selection in Polyploid Species.

G3 (Bethesda) 2019 02 7;9(2):327-334. Epub 2019 Feb 7.

Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, 08193 Bellaterra, Barcelona, Spain

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http://dx.doi.org/10.1534/g3.118.200942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385978PMC
February 2019

Can Deep Learning Improve Genomic Prediction of Complex Human Traits?

Genetics 2018 11 31;210(3):809-819. Epub 2018 Aug 31.

Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas (CSIC) - Institut de Recerca i Tecnologies Agroalimentaries (IRTA) - Universitat Autònoma de Barcelona (UAB) - Universitat de Barcelona (UB) Consortium, 08193 Bellaterra, Barcelona, Spain

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http://dx.doi.org/10.1534/genetics.118.301298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218236PMC
November 2018

Influence of epistasis on response to genomic selection using complete sequence data.

Genet Sel Evol 2017 08 25;49(1):66. Epub 2017 Aug 25.

Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, 08193, Bellaterra, Barcelona, Spain.

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http://gsejournal.biomedcentral.com/articles/10.1186/s12711-
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http://dx.doi.org/10.1186/s12711-017-0340-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5574158PMC
August 2017

A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia.

G3 (Bethesda) 2017 07 5;7(7):2171-2184. Epub 2017 Jul 5.

Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas-Instituto Recerca i Tecnologia Agroalimentaries-Universidad Autonoma de Barcelona-Universidad de Barcelona (CSIC-IRTA-UAB-UB) Consortium, 08193 Bellaterra, Spain

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http://dx.doi.org/10.1534/g3.117.042671DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499126PMC
July 2017

Evaluating Sequence-Based Genomic Prediction with an Efficient New Simulator.

Genetics 2017 02 2;205(2):939-953. Epub 2016 Dec 2.

INRA, UMR 1388 GENPHYSE, Castanet-Tolosan 31326, France.

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http://dx.doi.org/10.1534/genetics.116.194878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5289861PMC
February 2017

Sequence- vs. chip-assisted genomic selection: accurate biological information is advised.

Genet Sel Evol 2015 May 9;47:43. Epub 2015 May 9.

INRA, UMR 1388 GENPHYSE, Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, 31326, France.

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http://dx.doi.org/10.1186/s12711-015-0117-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424891PMC
May 2015

A deep catalog of autosomal single nucleotide variation in the pig.

PLoS One 2015 19;10(3):e0118867. Epub 2015 Mar 19.

Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain; Universitat Autònoma de Barcelona, Department of Animal Science, Bellaterra, Spain; Institut Català de Recerca I Estudis Avançats (ICREA), Carrer de Lluís Companys 23, Barcelona, Spain.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118867PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4366260PMC
December 2015

On genetic differentiation between domestic pigs and Tibetan wild boars.

Nat Genet 2015 Mar;47(3):190-2

Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas (CSIC)-Institut de Recerca i Tecnologia Agroalimentàries (IRTA)-Universitat Autònoma de Barcelona-Universitat de Barcelona Consortium, Bellaterra, Spain.

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http://dx.doi.org/10.1038/ng.3191DOI Listing
March 2015

Recombination of the porcine X chromosome: a high density linkage map.

BMC Genet 2014 Dec 20;15:148. Epub 2014 Dec 20.

Departamento de Mejora Genética Animal, INIA, Ctra. De la Coruña km. 7, Madrid, 28040, Spain.

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http://dx.doi.org/10.1186/s12863-014-0148-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4293812PMC
December 2014

Characterization of the porcine nutrient and taste receptor gene repertoire in domestic and wild populations across the globe.

BMC Genomics 2014 Dec 3;15:1057. Epub 2014 Dec 3.

Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193 Bellaterra, Spain.

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http://dx.doi.org/10.1186/1471-2164-15-1057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302110PMC
December 2014

Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula.

BMC Genet 2013 Oct 30;14:106. Epub 2013 Oct 30.

Departamento de Producción Animal, Fac, de Veterinaria, Área de Genética, C,P,30100 Murcia, Spain.

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http://dx.doi.org/10.1186/1471-2156-14-106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840735PMC
October 2013

Population genomics from pool sequencing.

Mol Ecol 2013 Nov 28;22(22):5561-76. Epub 2013 Oct 28.

Center for Research in Agricultural Genomics (CRAG), UAB, 08193, Bellaterra, Spain.

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http://dx.doi.org/10.1111/mec.12522DOI Listing
November 2013

Future implications of full-scale genomics for animal breeding: personalized indices?

J Anim Breed Genet 2013 Feb;130(1):2-3

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http://dx.doi.org/10.1111/jbg.12027DOI Listing
February 2013

Analyses of pig genomes provide insight into porcine demography and evolution.

Authors:
Martien A M Groenen Alan L Archibald Hirohide Uenishi Christopher K Tuggle Yasuhiro Takeuchi Max F Rothschild Claire Rogel-Gaillard Chankyu Park Denis Milan Hendrik-Jan Megens Shengting Li Denis M Larkin Heebal Kim Laurent A F Frantz Mario Caccamo Hyeonju Ahn Bronwen L Aken Anna Anselmo Christian Anthon Loretta Auvil Bouabid Badaoui Craig W Beattie Christian Bendixen Daniel Berman Frank Blecha Jonas Blomberg Lars Bolund Mirte Bosse Sara Botti Zhan Bujie Megan Bystrom Boris Capitanu Denise Carvalho-Silva Patrick Chardon Celine Chen Ryan Cheng Sang-Haeng Choi William Chow Richard C Clark Christopher Clee Richard P M A Crooijmans Harry D Dawson Patrice Dehais Fioravante De Sapio Bert Dibbits Nizar Drou Zhi-Qiang Du Kellye Eversole João Fadista Susan Fairley Thomas Faraut Geoffrey J Faulkner Katie E Fowler Merete Fredholm Eric Fritz James G R Gilbert Elisabetta Giuffra Jan Gorodkin Darren K Griffin Jennifer L Harrow Alexander Hayward Kerstin Howe Zhi-Liang Hu Sean J Humphray Toby Hunt Henrik Hornshøj Jin-Tae Jeon Patric Jern Matthew Jones Jerzy Jurka Hiroyuki Kanamori Ronan Kapetanovic Jaebum Kim Jae-Hwan Kim Kyu-Won Kim Tae-Hun Kim Greger Larson Kyooyeol Lee Kyung-Tai Lee Richard Leggett Harris A Lewin Yingrui Li Wansheng Liu Jane E Loveland Yao Lu Joan K Lunney Jian Ma Ole Madsen Katherine Mann Lucy Matthews Stuart McLaren Takeya Morozumi Michael P Murtaugh Jitendra Narayan Dinh Truong Nguyen Peixiang Ni Song-Jung Oh Suneel Onteru Frank Panitz Eung-Woo Park Hong-Seog Park Geraldine Pascal Yogesh Paudel Miguel Perez-Enciso Ricardo Ramirez-Gonzalez James M Reecy Sandra Rodriguez-Zas Gary A Rohrer Lauretta Rund Yongming Sang Kyle Schachtschneider Joshua G Schraiber John Schwartz Linda Scobie Carol Scott Stephen Searle Bertrand Servin Bruce R Southey Goran Sperber Peter Stadler Jonathan V Sweedler Hakim Tafer Bo Thomsen Rashmi Wali Jian Wang Jun Wang Simon White Xun Xu Martine Yerle Guojie Zhang Jianguo Zhang Jie Zhang Shuhong Zhao Jane Rogers Carol Churcher Lawrence B Schook

Nature 2012 Nov;491(7424):393-8

Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.

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http://www.umass.edu/vetimm/docs/Groenen_etal_2012.pdf
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http://www.nature.com/doifinder/10.1038/nature11622
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http://dx.doi.org/10.1038/nature11622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566564PMC
November 2012

SNP calling by sequencing pooled samples.

BMC Bioinformatics 2012 Sep 20;13:239. Epub 2012 Sep 20.

Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona, 08028, Spain.

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http://dx.doi.org/10.1186/1471-2105-13-239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475117PMC
September 2012

Exploring the gonad transcriptome of two extreme male pigs with RNA-seq.

BMC Genomics 2011 Nov 8;12:552. Epub 2011 Nov 8.

Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.

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http://dx.doi.org/10.1186/1471-2164-12-552DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3221674PMC
November 2011

Association between plasma metabolites and gene expression profiles in five porcine endocrine tissues.

Genet Sel Evol 2011 Jul 25;43:28. Epub 2011 Jul 25.

Department of Food and Animal Science, Veterinary School, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain.

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http://dx.doi.org/10.1186/1297-9686-43-28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149573PMC
July 2011

Qxpak.5: old mixed model solutions for new genomics problems.

BMC Bioinformatics 2011 May 25;12:202. Epub 2011 May 25.

ICREA-CRAG-Universitat Autònoma de Barcelona, Bellaterra, Spain.

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http://dx.doi.org/10.1186/1471-2105-12-202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123239PMC
May 2011

Disease liability prediction from large scale genotyping data using classifiers with a reject option.

IEEE/ACM Trans Comput Biol Bioinform 2012 Jan-Feb;9(1):88-97. Epub 2011 Mar 3.

Oviedo University, Gijón.

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http://dx.doi.org/10.1109/TCBB.2011.44DOI Listing
April 2014

Explaining the genetic basis of complex quantitative traits through prediction models.

J Comput Biol 2010 Dec;17(12):1711-23

Artificial Intelligence Center, University of Oviedo at Gijón, Asturias, Spain.

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http://dx.doi.org/10.1089/cmb.2009.0161DOI Listing
December 2010

Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip.

BMC Genomics 2010 Oct 22;11:593. Epub 2010 Oct 22.

Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.

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http://dx.doi.org/10.1186/1471-2164-11-593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091738PMC
October 2010

Leipzig: the dawn of the genomes era.

J Anim Breed Genet 2010 Oct;127(5):338

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http://dx.doi.org/10.1111/j.1439-0388.2010.00898.xDOI Listing
October 2010

Optimal neutrality tests based on the frequency spectrum.

Genetics 2010 Sep 6;186(1):353-65. Epub 2010 Jul 6.

Department of Animal Science and Food, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain.

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http://dx.doi.org/10.1534/genetics.110.118570DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940299PMC
September 2010

Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data.

Bioinformatics 2010 Apr 9;26(7):896-904. Epub 2010 Feb 9.

Bioinformatics Group, CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Brisbane, Queensland 4067, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btq051DOI Listing
April 2010

Plant polyphenol intake alters gene expression in canine leukocytes.

J Nutrigenet Nutrigenomics 2009 6;2(1):43-52. Epub 2009 Feb 6.

Affinity Petcare, Research and Development Department, Barcelona, Spain.

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https://www.karger.com/Article/FullText/200018
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http://dx.doi.org/10.1159/000200018DOI Listing
October 2009

Genomic scan for quantitative trait loci of chemical and physical body composition and deposition on pig chromosome X including the pseudoautosomal region of males.

Genet Sel Evol 2009 Mar 11;41:27. Epub 2009 Mar 11.

Animal Breeding and Development, Sustainable Livestock Systems Group, Scottish Agricultural College, West Mains Road, Edinburgh, UK.

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http://dx.doi.org/10.1186/1297-9686-41-27DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666071PMC
March 2009

Data modeling as a main source of discrepancies in single and multiple marker association methods.

BMC Proc 2009 Feb 23;3 Suppl 1:S9. Epub 2009 Feb 23.

Dept. Ciencia Animal i dels Aliments, Facultat de Veterinaria, Universitat Autonoma de Barcelona, 08193, Bellaterra, Spain.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654503PMC
http://dx.doi.org/10.1186/1753-6561-3-s1-s9DOI Listing
February 2009

Impact of breed and sex on porcine endocrine transcriptome: a bayesian biometrical analysis.

BMC Genomics 2009 Feb 24;10:89. Epub 2009 Feb 24.

Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.

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http://dx.doi.org/10.1186/1471-2164-10-89DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656523PMC
February 2009

A genome wide detection of quantitative trait loci on pig maternal infanticide behavior in a large scale White Duroc x Erhualian resource population.

Behav Genet 2009 Mar 6;39(2):213-9. Epub 2009 Jan 6.

Key Laboratory for Animal Biotechnology of Jiangxi Province and The Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, Jiangxi Province, People's Republic of China.

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http://link.springer.com/content/pdf/10.1007/s10519-008-9252
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http://link.springer.com/10.1007/s10519-008-9252-x
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http://dx.doi.org/10.1007/s10519-008-9252-xDOI Listing
March 2009

Population and quantitative genetics for a cause.

J Anim Breed Genet 2008 Aug;125(4):217-8

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http://dx.doi.org/10.1111/j.1439-0388.2008.00760.xDOI Listing
August 2008

Transcriptome architecture across tissues in the pig.

BMC Genomics 2008 Apr 16;9:173. Epub 2008 Apr 16.

Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.

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http://dx.doi.org/10.1186/1471-2164-9-173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2335121PMC
April 2008

Genetical genomics: use all data.

BMC Genomics 2007 Mar 12;8:69. Epub 2007 Mar 12.

Departament of Food and Animal Science, Veterinary School, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.

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http://dx.doi.org/10.1186/1471-2164-8-69DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1828729PMC
March 2007

Unexpected high polymorphism at the FABP4 gene unveils a complex history for pig populations.

Genetics 2006 Dec 22;174(4):2119-27. Epub 2006 Oct 22.

Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain.

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http://dx.doi.org/10.1534/genetics.106.063057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1698616PMC
December 2006

Many QTLs with minor additive effects are associated with a large difference in growth between two selection lines in chickens.

Genet Res 2005 Oct;86(2):115-25

Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, BMC, Uppsala.

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http://dx.doi.org/10.1017/S0016672305007767DOI Listing
October 2005

On growth, fatness, and form: a further look at porcine chromosome 4 in an Iberian x Landrace cross.

Mamm Genome 2005 May;16(5):374-82

Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.

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http://dx.doi.org/10.1007/s00335-004-2447-4DOI Listing
May 2005

A comparison between methods for linkage disequilibrium fine mapping of quantitative trait loci.

Genet Res 2004 Feb;83(1):41-7

Station d'amélioration génétique des animaux, Institut national de la recherche agronomique, Castanet-Tolosan, France.

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http://dx.doi.org/10.1017/s0016672303006554DOI Listing
February 2004

In silico study of transcriptome genetic variation in outbred populations.

Genetics 2004 Jan;166(1):547-54

Universitat Autònoma de Barcelona, Facultat de Veterinária, Departament de Ciència Animal i dels Aliments, 08193 Bellaterra, Spain.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1470684PMC
http://dx.doi.org/10.1534/genetics.166.1.547DOI Listing
January 2004

Detection of QTL affecting fatty acid composition in the pig.

Mamm Genome 2003 Sep;14(9):650-6

Department de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.

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http://www.animalgenome.org/QTLdb/references/14629115.pdf
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http://dx.doi.org/10.1007/s00335-002-2210-7DOI Listing
September 2003

Linkage disequilibrium fine mapping of quantitative trait loci: a simulation study.

Genet Sel Evol 2003 Sep-Oct;35(5):513-32

Station d'amélioration génétique des animaux, Institut national de la recherche agronomique, Auzeville BP 27, 31326 Castanet-Tolosan Cedex, France.

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http://dx.doi.org/10.1186/1297-9686-35-6-513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2697979PMC
April 2004

Combining gene expression and molecular marker information for mapping complex trait genes: a simulation study.

Genetics 2003 Aug;164(4):1597-606

Station d'Amélioration Génétique des Animaux, INRA, BP 27, 31326 Castanet-Tolosan, France.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462653PMC
August 2003

Fine mapping of complex trait genes combining pedigree and linkage disequilibrium information: a Bayesian unified framework.

Genetics 2003 Apr;163(4):1497-510

Institut National de la Recherche Agronomique, Station d'Amélioration Génétique des Animaux, 31326 Castanet-Tolosan, France.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462504PMC
April 2003

Prediction of clinical outcome with microarray data: a partial least squares discriminant analysis (PLS-DA) approach.

Hum Genet 2003 May 27;112(5-6):581-92. Epub 2003 Feb 27.

Station d'Amélioration Génétique des Animaux, Institut National de la Recherche Agronomique, BP 27, 31326 Castanet-Tolosan, France.

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http://dx.doi.org/10.1007/s00439-003-0921-9DOI Listing
May 2003

On marker-assisted prediction of genetic value: beyond the ridge.

Genetics 2003 Jan;163(1):347-65

Department of Animal Sciences, University of Wisconsin, Madison, Wisconsin 53706, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462425PMC
January 2003

A method for computing identity by descent probabilities and quantitative trait loci mapping with dominant (AFLP) markers.

Genet Res 2002 Jun;79(3):247-58

Station d'Amelioration Génétique des Animaux, INRA, Castanet-Tolosan, France.

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http://dx.doi.org/10.1017/s0016672302005645DOI Listing
June 2002

On the mapping of quantitative trait loci at marker and non-marker locations.

Genet Res 2002 Feb;79(1):97-106

Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS, UK.

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http://dx.doi.org/10.1017/s0016672301005420DOI Listing
February 2002