2017
A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia.
Leno-Colorado J, Hudson N, Reverter A, Pérez-Enciso M.
G3 (Bethesda). 2017 May 12. pii: g3.117.042671. doi: 10.1534/g3.117.042671
Using RNA-Seq SNP data to reveal potential causal mutations related to pig production traits and RNA editing.
Martínez-Montes AM, Fernández A, Pérez-Montarelo D, Alves E, Benítez RM, Nuñez Y, Óvilo C, Ibañez-Escriche N, Folch JM, Fernández AI.
Anim Genet. 2017 Apr;48(2):151-165. doi: 10.1111/age.12507. Epub 2016 Sep 18.
Deciphering the regulation of porcine genes influencing growth, fatness and yield-related traits through genetical genomics.
Martínez-Montes AM, Muiños-Bühl A, Fernández A, Folch JM, Ibáñez-Escriche N, Fernández AI.
Mamm Genome. 2017 Apr;28(3-4):130-142. doi: 10.1007/s00335-016-9674-3. Epub 2016 Dec 10.
Integration of liver gene co-expression networks and eGWAs analyses highlighted candidate regulators implicated in lipid metabolism in pigs.
Ballester M, Ramayo-Caldas Y, Revilla M, Corominas J, Castelló A, Estellé J, Fernández AI, Folch JM.
Sci Rep. 2017 Apr 19;7:46539. doi: 10.1038/srep46539.
A global analysis of CNVs in swine using whole genome sequence data and association analysis with fatty acid composition and growth traits.
Revilla M, Puig-Oliveras A, Castelló A, Crespo-Piazuelo D, Paludo E, Fernández AI, Ballester M, Folch JM.
PLoS One. 2017 May 4;12(5):e0177014. doi: 10.1371/journal.pone.0177014. eCollection 2017.
Evaluating Sequence-Based Genomic Prediction with an Efficient New Simulator.
Pérez-Enciso M, Forneris N, de Los Campos G, Legarra A.
Genetics. 2017 Feb;205(2):939-953. doi: 10.1534/genetics.116.194878. Epub 2016 Dec 2.
Animal Breeding learning from machine learning.
Pérez-Enciso M.
J Anim Breed Genet. 2017 Apr;134(2):85-86. doi: 10.1111/jbg.12263.
A genomic perspective on wild boar demography and evolution.
Marcel Amills eras , Hendrik Ian Megens, Arianna Manunza Sebastian E. Ramos-Onsins and Martien Groenen.
Chapter in the Book titled "Ecology, conservation and Management of Wild Pigs and Peccaries". Edited by Mario Melletti and Erik Meijaard.
Cambridge University Press
2016
A combined coalescence gene-dropping tool for evaluating genomic selection in complex scenarios (ms2gs).
Pérez-Enciso M, Legarra A.
J Anim Breed Genet. 2016 Apr;133(2):85-91. doi: 10.1111/jbg.12200. Epub 2016 Jan 6.
Analysis of the porcine APOA2 gene expression in liver, polymorphism identification and association with fatty acid composition traits.
Ballester M, Revilla M, Puig-Oliveras A, Marchesi JA, Castelló A, Corominas J, Fernández AI, Folch JM.
Anim Genet. 2016 Oct;47(5):552-9. doi: 10.1111/age.12462. Epub 2016 Jun 14.
Expression-based GWAS identifies variants, gene interactions and key regulators affecting intramuscular fatty acid content and composition in porcine meat.
Puig-Oliveras A, Revilla M, Castelló A, Fernández AI, Folch JM, Ballester M.
Sci Rep. 2016 Aug 18;6:31803. doi: 10.1038/srep31803.
The 'heritability' of domestication and its functional partitioning in the pig.
Pérez-Enciso M, de Los Campos G, Hudson N, Kijas J, Reverter A.
Heredity (Edinb). 2017 Feb;118(2):160-168. doi: 10.1038/hdy.2016.78. Epub 2016 Sep 21.
Identification of protein-damaging mutations in 10 swine taste receptors and 191 appetite-reward genes.
Clop A, Sharaf A, Castelló A, Ramos-Onsins S, Cirera S, Mercadé A, Derdak S, Beltran S, Huisman A, Fredholm M, van As P, Sánchez A.
BMC Genomics. 2016 Aug 26;17:685. doi: 10.1186/s12864-016-2972-z.
Approaching Long Genomic Regions and Large Recombination Rates with msParSm as an Alternative to MaCS.
Montemuiño C, Espinosa A, Moure JC, Vera G, Hernández P, Ramos-Onsins S.
Evol Bioinform Online. 2016 Oct 2;12:223-228. eCollection 2016.
2015
Epigenetic regulation of the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs.
Corominas J, Marchesi JA, Puig-Oliveras A, Revilla M, Estellé J, Alves E, Folch JM, Ballester M.
Genet Sel Evol. 2015 Mar 25;47:20. doi: 10.1186/s12711-015-0111-y. PubMed PMID: 25887840; PubMed
Central PMCID: PMC4371617.
On genetic differentiation between domestic pigs and Tibetan wild boars.
Pérez-Enciso M, Burgos-Paz W, Ramos-Onsins SE.
Nat Genet. 2015 Mar;47(3):190-2. doi: 10.1038/ng.3191. PubMed PMID: 25711861.
Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome.
Sanseverino W, Hénaff E, Vives C, Pinosio S, Burgos-Paz W, Morgante M, Ramos-Onsins SE, Garcia-Mas J, Casacuberta JM.
Mol Biol Evol. 2015 Oct;32(10):2760-74. doi: 10.1093/molbev/msv152. Epub 2015 Jul 14.
PubMed PMID: 26174143.
A deep catalog of autosomal single nucleotide variation in the pig.
Bianco E, Nevado B, Ramos-Onsins SE, Pérez-Enciso M.
PLoS One. 2015 Mar 19;10(3):e0118867. doi: 10.1371/journal.pone.0118867. eCollection 2015. PubMed
PMID: 25789620; PubMed Central PMCID: PMC4366260.
Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly.
Argyris JM, Ruiz-Herrera A, Madriz-Masis P, Sanseverino W, Morata J, Pujol M, Ramos-Onsins SE, Garcia-Mas J.
BMC Genomics. 2015 Jan 22;16:4. doi: 10.1186/s12864-014-1196-3. PubMed PMID: 25612459; PubMed
Central PMCID: PMC4316794.
A generalized Watterson estimator for next-generation sequencing: From trios to autopolyploids.
Ferretti L, Ramos-Onsins SE.
Theor Popul Biol. 2015 Jan 13;100C:79-87. doi: 10.1016/j.tpb.2015.01.001. [Epub ahead of print] PubMed PMID: 25595553.
Sequence- vs. chip-assisted genomic selection: accurate biological information is advised.
Pérez-Enciso M, Rincón JC, Legarra
Genet Sel Evol. 2015 May 9;47:43. doi: 10.1186/s12711-015-0117-5. PubMed PMID: 25956961; PubMed Central
PMCID: PMC4424891.
The chimerical genome of Isla del Coco feral pigs (Costa Rica), an isolated population since 1793 but with remarkable levels of diversity.
Bianco E, Soto HW, Vargas L, Pérez-Enciso M.
Mol Ecol. 2015 May;24(10):2364-78. doi: 10.1111/mec.13182. Epub 2015 Apr 22. PubMed PMID: 25827466.
2014
Characterization of the porcine nutrient and taste receptor gene repertoire in domestic and wild populations across the globe.
da Silva EC, de Jager N, Burgos-Paz W, Reverter A, Perez-Enciso M, Roura E.
BMC Genomics. 2014 Dec 3;15:1057. doi: 10.1186/1471-2164-15-1057.
A co-association network analysis of the genetic determination of pig conformation, growth and fatness.
Puig-Oliveras A, Ballester M, Corominas J, Revilla M, Estellé J, Fernández AI, Ramayo-Caldas Y, Folch JM.
PLoS One. 2014 Dec 11;9(12):e114862. doi: 10.1371/journal.pone.0114862. eCollection 2014.
Recombination of the porcine X chromosome: a high density linkage map.
Fernández AI, Muñoz M, Alves E, Folch JM, Noguera JL, Enciso MP, Rodríguez Mdel C, Silió L.
BMC Genet. 2014 Dec 20;15:148. doi: 10.1186/s12863-014-0148-x.
Differences in muscle transcriptome among pigs phenotypically extreme for fatty acid composition.
Puig-Oliveras A, Ramayo-Caldas Y, Corominas J, Estellé J, Pérez-Montarelo D, Hudson NJ, Casellas J, Folch JM, Ballester M.
PLoS One. 2014 Jun 13;9(6):e99720. doi: 10.1371/journal.pone.0099720. eCollection 2014. Erratum in: PLoS One. 2014 Jul;9(7):e103668.
New insight into the SSC8 genetic determination of fatty acid composition in pigs.
Revilla M, Ramayo-Caldas Y, Castelló A, Corominas J, Puig-Oliveras A, Ibáñez-Escriche N, Muñoz M, Ballester M, Folch JM.
Genet Sel Evol. 2014 Apr 23;46(1):28. doi: 10.1186/1297-9686-46-28.
From SNP co-association to RNA co-expression: novel insights into gene networks for intramuscular fatty acid composition in porcine.
Ramayo-Caldas Y, Ballester M, Fortes MR, Esteve-Codina A, Castelló A, Noguera JL, Fernández AI, Pérez-Enciso M, Reverter A, Folch JM.
BMC Genomics. 2014 Mar 26;15:232. doi: 10.1186/1471-2164-15-232.
Genome-wide analysis of porcine backfat and intramuscular fat fatty acid composition using high-density genotyping and expression data.
Muñoz M, Rodríguez MC, Alves E, Folch JM, Ibañez-Escriche N, Silió L, Fernández AI.
BMC Genomics. 2013 Dec 2;14:845. doi: 10.1186/1471-2164-14-845.
Analysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition.
Corominas J, Ramayo-Caldas Y, Puig-Oliveras A, Estellé J, Castelló A, Alves E, Pena RN, Ballester M, Folch JM.
BMC Genomics. 2013 Dec 1;14:843. doi: 10.1186/1471-2164-14-843.
Identification of genes regulating growth and fatness traits in pig through hypothalamic transcriptome analysis.
Pérez-Montarelo D, Madsen O, Alves E, Rodríguez MC, Folch JM, Noguera JL, Groenen MA, Fernández AI.
Physiol Genomics. 2014 Mar 15;46(6):195-206. doi: 10.1152/physiolgenomics.00151.2013. Epub 2013 Nov 26.
PopGenome: an efficient Swiss army knife for population genomic analyses in R.
Pfeifer B, Wittelsbürger U, Ramos-Onsins SE, Lercher MJ.
Mol Biol Evol. 2014 Jul;31(7):1929-36.
Mining the pig genome to investigate the domestication process.
Ramos-Onsins SE, Burgos-Paz W, Manunza A, Amills M.
Heredity (Edinb). 2014 Dec;113(6):471-484. doi: 10.1038/hdy.2014.68.
10th WCGALP in beautiful Vancouver.
Cantet RJ, Christensen OF, Pérez-Enciso M, van der Werf JH.
J Anim Breed Genet. 2014 Oct;131(5):409-12. doi: 10.1111/jbg.12119. No abstract available.
Genome data from a sixteenth century pig illuminate modern breed relationships.
Ramírez O, Burgos-Paz W, Casas E, Ballester M, Bianco E, Olalde I, Santpere G, Novella V, Gut M, Lalueza-Fox C, Saña M, Pérez-Enciso M.
Heredity (Edinb). 2014 Sep 10. doi: 10.1038/hdy.2014.81.
Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds.
Herrero-Medrano JM, Megens HJ, Groenen MA, Bosse M, Pérez-Enciso M, Crooijmans RP.
BMC Genomics. 2014 Jul 16;15:601. doi: 10.1186/1471-2164-15-601.
Pipeliner: software to evaluate the performance of bioinformatics pipelines for next-generation resequencing.
Nevado B, Perez-Enciso M.
Mol Ecol Resour. 2014 May 28. doi: 10.1111/1755-0998.12286.
From SNP co-association to RNA co-expression: novel insights into gene networks for intramuscular fatty acid composition in porcine.
Ramayo-Caldas Y, Ballester M, Fortes MR, Esteve-Codina A, Castelló A, Noguera JL, Fernández AI, Pérez-Enciso M, Reverter A, Folch JM.
BMC Genomics. 2014 Mar 26;15:232. doi: 10.1186/1471-2164-15-232.
Resequencing studies of nonmodel organisms using closely related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics.
Nevado B, Ramos-Onsins SE, Perez-Enciso M.
Mol Ecol. 2014 Apr;23(7):1764-79.
mspar: A Parallel Coalescent Simulator
Montemuiño C, Espinosa A, Moure JC, Vera Rodriguez G, Ramos-Onsins SE, Hernández Budé P (2014) .
D. an Mey et al. (Eds.): Euro-Par 2013 Workshops, LNCS 8374, pp. 321–330, 2014. © Springer-Verlag Berlin Heidelberg 2014
Genomic relationships computed from either next-generation sequence or array SNP data.
Pérez-Enciso M.
J Anim Breed Genet. 2014 Apr;131(2):85-96. doi: 10.1111/jbg.12074. Epub 2014 Jan 8.
2013
Worldwide genetic relationships of pigs as inferred from X chromosome SNPs.
Burgos-Paz W, Souza CA, Castelló A, Mercadé A, Okumura N, Sheremet'eva IN, Huang LS, Cho IC, Paiva SR, Ramos-Onsins S, Pérez-Enciso M.
Anim Genet. 2013 Apr;44(2):130-8. doi: 10.1111/j.1365-2052.2012.02374.x.
Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula.
Herrero-Medrano JM, Megens HJ, Groenen MA, Ramis G, Bosse M, Pérez-Enciso M, Crooijmans RP.
BMC Genet. 2013 Oct 30;14:106. doi: 10.1186/1471-2156-14-106.
Population genomics from pool sequencing.
Ferretti L, Ramos-Onsins SE, Pérez-Enciso M.
Mol Ecol. 2013 Nov;22(22):5561-76. doi: 10.1111/mec.12522. Epub 2013 Oct 28.
Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs.
Esteve-Codina A, Paudel Y, Ferretti L, Raineri E, Megens HJ, Silió L, Rodríguez MC, Groenen MA, Ramos-Onsins SE, Pérez-Enciso M.
BMC Genomics. 2013 Mar 5;14:148. doi: 10.1186/1471-2164-14-148.
Future implications of full-scale genomics for animal breeding: personalized indices?
Pérez-Enciso M.
J Anim Breed Genet. 2013 Feb;130(1):2-3. doi: 10.1111/jbg.12027. No abstract available.
Porcine colonization of the Americas: a 60k SNP story.
Burgos-Paz W, Souza CA, Megens HJ, Ramayo-Caldas Y, Melo M, Lemús-Flores C, Caal E, Soto HW, Martínez R, Alvarez LA, Aguirre L, Iñiguez V, Revidatti MA, Martínez-López OR, Llambi S, Esteve-Codina A, Rodríguez MC, Crooijmans RP, Paiva SR, Schook LB, Groenen MA, Pérez-Enciso M.
Heredity (Edinb). 2013 Apr;110(4):321-30. doi: 10.1038/hdy.2012.109. Epub 2012 Dec 19.
Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics.
Ottoni C, Flink LG, Evin A, Geörg C, De Cupere B, Van Neer W, Bartosiewicz L, Linderholm A, Barnett R, Peters J, Decorte R, Waelkens M, Vanderheyden N, Ricaut FX, Cakirlar C, Cevik O, Hoelzel AR, Mashkour M, Karimlu AF, Seno SS, Daujat J, Brock F, Pinhasi R, Hongo H, Perez-Enciso M, Rasmussen M, Frantz L, Megens HJ, Crooijmans R, Groenen M, Arbuckle B, Benecke N, Vidarsdottir US, Burger J, Cucchi T, Dobney K, Larson G.
Mol Biol Evol. 2013 Apr;30(4):824-32. doi: 10.1093/molbev/mss261. Epub 2012 Nov 22.
Genome-wide analysis of porcine backfat and intramuscular fat fatty acid composition using high-density genotyping and expression data.
Muñoz M, Rodríguez MC, Alves E, Folch JM, Ibañez-Escriche N, Silió L, Fernández AI.
BMC Genomics. 2013 Dec 2;14:845. doi: 10.1186/1471-2164-14-845.
Analysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition.
Corominas J, Ramayo-Caldas Y, Puig-Oliveras A, Estellé J, Castelló A, Alves E, Pena RN, Ballester M, Folch JM.
BMC Genomics. 2013 Dec 1;14:843. doi: 10.1186/1471-2164-14-843.
Identification of genes regulating growth and fatness traits in pig through hypothalamic transcriptome analysis.
Pérez-Montarelo D, Madsen O, Alves E, Rodríguez MC, Folch JM, Noguera JL, Groenen MA, Fernández AI.
Physiol Genomics. 2014 Mar 15;46(6):195-206. doi: 10.1152/physiolgenomics.00151.2013. Epub 2013 Nov 26.
DAG expression: high-throughput gene expression analysis of real-time PCR data using standard curves for relative quantification.
Ballester M, Cordón R, Folch JM.
PLoS One. 2013 Nov 18;8(11):e80385. doi: 10.1371/journal.pone.0080385. eCollection 2013.
Transcriptional analysis of intramuscular fatty acid composition in the longissimus thoracis muscle of Iberian × Landrace back-crossed pigs.
Pena RN, Noguera JL, Casellas J, Díaz I, Fernández AI, Folch JM, Ibáñez-Escriche N.
Anim Genet. 2013 Dec;44(6):648-60. doi: 10.1111/age.12066. Epub 2013 Jul 5.
Transcriptional Characterization of Porcine Leptin and Leptin Receptor Genes.
Pérez-Montarelo D, Fernández A, Barragán C, Noguera JL, Folch JM, Rodríguez MC, Ovilo C, Silió L, Fernández AI.
PLoS One. 2013 Jun 18;8(6):e66398. Print 2013.
Disentangling two QTL on porcine chromosome 12 for backfat fatty acid composition.
Muñoz M, Fernández AI, Benítez R, Pena RN, Folch JM, Rodríguez Mdel C, Silió L, Alves E.
Anim Biotechnol. 2013;24(3):168-86. doi: 10.1080/10495398.2012.763130.
Polymorphism in the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs.
Corominas J, Ramayo-Caldas Y, Puig-Oliveras A, Pérez-Montarelo D, Noguera JL, Folch JM, Ballester M.
PLoS One. 2013;8(1):e53687. doi: 10.1371/journal.pone.0053687. Epub 2013 Jan 14.
Identification of differentially expressed genes in the oviduct of two rabbit lines divergently selected for uterine capacity using suppression subtractive hybridization.
Ballester M, Castelló A, Peiró R, Argente MJ, Santacreu MA, Folch JM.
Anim Genet. 2013 Jun;44(3):296-304. doi: 10.1111/age.12005.
A quantitative real-time PCR method using an X-linked gene for sex typing in pigs.
Ballester M, Castelló A, Ramayo-Caldas Y, Folch JM.
Mol Biotechnol. 2013 Jun;54(2):493-6. doi: 10.1007/s12033-012-9589-5.
Evolution of recombination in eutherian mammals: insights into mechanisms that affect recombination rates and crossover interference.
Segura J, Ferretti L, Ramos-Onsins S, Capilla L, Farré M, Reis F, Oliver-Bonet M, Fernández-Bellón H, Garcia F, Garcia-Caldés M, Robinson TJ, Ruiz-Herrera A.
Proc Biol Sci. 2013 Sep 25;280(1771):20131945. doi: 10.1098/rspb.2013.1945. Print 2013 Nov 22.
2012
Genome-wide linkage analysis of QTL for growth and body composition employing the PorcineSNP60 BeadChip.
Fernández AI, Pérez-Montarelo D, Barragán C, Ramayo-Caldas Y, Ibáñez-Escriche N, Castelló A, Noguera JL, Silió L, Folch JM, Rodríguez MC.
BMC Genet. 2012 May 20;13:41. doi: 10.1186/1471-2156-13-41.
Evaluation of the porcine ACSL4 gene as a candidate gene for meat quality traits in pigs.
Corominas J, Ramayo-Caldas Y, Castelló A, Muñoz M, Ibáñez-Escriche N, Folch JM, Ballester M.
Anim Genet. 2012 Dec;43(6):714-20. doi: 10.1111/j.1365-2052.2012.02335.x. Epub 2012 Mar 11.
Joint effects of porcine leptin and leptin receptor polymorphisms on productivity and quality traits.
Pérez-Montarelo D, Fernández A, Folch JM, Pena RN, Ovilo C, Rodríguez C, Silió L, Fernández AI.
Anim Genet. 2012 Dec;43(6):805-9. doi: 10.1111/j.1365-2052.2012.02338.x. Epub 2012 Mar 6.
Recombination rates across porcine autosomes inferred from high-density linkage maps.
Muñoz M, Alves E, Ramayo-Caldas Y, Casellas J, Rodríguez C, Folch JM, Silió L, Fernández AI.
Anim Genet. 2012 Oct;43(5):620-3. doi: 10.1111/j.1365-2052.2011.02301.x. Epub 2011 Dec 7.
Survey of SSC12 Regions Affecting Fatty Acid Composition of Intramuscular Fat Using High-Density SNP Data.
Muñoz M, Alves E, Corominas J, Folch JM, Casellas J, Noguera JL, Silió L, Fernández AI.
Front Genet. 2012 Jan 5;2:101. doi: 10.3389/fgene.2011.00101. eCollection 2011.
Analyses of pig genomes provide insight into porcine demography and evolution.
Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi SH, Chow W, Clark RC, Clee C, Crooijmans RP, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB.
Nature. 2012 Nov 15;491(7424):393-8. doi: 10.1038/nature11622.
Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition.
Ramayo-Caldas Y, Mach N, Esteve-Codina A, Corominas J, Castelló A, Ballester M, Estellé J, Ibáñez-Escriche N, Fernández AI, Pérez-Enciso M, Folch JM.
BMC Genomics. 2012 Oct 11;13:547. doi: 10.1186/1471-2164-13-547.
SNP calling by sequencing pooled samples.
Raineri E, Ferretti L, Esteve-Codina A, Nevado B, Heath S, Pérez-Enciso M.
BMC Bioinformatics. 2012 Sep 20;13:239. doi: 10.1186/1471-2105-13-239.
International conference on quantitative genetics 4: big science for complex traits.
Simianer H, Pérez-Enciso M.
J Anim Breed Genet. 2012 Oct;129(5):343-4. doi: 10.1111/jbg.12000. No abstract available.
Genome-wide association study for intramuscular fatty acid composition in an Iberian × Landrace cross.
Ramayo-Caldas Y, Mercadé A, Castelló A, Yang B, Rodríguez C, Alves E, Díaz I, Ibáñez-Escriche N, Noguera JL, Pérez-Enciso M, Fernández AI, Folch JM.
J Anim Sci. 2012 Sep;90(9):2883-93. doi: 10.2527/jas.2011-4900. Epub 2012 Jul 10.
Neutrality tests for sequences with missing data.
Ferretti L, Raineri E, Ramos-Onsins S.
Genetics. 2012 Aug;191(4):1397-401. doi: 10.1534/genetics.112.139949. Epub 2012 Jun 1.
2011
Recombination rates across porcine autosomes inferred from high-density linkage maps.
Muñoz M, Alves E, Ramayo-Caldas Y, Casellas J, Rodríguez C, Folch JM, Silió L, Fernández AI.
Anim Genet. 2011 Dec 7. doi: 10.1111/j.1365-2052.2011.02301.x. PMID: 22497205.
Survey of SSC12 Regions Affecting Fatty Acid Composition of Intramuscular Fat Using High-Density SNP Data.
Muñoz M, Alves E, Corominas J, Folch JM, Casellas J, Noguera JL, Silió L, Fernández AI.
Front Genet. 2011;2:101. Epub 2012 Jan 5. PMID: 22303395.
Preferential attachment in growing spatial networks.
Ferretti L, Cortelezzi M.
Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Jul;84(1 Pt 2):016103. Epub 2011 Jul 8. PMID: 21867253.
Qxpak.5: old mixed model solutions for new genomics problems.
Pérez-Enciso M, Misztal I.
BMC Bioinformatics. 2011 May 25;12:202. PMID: 21612630.
Association between plasma metabolites and gene expression profiles in five porcine endocrine tissues.
Yang B, Bassols A, Saco Y, Pérez-Enciso M.
Genet Sel Evol. 2011 Jul 25;43:28. PMID: 21787428.
Exploring the gonad transcriptome of two extreme male pigs with RNA-seq.
Esteve-Codina A, Kofler R, Palmieri N, Bussotti G, Notredame C, Pérez-Enciso M.
BMC Genomics. 2011 Nov 8;12:552. PMID: 22067327.
Building phenotype networks to improve QTL detection: a comparative analysis of fatty acid and fat traits in pigs.
Yang B, Navarro N, Noguera JL, Muñoz M, Guo TF, Yang KX, Ma JW, Folch JM, Huang LS, Pérez-Enciso M.
J Anim Breed Genet. 2011 Oct;128(5):329-43. doi: 10.1111/j.1439-0388.2011.00928.x. Epub 2011 Jun 5. PMID: 21906179.
Partial short-read sequencing of a highly inbred Iberian pig and genomics inference thereof.
Esteve-Codina A, Kofler R, Himmelbauer H, Ferretti L, Vivancos AP, Groenen MA, Folch JM, Rodríguez MC, Pérez-Enciso M.
Heredity. 2011 Mar 16.
Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA.
Amaral AJ, Ferretti L, Megens H-J, Crooijmans RPMA, Nie H, et al.
PLoS ONE 6(4): e14782.
Disease Liability Prediction from Large Scale Genotyping Data Using Classifiers with a Reject Option.
Quevedo JR, Bahamonde A, Perez-Enciso M, Luaces O.
IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar 3.
Evolutionary study of a potential selection target region in the pig.
Ojeda A, Ramos-Onsins SE, Marletta D, Huang LS, Folch JM, Pérez-Enciso M.
Heredity. 2011 Feb;106(2):330-8.
Mitochondrial DNA diversity in wild boar from the Primorsky Krai Region (East Russia).
Ramayo Y, Shemeret'eva IN, Pérez-Enciso M.
Anim Genet. 2011 Feb;42(1):96-9.
2010
Explaining the genetic basis of complex quantitative traits through prediction models.
Luaces O, Quevedo JR, Pérez-Enciso M, Díez J, Del Coz JJ, Bahamonde A.
J Comput Biol. 2010 Dec;17(12):1711-23.
Nucleotide variability of the porcine SERPINA6 gene and the origin of a putative causal mutation associated with meat quality.
Esteve A, Ojeda A, Huang LS, Folch JM, Pérez-Enciso M.
Anim Genet. 2010 Nov 4.
Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip.
Ramayo-Caldas Y, Castelló A, Pena RN, Alves E, Mercadé A, Souza CA, Fernández AI, Perez-Enciso M, Folch JM.
BMC Genomics. 2010 Oct 22;11:593.
Leipzig: the dawn of the genomes era.
Perez-Enciso M.
J Anim Breed Genet. 2010 Oct;127(5):338.
Optimal neutrality tests based on the frequency spectrum.
Ferretti L, Perez-Enciso M, Ramos-Onsins S.
Genetics. 2010 Sep;186(1):353-65.
Massive parallel sequencing in animal genetics: wherefroms and wheretos.
Pérez-Enciso M, Ferretti L.
Anim Genet. 2010 Dec;41(6):561-9.
Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data.
Reverter A, Hudson NJ, Nagaraj SH, Pérez-Enciso M, Dalrymple BP.
Bioinformatics. 2010 Apr 1;26(7):896-904.
Large-scale SNP genotyping in crosses between outbred lines: how useful is it?
Ledur MC, Navarro N, Pérez-Enciso M.
Heredity. 2010 Aug;105(2):173-82.
Population history in Arabidopsis halleri using multilocus analysis.
Heidel AJ, Ramos-Onsins SE, Wang WK, Chiang TY, Mitchell-Olds T.
Mol Ecol. 2010 Aug;19(16):3364-79. Epub 2010 Jul 28.
Assessing the influence of adjacent gene orientation on the evolution of gene upstream regions in Arabidopsis thaliana.
He F, Chen WH, Collins S, Acquisti C, Goebel U, Ramos-Onsins S, Lercher MJ, de Meaux J.
Genetics. 2010 Jun;185(2):695-701.