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A genomic inference of the White Plymouth Rock genealogy.

Guo Y, Lillie M, Zan Y, Beranger J, Martin A, Honaker CF, Siegel PB, Carlborg Ö.

Poult Sci. 2019 Jul 15. pii: pez411. doi: 10.3382/ps/pez411. [Epub ahead of print]


Bidirectional Selection for Body Weight on Standing Genetic Variation in a Chicken Model.

Lillie M, Honaker CF, Siegel PB, Carlborg Ö.

G3 (Bethesda). 2019 Apr 9;9(4):1165-1173. doi: 10.1534/g3.119.400038.


A Polygenic Genetic Architecture of Flowering Time in the Worldwide Arabidopsis thaliana Population.

Zan Y, Carlborg Ö.

Mol Biol Evol. 2019 Jan 1;36(1):141-154. doi: 10.1093/molbev/msy203.


On the Relationship Between High-Order Linkage Disequilibrium and Epistasis.

Zan Y, Forsberg SKG, Carlborg Ö.

G3 (Bethesda). 2018 Jul 31;8(8):2817-2824. doi: 10.1534/g3.118.200513.


Genomic signatures of 60 years of bidirectional selection for 8-week body weight in chickens.

Lillie M, Sheng ZY, Honaker CF, Andersson L, Siegel PB, Carlborg Ö.

Poult Sci. 2018 Mar 1;97(3):781-790. doi: 10.3382/ps/pex383.


On the relationship between epistasis and genetic variance heterogeneity.

Forsberg SKG, Carlborg Ö.

J Exp Bot. 2017 Nov 28;68(20):5431-5438. doi: 10.1093/jxb/erx283. Review.


Artificial Selection Response due to Polygenic Adaptation from a Multilocus, Multiallelic Genetic Architecture.

Zan Y, Sheng Z, Lillie M, Rönnegård L, Honaker CF, Siegel PB, Carlborg Ö.

Mol Biol Evol. 2017 Oct 1;34(10):2678-2689. doi: 10.1093/molbev/msx194.


Accounting for genetic interactions improves modeling of individual quantitative trait phenotypes in yeast.

Forsberg SK, Bloom JS, Sadhu MJ, Kruglyak L, Carlborg Ö.

Nat Genet. 2017 Apr;49(4):497-503. doi: 10.1038/ng.3800. Epub 2017 Feb 27.


Genome-wide standing variation facilitates long-term response to bidirectional selection for antibody response in chickens.

Lillie M, Sheng Z, Honaker CF, Dorshorst BJ, Ashwell CM, Siegel PB, Carlborg Ö.

BMC Genomics. 2017 Jan 18;18(1):99. doi: 10.1186/s12864-016-3414-7.


Imputation-Based Fine-Mapping Suggests That Most QTL in an Outbred Chicken Advanced Intercross Body Weight Line Are Due to Multiple, Linked Loci.

Brandt M, Ahsan M, Honaker CF, Siegel PB, Carlborg Ö.

G3 (Bethesda). 2017 Jan 5;7(1):119-128. doi: 10.1534/g3.116.036012.


Genetics of Interactive Behavior in Silver Foxes (Vulpes vulpes).

Nelson RM, Temnykh SV, Johnson JL, Kharlamova AV, Vladimirova AV, Gulevich RG, Shepeleva DV, Oskina IN, Acland GM, Rönnegård L, Trut LN, Carlborg Ö, Kukekova AV.

Behav Genet. 2017 Jan;47(1):88-101. doi: 10.1007/s10519-016-9815-1. Epub 2016 Oct 18.


A Complex Structural Variation on Chromosome 27 Leads to the Ectopic Expression of HOXB8 and the Muffs and Beard Phenotype in Chickens.

Guo Y, Gu X, Sheng Z, Wang Y, Luo C, Liu R, Qu H, Shu D, Wen J, Crooijmans RP, Carlborg Ö, Zhao Y, Hu X, Li N.

PLoS Genet. 2016 Jun 2;12(6):e1006071. doi: 10.1371/journal.pgen.1006071. eCollection 2016 Jun.


Genetic Regulation of Transcriptional Variation in Natural Arabidopsis thaliana Accessions.

Zan Y, Shen X, Forsberg SK, Carlborg Ö.

G3 (Bethesda). 2016 Aug 9;6(8):2319-28. doi: 10.1534/g3.116.030874.


Correction: Genome-Wide Analysis in German Shepherd Dogs Reveals Association of a Locus on CFA 27 with Atopic Dermatitis.

Tengvall K, Kierczak M, Bergvall K, Olsson M, Frankowiack M, Farias FH, Pielberg G, Carlborg Ö, Leeb T, Andersson G, Hammarström L, Hedhammar Å, Lindblad-Toh K.

PLoS Genet. 2015 Dec 11;11(12):e1005740. doi: 10.1371/journal.pgen.1005740. eCollection 2015 Dec. No abstract available.


The Multi-allelic Genetic Architecture of a Variance-Heterogeneity Locus for Molybdenum Concentration in Leaves Acts as a Source of Unexplained Additive Genetic Variance.

Forsberg SK, Andreatta ME, Huang XY, Danku J, Salt DE, Carlborg Ö.

PLoS Genet. 2015 Nov 23;11(11):e1005648. doi: 10.1371/journal.pgen.1005648. eCollection 2015 Nov.


Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance.

Alexander M, Ho SY, Molak M, Barnett R, Carlborg Ö, Dorshorst B, Honaker C, Besnier F, Wahlberg P, Dobney K, Siegel P, Andersson L, Larson G.

Biol Lett. 2015 Oct;11(10). pii: 20150561. doi: 10.1098/rsbl.2015.0561.


Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment.

Sheng Z, Pettersson ME, Honaker CF, Siegel PB, Carlborg Ö.

Genome Biol. 2015 Oct 1;16:219. doi: 10.1186/s13059-015-0785-z.


A Genome-Wide Association Analysis Reveals Epistatic Cancellation of Additive Genetic Variance for Root Length in Arabidopsis thaliana.

Lachowiec J, Shen X, Queitsch C, Carlborg Ö.

PLoS Genet. 2015 Sep 23;11(9):e1005541. doi: 10.1371/journal.pgen.1005541. eCollection 2015.


cgmisc: enhanced genome-wide association analyses and visualization.

Kierczak M, Jabłońska J, Forsberg SK, Bianchi M, Tengvall K, Pettersson M, Scholz V, Meadows JR, Jern P, Carlborg Ö, Lindblad-Toh K.

Bioinformatics. 2015 Dec 1;31(23):3830-1. doi: 10.1093/bioinformatics/btv426. Epub 2015 Aug 6.


Reassess the t Test: Interact with All Your Data via ANOVA.

Brady SM, Burow M, Busch W, Carlborg Ö, Denby KJ, Glazebrook J, Hamilton ES, Harmer SL, Haswell ES, Maloof JN, Springer NM, Kliebenstein DJ.

Plant Cell. 2015 Aug;27(8):2088-94. doi: 10.1105/tpc.15.00238. Epub 2015 Jul 28.


Multiple Changes of Gene Expression and Function Reveal Genomic and Phenotypic Complexity in SLE-like Disease.

Wilbe M, Kozyrev SV, Farias FH, Bremer HD, Hedlund A, Pielberg GR, Seppälä EH, Gustafson U, Lohi H, Carlborg Ö, Andersson G, Hansson-Hamlin H, Lindblad-Toh K.

PLoS Genet. 2015 Jun 9;11(6):e1005248. doi: 10.1371/journal.pgen.1005248. eCollection 2015 Jun.


The Shepherds' Tale: A Genome-Wide Study across 9 Dog Breeds Implicates Two Loci in the Regulation of Fructosamine Serum Concentration in Belgian Shepherds.

Forsberg SK, Kierczak M, Ljungvall I, Merveille AC, Gouni V, Wiberg M, Lundgren Willesen J, Hanås S, Lequarré AS, Mejer Sørensen L, Tiret L, McEntee K, Seppälä E, Koch J, Battaille G, Lohi H, Fredholm M, Chetboul V, Häggström J, Carlborg Ö, Lindblad-Toh K, Höglund K.

PLoS One. 2015 May 13;10(5):e0123173. doi: 10.1371/journal.pone.0123173. eCollection 2015.


Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality.

Shen X, De Jonge J, Forsberg SK, Pettersson ME, Sheng Z, Hennig L, Carlborg Ö.

PLoS Genet. 2014 Dec 11;10(12):e1004842. doi: 10.1371/journal.pgen.1004842. eCollection 2014 Dec.


Capacitating epistasis--detection and role in the genetic architecture of complex traits.

Pettersson ME, Carlborg O.

Methods Mol Biol. 2015;1253:185-96. doi: 10.1007/978-1-4939-2155-3_10.


Genetic influences on brain gene expression in rats selected for tameness and aggression.

Heyne HO, Lautenschläger S, Nelson R, Besnier F, Rotival M, Cagan A, Kozhemyakina R, Plyusnina IZ, Trut L, Carlborg Ö, Petretto E, Kruglyak L, Pääbo S, Schöneberg T, Albert FW.

Genetics. 2014 Nov;198(3):1277-90. doi: 10.1534/genetics.114.168948. Epub 2014 Sep 3.


Variance heterogeneity in Saccharomyces cerevisiae expression data: trans-regulation and epistasis.

Nelson RM, Pettersson ME, Li X, Carlborg Ö.

PLoS One. 2013 Nov 4;8(11):e79507. doi: 10.1371/journal.pone.0079507. eCollection 2013.


Identification of candidate genes and mutations in QTL regions for chicken growth using bioinformatic analysis of NGS and SNP-chip data.

Ahsan M, Li X, Lundberg AE, Kierczak M, Siegel PB, Carlborg O, Marklund S.

Front Genet. 2013 Nov 5;4:226. doi: 10.3389/fgene.2013.00226. eCollection 2013.


Dynamics of adaptive alleles in divergently selected body weight lines of chickens.

Pettersson ME, Johansson AM, Siegel PB, Carlborg O.

G3 (Bethesda). 2013 Dec 9;3(12):2305-12. doi: 10.1534/g3.113.008375.


A century after Fisher: time for a new paradigm in quantitative genetics.

Nelson RM, Pettersson ME, Carlborg Ö.

Trends Genet. 2013 Dec;29(12):669-76. doi: 10.1016/j.tig.2013.09.006. Epub 2013 Oct 23.


MAPfastR: quantitative trait loci mapping in outbred line crosses.

Nelson RM, Nettelblad C, Pettersson ME, Shen X, Crooks L, Besnier F, Alvarez-Castro JM, Rönnegård L, Ek W, Sheng Z, Kierczak M, Holmgren S, Carlborg O.

G3 (Bethesda). 2013 Dec 9;3(12):2147-9. doi: 10.1534/g3.113.008623.


Higher order interactions: detection of epistasis using machine learning and evolutionary computation.

Nelson RM, Kierczak M, Carlborg O.

Methods Mol Biol. 2013;1019:499-518. doi: 10.1007/978-1-62703-447-0_24.


Beware of risk for increased false positive rates in genome-wide association studies for phenotypic variability.

Shen X, Carlborg O.

Front Genet. 2013 May 21;4:93. doi: 10.3389/fgene.2013.00093. eCollection 2013. No abstract available.


Identification of null alleles and deletions from SNP genotypes for an intercross between domestic and wild chickens.

Crooks L, Carlborg Ö, Marklund S, Johansson AM.

G3 (Bethesda). 2013 Aug 7;3(8):1253-60. doi: 10.1534/g3.113.006643.


Genome-wide analysis in German shepherd dogs reveals association of a locus on CFA 27 with atopic dermatitis.

Tengvall K, Kierczak M, Bergvall K, Olsson M, Frankowiack M, Farias FH, Pielberg G, Carlborg Ö, Leeb T, Andersson G, Hammarström L, Hedhammar Å, Lindblad-Toh K.

PLoS Genet. 2013 May;9(5):e1003475. doi: 10.1371/journal.pgen.1003475. Epub 2013 May 9. Erratum in: PLoS Genet. 2013 May;9(5). doi:10.1371/annotation/fd6f4425-3d84-4017-a012-a5df6ddee13a. PLoS Genet. 2015 Dec;11(12):e1005740.


PASE: a novel method for functional prediction of amino acid substitutions based on physicochemical properties.

Li X, Kierczak M, Shen X, Ahsan M, Carlborg O, Marklund S.

Front Genet. 2013 Mar 6;4:21. doi: 10.3389/fgene.2013.00021. eCollection 2013.


Genetic dissection of growth traits in a Chinese indigenous × commercial broiler chicken cross.

Sheng Z, Pettersson ME, Hu X, Luo C, Qu H, Shu D, Shen X, Carlborg O, Li N.

BMC Genomics. 2013 Mar 6;14:151. doi: 10.1186/1471-2164-14-151.


Modelling of genetic interactions improves prediction of hybrid patterns--a case study in domestic fowl.

Álvarez-Castro JM, Le Rouzic A, Andersson L, Siegel PB, Carlborg Ö.

Genet Res (Camb). 2012 Oct;94(5):255-66. doi: 10.1017/S001667231200047X.


Selection on variance-controlling genes: adaptability or stability.

Pettersson ME, Nelson RM, Carlborg O.

Evolution. 2012 Dec;66(12):3945-9. doi: 10.1111/j.1558-5646.2012.01753.x. Epub 2012 Aug 24.


Strong signatures of selection in the domestic pig genome.

Rubin CJ, Megens HJ, Martinez Barrio A, Maqbool K, Sayyab S, Schwochow D, Wang C, Carlborg Ö, Jern P, Jørgensen CB, Archibald AL, Fredholm M, Groenen MA, Andersson L.

Proc Natl Acad Sci U S A. 2012 Nov 27;109(48):19529-36. doi: 10.1073/pnas.1217149109. Epub 2012 Nov 14.


Inheritance beyond plain heritability: variance-controlling genes in Arabidopsis thaliana.

Shen X, Pettersson M, Rönnegård L, Carlborg Ö.

PLoS Genet. 2012;8(8):e1002839. doi: 10.1371/journal.pgen.1002839. Epub 2012 Aug 2.


Mapping QTL affecting a systemic sclerosis-like disorder in a cross between UCD-200 and red jungle fowl chickens.

Ek W, Sahlqvist AS, Crooks L, Sgonc R, Dietrich H, Wick G, Ekwall O, Andersson L, Carlborg Ö, Kämpe O, Kerje S.

Dev Comp Immunol. 2012 Oct;38(2):352-9. doi: 10.1016/j.dci.2012.06.006. Epub 2012 Jul 13. Erratum in: Dev Comp Immunol. 2012 Dec;38(4):561.


Estimation and interpretation of genetic effects with epistasis using the NOIA model.

Alvarez-Castro JM, Carlborg O, Rönnegård L.

Methods Mol Biol. 2012;871:191-204. doi: 10.1007/978-1-61779-785-9_10. Review.


Generation of a multi-locus chicken introgression line to study the effects of genetic interactions on metabolic phenotypes in chickens.

Ek W, Marklund S, Ragavendran A, Siegel P, Muir W, Carlborg O.

Front Genet. 2012 Mar 2;3:29. doi: 10.3389/fgene.2012.00029. eCollection 2012.


An Improved Method for Estimating Chromosomal Line Origin in QTL Analysis of Crosses Between Outbred Lines.

Crooks L, Nettelblad C, Carlborg O.

G3 (Bethesda). 2011 Jun;1(1):57-64. doi: 10.1534/g3.111.000109. Epub 2011 Jun 1.


Replication and explorations of high-order epistasis using a large advanced intercross line pedigree.

Pettersson M, Besnier F, Siegel PB, Carlborg O.

PLoS Genet. 2011 Jul;7(7):e1002180. doi: 10.1371/journal.pgen.1002180. Epub 2011 Jul 21.


How to deal with genotype uncertainty in variance component quantitative trait loci analyses.

Shen X, Rönnegård L, Carlborg O.

Genet Res (Camb). 2011 Oct;93(5):333-42. doi: 10.1017/S0016672311000152. Epub 2011 Jul 18.


Hierarchical likelihood opens a new way of estimating genetic values using genome-wide dense marker maps.

Shen X, Rönnegård L, Carlborg O.

BMC Proc. 2011 May 27;5 Suppl 3:S14. doi: 10.1186/1753-6561-5-S3-S14.


qtl.outbred: Interfacing outbred line cross data with the R/qtl mapping software.

Nelson RM, Shen X, Carlborg O.

BMC Res Notes. 2011 May 26;4:154. doi: 10.1186/1756-0500-4-154.

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