Publications

Complex genetic architecture of the chicken Growth1 QTL region

Ou, Jen-Hsiang; Rönneburg, Tilman; Carlborg, Örjan; Honaker, Christa F. et al.

Part of PLOS ONE, 2024

• DOI for Complex genetic architecture of the chicken Growth1 QTL region
• Download full text (pdf) of Complex genetic architecture of the chicken Growth1 QTL region

Selection against domestication alleles in introduced rabbit populations

Andrade, Pedro; Alves, Joel M.; Pereira, Paulo; Rubin, Carl-Johan et al.

Part of Nature Ecology & Evolution, 2024

• DOI for Selection against domestication alleles in introduced rabbit populations

Whole-genome selective sweep analyses identifies the region and candidate gene associated with white earlobe color in Mediterranean chickens

Guo, Ying; Rubin, Carl-Johan; Rönneburg, Tilman; Wang, Shouzhi et al.

Part of Poultry Science, 2024

• DOI for Whole-genome selective sweep analyses identifies the region and candidate gene associated with white earlobe color in Mediterranean chickens
• Download full text (pdf) of Whole-genome selective sweep analyses identifies the region and candidate gene associated with white earlobe color in Mediterranean chickens

A frame-shift mutation in COMTD1 is associated with impaired pheomelanin pigmentation in chicken

Bi, Huijuan; Tranell, Jonas; Harper, Dawn C.; Lin, Weifeng et al.

Part of PLOS Genetics, 2023

• DOI for A frame-shift mutation in COMTD1 is associated with impaired pheomelanin pigmentation in chicken
• Download full text (pdf) of A frame-shift mutation in COMTD1 is associated with impaired pheomelanin pigmentation in chicken

Community-wide genome sequencing reveals 30 years of Darwin's finch evolution

Enbody, Erik D.; Sendell-Price, Ashley T.; Sprehn, C. Grace; Rubin, Carl-Johan et al.

Part of Science, p. 1427-+, 2023

• DOI for Community-wide genome sequencing reveals 30 years of Darwin's finch evolution

Long-read whole-genome analysis of human single cells

Hård, Joanna; Mold, Jeff E; Eisfeldt, Jesper; Tellgren-Roth, Christian et al.

Part of Nature Communications, 2023

• DOI for Long-read whole-genome analysis of human single cells
• Download full text (pdf) of Long-read whole-genome analysis of human single cells

Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut

Edvardsen, Rolf Brudvik; Wallerman, Ola; Furmanek, Tomasz; Kleppe, Lene et al.

Part of PLOS Genetics, 2022

• DOI for Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut
• Download full text (pdf) of Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut

Rapid adaptive radiation of Darwin's finches depends on ancestral genetic modules

Rubin, Carl-Johan; Enbody, Erik D.; Dobreva, Mariya P.; Abzhanov, Arhat et al.

Part of Science Advances, 2022

• DOI for Rapid adaptive radiation of Darwin's finches depends on ancestral genetic modules
• Download full text (pdf) of Rapid adaptive radiation of Darwin's finches depends on ancestral genetic modules

Spatiotemporal variations in retrovirus-host interactions among Darwin’s finches

Hill, Jason; Lillie, Mette; Pettersson, Mats; Rubin, Carl-Johan et al.

Part of Nature Communications, 2022

• DOI for Spatiotemporal variations in retrovirus-host interactions among Darwin’s finches
• Download full text (pdf) of Spatiotemporal variations in retrovirus-host interactions among Darwin’s finches

A multispecies BCO2 beak color polymorphism in the Darwin's finch radiation

Enbody, Erik D.; Sprehn, Charlotte Grace; Abzhanov, Arhat; Bi, Huijuan et al.

Part of Current Biology, p. 5597-56040000000, 2021

• DOI for A multispecies BCO2 beak color polymorphism in the Darwin's finch radiation
• Download full text (pdf) of A multispecies BCO2 beak color polymorphism in the Darwin's finch radiation

Comparison of anadromous and landlocked Atlantic salmon genomes reveals signatures of parallel and relaxed selection across the Northern Hemisphere

Kjaerner-Semb, Erik; Edvardsen, Rolf B.; Ayllon, Fernando; Vogelsang, Petra et al.

Part of Evolutionary Applications, p. 446-461, 2021

• DOI for Comparison of anadromous and landlocked Atlantic salmon genomes reveals signatures of parallel and relaxed selection across the Northern Hemisphere

The Human Adenovirus 2 Transcriptome: An Amazing Complexity of Alternatively Spliced mRNAs

Westergren Jakobsson, Amanda; Segerman, Bo; Wallerman, Ola; Bergström Lind, Sara et al.

Part of Journal of Virology, 2021

• DOI for The Human Adenovirus 2 Transcriptome: An Amazing Complexity of Alternatively Spliced mRNAs
• Download full text (pdf) of The Human Adenovirus 2 Transcriptome: An Amazing Complexity of Alternatively Spliced mRNAs

The nedd-8 activating enzyme gene underlies genetic resistance to infectious pancreatic necrosis virus in Atlantic salmon

Pavelin, Jon; Jin, Ye Hwa; Gratacap, Remi L.; Taggart, John B. et al.

Part of Genomics, p. 3842-3850, 2021

• DOI for The nedd-8 activating enzyme gene underlies genetic resistance to infectious pancreatic necrosis virus in Atlantic salmon

The polarity protein Par3 coordinates positively self-renewal and negatively invasiveness in glioblastoma

Dadras, Mahsa Shahidi; Caja, Laia; Mezheyeuski, Artur; Liu, Sijia et al.

Part of Cell Death and Disease, 2021

• DOI for The polarity protein Par3 coordinates positively self-renewal and negatively invasiveness in glioblastoma
• Download full text (pdf) of The polarity protein Par3 coordinates positively self-renewal and negatively invasiveness in glioblastoma

Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes

Wojewodzic, Marcin W.; Leithaug, Magnus; Lauritzen, Marianne; Lyle, Robert et al.

Part of Clinical Epigenetics, 2021

• DOI for Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes
• Download full text (pdf) of Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes

Brain Transcriptomics of Wild and Domestic Rabbits Suggests That Changes in Dopamine Signaling and Ciliary Function Contributed to Evolution of Tameness

Sato, Daiki X.; Rafati, Nima; Ring, Henrik; Younis, Shady et al.

Part of Genome Biology and Evolution, p. 1918-1928, 2020

• DOI for Brain Transcriptomics of Wild and Domestic Rabbits Suggests That Changes in Dopamine Signaling and Ciliary Function Contributed to Evolution of Tameness

Reconstruction of the birth of a male sex chromosome present in Atlantic herring

Rafati, Nima; Chen, Junfeng; Herpin, Amaury; Pettersson, Mats et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 24359-24368, 2020

• DOI for Reconstruction of the birth of a male sex chromosome present in Atlantic herring
• Download full text (pdf) of Reconstruction of the birth of a male sex chromosome present in Atlantic herring

Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs

Bianchi, Matteo; Rafati, Nima; Karlsson, Åsa; Murén, Eva et al.

Part of BMC Genomics, 2020

• DOI for Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs
• Download full text (pdf) of Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs

Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species

Kurland, Sara; Wheat, Christopher W.; Mancera, Maria de la Paz Celorio; Kutschera, Verena E. et al.

Part of Ecology and Evolution, p. 11448-11463, 2019

• DOI for Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species
• Download full text (pdf) of Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species

Genetics of adaptation in modern chicken

Qanbari, Saber; Rubin, Carl-Johan; Maqbool, Khurram; Weigend, Steffen et al.

Part of PLOS Genetics, 2019

• DOI for Genetics of adaptation in modern chicken
• Download full text (pdf) of Genetics of adaptation in modern chicken

Identification and validation of genetic variants predictive of gait in standardbred horses

McCoy, Annette M.; Beeson, Samantha K.; Rubin, Carl-Johan; Andersson, Leif et al.

Part of PLOS Genetics, 2019

• DOI for Identification and validation of genetic variants predictive of gait in standardbred horses
• Download full text (pdf) of Identification and validation of genetic variants predictive of gait in standardbred horses

Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard

Andrade, Pedro; Pinho, Catarina; Perez i de lanuza, Guillem; Afonso, Sandra et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 5633-5642, 2019

• DOI for Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard

The horse Y chromosome as an informative marker for tracing sire lines

Felkel, Sabine; Vogl, Claus; Rigler, Doris; Dobretsberger, Viktoria et al.

Part of Scientific Reports, 2019

• DOI for The horse Y chromosome as an informative marker for tracing sire lines
• Download full text (pdf) of The horse Y chromosome as an informative marker for tracing sire lines

A genomic map of clinal variation across the European rabbit hybrid zone

Rafati, Nima; Blanco-Aguiar, Jose A.; Rubin, Carl-Johan; Sayyab, Shumaila et al.

Part of Molecular Ecology, p. 1457-1478, 2018

• DOI for A genomic map of clinal variation across the European rabbit hybrid zone

Analysis of porcine body size variation using re-sequencing data of miniature and large pigs

Reimer, C.; Rubin, Carl-Johan; Sharifi, A. R.; Ha, N. -T et al.

Part of BMC Genomics, 2018

• DOI for Analysis of porcine body size variation using re-sequencing data of miniature and large pigs
• Download full text (pdf) of Analysis of porcine body size variation using re-sequencing data of miniature and large pigs

Asian horses deepen the MSY phylogeny

Felkel, S.; Vogl, C.; Rigler, D.; Jagannathan, V. et al.

Part of Animal Genetics, p. 90-93, 2018

• DOI for Asian horses deepen the MSY phylogeny

Changes in brain architecture are consistent with altered fear processing in domestic rabbits

Brusini, Irene; Carneiro, Miguel; Wang, Chunliang; Rubin, Carl-Johan et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 7380-7385, 2018

• DOI for Changes in brain architecture are consistent with altered fear processing in domestic rabbits

Elevated proportions of deleterious genetic variation in domestic animals and plants

Makino, Takashi; Rubin, Carl-Johan; Carneiro, Miguel; Axelsson, Erik et al.

Part of Genome Biology and Evolution, p. 276-290, 2018

• DOI for Elevated proportions of deleterious genetic variation in domestic animals and plants
• Download full text (pdf) of Elevated proportions of deleterious genetic variation in domestic animals and plants

Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations

Rivas-Carrillo, Salvador Daniel; Pettersson, Mats; Rubin, Carl-Johan; Jern, Patric

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 11012-11017, 2018

• DOI for Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations
• Download full text (pdf) of Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations

Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus

Carneiro, Miguel; Hu, Dou; Archer, John; Feng, Chungang et al.

Part of Genetics, p. 955-965, 2017

• DOI for Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus

Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

Feng, Chungang; Pettersson, Mats; Lamichhaney, Sangeet; Rubin, Carl-Johan et al.

Part of eLIFE, 2017

• DOI for Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate
• Download full text (pdf) of Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

The evolutionary history of the DMRT3 'Gait keeper' haplotype

Staiger, E. A.; Almén, M. S.; Promerova, M.; Brooks, S. et al.

Part of Animal Genetics, p. 551-559, 2017

• DOI for The evolutionary history of the DMRT3 'Gait keeper' haplotype

Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions

Wallner, Barbara; Palmieri, Nicola; Vogl, Claus; Rigler, Doris et al.

Part of Current Biology, p. 2029-2035, 2017

• DOI for Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions

Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection

Kjaerner-Semb, Erik; Ayllon, Fernando; Furmanek, Tomasz; Wennevik, Vidar et al.

Part of BMC Genomics, 2016

• DOI for Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection
• Download full text (pdf) of Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection

Decreased fracture rate, pharmacogenetics and BMD response in 79 Swedish children with osteogenesis imperfecta types I, III and IV treated with Pamidronate

Lindahl, Katarina; Kindmark, Andreas; Rubin, Carl-Johan; Malmgren, B. et al.

Part of Bone, p. 11-18, 2016

• DOI for Decreased fracture rate, pharmacogenetics and BMD response in 79 Swedish children with osteogenesis imperfecta types I, III and IV treated with Pamidronate

Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies

Rafati, Nima; Andersson, Lisa S.; Mikko, Sofia; Feng, Chungang et al.

Part of G3, p. 2213-2223, 2016

• DOI for Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies
• Download full text (pdf) of Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies

Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation underlying Dun camouflage colour in horses

Imsland, Freyja; McGowan, Kelly; Rubin, Carl-Johan; Henegar, Corneliu et al.

Part of Nature Genetics, p. 152-158, 2016

• DOI for Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation underlying Dun camouflage colour in horses

Second generation sequencing of microRNA in Human Bone Cells treated with Parathyroid Hormone or Dexamethasone

Laxman, Navya; Rubin, Carl-Johan; Mallmin, Hans; Nilsson, Olle et al.

Part of Bone, p. 181-188, 2016

• DOI for Second generation sequencing of microRNA in Human Bone Cells treated with Parathyroid Hormone or Dexamethasone

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

Martínez Barrio, Álvaro; Lamichhaney, Sangeet; Fan, Guangyi; Rafati, Nima et al.

Part of eLIFE, 2016

• DOI for The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
• Download full text (pdf) of The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

A Genomic Duplication is Associated with Ectopic Eomesodermin Expression in the Embryonic Chicken Comb and Two Duplex-comb Phenotypes

Dorshorst, Ben; Harun-Or-Rashid, Mohammad; Bagherpoor, Alireza Jian; Rubin, Carl-Johan et al.

Part of PLOS Genetics, 2015

• DOI for A Genomic Duplication is Associated with Ectopic Eomesodermin Expression in the Embryonic Chicken Comb and Two Duplex-comb Phenotypes
• Download full text (pdf) of A Genomic Duplication is Associated with Ectopic Eomesodermin Expression in the Embryonic Chicken Comb and Two Duplex-comb Phenotypes

Candidate genes underlying heritable differences in reproductive seasonality between wild and domestic rabbits

Carneiro, Miguel; Piorno, Vicente; Rubin, Carl-Johan; Alves, Joel M. et al.

Part of Animal Genetics, p. 418-425, 2015

• DOI for Candidate genes underlying heritable differences in reproductive seasonality between wild and domestic rabbits

Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha (COPA) Gene

Dorshorst, Ben; Henegar, Corneliu; Liao, Xiaoping; Almén, Markus Sällman et al.

Part of PLOS ONE, 2015

• DOI for Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha (COPA) Gene
• Download full text (pdf) of Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha (COPA) Gene

Evolution of Darwin's finches and their beaks revealed by genome sequencing

Lamichhaney, Sangeet; Berglund, Jonas; Almen, Markus Sällman; Maqbool, Khurram et al.

Part of Nature, 2015

• DOI for Evolution of Darwin's finches and their beaks revealed by genome sequencing

Genetic epidemiology, prevalence, and genotype-phenotype correlations in the Swedish population with osteogenesis imperfecta

Lindahl, Katarina; Astrom, Eva; Rubin, Carl-Johan; Grigelioniene, Giedre et al.

Part of European Journal of Human Genetics, p. 1042-1050, 2015

• DOI for Genetic epidemiology, prevalence, and genotype-phenotype correlations in the Swedish population with osteogenesis imperfecta

Global miRNA expression and correlation with mRNA levels in primary human bone cells

Laxman, Navya; Rubin, Carl-Johan; Mallmin, Hans; Nilsson, Olle et al.

Part of RNA, p. 1433-1443, 2015

• DOI for Global miRNA expression and correlation with mRNA levels in primary human bone cells
• Download full text (pdf) of Global miRNA expression and correlation with mRNA levels in primary human bone cells

The vgll3 Locus Controls Age at Maturity in Wild and Domesticated Atlantic Salmon (Salmo salar L.) Males

Ayllon, Fernando; Kjaerner-Semb, Erik; Furmanek, Tomasz; Wennevik, Vidar et al.

Part of PLOS Genetics, 2015

• DOI for The vgll3 Locus Controls Age at Maturity in Wild and Domesticated Atlantic Salmon (Salmo salar L.) Males
• Download full text (pdf) of The vgll3 Locus Controls Age at Maturity in Wild and Domesticated Atlantic Salmon (Salmo salar L.) Males

A cis-Regulatory Mutation of PDSS2 Causes Silky-Feather in Chickens

Feng, Chungang; Gao, Yu; Dorshorst, Ben; Song, Chi et al.

Part of PLOS Genetics, 2014

• DOI for A cis-Regulatory Mutation of PDSS2 Causes Silky-Feather in Chickens
• Download full text (pdf) of A cis-Regulatory Mutation of PDSS2 Causes Silky-Feather in Chickens

Differentiation and Phylogenetic Relationships in Mycobacterium spp with Special Reference to the RNase P RNA Gene rnpB

Herrmann, Björn; Stolt, Pelle; Abdeldaim, Guma; Rubin, Carl-Johan et al.

Part of Current Microbiology, p. 634-639, 2014

• DOI for Differentiation and Phylogenetic Relationships in Mycobacterium spp with Special Reference to the RNase P RNA Gene rnpB

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

Schubert, Mikkel; Jonsson, Hakon; Chang, Dan; Sarkissian, Clio Der et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, 2014

• DOI for Prehistoric genomes reveal the genetic foundation and cost of horse domestication

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

Carneiro, Miguel; Rubin, Carl-Johan; Di Palma, Federica; Albert, Frank W. et al.

Part of Science, p. 1074-1079, 2014

• DOI for Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication