Publications

Spatiotemporal variations in retrovirus-host interactions among Darwin’s finches.
Hill, J., Lillie, M., Pettersson, M., Rubin, C., Grant, B. et al. (2022). Nature Communications, . vol. 13 DOI
Rapid adaptive radiation of Darwin's finches depends on ancestral genetic modules.
Rubin, C., Enbody, E., Dobreva, M., Abzhanov, A., Davis, B. et al. (2022). Science Advances, . vol. 8 DOI
Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut.
Edvardsen, R., Wallerman, O., Furmanek, T., Kleppe, L., Jern, P. et al. (2022). PLOS Genetics, . vol. 18 DOI
A multispecies BCO2 beak color polymorphism in the Darwin's finch radiation.
Enbody, E., Sprehn, C., Abzhanov, A., Bi, H., Dobreva, M. et al. (2021). Current Biology, . vol. 31, ss. 5597-5604.e7 DOI
The nedd-8 activating enzyme gene underlies genetic resistance to infectious pancreatic necrosis virus in Atlantic salmon.
Pavelin, J., Jin, Y., Gratacap, R., Taggart, J., Hamilton, A. et al. (2021). Genomics, . vol. 113, ss. 3842-3850 DOI
The polarity protein Par3 coordinates positively self-renewal and negatively invasiveness in glioblastoma.
Dadras, M., Caja, L., Mezheyeuski, A., Liu, S., Gelabert, C. et al. (2021). Cell Death and Disease, . vol. 12 DOI
Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes.
Wojewodzic, M., Leithaug, M., Lauritzen, M., Lyle, R., Haglund, S. et al. (2021). Clinical Epigenetics, . vol. 13 DOI
Comparison of anadromous and landlocked Atlantic salmon genomes reveals signatures of parallel and relaxed selection across the Northern Hemisphere.
Kjaerner-Semb, E., Edvardsen, R., Ayllon, F., Vogelsang, P., Furmanek, T. et al. (2021). Evolutionary Applications, . vol. 14, ss. 446-461 DOI
The Human Adenovirus 2 Transcriptome: An Amazing Complexity of Alternatively Spliced mRNAs.
Westergren Jakobsson, A., Segerman, B., Wallerman, O., Bergström Lind, S., Zhao, H. et al. (2021). Journal of Virology, vol. 95 DOI
Brain Transcriptomics of Wild and Domestic Rabbits Suggests That Changes in Dopamine Signaling and Ciliary Function Contributed to Evolution of Tameness.
Sato, D., Rafati, N., Ring, H., Younis, S., Feng, C. et al. (2020). Genome Biology and Evolution, . vol. 12, ss. 1918-1928 DOI
Reconstruction of the birth of a male sex chromosome present in Atlantic herring.
Rafati, N., Chen, J., Herpin, A., Pettersson, M., Han, F. et al. (2020). Proceedings of the National Academy of Sciences of the United States of America, . vol. 117, ss. 24359-24368 DOI
Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs.
Bianchi, M., Rafati, N., Karlsson, Å., Murén, E., Rubin, C. et al. (2020). BMC Genomics, . vol. 21 DOI
Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species.
Kurland, S., Wheat, C., Mancera, M., Kutschera, V., Hill, J. et al. (2019). Ecology and Evolution, . vol. 9, ss. 11448-11463 DOI
Identification and validation of genetic variants predictive of gait in standardbred horses.
McCoy, A., Beeson, S., Rubin, C., Andersson, L., Caputo, P. et al. (2019). PLOS Genetics, . vol. 15 DOI
Genetics of adaptation in modern chicken.
Qanbari, S., Rubin, C., Maqbool, K., Weigend, S., Weigend, A. et al. (2019). PLOS Genetics, . vol. 15 DOI
The horse Y chromosome as an informative marker for tracing sire lines.
Felkel, S., Vogl, C., Rigler, D., Dobretsberger, V., Chowdhary, B. et al. (2019). Scientific Reports, vol. 9 DOI
Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard.
Andrade, P., Pinho, C., Perez i de lanuza, G., Afonso, S., Brejcha, J. et al. (2019). Proceedings of the National Academy of Sciences of the United States of America, vol. 116, ss. 5633-5642 DOI
Analysis of porcine body size variation using re-sequencing data of miniature and large pigs.
Reimer, C., Rubin, C., Sharifi, A., Ha, N., Weigend, S. et al. (2018). BMC Genomics, . vol. 19 DOI
Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations.
Rivas-Carrillo, S., Pettersson, M., Rubin, C., Jern, P. (2018). Proceedings of the National Academy of Sciences of the United States of America, vol. 115, ss. 11012-11017 DOI
Changes in brain architecture are consistent with altered fear processing in domestic rabbits.
Brusini, I., Carneiro, M., Wang, C., Rubin, C., Ring, H. et al. (2018). Proceedings of the National Academy of Sciences of the United States of America, vol. 115, ss. 7380-7385 DOI
Asian horses deepen the MSY phylogeny.
Felkel, S., Vogl, C., Rigler, D., Jagannathan, V., Leeb, T. et al. (2018). Animal Genetics, . vol. 49, ss. 90-93 DOI
Elevated proportions of deleterious genetic variation in domestic animals and plants.
Makino, T., Rubin, C., Carneiro, M., Axelsson, E., Andersson, L. et al. (2018). Genome Biology and Evolution, . vol. 10, ss. 276-290 DOI
The evolutionary history of the DMRT3 'Gait keeper' haplotype.
Staiger, E., Almén, M., Promerova, M., Brooks, S., Cothran, E. et al. (2017). Animal Genetics, . vol. 48, ss. 551-559 DOI
Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate.
Feng, C., Pettersson, M., Lamichhaney, S., Rubin, C., Rafati, N. et al. (2017). eLIFE, . vol. 6 DOI
Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions.
Wallner, B., Palmieri, N., Vogl, C., Rigler, D., Bozlak, E. et al. (2017). Current Biology, . vol. 27, ss. 2029-2035 DOI
Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus.
Carneiro, M., Hu, D., Archer, J., Feng, C., Afonso, S. et al. (2017). Genetics, . vol. 205, ss. 955-965 DOI
A genomic map of clinal variation across the European rabbit hybrid zone.
Rafati, N., Blanco-Aguiar, J., Rubin, C., Sayyab, S., Sabatino, S. et al. (2018). Molecular Ecology, . vol. 27, ss. 1457-1478 DOI
Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection.
Kjaerner-Semb, E., Ayllon, F., Furmanek, T., Wennevik, V., Dahle, G. et al. (2016). BMC Genomics, vol. 17 DOI
Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies.
Rafati, N., Andersson, L., Mikko, S., Feng, C., Raudsepp, T. et al. (2016). G3, vol. 6, ss. 2213-2223 DOI
Decreased fracture rate, pharmacogenetics and BMD response in 79 Swedish children with osteogenesis imperfecta types I, III and IV treated with Pamidronate.
Lindahl, K., Kindmark, A., Rubin, C., Malmgren, B., Grigelioniene, G. et al. (2016). Bone, vol. 87, ss. 11-18 DOI
The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing.
Martínez Barrio, Á., Lamichhaney, S., Fan, G., Rafati, N., Pettersson, M. et al. (2016). eLIFE, vol. 5 DOI
The vgll3 Locus Controls Age at Maturity in Wild and Domesticated Atlantic Salmon (Salmo salar L.) Males.
Ayllon, F., Kjaerner-Semb, E., Furmanek, T., Wennevik, V., Solberg, M. et al. (2015). PLOS Genetics, vol. 11 DOI
Second generation sequencing of microRNA in Human Bone Cells treated with Parathyroid Hormone or Dexamethasone.
Laxman, N., Rubin, C., Mallmin, H., Nilsson, O., Tellgren-Roth, C. et al. (2016). Bone, vol. 84, ss. 181-188 DOI
Candidate genes underlying heritable differences in reproductive seasonality between wild and domestic rabbits.
Carneiro, M., Piorno, V., Rubin, C., Alves, J., Ferrand, N. et al. (2015). Animal Genetics, vol. 46, ss. 418-425 DOI
Genetic epidemiology, prevalence, and genotype-phenotype correlations in the Swedish population with osteogenesis imperfecta.
Lindahl, K., Astrom, E., Rubin, C., Grigelioniene, G., Malmgren, B. et al. (2015). European Journal of Human Genetics, vol. 23, ss. 1042-1050 DOI
Global miRNA expression and correlation with mRNA levels in primary human bone cells.
Laxman, N., Rubin, C., Mallmin, H., Nilsson, O., Pastinen, T. et al. (2015). RNA, vol. 21, ss. 1433-1443 DOI
Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation underlying Dun camouflage colour in horses.
Imsland, F., McGowan, K., Rubin, C., Henegar, C., Sundström, E. et al. (2016). Nature Genetics, vol. 48, ss. 152-158 DOI
Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha (COPA) Gene.
Dorshorst, B., Henegar, C., Liao, X., Almén, M., Rubin, C. et al. (2015). PLOS ONE, vol. 10 DOI
A Genomic Duplication is Associated with Ectopic Eomesodermin Expression in the Embryonic Chicken Comb and Two Duplex-comb Phenotypes.
Dorshorst, B., Harun-Or-Rashid, M., Bagherpoor, A., Rubin, C., Ashwell, C. et al. (2015). PLOS Genetics, vol. 11 DOI
Evolution of Darwin's finches and their beaks revealed by genome sequencing.
Lamichhaney, S., Berglund, J., Almen, M., Maqbool, K., Grabherr, M. et al. (2015). Nature, vol. 518 DOI
Prehistoric genomes reveal the genetic foundation and cost of horse domestication.
Schubert, M., Jonsson, H., Chang, D., Sarkissian, C., Ermini, L. et al. (2014). Proceedings of the National Academy of Sciences of the United States of America, vol. 111, ss. E5661-E5669 DOI
Differentiation and Phylogenetic Relationships in Mycobacterium spp with Special Reference to the RNase P RNA Gene rnpB.
Herrmann, B., Stolt, P., Abdeldaim, G., Rubin, C., Kirsebom, L. et al. (2014). Current Microbiology, vol. 69, ss. 634-639 DOI
A cis-Regulatory Mutation of PDSS2 Causes Silky-Feather in Chickens.
Feng, C., Gao, Y., Dorshorst, B., Song, C., Gu, X. et al. (2014). PLOS Genetics, vol. 10, ss. e1004576- DOI
Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.
Carneiro, M., Rubin, C., Di Palma, F., Albert, F., Alfoeldi, J. et al. (2014). Science, vol. 345, ss. 1074-1079 DOI
The role of pleiotropy and linkage in genes affecting a sexual ornament and bone allocation in the chicken.
Johnsson, M., Rubin, C., Hoglund, A., Sahlqvist, A., Jonsson, K. et al. (2014). Molecular Ecology, vol. 23, ss. 2275-2286 DOI
ZBED6 Modulates the Transcription of Myogenic Genes in Mouse Myoblast Cells.
Jiang, L., Wallerman, O., Younis, S., Rubin, C., Gilbert, E. et al. (2014). PLOS ONE, vol. 9, ss. e94187- DOI
Allele Dependent Silencing of Collagen Type I Using Small Interfering RNAs Targeting 3'UTR Indels: a Novel Therapeutic Approach in Osteogenesis Imperfecta.
Lindahl, K., Kindmark, A., Laxman, N., Åström, E., Rubin, C. et al. (2013). International Journal of Medical Sciences, vol. 10, ss. 1333-1343 DOI
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.
Orlando, L., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, A. et al. (2013). Nature, vol. 499, ss. 74-+ DOI
Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring.
Lamichhaney, S., Barrio, A., Rafati, N., Sundström, G., Rubin, C. et al. (2012). Proceedings of the National Academy of Sciences of the United States of America, vol. 109, ss. 19345-19350 DOI
Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens.
Natt, D., Rubin, C., Wright, D., Johnsson, M., Belteky, J. et al. (2012). BMC Genomics, vol. 13, ss. 59- DOI
Strong signatures of selection in the domestic pig genome.
Rubin, C., Megens, H., Barrio, A., Maqbool, K., Sayyab, S. et al. (2012). Proceedings of the National Academy of Sciences of the United States of America, vol. 109, ss. 19529-19536 DOI
A Sexual Ornament in Chickens Is Affected by Pleiotropic Alleles at HAO1 and BMP2, Selected during Domestication.
Johnsson, M., Gustafson, I., Rubin, C., Sahlqvist, A., Jonsson, K. et al. (2012). PLOS Genetics, vol. 8, ss. e1002914- DOI
The role of ZBED6 in transcriptional regulation studied by transcriptome analysis after RNAi in mouse myoblasts.
Jiang, L., Rubin, C., Gilbert, E., Sundström, E., Wallerman, O. et al.
Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice.
Andersson, L., Larhammar, M., Memic, F., Wootz, H., Schwochow, D. et al. (2012). Nature, vol. 488, ss. 642-646 DOI
The Rose-comb Mutation in Chickens Constitutes a Structural Rearrangement Causing Both Altered Comb Morphology and Defective Sperm Motility.
Imsland, F., Feng, C., Boije, H., Bed'hom, B., Fillon, V. et al. (2012). PLOS Genetics, vol. 8, ss. e1002775- DOI
Genotype-phenotype correlations and pharmacogenetic studies in 140 Swedish families with osteogenesis imperfecta.
Lindahl, K., Rubin, C., Astrom, E., Malmgren, B., Kindmark, A. et al. (2012). Bone, vol. 50, ss. S109-S109 DOI
Allele-specific gene silencing in osteogenesis imperfecta.
Ljunggren, Ö., Lindahl, K., Rubin, C., Kindmark, A. (2011). Endocrine Development, vol. 21, ss. 85-90 DOI
A Complex Genomic Rearrangement Involving the Endothelin 3 Locus Causes Dermal Hyperpigmentation in the Chicken.
Dorshorst, B., Molin, A., Rubin, C., Johansson, A., Stromstedt, L. et al. (2011). PLoS Genetics, vol. 7, ss. e1002412- DOI
Onset of Sexual Maturity in Female Chickens is Genetically Linked to Loci Associated with Fecundity and a Sexual Ornament.
Wright, D., Rubin, C., Schutz, K., Kerje, S., Kindmark, A. et al. (2012). Reproduction in domestic animals, vol. 47, ss. 31-36 DOI
ZBED6: the birth of a new transcription factor in the common ancestor of placental mammals.
Andersson, L., Andersson, G., Hjälm, G., Jiang, L., Lindblad-Toh, K. et al. (2010). Transcription, vol. 1, ss. 144-148 DOI
COL1 C-Propeptide Cleavage Site Mutations Cause High Bone Mass Osteogenesis Imperfecta.
Lindahl, K., Barnes, A., Fratzl-Zelman, N., Whyte, M., Hefferan, T. et al. (2011). Human Mutation, vol. 32, ss. 598-609 DOI
The genetic architecture of domestication in the chicken: effects of pleiotropy and linkage.
Wright, D., Rubin, C., Martinez Barrio, A., Schütz, K., Kerje, S. et al. (2010). Molecular Ecology, vol. 19, ss. 5140-5156 DOI
Allele dependent silencing of COL1A2 using small interfering RNAs.
Lindahl, K., Rubin, C., Kindmark, A., Ljunggren, Ö. (2008). International journal of medical sciences, vol. 5, ss. 361-365
Copy number variation in intron 1 of SOX5 causes the Pea-comb phenotype in chickens.
Wright, D., Boije, H., Meadows, J., Bed'hom, B., Gourichon, D. et al. (2009). PLoS Genetics, vol. 5, ss. e1000512- DOI
Heterozygosity for a coding SNP in COL1A2 confers a lower BMD and an increased stroke risk.
Lindahl, K., Rubin, C., Brändström, H., Karlsson, M., Holmberg, A. et al. (2009). Biochemical and Biophysical Research Communications - BBRC, vol. 384, ss. 501-505 DOI
Whole genome resequencing reveals loci under selection during chicken domestication.
Rubin, C., Zody, M., Eriksson, J., Meadows, J., Sherwood, E. et al. (2010). Nature, vol. 464, ss. 587-591 DOI
Phylogenetic relationships and species differentiation of 39 Legionella species by sequence determination of the RNase P RNA gene rnpB.
Rubin, C., Thollesson, M., Kirsebom, L., Herrmann, B. (2005). Int J Syst Evol Microbiol, vol. 55, ss. 2039-49
Characterization of ompA genotypes by sequence analysis of DNA from all detected cases of Chlamydia trachomatis infections during 1 year of contact tracing in a Swedish County..
Lysén, M., Osterlund, A., Rubin, C., Persson, T., Persson, I. et al. (2004). J Clin Microbiol, vol. 42, ss. 1641-7
Comparison of a duplex quantitative real-time PCR assay and the COBAS Amplicor CMV Monitor test for detection of cytomegalovirus.
Herrmann, B., Larsson, V., Rubin, C., Sund, F., Eriksson, B. et al. (2004). Journal of Clinical Microbiology, vol. 42, ss. 1909-14 DOI
Functional Genomics of Bone Metabolism: Novel Candidate Genes Identified by Studies in Chicken Models.
Rubin, Carl-Johan, 2008 Download fulltext
Quantitative Trait Loci for BMD and Bone Strength in an Intercross Between Domestic and Wildtype Chickens.
Rubin, C., Brändström, H., Wright, D., Kerje, S., Gunnarsson, U. et al. (2007). Journal of Bone and Mineral Research, vol. 22, ss. 375-384 DOI
Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits.
Rubin, C., Lindberg, J., Fitzsimmons, C., Savolainen, P., Jensen, P. et al. (2007). BMC Genomics, vol. 8, ss. 208- DOI