Publications (Bioinformatics)
Before 2013 the Bioinformatics Core Faility was a part of the Genomics Core Facility. Hence the older publications listed here are from bioinformatics/statistics projects run at the Genomics Core Facility by the current Bioinformatics Core Facility staff.
2018
Hofving, T., et al., The neuroendocrine phenotype, genomic profile and therapeutic sensitivity of GEPNET cell lines. Endocr Relat Cancer, 2018. 25(4): p. X1-X2.
Nymo, S.H., et al., Serum neutrophil gelatinase-associated lipocalin (NGAL) concentration is independently associated with mortality in patients with acute coronary syndrome. Int J Cardiol, 2018. 262: p. 79-84.
Orebaugh, C.D., et al., Mapping Ribonucleotides Incorporated into DNA by Hydrolytic End-Sequencing. Methods Mol Biol, 2018. 1672: p. 329-345.
Parris, T.Z., et al., Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma. Oncotarget, 2018. 9(35): p. 24140-24154.
2017
Asghar, N., et al., Deep sequencing analysis of tick-borne encephalitis virus from questing ticks at natural foci reveals similarities between quasispecies pools of the virus. Journal of General Virology, 2017. 98(3): p. 413-421
Ben-Avraham, D., et al., The complex genetics of gait speed: genome-wide meta-analysis approach. Aging (Albany NY), 2017. 9(1): p. 209-246.
Bygdell, M., et al., The rise and the recent decline of childhood obesity in Swedish boys: the BEST cohort. Int J Obes (Lond), 2017.
Eriksson, J., et al., Causal relationship between obesity and serum testosterone status in men: A bi-directional mendelian randomization analysis. Plos One, 2017. 12(4).
Kariminejad, A., et al., TOR1A variants cause a severe arthrogryposis with developmental delay, strabismus and tremor. Neuromuscular Disorders, 2017. 27: p. S243-S243.
Ohlsson, C., et al., Low Serum DHEAS Predicts Increased Fracture Risk in Older Men - the MrOS Sweden Study. J Bone Miner Res, 2017.
Ohlsson, C., et al., BMI increase through puberty and adolescence is associated with risk of adult stroke. Neurology, 2017. 89(4): p. 363-369.
Orwoll, E.S., et al., The Limited Clinical Utility of Testosterone, Estradiol, and Sex Hormone Binding Globulin Measurements in the Prediction of Fracture Risk and Bone Loss in Older Men. J Bone Miner Res, 2017. 32(3): p. 633-640.
Robinson-Cohen, C., et al., Genetic Variants Associated with Circulating Parathyroid Hormone. J Am Soc Nephrol, 2016.
Szilagyi, Z., et al., Correction for Szilagyi et al., "Cyclin-Dependent Kinase 8 Regulates Mitotic Commitment in Fission Yeast". Mol Cell Biol, 2017. 37(17).
Tomic, T.T., et al., A new GTF2I-BRAF fusion mediating MAPK pathway activation in pilocytic astrocytoma. PLoS One, 2017. 12(4): p. e0175638.
Vandenput, L., et al., Low Testosterone, but Not Estradiol, Is Associated With Incident Falls in Older Men: The International MrOS Study. J Bone Miner Res, 2017
Vizlin-Hodzic, D., et al., Early onset of inflammation during ontogeny of bipolar disorder: the NLRP2 inflammasome gene distinctly differentiates between patients and healthy controls in the transition between iPS cell and neural stem cell stages. Transl Psychiatry, 2017. 7(1): p. e1010.
2016
Asghar, N., et al., The role of the poly(A) tract in the replication and virulence of tick-borne encephalitis virus. Sci Rep, 2016. 6: p. 39265.
Banyai, G., et al., Cdk1 activity acts as a quantitative platform for coordinating cell cycle progression with periodic transcription. Nat Commun, 2016. 7: p. 11161.
Bhadury, J., et al., Hypoxia-regulated gene expression explains differences between melanoma cell line-derived xenografts and patient-derived xenografts. Oncotarget, 2016. 7(17): p. 23801-23811.
Carlsten, J.O., et al., Loss of the Mediator subunit Med20 affects transcription of tRNA and other non-coding RNA genes in fission yeast. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 2016. 1859(2): p. 339-347.
Fransson, S., et al., Estimation of copy number aberrations: Comparison of exome sequencing data with SNP microarrays identifies homozygous deletions of 19q13.2 and CIC in neuroblastoma. Int J Oncol, 2016. 48(3): p. 1103-16.
Joydeep Bhadury, L.M.N., Marcela D López, Jonas A Nilsson. Trp53 mutational status correlates with tumorigenicity in TRAMP-C mouse prostate cancer cell lines. Science Matters 2016 Aug 30th, 2016.
Kariminejad, A., et al., Truncating CHRNG mutations associated with interfamilial variability of the severity of the Escobar variant of multiple pterygium syndrome. BMC Genet, 2016. 17(1): p. 71.
Kariminejad, A., et al., Lethal multiple pterygium syndrome, the extreme end of the RYR1 spectrum. BMC Musculoskelet Disord, 2016. 17: p. 109.
Langen, B., et al., Microarray Studies on 211At Administration in BALB/c Nude Mice Indicate Systemic Effects on Transcriptional Regulation in Non-Thyroid Tissues. J Nucl Med, 2016.
Langen, B., et al., Non-targeted transcriptomic effects upon thyroid irradiation: similarity between in-field and out-of-field responses varies with tissue type. Sci Rep, 2016. 6: p. 30738.
Nielson, C.M., et al., Novel Genetic Variants Associated With Increased Vertebral Volumetric BMD, Reduced Vertebral Fracture Risk, and Increased Expression of SLC1A3 and EPHB2. Journal of Bone and Mineral Research, 2016. 31(12): p. 2085-2097.
Ohlsson, C., et al., Association between excessive BMI increase during puberty and risk of cardiovascular mortality in adult men: a population-based cohort study. Lancet Diabetes Endocrinol, 2016. 4(12): p. 1017-1024.
Olafsdottir, T.A., et al., Comparative Systems Analyses Reveal Molecular Signatures of Clinically tested Vaccine Adjuvants. Sci Rep, 2016. 6: p. 39097.
Orwoll, E.S., et al., The Limited Clinical Utility of Testosterone, Estradiol, and Sex Hormone Binding Globulin Measurements in the Prediction of Fracture Risk and Bone Loss in Older Men. J Bone Miner Res, 2016.
Rohlin, A., et al., GREM1 and POLE variants in hereditary colorectal cancer syndromes. Genes, Chromosomes and Cancer, 2016. 55(1): p. 95-106.
Teumer, A., et al., Genomewide meta-analysis identifies loci associated with IGF-I and IGFBP-3 levels with impact on age-related traits. Aging Cell, 2016. 15(5): p. 811-24.
Truve, K., et al., Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development-Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus. PLoS Genet, 2016. 12(5): p. e1006000.
2015
Carlsten, J.O., et al., Loss of the Mediator subunit Med20 affects transcription of tRNA and other non-coding RNA genes in fission yeast. Biochim Biophys Acta, 2015.
Ek, C.J., et al., Transcriptomal changes and functional annotation of the developing non-human primate choroid plexus. Front Neurosci, 2015. 9: p. 82.
Ek, C.J., et al., Expression of tight junction proteins and transporters for xenobiotic metabolism at the blood-CSF barrier during development in the nonhuman primate (P. hamadryas). Reprod Toxicol, 2015. 56: p. 32-44.
Fransson, S., et al., Intragenic anaplastic lymphoma kinase (ALK) rearrangements: Translocations as a novel mechanism of ALK activation in neuroblastoma tumors. Genes Chromosomes Cancer, 2015. 54(2): p. 99-109.
Jemt, E., et al., Regulation of DNA replication at the end of the mitochondrial D-loop involves the helicase TWINKLE and a conserved sequence element. Nucleic Acids Res, 2015.
Kling, T., et al., Efficient exploration of pan-cancer networks by generalized covariance selection and interactive web content. Nucleic Acids Res, 2015. 43(15): p. e98.
Lunavat, T.R., et al., Small RNA deep sequencing discriminates subsets of extracellular vesicles released by melanoma cells - Evidence of unique microRNA cargos. RNA Biol, 2015. 12(8): p. 810-23.
Odin, E., et al., Expression of Folate Pathway Genes in Stage III Colorectal Cancer Correlates with Recurrence Status Following Adjuvant Bolus 5-FU-Based Chemotherapy. Mol Med, 2015. 21(1): p. 597-604.
2014
Banyai, G., et al., Mediator can regulate mitotic entry and direct periodic transcription in fission yeast. Mol Cell Biol, 2014.
Einarsdottir, B.O., et al., Melanoma patient-derived xenografts accurately model the disease and develop fast enough to guide treatment decisions. Oncotarget, 2014. 5(20): p. 9609-18.
Jabbar, K.S., et al., Proteomic mucin profiling for the identification of cystic precursors of pancreatic cancer. J Natl Cancer Inst, 2014. 106(2): p. djt439.
Kalliopi Sofou, et al., Whole exome sequencing reveals mutations in NARS2 and PARS2, encoding the mitochondrial asparaginyl-tRNA synthetase and prolyl-tRNA synthetase, in patients with Alpers syndrome. Molecular Genetics & Genomic Medicine 2014. 3(1): p. 59-68.
Rohlin, A., et al., A mutation in POLE predisposing to a multi-tumour phenotype. Int J Oncol, 2014. 45(1): p. 77-81.
2013
Bhadury, J., et al., Identification of tumorigenic and therapeutically actionable mutations in transplantable mouse tumor cells by exome sequencing. Oncogenesis, 2013. 2: p. e44.
Djos, A., et al., Aneuploidy in neuroblastoma tumors is not associated with inactivating point mutations in the STAG2 gene. BMC Med Genet, 2013. 14: p. 102.
Nilsson, J., et al., Polyglucosan body myopathy caused by defective ubiquitin ligase RBCK1. Ann Neurol, 2013.
Terzioglu, M., et al., MTERF1 Binds mtDNA to Prevent Transcriptional Interference at the Light-Strand Promoter but Is Dispensable for rRNA Gene Transcription Regulation. Cell Metab, 2013. 17(4): p. 618-26.
2012
Carlsten, J.O., et al., Mediator promotes CENP-a incorporation at fission yeast centromeres. Mol Cell Biol, 2012. 32(19): p. 4035-43.
Estrada, K., et al., Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. Nat Genet, 2012. 44(5): p. 491-501.
Medina-Gomez, C., et al., Meta-analysis of genome-wide scans for total body BMD in children and adults reveals allelic heterogeneity and age-specific effects at the WNT16 locus. PLoS Genet, 2012. 8(7): p. e1002718.
Szilagyi, Z., et al., Cyclin-dependent kinase 8 regulates mitotic commitment in fission yeast. Mol Cell Biol, 2012. 32(11): p. 2099-109.
Zheng, H.F., et al., WNT16 influences bone mineral density, cortical bone thickness, bone strength, and osteoporotic fracture risk. PLoS Genet, 2012. 8(7): p. e1002745.
2011
Abel, F., et al., A 6-gene signature identifies four molecular subgroups of neuroblastoma. Cancer Cell Int, 2011. 11: p. 9.
Caren, H., et al., Identification of epigenetically regulated genes that predict patient outcome in neuroblastoma. BMC Cancer, 2011. 11: p. 66.
Ohlsson, C., et al., Genetic determinants of serum testosterone concentrations in men. PLoS Genet, 2011. 7(10): p. e1002313.
Zhu, X., et al., Histone modifications influence mediator interactions with chromatin. Nucleic Acids Res, 2011. 39(19): p. 8342-54.