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University of Gothenburg

Publications from BCF users and staff

Before 2013 the Bioinformatics Core Facility 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.

Ilinca, A., E. Englund, S. Samuelsson, K. Truve, E. Kafantari, N. Martinez-Majander, J. Putaala, C. Hakansson, A. G. Lindgren and A. Puschmann (2021). "MAP3K6 Mutations in a Neurovascular Disease Causing Stroke, Cognitive Impairment, and Tremor." Neurol Genet 7(1): e548.

Lu, T., V. Forgetta, J. Keller-Baruch, M. Nethander, D. Bennett, M. Forest, S. Bhatnagar, R. G. Walters, K. Lin, Z. Chen, L. Li, M. Karlsson, D. Mellstrom, E. Orwoll, E. V. McCloskey, J. A. Kanis, W. D. Leslie, R. J. Clarke, C. Ohlsson, C. M. T. Greenwood and J. B. Richards (2021). "Improved prediction of fracture risk leveraging a genome-wide polygenic risk score." Genome Med 13(1): 16.


Celind, J., C. Ohlsson, M. Bygdell, J. Martikainen, C. Lewerin and J. M. Kindblom (2020). "Childhood body mass index is associated with the risk of adult hematologic malignancies in men-The best Gothenburg cohort." Int J Cancer 147(9): 2355-2362.

Garcia, P., C. Bizama, L. Rosa, J. A. Espinoza, H. Weber, J. Cerda-Infante, M. Sanchez, V. P. Montecinos, J. Lorenzo-Bermejo, F. Boekstegers, M. Davila-Lopez, F. Alfaro, C. Leiva-Acevedo, Z. Parra, D. Romero, S. Kato, P. Leal, M. Lagos and J. C. Roa (2020). "Functional and genomic characterization of three novel cell lines derived from a metastatic gallbladder cancer tumor." Biol Res 53(1): 13.

Ilinca, A., N. Martinez-Majander, S. Samuelsson, P. Piccinelli, K. Truve, J. Cole, S. Kittner, M. Soller, U. Kristoffersson, T. Tatlisumak, A. Puschmann, J. Putaala and A. Lindgren (2020). "Whole-Exome Sequencing in 22 Young Ischemic Stroke Patients With Familial Clustering of Stroke." Stroke 51(4): 1056-1063.

Javanmardi, N., S. Fransson, A. Djos, G. Umapathy, M. Ostensson, J. Milosevic, M. Borenas, B. Hallberg, P. Kogner, T. Martinsson and R. H. Palmer (2019). "Analysis of ALK, MYCN, and the ALK ligand ALKAL2 (FAM150B/AUGalpha) in neuroblastoma patient samples with chromosome arm 2p rearrangements." Genes Chromosomes Cancer.

Marild, K., C. Ohlsson, M. Bygdell, J. Martikainen, L. Savendahl, K. Stordal and J. M. Kindblom (2020). "Growth and Pubertal Timing in Boys With Adult-diagnosed Celiac Disease: A Population-based Longitudinal Cohort Study." J Pediatr Gastroenterol Nutr 70(6): 853-857.

Masoudzadeh, N., M. Ostensson, J. Persson, V. Mashayekhi Goyonlo, C. Agbajogu, Y. Taslimi, R. Erfanian Salim, F. Zahedifard, A. Mizbani, H. Malekafzali Ardekani, B. M. Gunn, S. Rafati and A. M. Harandi (2020). "Molecular signatures of anthroponotic cutaneous leishmaniasis in the lesions of patients infected with Leishmania tropica." Sci Rep 10(1): 16198.

Nethander, M., U. Pettersson-Kymmer, L. Vandenput, M. Lorentzon, M. Karlsson, D. Mellstrom and C. Ohlsson (2020). "BMD-Related Genetic Risk Scores Predict Site-Specific Fractures as Well as Trabecular and Cortical Bone Microstructure." J Clin Endocrinol Metab 105(4).

Nwaru, B. I., C. Ohlsson, M. Bygdell, J. Martikainen and J. M. Kindblom (2020). "Pubertal BMI change and adult-onset asthma in men: Population-based cohort study in Sweden." Clin Exp Allergy 50(1): 51-60.

Olsson Lindvall, M., A. Angerfors, B. Andersson, S. Nilsson, M. Davila Lopez, L. Hansson, T. M. Stanne and C. Jern (2020). "Comparison of DNA Methylation Profiles of Hemostatic Genes between Liver Tissue and Peripheral Blood within Individuals." Thromb Haemost.

Olsson Lindvall, M., M. Davila Lopez, S. Klasson, L. Hansson, S. Nilsson, T. M. Stanne and C. Jern (2020). "A Comprehensive Sequencing-Based Analysis of Allelic Methylation Patterns in Hemostatic Genes in Human Liver." Thromb Haemost 120(2): 229-242.

Purhonen, J., V. Grigorjev, R. Ekiert, N. Aho, J. Rajendran, R. Pietras, K. Truve, M. Wikstrom, V. Sharma, A. Osyczka, V. Fellman and J. Kallijarvi (2020). "A spontaneous mitonuclear epistasis converging on Rieske Fe-S protein exacerbates complex III deficiency in mice." Nat Commun 11(1): 322.

Ringlander, J., C. Skoglund, K. Prakash, M. E. Andersson, S. B. Larsson, K. W. Tang, G. E. Rydell, S. Abrahamsson, M. Castedal, H. Norder, K. Hellstrand and M. Lindh (2020). "Deep sequencing of liver explant transcriptomes reveals extensive expression from integrated hepatitis B virus DNA." J Viral Hepat 27(11): 1162-1170.

Scherer, D., M. D. Davila Lopez, B. Goeppert, S. Abrahamsson, R. G. Gonzalez Silos, I. Nova, K. Marcelain, J. C. Roa, D. Ibberson, S. U. Umu, T. B. Rounge, S. Roessler and J. L. Bermejo (2020). "RNA Sequencing of Hepatobiliary Cancer Cell Lines: Data and Applications to Mutational and Transcriptomic Profiling." Cancers (Basel) 12(9).

Siaw, J. T., N. Javanmardi, J. Van den Eynden, D. E. Lind, S. Fransson, A. Martinez-Monleon, A. Djos, R. M. Sjoberg, M. Ostensson, H. Caren, G. Troen, K. Beiske, A. P. Berbegall, R. Noguera, W. Y. Lai, P. Kogner, R. H. Palmer, B. Hallberg and T. Martinsson (2020). "11q Deletion or ALK Activity Curbs DLG2 Expression to Maintain an Undifferentiated State in Neuroblastoma." Cell Rep 32(12): 108171.

Taslimi, Y., C. Agbajogu, S. F. Brynjolfsson, N. Masoudzadeh, V. Mashayekhi, S. Gharibzadeh, M. Ostensson, S. S. Nakka, A. Mizbani, S. Rafati and A. M. Harandi (2020). "Profiling inflammatory response in lesions of cutaneous leishmaniasis patients using a non-invasive sampling method combined with a high-throughput protein detection assay." Cytokine 130: 155056.
Tengvall, S., C. Ohlsson, M. Bygdell, J. Martikainen, A. Andersson and J. M. Kindblom (2020). "Pubertal-onset overweight and COPD in men: a cohort study." ERJ Open Res 6(1).

Truve, K., T. Z. Parris, D. Vizlin-Hodzic, S. Salmela, E. Berger, H. Agren and K. Funa (2020). "Identification of candidate genetic variants and altered protein expression in neural stem and mature neural cells support altered microtubule function to be an essential component in bipolar disorder." Transl Psychiatry 10(1): 390.

Truve, K., T. Z. Parris, D. Vizlin-Hodzic, S. Salmela, E. Berger, H. Agren and K. Funa (2020). "Identification of candidate genetic variants and altered protein expression in neural stem and mature neural cells support altered microtubule function to be an essential component in bipolar disorder." Transl Psychiatry 10(1): 390.

Uribe, P., A. Johansson, R. Jugdaohsingh, J. J. Powell, C. Magnusson, M. Davila, A. Westerlund and M. Ransjo (2020). "Soluble silica stimulates osteogenic differentiation and gap junction communication in human dental follicle cells." Sci Rep 10(1): 9923.

Bostrom, M., et al., Chronic disturbance in the thalamus following cranial irradiation to the developing mouse brain. Sci Rep, 2019. 9(1): p. 9588.

Celind, J., et al., Childhood Body Mass Index Is Associated with Risk of Adult Colon Cancer in Men: An Association Modulated by Pubertal Change in Body Mass Index. Cancer Epidemiol Biomarkers Prev, 2019. 28(5): p. 974-979.

Funck-Brentano, T., et al., Causal Factors for Knee, Hip, and Hand Osteoarthritis: A Mendelian Randomization Study in the UK Biobank. Arthritis Rheumatol, 2019. 71(10): p. 1634-1641.

Hedberg-Oldfors, C., et al., Cardiomyopathy with lethal arrhythmias associated with inactivation of KLHL24. Hum Mol Genet, 2019. 28(11): p. 1919-1929.

Javanmardi, N., et al., Low Frequency ALK Hotspots Mutations In Neuroblastoma Tumours Detected By Ultra-deep Sequencing: Implications For ALK Inhibitor Treatment. Sci Rep, 2019. 9(1): p. 2199.

Javanmardi, N., et al., Analysis of ALK, MYCN, and the ALK ligand ALKAL2 (FAM150B/AUGalpha) in neuroblastoma patient samples with chromosome arm 2p rearrangements. Genes Chromosomes Cancer, 2019.

Karasik, D., et al., Disentangling the genetics of lean mass. Am J Clin Nutr, 2019. 109(2): p. 276-287.

Laiz Heckmann Barbalho de Figueroa, R. S., Jennifer Horkoff, Soni Chauhan, Marcela Davila Lopez, Francisco Gomes de Oliveira Neto and Alexander Schliep (2019). "A Modeling Approach for Bioinformatics Workflows." PoEM 2019. Lecture Notes in Business Information Processing 369.

Nethander, M., et al., Evidence of a Causal Effect of Estradiol on Fracture Risk in Men. J Clin Endocrinol Metab, 2019. 104(2): p. 433-442.

Nwaru, B.I., et al., Pubertal BMI change and adult-onset asthma in men: Population-based cohort study in Sweden. Clin Exp Allergy, 2019.

Ohlsson, C., et al., BMI Change During Puberty Is an Important Determinant of Adult Type 2 Diabetes Risk in Men. J Clin Endocrinol Metab, 2019. 104(5): p. 1823-1832.

Olsson Lindvall, M., et al., Hemostatic Genes Exhibit a High Degree of Allele-Specific Regulation in Liver. Thromb Haemost, 2019. 119(7): p. 1072-1083.

Purhonen, J., et al., A spontaneous mitonuclear epistasis converging on Rieske Fe-S protein exacerbates complex III deficiency in mice. Nat Commun, 2020. 11(1): p. 322.Moverare-Skrtic, S., et al., Osteoblast-derived NOTUM reduces cortical bone mass in mice and the NOTUM locus is associated with bone mineral density in humans. FASEB J, 2019. 33(10): p. 11163-11179.

Samelson, E.J., et al., Cortical and trabecular bone microarchitecture as an independent predictor of incident fracture risk in older women and men in the Bone Microarchitecture International Consortium (BoMIC): a prospective study. Lancet Diabetes Endocrinol, 2019. 7(1): p. 34-43.

Zheng, J., et al., Mendelian Randomization Analysis Reveals a Causal Influence of Circulating Sclerostin Levels on Bone Mineral Density and Fractures. J Bone Miner Res, 2019. 34(10): p. 1824-1836.

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.

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.

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.

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.

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.

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.

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.

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.