The Bioinformatics Core Facility
- Prosjektnummer
- 2015097
- Ansvarlig person
- Eivind Hovig
- Institusjon
- Oslo universitetssykehus HF
- Prosjektkategori
- Regional teknologisk kjernefasilitet
- Helsekategori
- Cancer, Generic Health Relevance
- Forskningsaktivitet
- 1. Underpinning
Single-cell m
Nat Biotechnol 2023 Jun 22. Epub 2023 jun 22
PMID: 37349523
A Breast Cancer Polygenic Risk Score Is Feasible for Risk Stratification in the Norwegian Population.
Cancers (Basel) 2023 Aug 16;15(16). Epub 2023 aug 16
PMID: 37627152
hGSuite HyperBrowser: A web-based toolkit for hierarchical metadata-informed analysis of genomic tracks.
PLoS One 2023;18(7):e0286330. Epub 2023 jul 19
PMID: 37467208
A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer.
NAR Cancer 2022 Mar;4(1):zcab051. Epub 2022 jan 14
PMID: 35047825
Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for
Biology (Basel) 2022 Jan 13;11(1). Epub 2022 jan 13
PMID: 35053128
A national precision cancer medicine implementation initiative for Norway.
Nat Med 2022 May;28(5):885.
PMID: 35513529
Improving public cancer care by implementing precision medicine in Norway: IMPRESS-Norway.
J Transl Med 2022 May 14;20(1):225. Epub 2022 mai 14
PMID: 35568909
Expression Analysis in Atlantic Salmon Liver Reveals miRNAs Associated with Smoltification and Seawater Adaptation.
Biology (Basel) 2022 Apr 30;11(5). Epub 2022 apr 30
PMID: 35625416
Clonal evolution in primary breast cancers under sequential epirubicin and docetaxel monotherapy.
Genome Med 2022 Aug 11;14(1):86. Epub 2022 aug 11
PMID: 35948919
Differential Expression of miRNAs and Their Predicted Target Genes Indicates That Gene Expression in Atlantic Salmon Gill Is Post-Transcriptionally Regulated by miRNAs in the Parr-Smolt Transformation and Adaptation to Sea Water.
Int J Mol Sci 2022 Aug 08;23(15). Epub 2022 aug 8
PMID: 35955964
Whole exome sequencing of high-risk neuroblastoma identifies novel non-synonymous variants.
PLoS One 2022;17(8):e0273280. Epub 2022 aug 29
PMID: 36037157
Mutational analysis and protein profiling predict drug sensitivity in multiple myeloma cell lines.
Front Oncol 2022;12():1040730. Epub 2022 nov 29
PMID: 36523963
Genetic Characterization in High-Risk Individuals from a Low-Resource City of Peru.
Cancers (Basel) 2022 Nov 15;14(22). Epub 2022 nov 15
PMID: 36428697
The population genomic legacy of the second plague pandemic.
Curr Biol 2022 Nov 07;32(21):4743. Epub 2022 okt 1
PMID: 36182700
Functional precision cancer medicine: drug sensitivity screening enabled by cell culture models.
Trends Pharmacol Sci 2022 Nov;43(11):973. Epub 2022 sep 23
PMID: 36163057
Cooperative induction of receptor tyrosine kinases contributes to adaptive MAPK drug resistance in melanoma through the PI3K pathway.
Cancer Rep (Hoboken) 2023 Feb;6(2):e1736. Epub 2022 okt 17
PMID: 36251678
Colorectal cancer incidences in Lynch syndrome: a comparison of results from the prospective lynch syndrome database and the international mismatch repair consortium.
Hered Cancer Clin Pract 2022 Oct 01;20(1):36. Epub 2022 okt 1
PMID: 36182917
Characterization of the T cell receptor repertoire and melanoma tumor microenvironment upon combined treatment with ipilimumab and hTERT vaccination.
J Transl Med 2022 Sep 11;20(1):419. Epub 2022 sep 11
PMID: 36089578
Combining a Universal Telomerase Based Cancer Vaccine With Ipilimumab in Patients With Metastatic Melanoma - Five-Year Follow Up of a Phase I/IIa Trial.
Front Immunol 2021;12():663865. Epub 2021 mai 11
PMID: 34046035
Gene expression profile in cases of infectious death in infancy.
Pediatr Res 2021 02;89(3):483-487. Epub 2020 apr 16
PMID: 32299088
Rapid nanopore-based DNA sequencing protocol of antibiotic-resistant bacteria for use in surveillance and outbreak investigation.
Microb Genom 2021 04;7(4).
PMID: 33885360
Tissue distribution and transcriptional regulation of CCN5 in the heart after myocardial infarction.
J Cell Commun Signal 2022 Sep;16(3):377. Epub 2021 des 1
PMID: 34854055
Identification of response signatures for tankyrase inhibitor treatment in tumor cell lines.
iScience 2021 Jul 23;24(7):102807. Epub 2021 jul 1
PMID: 34337362
Proteomic analyses identify major vault protein as a prognostic biomarker for fatal prostate cancer.
Carcinogenesis 2021 05 28;42(5):685-693.
PMID: 33609362
DNA glycosylase Neil3 regulates vascular smooth muscle cell biology during atherosclerosis development.
Atherosclerosis 2021 05;324():123-132. Epub 2021 feb 23
PMID: 33714552
Cancer Predisposition Sequencing Reporter (CPSR): A flexible variant report engine for high-throughput germline screening in cancer.
Int J Cancer 2021 12 01;149(11):1955-1960. Epub 2021 aug 4
PMID: 34310709
Recommendations for the FAIRification of genomic track metadata.
F1000Res 2021;10(). Epub 2021 apr 1
PMID: 34249331
No association to sudden infant death syndrome detected by targeted amplicon sequencing of 24 genes.
Acta Paediatr 2020 12;109(12):2636-2640. Epub 2020 mai 18
PMID: 32271962
Molecularly matched therapy in the context of sensitivity, resistance, and safety; patient outcomes in end-stage cancer - the MetAction study.
Acta Oncol 2020 Jul;59(7):733-740. Epub 2020 mar 25
PMID: 32208873
miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection.
Front Immunol 2020;11():2113. Epub 2020 sep 11
PMID: 33013890
A framework to assess the quality and impact of bioinformatics training across ELIXIR.
PLoS Comput Biol 2020 07;16(7):e1007976. Epub 2020 jul 23
PMID: 32702016
Accuracy and efficiency of germline variant calling pipelines for human genome data.
Sci Rep 2020 11 19;10(1):20222. Epub 2020 nov 19
PMID: 33214604
MirGeneDB 2.0: the metazoan microRNA complement.
Nucleic Acids Res 2020 01 08;48(D1):D132-D141.
PMID: 31598695
Mutational dynamics and immune evasion in diffuse large B-cell lymphoma explored in a relapse-enriched patient series.
Blood Adv 2020 05 12;4(9):1859-1866.
PMID: 32374878
A Three-dimensional Ex Vivo Viability Assay Reveals a Strong Correlation Between Response to Targeted Inhibitors and Mutation Status in Melanoma Lymph Node Metastases.
Transl Oncol 2019 Jul;12(7):951-958. Epub 2019 mai 13
PMID: 31096111
Responsiveness to PD-1 Blockade in End-Stage Colon Cancer with Gene Locus 9p24.1 Copy-Number Gain.
Cancer Immunol Res 2019 May;7(5):701-706. Epub 2019 feb 25
PMID: 30804006
PathTracer: High-sensitivity detection of differential pathway activity in tumours.
Sci Rep 2019 Nov 08;9(1):16332. Epub 2019 nov 8
PMID: 31704995
The extracellular matrix proteoglycan lumican improves survival and counteracts cardiac dilatation and failure in mice subjected to pressure overload.
Sci Rep 2019 Jun 24;9(1):9206. Epub 2019 jun 24
PMID: 31235849
Integrative genomic analysis of peritoneal malignant mesothelioma: understanding a case with extraordinary chemotherapy response.
Cold Spring Harb Mol Case Stud 2019 04;5(2). Epub 2019 apr 1
PMID: 30862609
Long-term effects on survival after a 1-year multifactorial vascular risk factor intervention after stroke or TIA: secondary analysis of a randomized controlled trial, a 7-year follow-up study.
Vasc Health Risk Manag 2019;15():11-18. Epub 2019 feb 7
PMID: 30799926
Circulating Secretoneurin Concentrations After Cardiac Surgery: Data From the FINNish Acute Kidney Injury Heart Study.
Crit Care Med 2019 05;47(5):e412-e419.
PMID: 30730440
Carotid Atherosclerosis and Cognitive Function in a General Population Aged 63-65 Years: Data from the Akershus Cardiac Examination (ACE) 1950 Study.
J Alzheimers Dis 2019;70(4):1041-1049.
PMID: 31306128
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.
Nat Commun 2019 06 17;10(1):2674. Epub 2019 jun 17
PMID: 31209238
Roadmap for a precision-medicine initiative in the Nordic region.
Nat Genet 2019 06;51(6):924-930.
PMID: 30988515
Colocalization analyses of genomic elements: approaches, recommendations and challenges.
Bioinformatics 2019 May 01;35(9):1615-1624.
PMID: 30307532
Diagnostic Profiling of the Human Public IgM Repertoire With Scalable Mimotope Libraries.
Front Immunol 2019;10():2796. Epub 2019 des 3
PMID: 31849974
Signalling pathways identified in salivary glands from primary Sjögren's syndrome patients reveal enhanced adipose tissue development.
Autoimmunity 2018 May;51(3):135-146. Epub 2018 mar 5
PMID: 29504848
The predictive value of NT-proBNP and hs-TnT for risk of death in cardiac surgical patients.
Clin Biochem 2018 Mar;53():65-71. Epub 2018 jan 31
PMID: 29371002
Prevalence of Carotid Plaque in a 63- to 65-Year-Old Norwegian Cohort From the General Population: The ACE (Akershus Cardiac Examination) 1950 Study.
J Am Heart Assoc 2018 May 08;7(10). Epub 2018 mai 8
PMID: 29739796
Ex vivo metabolic fingerprinting identifies biomarkers predictive of prostate cancer recurrence following radical prostatectomy.
Br J Cancer 2018 Mar 20;118(6):e11. Epub 2018 feb 20
PMID: 29462127
Sample-Index Misassignment Impacts Tumour Exome Sequencing.
Sci Rep 2018 Mar 28;8(1):5307. Epub 2018 mar 28
PMID: 29593270
Challenges in the identification of methicillin-resistant Staphylococcus argenteus by routine diagnostics.
APMIS 2018 Jun;126(6):533-537.
PMID: 29924450
Personal Cancer Genome Reporter: variant interpretation report for precision oncology.
Bioinformatics 2018 05 15;34(10):1778-1780.
PMID: 29272339
Main title: pulmonary vascular disease is evident in gene regulation of experimental bronchopulmonary dysplasia.
J Matern Fetal Neonatal Med 2018 Nov 14. Epub 2018 nov 14
PMID: 30428746
Expression of nucleotide excision repair in Alzheimer's disease is higher in brain tissue than in blood.
Neurosci Lett 2018 04 13;672():53-58. Epub 2018 feb 21
PMID: 29474873
Each pregnancy linearly changes immune gene expression in the blood of healthy women compared with breast cancer patients.
Clin Epidemiol 2018;10():931-940. Epub 2018 aug 6
PMID: 30123005
Excision of the doubly methylated base
Philos Trans R Soc Lond B Biol Sci 2018 Jun 05;373(1748).
PMID: 29685966
Norwegian e-Infrastructure for Life Sciences (NeLS).
F1000Res 2018;7(). Epub 2018 jun 29
PMID: 30271575
Development of a clinical prediction model for diagnosing adenomyosis.
Fertil Steril 2018 Oct;110(5):957-964.e3.
PMID: 30316443
Serological markers of extracellular matrix remodeling predict transplant-free survival in primary sclerosing cholangitis.
Aliment Pharmacol Ther 2018 Jul;48(2):179-189. Epub 2018 mai 30
PMID: 29851098
Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection.
BMC Genomics 2017 05 04;18(1):349. Epub 2017 mai 4
PMID: 28472924
Ex vivo metabolic fingerprinting identifies biomarkers predictive of prostate cancer recurrence following radical prostatectomy.
Br J Cancer 2017 Nov 21;117(11):1656-1664. Epub 2017 okt 3
PMID: 28972967
Enhanced liver fibrosis test predicts transplant-free survival in primary sclerosing cholangitis, a multi-centre study.
Liver Int 2017 Oct;37(10):1554-1561. Epub 2017 apr 13
PMID: 28267887
HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization.
PLoS One 2017;12(1):e0169074. Epub 2017 jan 3
PMID: 28045981
Circulating chromogranin B levels in patients with acute respiratory failure: data from the FINNALI Study.
Biomarkers 2017 Dec;22(8):775-781. Epub 2017 jan 3
PMID: 28049363
Evolution of the cAMP-dependent protein kinase (PKA) catalytic subunit isoforms.
PLoS One 2017;12(7):e0181091. Epub 2017 jul 25
PMID: 28742821
Novel serum and bile protein markers predict primary sclerosing cholangitis disease severity and prognosis.
J Hepatol 2017 Jun;66(6):1214-1222. Epub 2017 feb 2
PMID: 28161472
Prognostic and diagnostic significance of copeptin in acute exacerbation of chronic obstructive pulmonary disease and acute heart failure: data from the ACE 2 study.
Respir Res 2017 Nov 03;18(1):184. Epub 2017 nov 3
PMID: 29100503
Implementing precision cancer medicine in the public health services of Norway: the diagnostic infrastructure and a cost estimate.
ESMO Open 2017;2(2):e000158. Epub 2017 mai 2
PMID: 28761742
Th17 Polarization under Hypoxia Results in Increased IL-10 Production in a Pathogen-Independent Manner.
Front Immunol 2017;8():698. Epub 2017 jun 19
PMID: 28674533
Mutations affecting the transmembrane domain of the LDL receptor: impact of charged residues on the membrane insertion.
Hum Mol Genet 2017 05 01;26(9):1634-1642.
PMID: 28334946
The rainfall plot: its motivation, characteristics and pitfalls.
BMC Bioinformatics 2017 May 18;18(1):264. Epub 2017 mai 18
PMID: 28521741
Bioinformatics Approaches to Profile the Tumor Microenvironment for Immunotherapeutic Discovery.
Curr Pharm Des 2017;23(32):4716-4725.
PMID: 28699527
Genome build information is an essential part of genomic track files.
Genome Biol 2017 Sep 14;18(1):175. Epub 2017 sep 14
PMID: 28911336
GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome.
Gigascience 2017 Jul 01;6(7):1-12.
PMID: 28459977
Use of liquid biopsies to monitor disease progression in a sarcoma patient: a case report.
BMC Cancer 2017 Jan 06;17(1):29. Epub 2017 jan 6
PMID: 28061772
Impact of Smoking on Circulating Cardiac Troponin I Concentrations and Cardiovascular Events in the General Population: The HUNT Study (Nord-Trøndelag Health Study).
Circulation 2016 Dec 13;134(24):1962-1972. Epub 2016 nov 4
PMID: 27815376
Pathogenic variants in KCTD7 perturb neuronal K+ fluxes and glutamine transport.
Brain 2016 Dec;139(Pt 12):3109-3120. Epub 2016 okt 14
PMID: 27742667
NAD(+) Replenishment Improves Lifespan and Healthspan in Ataxia Telangiectasia Models via Mitophagy and DNA Repair.
Cell Metab 2016 Oct 11;24(4):566-581.
PMID: 27732836
Prognostic Value of Secretoneurin in Patients with Acute Respiratory Failure: Data from the FINNALI Study.
Clin Chem 2016 Oct;62(10):1380-9. Epub 2016 aug 18
PMID: 27540029
Gender, High-Sensitivity Troponin I, and the Risk of Cardiovascular Events (from the Nord-Trøndelag Health Study).
Am J Cardiol 2016 Sep 15;118(6):816-21. Epub 2016 jun 28
PMID: 27453509
Prognostic Value of Secretoneurin in Critically Ill Patients With Infections.
Crit Care Med 2016 Oct;44(10):1882-90.
PMID: 27414477
Discovery of miRNAs and Their Corresponding miRNA Genes in Atlantic Cod (Gadus morhua): Use of Stable miRNAs as Reference Genes Reveals Subgroups of miRNAs That Are Highly Expressed in Particular Organs.
PLoS One 2016;11(4):e0153324. Epub 2016 apr 29
PMID: 27128807
Altered gene expression and possible immunodeficiency in cases of sudden infant death syndrome.
Pediatr Res 2016 07;80(1):77-84. Epub 2016 mar 9
PMID: 26959483
The gut microbial profile in patients with primary sclerosing cholangitis is distinct from patients with ulcerative colitis without biliary disease and healthy controls.
Gut 2017 Apr;66(4):611-619. Epub 2016 feb 17
PMID: 26887816
The PBMC transcriptome profile after intake of oxidized versus high-quality fish oil: an explorative study in healthy subjects.
Genes Nutr 2016;11():16. Epub 2016 mai 31
PMID: 27551317
Altered DNA base excision repair profile in brain tissue and blood in Alzheimer's disease.
Mol Brain 2016 May 28;9(1):61. Epub 2016 mai 28
PMID: 27234294
Wnt inhibition is dysregulated in gliomas and its re-establishment inhibits proliferation and tumor sphere formation.
Exp Cell Res 2016 Jan 01;340(1):53-61. Epub 2015 des 19
PMID: 26712519
Subtype-specific micro-RNA expression signatures in breast cancer progression.
Int J Cancer 2016 Sep 01;139(5):1117-28. Epub 2016 mai 9
PMID: 27082076
Transcriptomic Profiling of Tumor Aggressiveness in Sporadic Nonfunctioning Pancreatic Neuroendocrine Neoplasms.
Pancreas 2016 Sep;45(8):1196-203.
PMID: 26918873
[Diagnostic accuracy for heart failure – data from the Akershus Cardiac Examination 2 Study].
Tidsskr Nor Laegeforen 2015 Oct 20;135(19):1738-44. Epub 2015 okt 20
PMID: 26486668
Gene expression profiling of Gram-negative bacteria-induced inflammation in human whole blood: The role of complement and CD14-mediated innate immune response.
Genom Data 2015 Sep;5():176-83. Epub 2015 mai 30
PMID: 26484252
Combined expressional analysis, bioinformatics and targeted proteomics identify new potential therapeutic targets in glioblastoma stem cells.
Oncotarget 2015 Sep 22;6(28):26192-215.
PMID: 26295306
Mapping the global mRNA transcriptome during development of the murine first molar.
Front Genet 2015;6():47. Epub 2015 feb 26
PMID: 25852735
Enhanced liver fibrosis score predicts transplant-free survival in primary sclerosing cholangitis.
Hepatology 2015 Jul;62(1):188-97. Epub 2015 apr 28
PMID: 25833813
CD14 and complement crosstalk and largely mediate the transcriptional response to Escherichia coli in human whole blood as revealed by DNA microarray.
PLoS One 2015;10(2):e0117261. Epub 2015 feb 23
PMID: 25706641
Impact of sex on the prognostic value of high-sensitivity cardiac troponin I in the general population: the HUNT study.
Clin Chem 2015 Apr;61(4):646-56. Epub 2015 feb 18
PMID: 25695851
Secretoneurin is a novel prognostic cardiovascular biomarker associated with cardiomyocyte calcium handling.
J Am Coll Cardiol 2015 Feb 3;65(4):339-51.
PMID: 25634832
Reduced expression of aquaporins in human intestinal mucosa in early stage inflammatory bowel disease.
Clin Exp Gastroenterol 2015;8():49-67. Epub 2015 jan 9
PMID: 25624769
Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires.
Immunogenetics 2015 Feb;67(2):73-84. Epub 2014 des 12
PMID: 25502872
Automated amplicon design suitable for analysis of DNA variants by melting techniques.
BMC Res Notes 2015;8():667. Epub 2015 nov 11
PMID: 26559640
A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome.
Annu Rev Genet 2015 Nov 23;49():213-42. Epub 2015 okt 14
PMID: 26473382
The androgen receptor controls expression of the cancer-associated sTn antigen and cell adhesion through induction of ST6GalNAc1 in prostate cancer.
Oncotarget 2015 Oct 27;6(33):34358-74.
PMID: 26452038
Glucocorticoid receptor and Klf4 co-regulate anti-inflammatory genes in keratinocytes.
Mol Cell Endocrinol 2015 Sep 5;412():281-9. Epub 2015 mai 19
PMID: 26001834
Unscrambling the genomic chaos of osteosarcoma reveals extensive transcript fusion, recurrent rearrangements and frequent novel TP53 aberrations.
Oncotarget 2016 Feb 02;7(5):5273-88.
PMID: 26672768
COGEDAP: A COmprehensive GEnomic Data Analysis Platform
arxiv, 2022
OncoEnrichR: cancer-dedicated gene set interpretation
arxiv, 2022
Finemap-MiXeR: A variational Bayesian approach for genetic finemapping
biorxiv, 2022
- Victor Micahel Kalbskopf Prosjektdeltaker
- Annbjørg Helene Barbakken Prosjektdeltaker
- Monica Hongrø Solbakken Prosjektdeltaker
- Daniel Vodák Prosjektdeltaker
- Joshua Baskaran Prosjektdeltaker
- Clara-Cecilie Günther Prosjektdeltaker
- Marit Holden Prosjektdeltaker
- Hildur Sif Thorarensen Prosjektdeltaker
- Johannes Eivind Hovig Prosjektleder
- Tina Visnovska Prosjektdeltaker
- Ksenia Khelik Prosjektdeltaker
- Jon Kristen Lærdahl Prosjektdeltaker
- Oleg Agafonov Prosjektdeltaker
- Sumana Kalyanasund Prosjektdeltaker
- Vegard Nygaard Prosjektdeltaker
- Morten Johansen Prosjektdeltaker
- Charitra Kumar Mishra Prosjektdeltaker
- Ståle Nygård Prosjektleder
- Sumana Kalyanasundaram Prosjektdeltaker
eRapport er utarbeidet av Sølvi Lerfald og Reidar Thorstensen, Regionalt kompetansesenter for klinisk forskning, Helse Vest RHF, og videreutvikles av de fire RHF-ene i fellesskap, med støtte fra Helse Vest IKT
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