Publications

Publications 2022

Kidd SG, Bogaard M, Carm KT, Bakken AC, Maltau AMV, Løvf M, Lothe RA, Axcrona K, Axcrona U, Skotheim RI (2022)
In situ expression of ERG protein in the context of tumor heterogeneity identifies prostate cancer patients with inferior prognosis
Mol Oncol (in press)
DOI 10.1002/1878-0261.13225, PubMed 35574900

Helland Å, Russnes HG, Fagereng GL, Al-Shibli K, Andersson Y, Berg T, Bjørge L, Blix E, Bjerkehagen B, Brabrand S, Cameron MG, Dalhaug A, Dietzel D, Dønnem T, Enerly E, Flobak Å, Fluge S, Gilje B, Gjertsen BT, Grønberg BH, Grønås K, Guren T, Hamre H, Haug Å, Heinrich D et al. (2022)
Improving public cancer care by implementing precision medicine in Norway: IMPRESS-Norway
J Transl Med, 20 (1), 225
DOI 10.1186/s12967-022-03432-5, PubMed 35568909

Torgersen K, Rahman Z, Bahrami S, Hindley GFL, Parker N, Frei O, Shadrin A, O'Connell KS, Tesli M, Smeland OB, Munkhaugen J, Djurovic S, Dammen T, Andreassen OA (2022)
Shared genetic loci between depression and cardiometabolic traits
PLoS Genet, 18 (5), e1010161 (in press)
DOI 10.1371/journal.pgen.1010161, PubMed 35560157

Fan CC, Loughnan R, Makowski C, Pecheva D, Chen CH, Hagler DJ, Thompson WK, Parker N, van der Meer D, Frei O, Andreassen OA, Dale AM (2022)
Multivariate genome-wide association study on tissue-sensitive diffusion metrics highlights pathways that shape the human brain
Nat Commun, 13 (1), 2423
DOI 10.1038/s41467-022-30110-3, PubMed 35505052

Taskén K, Russnes HEG, Aas E, Bjørge L, Blix ES, CONNECT Public–Private Partnership Consortium, Enerly E, Fagereng GL, Flobak Å, Gilje B, Gjertsen BT, Guren TK, Heix J, Hovig E, Hovland R, InPreD-Norway and National Molecular Tumor Board Consortium, IMPRESS-Norway Consortium, Lønning PE, Meza-Zepeda LA, Mæhle PM, Nilsen HL, Thoresen SØ, Widerberg K, Smeland S, Helland Å (2022)
A national precision cancer medicine implementation initiative for Norway
Nat Med, 28 (5), 885-887
DOI 10.1038/s41591-022-01777-4, PubMed 35513529

Khadse A, Haakensen VD, Silwal-Pandit L, Hamfjord J, Micke P, Botling J, Brustugun OT, Lingjærde OC, Helland Å, Kure EH (2022)
Prognostic Significance of the Loss of Heterozygosity of KRAS in Early-Stage Lung Adenocarcinoma
Front Oncol, 12, 873532
DOI 10.3389/fonc.2022.873532, PubMed 35574381

Saevarsdottir S, Stefansdottir L, Sulem P, Thorleifsson G, Ferkingstad E, Rutsdottir G, Glintborg B, Westerlind H, Grondal G, Loft IC, Sorensen SB, Lie BA, Brink M, Ärlestig L, Arnthorsson AO, Baecklund E, Banasik K, Bank S, Bjorkman LI, Ellingsen T, Erikstrup C, Frei O, Gjertsson I, Gudbjartsson DF, Gudjonsson SA et al. (2022)
Multiomics analysis of rheumatoid arthritis yields sequence variants that have large effects on risk of the seropositive subset
Ann Rheum Dis (in press)
DOI 10.1136/annrheumdis-2021-221754, PubMed 35470158

Wolowczyk C, Neckmann U, Aure MR, Hall M, Johannessen B, Zhao S, Skotheim RI, Andersen SB, Zwiggelaar R, Steigedal TS, Lingjærde OC, Sahlberg KK, Almaas E, Bjørkøy G (2022)
NRF2 drives an oxidative stress response predictive of breast cancer
Free Radic Biol Med, 184, 170-184
DOI 10.1016/j.freeradbiomed.2022.03.029, PubMed 35381325

Trubetskoy V, Pardiñas AF, Qi T, Panagiotaropoulou G, Awasthi S, Bigdeli TB, Bryois J, Chen CY, Dennison CA, Hall LS, Lam M, Watanabe K, Frei O, Ge T, Harwood JC, Koopmans F, Magnusson S, Richards AL, Sidorenko J, Wu Y, Zeng J, Grove J, Kim M, Li Z, Voloudakis G et al. (2022)
Mapping genomic loci implicates genes and synaptic biology in schizophrenia
Nature, 604 (7906), 502-508
DOI 10.1038/s41586-022-04434-5, PubMed 35396580

Bahrami S, Hindley G, Winsvold BS, O'Connell KS, Frei O, Shadrin A, Cheng W, Bettella F, Rødevand L, Odegaard KJ, Fan CC, Pirinen MJ, Hautakangas HM, , Dale AM, Djurovic S, Smeland OB, Andreassen OA (2022)
Dissecting the shared genetic basis of migraine and mental disorders using novel statistical tools
Brain, 145 (1), 142-153
DOI 10.1093/brain/awab267, PubMed 34273149

Dahal-Koirala S, Balaban G, Neumann RS, Scheffer L, Lundin KEA, Greiff V, Sollid LM, Qiao SW, Sandve GK (2022)
TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences
Brief Bioinform, 23 (2)
DOI 10.1093/bib/bbab566, PubMed 35062022

Jorgensen M, Halkjelsvik T, Liestol K (2022)
When should we (not) use the mean magnitude of relative error (MMRE) as an error measure in software development effort estimation?
Inf. Softw. Technol., 143, 106784
DOI 10.1016/j.infsof.2021.106784

Strømme JM, Johannessen B, Kidd SG, Bogaard M, Carm KT, Zhang X, Sveen A, Mathelier A, Lothe RA, Axcrona U, Axcrona K, Skotheim RI (2022)
Expressed prognostic biomarkers for primary prostate cancer independent of multifocality and transcriptome heterogeneity
Cancer Gene Ther (in press)
DOI 10.1038/s41417-022-00444-7, PubMed 35194199

Fontugne J, Cai PY, Alnajar H, Bhinder B, Park K, Ye H, Beg S, Sailer V, Siddiqui J, Blattner-Johnson M, Croyle JA, Noorzad Z, Calagua C, MacDonald TY, Axcrona U, Bogaard M, Axcrona K, Scherr DS, Sanda MG, Johannessen B, Chinnaiyan AM, Elemento O, Skotheim RI, Rubin MA, Barbieri CE et al. (2022)
Collision tumors revealed by prospectively assessing subtype-defining molecular alterations in 904 individual prostate cancer foci
JCI Insight, 7 (4)
DOI 10.1172/jci.insight.155309, PubMed 35050902

Umu SU, Langseth H, Zuber V, Helland Å, Lyle R, Rounge TB (2022)
Serum RNAs can predict lung cancer up to 10 years prior to diagnosis
Elife, 11
DOI 10.7554/eLife.71035, PubMed 35147498

van der Meer D, Shadrin AA, O'Connell K, Bettella F, Djurovic S, Wolfers T, Alnæs D, Agartz I, Smeland OB, Melle I, Sánchez JM, Linden DEJ, Dale AM, Westlye LT, Andreassen OA, Frei O, Kaufmann T (2022)
Boosting Schizophrenia Genetics by Utilizing Genetic Overlap With Brain Morphology
Biol Psychiatry (in press)
DOI 10.1016/j.biopsych.2021.12.007, PubMed 35164939

Blandino A, Scherer D, Rounge TB, Umu SU, Boekstegers F, Barahona Ponce C, Marcelain K, Gárate-Calderón V, Waldenberger M, Morales E, Rojas A, Munoz C, Retamales J, de Toro G, Barajas O, Rivera MT, Cortés A, Loader D, Saavedra J, Gutiérrez L, Ortega A, Bertrán ME, Gabler F, Campos M, Alvarado J et al. (2022)
Identification of Circulating lncRNAs Associated with Gallbladder Cancer Risk by Tissue-Based Preselection, Cis-eQTL Validation, and Analysis of Association with Genotype-Based Expression
Cancers (Basel), 14 (3)
DOI 10.3390/cancers14030634, PubMed 35158906

Høye E, Fromm B, Böttger PHM, Domanska D, Torgunrud A, Lund-Andersen C, Abrahamsen TW, Fretland ÅA, Dagenborg VJ, Lorenz S, Edwin B, Hovig E, Flatmark K (2022)
A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer
NAR Cancer, 4 (1), zcab051
DOI 10.1093/narcan/zcab051, PubMed 35047825

Skotheim RI, Axcrona U, Axcrona K (2022)
Re: Fibroblast Growth Factor Receptor 1 Drives the Metastatic Progression of Prostate Cancer
Eur Urol, 81 (4), 431
DOI 10.1016/j.eururo.2021.12.031, PubMed 35031159

Fromm B, Høye E, Domanska D, Zhong X, Aparicio-Puerta E, Ovchinnikov V, Umu SU, Chabot PJ, Kang W, Aslanzadeh M, Tarbier M, Mármol-Sánchez E, Urgese G, Johansen M, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ (2022)
MirGeneDB 2.1: toward a complete sampling of all major animal phyla
Nucleic Acids Res, 50 (D1), D204-D210
DOI 10.1093/nar/gkab1101, PubMed 34850127

Paulsen J, Collas P (2022)
Modeling the 3D Genome Using Hi-C and Nuclear Lamin-Genome Contacts
Methods Mol Biol, 2301, 337-352
DOI 10.1007/978-1-0716-1390-0_18, PubMed 34415545

Akbar R, Robert PA, Weber CR, Widrich M, Frank R, Pavlović M, Scheffer L, Chernigovskaya M, Snapkov I, Slabodkin A, Mehta BB, Miho E, Lund-Johansen F, Andersen JT, Hochreiter S, Hobæk Haff I, Klambauer G, Sandve GK, Greiff V (2022)
In silico proof of principle of machine learning-based antibody design at unconstrained scale
MAbs, 14 (1), 2031482
DOI 10.1080/19420862.2022.2031482, PubMed 35377271

Publications 2021

Balaban G, Halliday BP, Hammersley D, Rinaldi CA, Prasad SK, Bishop MJ, Lamata P (2021)
Left ventricular shape predicts arrhythmic risk in fibrotic dilated cardiomyopathy
Europace (in press)
DOI 10.1093/europace/euab306, PubMed 34907426

van der Meer D, Kaufmann T, Shadrin AA, Makowski C, Frei O, Roelfs D, Monereo-Sánchez J, Linden DEJ, Rokicki J, Alnæs D, de Leeuw C, Thompson WK, Loughnan R, Fan CC, Westlye LT, Andreassen OA, Dale AM (2021)
The genetic architecture of human cortical folding
Sci Adv, 7 (51), eabj9446
DOI 10.1126/sciadv.abj9446, PubMed 34910505

Lien TG, Ohnstad HO, Lingjærde OC, Vallon-Christersson J, Aaserud M, Sveli MAT, Borg Å, Osbreac OBO, Garred Ø, Borgen E, Naume B, Russnes H, Sørlie T (2021)
Sample Preparation Approach Influences PAM50 Risk of Recurrence Score in Early Breast Cancer
Cancers (Basel), 13 (23)
DOI 10.3390/cancers13236118, PubMed 34885228

Simões RF, Pino R, Moreira-Soares M, Kovarova J, Neuzil J, Travasso R, Oliveira PJ, Cunha-Oliveira T, Pereira FB (2021)
Quantitative analysis of neuronal mitochondrial movement reveals patterns resulting from neurotoxicity of rotenone and 6-hydroxydopamine
FASEB J, 35 (12), e22024
DOI 10.1096/fj.202100899R, PubMed 34751984

Jorgensen M, Bergersen GR, Liestol K (2021)
Relations Between Effort Estimates, Skill Indicators, and Measured Programming Skill
IEEE Trans. Softw. Eng., 47 (12), 2892-2906
DOI 10.1109/TSE.2020.2973638

Slabodkin A, Chernigovskaya M, Mikocziova I, Akbar R, Scheffer L, Pavlović M, Bashour H, Snapkov I, Mehta BB, Weber CR, Gutierrez-Marcos J, Sollid LM, Haff IH, Sandve GK, Robert PA, Greiff V (2021)
Individualized VDJ recombination predisposes the available Ig sequence space
Genome Res (in press)
DOI 10.1101/gr.275373.121, PubMed 34815307

Isaksen KT, Mastroianni MA, Rinde M, Rusten LS, Barzenje DA, Ramslien LF, Slaaen M, Jerm MB, Smeland EB, Rostoft S, Liestøl K, Brodtkorb M, Holte H (2021)
A simplified frailty score predicts survival and can aid treatment-intensity decisions in older patients with DLBCL
Blood Adv, 5 (22), 4771-4782
DOI 10.1182/bloodadvances.2021004777, PubMed 34543384

Pavlovic M, Scheffer L, Motwani K, Kanduri C, Kompova R, Vazov N, Waagan K, Bernal FLM, Costa AA, Corrie B, Akbar R, Al Hajj GS, Balaban G, Brusko TM, Chernigovskaya M, Christley S, Cowell LG, Frank R, Grytten I, Gundersen S, Haff IH, Hovig E, Hsieh PH, Klambauer G, Kuijjer ML et al. (2021)
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires
Nat. Mach. Intell., 3 (11), 936-+
DOI 10.1038/s42256-021-00413-z

Falk RS, Mariampillai JE, Prestgaard EE, Heir T, Bodegård J, Robsahm TE, Grundvold I, Skretteberg PT, Engeseth K, Bjornholt JV, Stavem K, Liestøl K, Sandvik L, Thaulow E, Erikssen G, Kjeldsen SE, Gjesdal K, Erikssen JE (2021)
The Oslo Ischaemia Study: cohort profile
BMJ Open, 11 (10), e049111
DOI 10.1136/bmjopen-2021-049111, PubMed 34645662

Bjaanæs MM, Nilsen G, Halvorsen AR, Russnes HG, Solberg S, Jørgensen L, Brustugun OT, Lingjærde OC, Helland Å (2021)
Whole genome copy number analyses reveal a highly aberrant genome in TP53 mutant lung adenocarcinoma tumors
BMC Cancer, 21 (1), 1089
DOI 10.1186/s12885-021-08811-7, PubMed 34625038

Yao Y, Wyrozżemski Ł, Lundin KEA, Sandve GK, Qiao SW (2021)
Differential expression profile of gluten-specific T cells identified by single-cell RNA-seq
PLoS One, 16 (10), e0258029
DOI 10.1371/journal.pone.0258029, PubMed 34618841

Pihlstrøm L, Fan CC, Frei O, Tan M, Karunamuni RA, Blauwendraat C, Bandres-Ciga S, Gan-Or Z, Grosset DG, International Parkinson's Disease Genomics Consortium (IPDGC), Dale AM, Seibert TM, Andreassen OA (2021)
Genetic Stratification of Age-Dependent Parkinson's Disease Risk by Polygenic Hazard Score
Mov Disord, 37 (1), 62-69
DOI 10.1002/mds.28808, PubMed 34612543

Wiström ED, O'Connell KS, Karadag N, Bahrami S, Hindley GFL, Lin A, Cheng W, Steen NE, Shadrin A, Frei O, Djurovic S, Dale AM, Andreassen OA, Smeland OB (2021)
Genome-wide analysis reveals genetic overlap between alcohol use behaviours, schizophrenia and bipolar disorder and identifies novel shared risk loci
Addiction, 117 (3), 600-610
DOI 10.1111/add.15680, PubMed 34472679

Mariampillai JE, Prestgaard EE, Kjeldsen SE, Liestøl K, Grundvold I, Bodegård J, Gjesdal K, Erikssen JE, Skretteberg PT (2021)
Novel insights into stroke risk beyond resting and maximal bicycle exercise systolic blood pressure
J Hypertens, 39 (10), 2022-2029
DOI 10.1097/HJH.0000000000002894, PubMed 34102659

Hindley G, Bahrami S, Steen NE, O'Connell KS, Frei O, Shadrin A, Bettella F, Rødevand L, Fan CC, Dale AM, Djurovic S, Smeland OB, Andreassen OA (2021)
Characterising the shared genetic determinants of bipolar disorder, schizophrenia and risk-taking
Transl Psychiatry, 11 (1), 466
DOI 10.1038/s41398-021-01576-4, PubMed 34497263

Sveen A, Johannessen B, Eilertsen IA, Røsok BI, Gulla M, Eide PW, Bruun J, Kryeziu K, Meza-Zepeda LA, Myklebost O, Bjørnbeth BA, Skotheim RI, Nesbakken A, Lothe RA (2021)
The expressed mutational landscape of microsatellite stable colorectal cancers
Genome Med, 13 (1), 142
DOI 10.1186/s13073-021-00955-2, PubMed 34470667

Kværner AS, Birkeland E, Bucher-Johannessen C, Vinberg E, Nordby JI, Kangas H, Bemanian V, Ellonen P, Botteri E, Natvig E, Rognes T, Hovig E, Lyle R, Ambur OH, de Vos WM, Bultman S, Hjartåker A, Landberg R, Song M, Blix HS, Ursin G, Randel KR, de Lange T, Hoff G, Holme Ø et al. (2021)
The CRCbiome study: a large prospective cohort study examining the role of lifestyle and the gut microbiome in colorectal cancer screening participants
BMC Cancer, 21 (1), 930
DOI 10.1186/s12885-021-08640-8, PubMed 34407780

Nakken S, Saveliev V, Hofmann O, Møller P, Myklebost O, Hovig E (2021)
Cancer Predisposition Sequencing Reporter (CPSR): A flexible variant report engine for high-throughput germline screening in cancer
Int J Cancer, 149 (11), 1955-1960
DOI 10.1002/ijc.33749, PubMed 34310709

Rødevand L, Bahrami S, Frei O, Chu Y, Shadrin A, O'Connell KS, Smeland OB, Elvsåshagen T, Hindley GFL, Djurovic S, Dale AM, Lagerberg TV, Steen NE, Andreassen OA (2021)
Extensive bidirectional genetic overlap between bipolar disorder and cardiovascular disease phenotypes
Transl Psychiatry, 11 (1), 407
DOI 10.1038/s41398-021-01527-z, PubMed 34301917

Pluta J, Pyle LC, Nead KT, Wilf R, Li M, Mitra N, Weathers B, D'Andrea K, Almstrup K, Anson-Cartwright L, Benitez J, Brown CD, Chanock S, Chen C, Cortessis VK, Ferlin A, Foresta C, Gamulin M, Gietema JA, Grasso C, Greene MH, Grotmol T, Hamilton RJ, Haugen TB, Hauser R et al. (2021)
Identification of 22 susceptibility loci associated with testicular germ cell tumors
Nat Commun, 12 (1), 4487
DOI 10.1038/s41467-021-24334-y, PubMed 34301922

Bergland OU, Halvorsen LV, Søraas CL, Hjørnholm U, Kjær VN, Rognstad S, Brobak KM, Aune A, Olsen E, Fauchald YM, Heimark S, Thorstensen CW, Liestøl K, Solbu MD, Gerdts E, Mo R, Rostrup M, Kjeldsen SE, Høieggen A, Opdal MS, Larstorp ACK, Fadl Elmula FEM (2021)
Detection of Nonadherence to Antihypertensive Treatment by Measurements of Serum Drug Concentrations
Hypertension, 78 (3), 617-628
DOI 10.1161/HYPERTENSIONAHA.121.17514, PubMed 34275336

Rye IH, Huse K, Josefsson SE, Kildal W, Danielsen HE, Schlichting E, Garred Ø, Riis ML, Osbreac, Lingjaerde OC, Myklebust JH, Russnes HG (2021)
Breast cancer metastasis: immune profiling of lymph nodes reveals exhaustion of effector T cells and immunosuppression
Mol Oncol, 16 (1), 88-103
DOI 10.1002/1878-0261.13047, PubMed 34165864

Mahé F, Czech L, Stamatakis A, Quince C, de Vargas C, Dunthorn M, Rognes T (2021)
Swarm v3: towards tera-scale amplicon clustering
Bioinformatics, 38 (1), 267-269
DOI 10.1093/bioinformatics/btab493, PubMed 34244702

Monereo-Sánchez J, Schram MT, Frei O, O'Connell K, Shadrin AA, Smeland OB, Westlye LT, Andreassen OA, Kaufmann T, Linden DEJ, van der Meer D (2021)
Genetic Overlap Between Alzheimer's Disease and Depression Mapped Onto the Brain
Front Neurosci, 15, 653130
DOI 10.3389/fnins.2021.653130, PubMed 34290577

Ellingsen EB, Mangsbo SM, Hovig E, Gaudernack G (2021)
Telomerase as a Target for Therapeutic Cancer Vaccines and Considerations for Optimizing Their Clinical Potential
Front Immunol, 12, 682492
DOI 10.3389/fimmu.2021.682492, PubMed 34290704

Liyakat Ali TM, Brunet A, Collas P, Paulsen J (2021)
TAD cliques predict key features of chromatin organization
BMC Genomics, 22 (1), 499
DOI 10.1186/s12864-021-07815-8, PubMed 34217222

Dominguez-Valentin M, Plazzer JP, Sampson JR, Engel C, Aretz S, Jenkins MA, Sunde L, Bernstein I, Capella G, Balaguer F, Macrae F, Winship IM, Thomas H, Evans DG, Burn J, Greenblatt M, de Vos Tot Nederveen Cappel WH, Sijmons RH, Nielsen M, Bertario L, Bonanni B, Tibiletti MG, Cavestro GM, Lindblom A, Valle AD et al. (2021)
No Difference in Penetrance between Truncating and Missense/Aberrant Splicing Pathogenic Variants in MLH1 and MSH2: A Prospective Lynch Syndrome Database Study
J Clin Med, 10 (13)
DOI 10.3390/jcm10132856, PubMed 34203177

Lagström S, Løvestad AH, Umu SU, Ambur OH, Nygård M, Rounge TB, Christiansen IK (2021)
HPV16 and HPV18 type-specific APOBEC3 and integration profiles in different diagnostic categories of cervical samples
Tumour Virus Res, 12, 200221
DOI 10.1016/j.tvr.2021.200221, PubMed 34175494

Torgersen K, Bahrami S, Frei O, Shadrin A, Connell KSO, Smeland OB, Munkhaugen J, Djurovic S, Dammen T, Andreassen OA (2021)
Shared genetic architecture between neuroticism, coronary artery disease and cardiovascular risk factors
Transl Psychiatry, 11 (1), 368
DOI 10.1038/s41398-021-01466-9, PubMed 34226488

Brägelmann J, Barahona Ponce C, Marcelain K, Roessler S, Goeppert B, Gallegos I, Colombo A, Sanhueza V, Morales E, Rivera MT, de Toro G, Ortega A, Müller B, Gabler F, Scherer D, Waldenberger M, Reischl E, Boekstegers F, Garate-Calderon V, Umu SU, Rounge TB, Popanda O, Lorenzo Bermejo J (2021)
Epigenome-Wide Analysis of Methylation Changes in the Sequence of Gallstone Disease, Dysplasia, and Gallbladder Cancer
Hepatology, 73 (6), 2293-2310
DOI 10.1002/hep.31585, PubMed 33020926

Kidd SG, Carm KT, Bogaard M, Olsen LG, Bakken AC, Løvf M, Lothe RA, Axcrona K, Axcrona U, Skotheim RI (2021)
High expression of SCHLAP1 in primary prostate cancer is an independent predictor of biochemical recurrence, despite substantial heterogeneity
Neoplasia, 23 (6), 634-641
DOI 10.1016/j.neo.2021.05.012, PubMed 34107378

Ramberg H, Richardsen E, de Souza GA, Rakaee M, Stensland ME, Braadland PR, Nygård S, Ögren O, Guldvik IJ, Berge V, Svindland A, Taskén KA, Andersen S (2021)
Proteomic analyses identify major vault protein as a prognostic biomarker for fatal prostate cancer
Carcinogenesis, 42 (5), 685-693
DOI 10.1093/carcin/bgab015, PubMed 33609362

Hamfjord J, Guren TK, Glimelius B, Sorbye H, Pfeiffer P, Dajani O, Lingjaerde OC, Tveit KM, Pallisgaard N, Spindler KG, Kure EH (2021)
Clinicopathological factors associated with tumour-specific mutation detection in plasma of patients with RAS-mutated or BRAF-mutated metastatic colorectal cancer
Int J Cancer, 149 (6), 1385-1397
DOI 10.1002/ijc.33672, PubMed 33961700

Eriksson AM, Leikfoss IS, Abrahamsen G, Sundvold V, Isom MM, Keshari PK, Rognes T, Landsverk OJB, Bos SD, Harbo HF, Spurkland A, Berge T (2021)
Exploring the role of the multiple sclerosis susceptibility gene CLEC16A in T cells
Scand J Immunol, 94 (1), e13050
DOI 10.1111/sji.13050, PubMed 34643957

Elvsåshagen T, Shadrin A, Frei O, van der Meer D, Bahrami S, Kumar VJ, Smeland O, Westlye LT, Andreassen OA, Kaufmann T (2021)
The genetic architecture of the human thalamus and its overlap with ten common brain disorders
Nat Commun, 12 (1), 2909
DOI 10.1038/s41467-021-23175-z, PubMed 34006833

Mattingsdal M, Ebenesersdóttir SS, Moore KHS, Andreassen OA, Hansen TF, Werge T, Kockum I, Olsson T, Alfredsson L, Helgason A, Stefánsson K, Hovig E (2021)
The genetic structure of Norway
Eur J Hum Genet, 29 (11), 1710-1718
DOI 10.1038/s41431-021-00899-6, PubMed 34002043

Wojewodzic MW, Leithaug M, Lauritzen M, Lyle R, Haglund S, Rubin CJ, Ewels PA, Grotmol T, Rounge TB (2021)
Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes
Clin Epigenetics, 13 (1), 107
DOI 10.1186/s13148-021-01097-3, PubMed 33980276

Aamdal E, Inderberg EM, Ellingsen EB, Rasch W, Brunsvig PF, Aamdal S, Heintz KM, Vodák D, Nakken S, Hovig E, Nyakas M, Guren TK, Gaudernack G (2021)
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, 12, 663865
DOI 10.3389/fimmu.2021.663865, PubMed 34046035

Lemma RB, Ledsaak M, Fuglerud BM, Sandve GK, Eskeland R, Gabrielsen OS (2021)
Chromatin occupancy and target genes of the haematopoietic master transcription factor MYB
Sci Rep, 11 (1), 9008
DOI 10.1038/s41598-021-88516-w, PubMed 33903675

Dube Mandishora RS, Rounge TB, Fitzpatrick M, Christiansen IK, Ambur OH, Lagström S, Stray-Pedersen B, Tommasino M, Palefsky J, Chirenje ZM (2021)
Self-collected and clinician-collected anal swabs show modest agreement for HPV genotyping
PLoS One, 16 (4), e0250426
DOI 10.1371/journal.pone.0250426, PubMed 33901223

Nakken S, Lilleby W, Switlyk MD, Knudsen KE, Lilleby O, Zhao S, Kaveh F, Ekstrøm PO, Urbanucci A, Hovig E (2021)
The Quandary of DNA-Based Treatment Assessment in De Novo Metastatic Prostate Cancer in the Era of Precision Oncology
J Pers Med, 11 (5)
DOI 10.3390/jpm11050330, PubMed 33922147

Dahal-Koirala S, Risnes LF, Neumann RS, Christophersen A, Lundin KEA, Sandve GK, Qiao SW, Sollid LM (2021)
Comprehensive Analysis of CDR3 Sequences in Gluten-Specific T-Cell Receptors Reveals a Dominant R-Motif and Several New Minor Motifs
Front Immunol, 12, 639672
DOI 10.3389/fimmu.2021.639672, PubMed 33927715

Gundersen S, Boddu S, Capella-Gutierrez S, Drabløs F, Fernández JM, Kompova R, Taylor K, Titov D, Zerbino D, Hovig E (2021)
Recommendations for the FAIRification of genomic track metadata
F1000Res, 10
DOI 10.12688/f1000research.28449.1, PubMed 34249331

Maximov II, van der Meer D, de Lange AG, Kaufmann T, Shadrin A, Frei O, Wolfers T, Westlye LT (2021)
Fast qualitY conTrol meThod foR derIved diffUsion Metrics (YTTRIUM) in big data analysis: U.K. Biobank 18,608 example
Hum Brain Mapp, 42 (10), 3141-3155
DOI 10.1002/hbm.25424, PubMed 33788350

Snipen L, Angell IL, Rognes T, Rudi K (2021)
Reduced metagenome sequencing for strain-resolution taxonomic profiles
Microbiome, 9 (1), 79
DOI 10.1186/s40168-021-01019-8, PubMed 33781324

Seppälä TT, Dominguez-Valentin M, Crosbie EJ, Engel C, Aretz S, Macrae F, Winship I, Capella G, Thomas H, Hovig E, Nielsen M, Sijmons RH, Bertario L, Bonanni B, Tibiletti MG, Cavestro GM, Mints M, Gluck N, Katz L, Heinimann K, Vaccaro CA, Green K, Lalloo F, Hill J, Schmiegel W et al. (2021)
Uptake of hysterectomy and bilateral salpingo-oophorectomy in carriers of pathogenic mismatch repair variants: a Prospective Lynch Syndrome Database report
Eur J Cancer, 148, 124-133
DOI 10.1016/j.ejca.2021.02.022, PubMed 33743481

Akbar R, Robert PA, Pavlović M, Jeliazkov JR, Snapkov I, Slabodkin A, Weber CR, Scheffer L, Miho E, Haff IH, Haug DTT, Lund-Johansen F, Safonova Y, Sandve GK, Greiff V (2021)
A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding
Cell Rep, 34 (11), 108856
DOI 10.1016/j.celrep.2021.108856, PubMed 33730590

Balaban G, Grytten I, Rand KD, Scheffer L, Sandve GK (2021)
Ten simple rules for quick and dirty scientific programming
PLoS Comput Biol, 17 (3), e1008549
DOI 10.1371/journal.pcbi.1008549, PubMed 33705383

Jiang X, Bergquist A, Löscher BS, Venkatesh G, Mold JE, Holm K, Laerdahl JK, Skånland SS, Maleki KT, Cornillet M, Taskén K, Franke A, Karlsen TH, Björkström NK, Melum E (2021)
A heterozygous germline CD100 mutation in a family with primary sclerosing cholangitis
Sci Transl Med, 13 (582)
DOI 10.1126/scitranslmed.abb0036, PubMed 33627483

Ask EH, Tschan-Plessl A, Gjerdingen TJ, Saetersmoen ML, Hoel HJ, Wiiger MT, Olweus J, Wahlin BE, Lingjaerde OC, Horowitz A, Cashen AF, Watkins M, Fehniger TA, Holte H, Kolstad A, Malmberg KJ (2021)
A Systemic Protein Deviation Score Linked to PD-1(+) CD8(+) T Cell Expansion That Predicts Overall Survival in Diffuse Large B Cell Lymphoma
Med, 2 (2), 180-+
DOI 10.1016/j.medj.2020.10.006

Kleppe A, Skrede OJ, De Raedt S, Liestøl K, Kerr DJ, Danielsen HE (2021)
Designing deep learning studies in cancer diagnostics
Nat Rev Cancer, 21 (3), 199-211
DOI 10.1038/s41568-020-00327-9, PubMed 33514930

Haugen MH, Lingjærde OC, Hedenfalk I, Garred Ø, Borgen E, Loman N, Hatschek T, Børresen-Dale AL, Naume B, Mills GB, Mælandsmo GM, Engebraaten O (2021)
Protein Signature Predicts Response to Neoadjuvant Treatment With Chemotherapy and Bevacizumab in HER2-Negative Breast Cancers
JCO Precis Oncol, 5
DOI 10.1200/PO.20.00086, PubMed 34036235

Kanduri C, Sandve GK, Hovig E, De S, Layer RM (2021)
Editorial: Genomic Colocalization and Enrichment Analyses
Front Genet, 11, 617876
DOI 10.3389/fgene.2020.617876, PubMed 33574832

Liestøl K, Kleppe A, Skrede OJ, De Raedt S, Kerr DJ, Danielsen HE (2021)
Deep learning and cancer biomarkers: recognising lead-time bias - Authors' reply
Lancet, 397 (10270), 194-195
DOI 10.1016/S0140-6736(21)00035-0, PubMed 33453777

Safavi S, Larouche A, Zahn A, Patenaude AM, Domanska D, Dionne K, Rognes T, Dingler F, Kang SK, Liu Y, Johnson N, Hébert J, Verdun RE, Rada CA, Vega F, Nilsen H, Noia JMD (2021)
Erratum: The uracil-DNA glycosylase UNG protects the fitness of normal and cancer B cells expressing AID
NAR Cancer, 3 (1), zcaa045
DOI 10.1093/narcan/zcaa045, PubMed 34316697

Rødevand L, Bahrami S, Frei O, Lin A, Gani O, Shadrin A, Smeland OB, Connell KSO, Elvsåshagen T, Winterton A, Quintana DS, Hindley GFL, Werner MCF, Djurovic S, Dale AM, Lagerberg TV, Steen NE, Andreassen OA (2021)
Polygenic overlap and shared genetic loci between loneliness, severe mental disorders, and cardiovascular disease risk factors suggest shared molecular mechanisms
Transl Psychiatry, 11 (1), 3
DOI 10.1038/s41398-020-01142-4, PubMed 33414458

Nikolaidis K, Kristiansen S, Plagemann T, Goebel V, Liestol K, Kankanhalli M, Traaen GM, Overland B, Akre H, Aakeroy L, Steinshamn S (2021)
Learning Realistic Patterns from Visually Unrealistic Stimuli: Generalization and Data Anonymization
J. Artif. Intell. Res., 72, 1163-1214

Publications 2020

Dominguez-Valentin M, Crosbie EJ, Engel C, Aretz S, Macrae F, Winship I, Capella G, Thomas H, Nakken S, Hovig E, Nielsen M, Sijmons RH, Bertario L, Bonanni B, Tibiletti MG, Cavestro GM, Mints M, Gluck N, Katz L, Heinimann K, Vaccaro CA, Green K, Lalloo F, Hill J, Schmiegel W et al. (2020)
Risk-reducing hysterectomy and bilateral salpingo-oophorectomy in female heterozygotes of pathogenic mismatch repair variants: a Prospective Lynch Syndrome Database report
Genet Med, 23 (4), 705-712
DOI 10.1038/s41436-020-01029-1, PubMed 33257847

Di Stefano M, Paulsen J, Jost D, Marti-Renom MA (2020)
4D nucleome modeling
Curr Opin Genet Dev, 67, 25-32
DOI 10.1016/j.gde.2020.10.004, PubMed 33253996

Zhao S, Agafonov O, Azab A, Stokowy T, Hovig E (2020)
Accuracy and efficiency of germline variant calling pipelines for human genome data
Sci Rep, 10 (1), 20222
DOI 10.1038/s41598-020-77218-4, PubMed 33214604

Yao Y, Zia A, Neumann RS, Pavlovic M, Balaban G, Lundin KEA, Sandve GK, Qiao SW (2020)
T cell receptor repertoire as a potential diagnostic marker for celiac disease
Clin Immunol, 222, 108621
DOI 10.1016/j.clim.2020.108621, PubMed 33197618

Balaban G, Halliday BP, Porter B, Bai W, Nygåard S, Owen R, Hatipoglu S, Ferreira ND, Izgi C, Tayal U, Corden B, Ware J, Pennell DJ, Rueckert D, Plank G, Rinaldi CA, Prasad SK, Bishop MJ (2020)
Late-Gadolinium Enhancement Interface Area and Electrophysiological Simulations Predict Arrhythmic Events in Patients With Nonischemic Dilated Cardiomyopathy
JACC Clin Electrophysiol, 7 (2), 238-249
DOI 10.1016/j.jacep.2020.08.036, PubMed 33602406

Burton J, Umu SU, Langseth H, Grotmol T, Grimsrud TK, Haugen TB, Rounge TB (2020)
Serum RNA Profiling in the 10-Years Period Prior to Diagnosis of Testicular Germ Cell Tumor
Front Oncol, 10, 574977
DOI 10.3389/fonc.2020.574977, PubMed 33251139

Salgado D, Armean IM, Baudis M, Beltran S, Capella-Gutierrez S, Carvalho-Silva D, Dominguez Del Angel V, Dopazo J, Furlong LI, Gao B, Garcia L, Gerloff D, Gut I, Gyenesei A, Habermann N, Hancock JM, Hanauer M, Hovig E, Johansson LF, Keane T, Korbel J, Lauer KB, Laurie S, Leskošek B, Lloyd D et al. (2020)
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research
F1000Res, 9
DOI 10.12688/f1000research.24887.1, PubMed 34367618

Farooq A, Grønmyr S, Ali O, Rognes T, Scheffler K, Bjørås M, Wang J (2020)
HMST-Seq-Analyzer: A new python tool for differential methylation and hydroxymethylation analysis in various DNA methylation sequencing data
Comput Struct Biotechnol J, 18, 2877-2889
DOI 10.1016/j.csbj.2020.09.038, PubMed 33163148

Salvatore S, Dagestad Rand K, Grytten I, Ferkingstad E, Domanska D, Holden L, Gheorghe M, Mathelier A, Glad I, Kjetil Sandve G (2020)
Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis
Brief Bioinform, 21 (5), 1523-1530
DOI 10.1093/bib/bbz083, PubMed 31624847

Figueiredo RAO, Kajantie E, Neuvonen PJ, Rounge TB, Weiderpass E, Viljakainen H (2020)
Lifetime antimicrobial use is associated with weight status in early adolescence-A register-based cohort study
Pediatr Obes, 16 (3), e12727
DOI 10.1111/ijpo.12727, PubMed 32959492

Shadrin AA, Frei O, Smeland OB, Bettella F, O'Connell KS, Gani O, Bahrami S, Uggen TKE, Djurovic S, Holland D, Andreassen OA, Dale AM (2020)
Phenotype-specific differences in polygenicity and effect size distribution across functional annotation categories revealed by AI-MiXeR
Bioinformatics, 36 (18), 4749-4756
DOI 10.1093/bioinformatics/btaa568, PubMed 32539089

Mirza Y, Prestgaard EE, Selmer R, Liestøl K, Grundvold I, Erikssen JE, Kjeldsen SE, Gjesdal K (2020)
Ten-year prediction of cardiovascular disease in healthy Norwegian men, based on NORRISK-2
Tidsskr Nor Laegeforen, 140 (12)
DOI 10.4045/tidsskr.20.0089, PubMed 32900157

Scherer D, Dávila López MD, Goeppert B, Abrahamsson S, González Silos RG, Nova I, Marcelain K, Roa JC, Ibberson D, Umu SU, Rounge TB, Roessler S, Bermejo JL (2020)
RNA Sequencing of Hepatobiliary Cancer Cell Lines: Data and Applications to Mutational and Transcriptomic Profiling
Cancers (Basel), 12 (9)
DOI 10.3390/cancers12092510, PubMed 32899426

Hoff AM, Kraggerud SM, Alagaratnam S, Berg KCG, Johannessen B, Høland M, Nilsen G, Lingjærde OC, Andrews PW, Lothe RA, Skotheim RI (2020)
Frequent copy number gains of SLC2A3 and ETV1 in testicular embryonal carcinomas
Endocr Relat Cancer, 27 (9), 457-468
DOI 10.1530/ERC-20-0064, PubMed 32580154

Safavi S, Larouche A, Zahn A, Patenaude AM, Domanska D, Dionne K, Rognes T, Dingler F, Kang SK, Liu Y, Johnson N, Hébert J, Verdun RE, Rada CA, Vega F, Nilsen H, Di Noia JM (2020)
The uracil-DNA glycosylase UNG protects the fitness of normal and cancer B cells expressing AID
NAR Cancer, 2 (3), zcaa019
DOI 10.1093/narcan/zcaa019, PubMed 33554121

Raju SC, Viljakainen H, Figueiredo RAO, Neuvonen PJ, Eriksson JG, Weiderpass E, Rounge TB (2020)
Antimicrobial drug use in the first decade of life influences saliva microbiota diversity and composition
Microbiome, 8 (1), 121
DOI 10.1186/s40168-020-00893-y, PubMed 32825849

Gurwitz KT, Singh Gaur P, Bellis LJ, Larcombe L, Alloza E, Balint BL, Botzki A, Dimec J, Dominguez Del Angel V, Fernandes PL, Korpelainen E, Krause R, Kuzak M, Le Pera L, Leskošek B, Lindvall JM, Marek D, Martinez PA, Muyldermans T, Nygård S, Palagi PM, Peterson H, Psomopoulos F, Spiwok V, van Gelder CWG et al. (2020)
A framework to assess the quality and impact of bioinformatics training across ELIXIR
PLoS Comput Biol, 16 (7), e1007976
DOI 10.1371/journal.pcbi.1007976, PubMed 32702016

Dominguez-Valentin M, Seppälä TT, Engel C, Aretz S, Macrae F, Winship I, Capella G, Thomas H, Hovig E, Nielsen M, Sijmons RH, Bertario L, Bonanni B, Tibiletti MG, Cavestro GM, Mints M, Gluck N, Katz L, Heinimann K, Vaccaro CA, Green K, Lalloo F, Hill J, Schmiegel W, Vangala D et al. (2020)
Risk-Reducing Gynecological Surgery in Lynch Syndrome: Results of an International Survey from the Prospective Lynch Syndrome Database
J Clin Med, 9 (7)
DOI 10.3390/jcm9072290, PubMed 32708519

van der Meer D, Frei O, Kaufmann T, Shadrin AA, Devor A, Smeland OB, Thompson WK, Fan CC, Holland D, Westlye LT, Andreassen OA, Dale AM (2020)
Understanding the genetic determinants of the brain with MOSTest
Nat Commun, 11 (1), 3512
DOI 10.1038/s41467-020-17368-1, PubMed 32665545

Myrstad M, Ihle-Hansen H, Tveita AA, Andersen EL, Nygård S, Tveit A, Berge T (2020)
National Early Warning Score 2 (NEWS2) on admission predicts severe disease and in-hospital mortality from Covid-19 - a prospective cohort study
Scand J Trauma Resusc Emerg Med, 28 (1), 66
DOI 10.1186/s13049-020-00764-3, PubMed 32660623

Gemmell PM, Gillette K, Balaban G, Rajani R, Vigmond EJ, Plank G, Bishop MJ (2020)
A computational investigation into rate-dependant vectorcardiogram changes due to specific fibrosis patterns in non-ischæmic dilated cardiomyopathy
Comput Biol Med, 123, 103895
DOI 10.1016/j.compbiomed.2020.103895, PubMed 32741753

Lavelle TJ, Alver TN, Heintz KM, Wernhoff P, Nygaard V, Nakken S, Øy GF, Bøe SL, Urbanucci A, Hovig E (2020)
Dysregulation of MITF Leads to Transformation in MC1R-Defective Melanocytes
Cancers (Basel), 12 (7)
DOI 10.3390/cancers12071719, PubMed 32605315

von der Lippe Gythfeldt H, Lien T, Tekpli X, Silwal-Pandit L, Borgen E, Garred Ø, Skjerven H, Schlichting E, Lundgren S, Wist E, Naume B, Kristensen V, Børresen-Dale AL, Lingjaerde OC, Engebraaten O (2020)
Immune phenotype of tumor microenvironment predicts response to bevacizumab in neoadjuvant treatment of ER-positive breast cancer
Int J Cancer, 147 (9), 2515-2525
DOI 10.1002/ijc.33108, PubMed 32488909

Pace M, Falappa M, Freschi A, Balzani E, Berteotti C, Lo Martire V, Kaveh F, Hovig E, Zoccoli G, Amici R, Cerri M, Urbanucci A, Tucci V (2020)
Loss of Snord116 impacts lateral hypothalamus, sleep, and food-related behaviors
JCI Insight, 5 (12)
DOI 10.1172/jci.insight.137495, PubMed 32365348

Keller A, Fehlmann T, Backes C, Kern F, Gislefoss R, Langseth H, Rounge TB, Ludwig N, Meese E (2020)
Competitive learning suggests circulating miRNA profiles for cancers decades prior to diagnosis
RNA Biol, 17 (10), 1416-1426
DOI 10.1080/15476286.2020.1771945, PubMed 32456538

Weber CR, Akbar R, Yermanos A, Pavlović M, Snapkov I, Sandve GK, Reddy ST, Greiff V (2020)
immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking
Bioinformatics, 36 (11), 3594-3596
DOI 10.1093/bioinformatics/btaa158, PubMed 32154832

Fan Q, Nørgaard RC, Grytten I, Ness CM, Lucas C, Vekterud K, Soedling H, Matthews J, Lemma RB, Gabrielsen OS, Bindesbøll C, Ulven SM, Nebb HI, Grønning-Wang LM, Sæther T (2020)
LXRα Regulates ChREBPα Transactivity in a Target Gene-Specific Manner through an Agonist-Modulated LBD-LID Interaction
Cells, 9 (5)
DOI 10.3390/cells9051214, PubMed 32414201

Wise JF, Nakken S, Steen CB, Vodák D, Trøen G, Johannessen B, Lingjærde OC, Hilden V, Blaker YN, Bai B, Aasheim LB, Pasanen A, Lorenz S, Sveen A, Lothe RA, Myklebost O, Leppä S, Meza-Zepeda LA, Beiske K, Lawrence MS, Hovig E, Myklebust JH, Smeland EB, Holte H (2020)
Mutational dynamics and immune evasion in diffuse large B-cell lymphoma explored in a relapse-enriched patient series
Blood Adv, 4 (9), 1859-1866
DOI 10.1182/bloodadvances.2019001325, PubMed 32374878

Leppä S, Jørgensen J, Tierens A, Meriranta L, Østlie I, de Nully Brown P, Fagerli UM, Larsen TS, Mannisto S, Munksgaard L, Maisenhölder M, Vasala K, Meyer P, Jerkeman M, Björkholm M, Fluge Ø, Jyrkkiö S, Liestøl K, Ralfkiaer E, Spetalen S, Beiske K, Karjalainen-Lindsberg ML, Holte H (2020)
Patients with high-risk DLBCL benefit from dose-dense immunochemotherapy combined with early systemic CNS prophylaxis
Blood Adv, 4 (9), 1906-1915
DOI 10.1182/bloodadvances.2020001518, PubMed 32380536

Rønningen PS, Berge T, Solberg MG, Enger S, Nygård S, Pervez MO, Orstad EB, Kvisvik B, Aagaard EN, Røsjø H, Tveit A, Steine K (2020)
Sex differences and higher upper normal limits for left atrial end-systolic volume in individuals in their mid-60s: data from the ACE 1950 Study
Eur Heart J Cardiovasc Imaging, 21 (5), 501-507
DOI 10.1093/ehjci/jeaa004, PubMed 32031593

Chandra A, Røsjø H, Svensson M, Vigen T, Ihle-Hansen H, Orstad EB, Rønning OM, Lyngbakken MN, Nygård S, Berge T, Schmidt EB, Omland T, Tveit A, Eide IA (2020)
Plasma linoleic acid levels and cardiovascular risk factors: results from the Norwegian ACE 1950 Study
Eur J Clin Nutr, 74 (12), 1707-1717
DOI 10.1038/s41430-020-0641-4, PubMed 32341488

Mehlum MH, Liestøl K, Kjeldsen SE, Wyller TB, Julius S, Rothwell PM, Mancia G, Parati G, Weber MA, Berge E (2020)
Blood Pressure-Lowering Profiles and Clinical Effects of Angiotensin Receptor Blockers Versus Calcium Channel Blockers
Hypertension, 75 (6), 1584-1592
DOI 10.1161/HYPERTENSIONAHA.119.14443, PubMed 32336236

Viljakainen J, Raju SC, Viljakainen H, Figueiredo RAO, Roos E, Weiderpass E, Rounge TB (2020)
Meal Regularity Plays a Role in Shaping the Saliva Microbiota
Front Microbiol, 11, 757
DOI 10.3389/fmicb.2020.00757, PubMed 32390990

Waaler J, Mygland L, Tveita A, Strand MF, Solberg NT, Olsen PA, Aizenshtadt A, Fauskanger M, Lund K, Brinch SA, Lycke M, Dybing E, Nygaard V, Bøe SL, Heintz KM, Hovig E, Hammarström C, Corthay A, Krauss S (2020)
Tankyrase inhibition sensitizes melanoma to PD-1 immune checkpoint blockade in syngeneic mouse models
Commun Biol, 3 (1), 196
DOI 10.1038/s42003-020-0916-2, PubMed 32332858

Prestgaard E, Mariampillai J, Engeseth K, Erikssen J, Bodegård J, Liestøl K, Kjeldsen S, Grundvold I, Berge E (2020)
Change in Body Weight and Long-Term Risk of Stroke and Death in Healthy Men
Stroke, 51 (5), 1435-1441
DOI 10.1161/STROKEAHA.119.027233, PubMed 32268850

Grytten I, Rand KD, Nederbragt AJ, Sandve GK (2020)
Assessing graph-based read mappers against a baseline approach highlights strengths and weaknesses of current methods
BMC Genomics, 21 (1), 282
DOI 10.1186/s12864-020-6685-y, PubMed 32252628

Balaban G, Costa CM, Porter B, Halliday B, Rinaldi CA, Prasad S, Plank G, Ismail TF, Bishop MJ (2020)
3D Electrophysiological Modeling of Interstitial Fibrosis Networks and Their Role in Ventricular Arrhythmias in Non-Ischemic Cardiomyopathy
IEEE Trans Biomed Eng, 67 (11), 3125-3133
DOI 10.1109/TBME.2020.2976924, PubMed 32275581

Pladsen AV, Nilsen G, Rueda OM, Aure MR, Borgan Ø, Liestøl K, Vitelli V, Frigessi A, Langerød A, Mathelier A, OSBREAC, Engebråten O, Kristensen V, Wedge DC, Van Loo P, Caldas C, Børresen-Dale AL, Russnes HG, Lingjærde OC (2020)
DNA copy number motifs are strong and independent predictors of survival in breast cancer
Commun Biol, 3 (1), 153
DOI 10.1038/s42003-020-0884-6, PubMed 32242091

Molyneux SD, Waterhouse PD, Shelton D, Shao YW, Watling CM, Tang QL, Harris IS, Dickson BC, Tharmapalan P, Sandve GK, Zhang X, Bailey SD, Berman H, Wunder JS, Izsvák Z, Lupien M, Mak TW, Khokha R (2020)
Author Correction: Human somatic cell mutagenesis creates genetically tractable sarcomas
Nat Genet, 52 (4), 464
DOI 10.1038/s41588-020-0589-2, PubMed 32094913

Backe PH, Laerdahl JK, Kittelsen LS, Dalhus B, Mørkrid L, Bjørås M (2020)
Structural basis for substrate and product recognition in human phosphoglucomutase-1 (PGM1) isoform 2, a member of the α-D-phosphohexomutase superfamily
Sci Rep, 10 (1), 5656
DOI 10.1038/s41598-020-62548-0, PubMed 32221390

Ree AH, Nygaard V, Boye K, Heinrich D, Dueland S, Bergheim IR, Johansen C, Beiske K, Negård A, Lund-Iversen M, Nygaard V, Hovig E, Nakken S, Nasser S, Julsrud L, Reisse CH, Ruud EA, Kristensen VN, Flørenes VA, Geitvik GA, Lingjærde OC, Børresen-Dale AL, Russnes HG, Mælandsmo GM, Flatmark K (2020)
Molecularly matched therapy in the context of sensitivity, resistance, and safety; patient outcomes in end-stage cancer - the MetAction study
Acta Oncol, 59 (7), 733-740
DOI 10.1080/0284186X.2020.1742377, PubMed 32208873

Khelik K, Sandve GK, Nederbragt AJ, Rognes T (2020)
NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads
BMC Bioinformatics, 21 (1), 66
DOI 10.1186/s12859-020-3414-0, PubMed 32085722

Møller P, Dominguez-Valentin M, Rødland EA, Hovig E (2020)
Correction: Møller, P.; et al. Causes for Frequent Pathogenic BRCA1 Variants Include Low Penetrance in Fertile Ages, Recurrent De-Novo Mutations and Genetic Drift. Cancers 2019, 11, 132
Cancers (Basel), 12 (2)
DOI 10.3390/cancers12020410, PubMed 32050665

du Pré MF, Blazevski J, Dewan AE, Stamnaes J, Kanduri C, Sandve GK, Johannesen MK, Lindstad CB, Hnida K, Fugger L, Melino G, Qiao SW, Sollid LM (2020)
B cell tolerance and antibody production to the celiac disease autoantigen transglutaminase 2
J Exp Med, 217 (2)
DOI 10.1084/jem.20190860, PubMed 31727780

Skrede OJ, De Raedt S, Kleppe A, Hveem TS, Liestøl K, Maddison J, Askautrud HA, Pradhan M, Nesheim JA, Albregtsen F, Farstad IN, Domingo E, Church DN, Nesbakken A, Shepherd NA, Tomlinson I, Kerr R, Novelli M, Kerr DJ, Danielsen HE (2020)
Deep learning for prediction of colorectal cancer outcome: a discovery and validation study
Lancet, 395 (10221), 350-360
DOI 10.1016/S0140-6736(19)32998-8, PubMed 32007170

Zhao S, Hoff AM, Skotheim RI (2020)
ScaR-a tool for sensitive detection of known fusion transcripts: establishing prevalence of fusions in testicular germ cell tumors
NAR Genom Bioinform, 2 (1), lqz025
DOI 10.1093/nargab/lqz025, PubMed 33575572

Umu SU, Langseth H, Keller A, Meese E, Helland Å, Lyle R, Rounge TB (2020)
A 10-year prediagnostic follow-up study shows that serum RNA signals are highly dynamic in lung carcinogenesis
Mol Oncol, 14 (2), 235-247
DOI 10.1002/1878-0261.12620, PubMed 31851411

Fromm B, Domanska D, Høye E, Ovchinnikov V, Kang W, Aparicio-Puerta E, Johansen M, Flatmark K, Mathelier A, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ (2020)
MirGeneDB 2.0: the metazoan microRNA complement
Nucleic Acids Res, 48 (D1), D1172
DOI 10.1093/nar/gkz1016, PubMed 31642479

Fromm B, Domanska D, Høye E, Ovchinnikov V, Kang W, Aparicio-Puerta E, Johansen M, Flatmark K, Mathelier A, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ (2020)
MirGeneDB 2.0: the metazoan microRNA complement
Nucleic Acids Res, 48 (D1), D132-D141
DOI 10.1093/nar/gkz885, PubMed 31598695

Nikolaidis K, Kristiansen S, Goebel V, Plagemann T, Liestol K, Kankanhalli M (2020)
Augmenting Physiological Time Series Data: A Case Study for Sleep Apnea Detection
LECT NOTES ARTIF INT, 11908, 376-399
DOI 10.1007/978-3-030-46133-1_23

Muscianisi G, Fiameni G, Azab A (2020)
Singularity GPU Containers Execution on HPC Cluster
LECT NOTES COMPUT SC, 11887, 61-68
DOI 10.1007/978-3-030-34356-9_6

Publications 2019

Dominguez-Valentin M, Nakken S, Tubeuf H, Vodak D, Ekstrøm PO, Nissen AM, Morak M, Holinski-Feder E, Holth A, Capella G, Davidson B, Evans DG, Martins A, Møller P, Hovig E (2019)
Results of multigene panel testing in familial cancer cases without genetic cause demonstrated by single gene testing
Sci Rep, 9 (1), 18555
DOI 10.1038/s41598-019-54517-z, PubMed 31811167

Ersvær E, Kildal W, Vlatkovic L, Cyll K, Pradhan M, Kleppe A, Hveem TS, Askautrud HA, Novelli M, Wæhre H, Liestøl K, Danielsen HE (2019)
Prognostic value of mitotic checkpoint protein BUB3, cyclin B1, and pituitary tumor-transforming 1 expression in prostate cancer
Mod Pathol, 33 (5), 905-915
DOI 10.1038/s41379-019-0418-2, PubMed 31801961

Pashov A, Shivarov V, Hadzhieva M, Kostov V, Ferdinandov D, Heintz KM, Pashova S, Todorova M, Vassilev T, Kieber-Emmons T, Meza-Zepeda LA, Hovig E (2019)
Diagnostic Profiling of the Human Public IgM Repertoire With Scalable Mimotope Libraries
Front Immunol, 10, 2796
DOI 10.3389/fimmu.2019.02796, PubMed 31849974

Mariampillai JE, Liestøl K, Kjeldsen SE, Prestgaard EE, Engeseth K, Bodegard J, Berge E, Gjesdal K, Erikssen J, Grundvold I, Skretteberg PT (2019)
Exercise Systolic Blood Pressure at Moderate Workload Is Linearly Associated With Coronary Disease Risk in Healthy Men
Hypertension, 75 (1), 44-50
DOI 10.1161/HYPERTENSIONAHA.119.13528, PubMed 31735088

Tellum T, Nygaard S, Lieng M (2019)
Noninvasive Diagnosis of Adenomyosis: A Structured Review and Meta-analysis of Diagnostic Accuracy in Imaging
J Minim Invasive Gynecol, 27 (2), 408-418.e3
DOI 10.1016/j.jmig.2019.11.001, PubMed 31712162

Nygård S, Lingjærde OC, Caldas C, Hovig E, Børresen-Dale AL, Helland Å, Haakensen VD (2019)
PathTracer: High-sensitivity detection of differential pathway activity in tumours
Sci Rep, 9 (1), 16332
DOI 10.1038/s41598-019-52529-3, PubMed 31704995

Neckmann U, Wolowczyk C, Hall M, Almaas E, Ren J, Zhao S, Johannessen B, Skotheim RI, Bjørkøy G, Ten Dijke P, Holien T (2019)
GREM1 is associated with metastasis and predicts poor prognosis in ER-negative breast cancer patients
Cell Commun Signal, 17 (1), 140
DOI 10.1186/s12964-019-0467-7, PubMed 31694641

Varadharajan S, Rastas P, Löytynoja A, Matschiner M, Calboli FCF, Guo B, Nederbragt AJ, Jakobsen KS, Merilä J (2019)
A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome
Genome Biol Evol, 11 (11), 3291-3308
DOI 10.1093/gbe/evz240, PubMed 31687752

Strøm TB, Vinje T, Bjune K, da Costa LT, Laerdahl JK, Leren TP (2019)
Lysosomal acid lipase does not have a propeptide and should not be considered being a proprotein
Proteins, 88 (3), 440-448
DOI 10.1002/prot.25821, PubMed 31587363

Tolios A, De Las Rivas J, Hovig E, Trouillas P, Scorilas A, Mohr T (2019)
Computational approaches in cancer multidrug resistance research: Identification of potential biomarkers, drug targets and drug-target interactions
Drug Resist Updat, 48, 100662
DOI 10.1016/j.drup.2019.100662, PubMed 31927437

Dominguez-Valentin M, Seppälä TT, Sampson JR, Macrae F, Winship I, Evans DG, Scott RJ, Burn J, Möslein G, Bernstein I, Pylvänäinen K, Renkonen-Sinisalo L, Lepistö A, Lindblom A, Plazzer JP, Tjandra D, Thomas H, Green K, Lalloo F, Crosbie EJ, Hill J, Capella G, Pineda M, Navarro M, Vidal JB et al. (2019)
Survival by colon cancer stage and screening interval in Lynch syndrome: a prospective Lynch syndrome database report
Hered Cancer Clin Pract, 17, 28
DOI 10.1186/s13053-019-0127-3, PubMed 31636762

Lie-Jensen A, Ivanauskiene K, Malerød L, Jain A, Tan KW, Laerdahl JK, Liestøl K, Stenmark H, Haglund K (2019)
Centralspindlin Recruits ALIX to the Midbody during Cytokinetic Abscission in Drosophila via a Mechanism Analogous to Virus Budding
Curr Biol, 29 (20), 3538-3548.e7
DOI 10.1016/j.cub.2019.09.025, PubMed 31607533

Carm KT, Hoff AM, Bakken AC, Axcrona U, Axcrona K, Lothe RA, Skotheim RI, Løvf M (2019)
Interfocal heterogeneity challenges the clinical usefulness of molecular classification of primary prostate cancer
Sci Rep, 9 (1), 13579
DOI 10.1038/s41598-019-49964-7, PubMed 31537872

Vinje T, Laerdahl JK, Bjune K, Leren TP, Strøm TB (2019)
Characterization of the mechanisms by which missense mutations in the lysosomal acid lipase gene disrupt enzymatic activity
Hum Mol Genet, 28 (18), 3043-3052
DOI 10.1093/hmg/ddz114, PubMed 31131398

Lindholm EM, Ragle Aure M, Haugen MH, Kleivi Sahlberg K, Kristensen VN, Nebdal D, Børresen-Dale AL, Lingjaerde OC, Engebraaten O (2019)
miRNA expression changes during the course of neoadjuvant bevacizumab and chemotherapy treatment in breast cancer
Mol Oncol, 13 (10), 2278-2296
DOI 10.1002/1878-0261.12561, PubMed 31402562

Gheorghe M, Sandve GK, Khan A, Chèneby J, Ballester B, Mathelier A (2019)
A map of direct TF-DNA interactions in the human genome
Nucleic Acids Res, 47 (14), 7715
DOI 10.1093/nar/gkz582, PubMed 31251803

Della Valle A, Rossi BM, Palmero EI, Antelo M, Vaccaro CA, López-Kostner F, Alvarez K, Cruz-Correa M, Bruno LI, Forones NM, Mindiola JAR, Buleje J, Spirandelli F, Bohorquez M, Cock-Rada AM, Sullcahuaman Y, Nascimento I, Abe-Sandes K, Lino-Silva LS, Petracchi F, Mampel A, Rodriguez Y, Rossi NT, Yañez CB, Rubio C et al. (2019)
A snapshot of current genetic testing practice in Lynch syndrome: The results of a representative survey of 33 Latin American existing centres/registries
Eur J Cancer, 119, 112-121
DOI 10.1016/j.ejca.2019.07.017, PubMed 31442815

Brown AJ, Snapkov I, Akbar R, Pavlovic M, Miho E, Sandve GK, Greiff V (2019)
Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires
Mol. Syst. Des. Eng., 4 (4), 701-736
DOI 10.1039/c9me00071b

Snir O, Kanduri C, Lundin KEA, Sandve GK, Sollid LM (2019)
Transcriptional profiling of human intestinal plasma cells reveals effector functions beyond antibody production
United European Gastroenterol J, 7 (10), 1399-1407
DOI 10.1177/2050640619862461, PubMed 31839965

Hamfjord J, Guren TK, Dajani O, Johansen JS, Glimelius B, Sorbye H, Pfeiffer P, Lingjærde OC, Tveit KM, Kure EH, Pallisgaard N, Spindler KG (2019)
Total circulating cell-free DNA as a prognostic biomarker in metastatic colorectal cancer before first-line oxaliplatin-based chemotherapy
Ann Oncol, 30 (7), 1088-1095
DOI 10.1093/annonc/mdz139, PubMed 31046124

Tellum T, Matic GV, Dormagen JB, Nygaard S, Viktil E, Qvigstad E, Lieng M (2019)
Diagnosing adenomyosis with MRI: a prospective study revisiting the junctional zone thickness cutoff of 12 mm as a diagnostic marker
Eur Radiol, 29 (12), 6971-6981
DOI 10.1007/s00330-019-06308-3, PubMed 31264010

Mohammadzadeh N, Lunde IG, Andenæs K, Strand ME, Aronsen JM, Skrbic B, Marstein HS, Bandlien C, Nygård S, Gorham J, Sjaastad I, Chakravarti S, Christensen G, Engebretsen KVT, Tønnessen T (2019)
The extracellular matrix proteoglycan lumican improves survival and counteracts cardiac dilatation and failure in mice subjected to pressure overload
Sci Rep, 9 (1), 9206
DOI 10.1038/s41598-019-45651-9, PubMed 31235849

Njølstad PR, Andreassen OA, Brunak S, Børglum AD, Dillner J, Esko T, Franks PW, Freimer N, Groop L, Heimer H, Hougaard DM, Hovig E, Hveem K, Jalanko A, Kaprio J, Knudsen GP, Melbye M, Metspalu A, Mortensen PB, Palmgren J, Palotie A, Reed W, Stefánsson H, Stitziel NO, Sullivan PF et al. (2019)
Roadmap for a precision-medicine initiative in the Nordic region
Nat Genet, 51 (6), 924-930
DOI 10.1038/s41588-019-0391-1, PubMed 30988515

Newman AM, Steen CB, Liu CL, Gentles AJ, Chaudhuri AA, Scherer F, Khodadoust MS, Esfahani MS, Luca BA, Steiner D, Diehn M, Alizadeh AA (2019)
Determining cell type abundance and expression from bulk tissues with digital cytometry
Nat Biotechnol, 37 (7), 773-782
DOI 10.1038/s41587-019-0114-2, PubMed 31061481

Brynildsen J, Petäjä L, Myhre PL, Lyngbakken MN, Nygård S, Stridsberg M, Christensen G, Ottesen AH, Pettilä V, Omland T, Røsjø H (2019)
Circulating Secretoneurin Concentrations After Cardiac Surgery: Data From the FINNish Acute Kidney Injury Heart Study
Crit Care Med, 47 (5), e412-e419
DOI 10.1097/CCM.0000000000003670, PubMed 30730440

Mariampillai JE, Prestgaard EE, Kjeldsen SE, Liestøl K, Engeseth K, Erikssen J, Bodegard J, Berge E, Grundvold I, Skretteberg PT (2019)
SBP above 180 mmHg at moderate exercise workload increases coronary heart disease risk in healthy men during 28-year follow-up
J Hypertens, 37 (5), 949-955
DOI 10.1097/HJH.0000000000001959, PubMed 30325341

Kanduri C, Bock C, Gundersen S, Hovig E, Sandve GK (2019)
Colocalization analyses of genomic elements: approaches, recommendations and challenges
Bioinformatics, 35 (9), 1615-1624
DOI 10.1093/bioinformatics/bty835, PubMed 30307532

Öjlert ÅK, Halvorsen AR, Nebdal D, Lund-Iversen M, Solberg S, Brustugun OT, Lingjaerde OC, Helland Å (2019)
The immune microenvironment in non-small cell lung cancer is predictive of prognosis after surgery
Mol Oncol, 13 (5), 1166-1179
DOI 10.1002/1878-0261.12475, PubMed 30854794

Lund-Andersen C, Nakken S, Nygård S, Fromm B, Aasheim LB, Davidson B, Julsrud L, Abrahamsen TW, Kristensen AT, Dybdahl B, Larsen SG, Hovig E, Flatmark K (2019)
Integrative genomic analysis of peritoneal malignant mesothelioma: understanding a case with extraordinary chemotherapy response
Cold Spring Harb Mol Case Stud, 5 (2)
DOI 10.1101/mcs.a003566, PubMed 30862609

Christophersen A, Lund EG, Snir O, Solà E, Kanduri C, Dahal-Koirala S, Zühlke S, Molberg Ø, Utz PJ, Rohani-Pichavant M, Simard JF, Dekker CL, Lundin KEA, Sollid LM, Davis MM (2019)
Distinct phenotype of CD4⁺ T cells driving celiac disease identified in multiple autoimmune conditions
Nat Med, 25 (5), 734-737
DOI 10.1038/s41591-019-0403-9, PubMed 30911136

Steen CB, Leich E, Myklebust JH, Lockmer S, Wise JF, Wahlin BE, Østenstad B, Liestøl K, Kimby E, Rosenwald A, Smeland EB, Holte H, Lingjærde OC, Brodtkorb M (2019)
A clinico-molecular predictor identifies follicular lymphoma patients at risk of early transformation after first-line immunotherapy
Haematologica, 104 (10), e460-e464
DOI 10.3324/haematol.2018.209080, PubMed 30846496

Gheorghe M, Sandve GK, Khan A, Chèneby J, Ballester B, Mathelier A (2019)
A map of direct TF-DNA interactions in the human genome
Nucleic Acids Res, 47 (4), e21
DOI 10.1093/nar/gky1210, PubMed 30517703

Seppälä TT, Ahadova A, Dominguez-Valentin M, Macrae F, Evans DG, Therkildsen C, Sampson J, Scott R, Burn J, Möslein G, Bernstein I, Holinski-Feder E, Pylvänäinen K, Renkonen-Sinisalo L, Lepistö A, Lautrup CK, Lindblom A, Plazzer JP, Winship I, Tjandra D, Katz LH, Aretz S, Hüneburg R, Holzapfel S, Heinimann K et al. (2019)
Lack of association between screening interval and cancer stage in Lynch syndrome may be accounted for by over-diagnosis; a prospective Lynch syndrome database report
Hered Cancer Clin Pract, 17, 8
DOI 10.1186/s13053-019-0106-8, PubMed 30858900

Ree AH, Nygaard V, Russnes HG, Heinrich D, Nygaard V, Johansen C, Bergheim IR, Hovig E, Beiske K, Negård A, Børresen-Dale AL, Flatmark K, Mælandsmo GM (2019)
Responsiveness to PD-1 Blockade in End-Stage Colon Cancer with Gene Locus 9p24.1 Copy-Number Gain
Cancer Immunol Res, 7 (5), 701-706
DOI 10.1158/2326-6066.CIR-18-0777, PubMed 30804006

Grytten I, Rand KD, Nederbragt AJ, Storvik GO, Glad IK, Sandve GK (2019)
Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes
PLoS Comput Biol, 15 (2), e1006731
DOI 10.1371/journal.pcbi.1006731, PubMed 30779737

Hagberg G, Fure B, Sandset EC, Thommessen B, Ihle-Hansen H, Øksengård AR, Nygård S, Wyller TB, Ihle-Hansen H (2019)
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, 15, 11-18
DOI 10.2147/VHRM.S191873, PubMed 30799926

Cheng J, Demeulemeester J, Wedge DC, Vollan HKM, Pitt JJ, Russnes HG, Pandey BP, Nilsen G, Nord S, Bignell GR, White KP, Børresen-Dale AL, Campbell PJ, Kristensen VN, Stratton MR, Lingjærde OC, Moreau Y, Van Loo P (2019)
Author Correction: Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors
Nat Commun, 10 (1), 525
DOI 10.1038/s41467-019-08512-7, PubMed 30692535

Møller P, Dominguez-Valentin M, Rødland EA, Hovig E (2019)
Causes for Frequent Pathogenic BRCA1 Variants Include Low Penetrance in Fertile Ages, Recurrent De-Novo Mutations and Genetic Drift
Cancers (Basel), 11 (2)
DOI 10.3390/cancers11020132, PubMed 30678073

Mehlum MH, Liestøl K, Wyller TB, Hua TA, Rostrup M, Berge E (2019)
Blood pressure variability in hypertensive patients with atrial fibrillation in the VALUE trial
Blood Press, 28 (2), 77-83
DOI 10.1080/08037051.2018.1524707, PubMed 30614275

Ihle-Hansen H, Vigen T, Berge T, Hagberg G, Engedal K, Rønning OM, Thommessen B, Lyngbakken MN, Nygård S, Røsjø H, Tveit A, Ihle-Hansen H (2019)
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, 70 (4), 1041-1049
DOI 10.3233/JAD-190327, PubMed 31306128

Hagberg G, Fure B, Thommessen B, Ihle-Hansen H, Øksengård AR, Nygård S, Pendlebury ST, Beyer MK, Wyller TB, Ihle-Hansen H (2019)
Predictors for Favorable Cognitive Outcome Post-Stroke: A-Seven-Year Follow-Up Study
Dement Geriatr Cogn Disord, 48 (1-2), 45-55
DOI 10.1159/000501850, PubMed 31461703