Publications

Publications published since 2000 from OUS - Department of Cancer Genetics

1092 publications found (only first 1000 shown)

Publications 2024

1. Adnan Awad S, Dufva O, Klievink J, Karjalainen E, Ianevski A, Pietarinen P, Kim D, Potdar S, Wolf M, Lotfi K, Aittokallio T, Wennerberg K, Porkka K, Mustjoki S (2024)
   Integrated drug profiling and CRISPR screening identify BCR::ABL1-independent vulnerabilities in chronic myeloid leukemia
   Cell Rep Med, 5 (5), 101521
   DOI 10.1016/j.xcrm.2024.101521, PubMed 38653245
2. Aittokallio T, Fang EF (2024)
   Editorial overview-Artificial intelligence methodologies in structural biology: Bridging the gap to medical applications
   Curr Opin Struct Biol, 87, 102862
   DOI 10.1016/j.sbi.2024.102862, PubMed 38870638
3. Andresen NK, Røssevold AH, Borgen E, Schirmer CB, Gilje B, Garred Ø, Lømo J, Stensland M, Nordgård O, Falk RS, Mathiesen RR, Russnes HG, Kyte JA, Naume B (2024)
   Circulating tumor cells in metastatic breast cancer patients treated with immune checkpoint inhibitors - a biomarker analysis of the ALICE and ICON trials
   Mol Oncol (in press)
   DOI 10.1002/1878-0261.13675, PubMed 38978352
4. Andresen NK, Røssevold AH, Quaghebeur C, Gilje B, Boge B, Gombos A, Falk RS, Mathiesen RR, Julsrud L, Garred Ø, Russnes HG, Lereim RR, Chauhan SK, Lingjærde OC, Dunn C, Naume B, Kyte JA (2024)
   Ipilimumab and nivolumab combined with anthracycline-based chemotherapy in metastatic hormone receptor-positive breast cancer: a randomized phase 2b trial
   J Immunother Cancer, 12 (1)
   DOI 10.1136/jitc-2023-007990, PubMed 38242720
5. Ankill J, Zhao Z, Tekpli X, Kure EH, Kristensen VN, Mathelier A, Fleischer T (2024)
   Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation
   PLoS Comput Biol, 20 (11), e1012565
   DOI 10.1371/journal.pcbi.1012565, PubMed 39556603
6. Arner EN, Alzhanova D, Westcott JM, Hinz S, Tiron CE, Blø M, Mai A, Virtakoivu R, Phinney N, Nord S, Aguilera KY, Rizvi A, Toombs JE, Reese TC, Fey V, Micklem D, Gausdal G, Ivaska J, Lorens JB, Brekken RA (2024)
   AXL-TBK1 driven AKT3 activation promotes metastasis
   Sci Signal, 17 (867), eado6057
   DOI 10.1126/scisignal.ado6057, PubMed 39689180
7. Bai B, Wise JF, Vodák D, Nakken S, Sharma A, Blaker YN, Brodtkorb M, Hilden V, Trøen G, Ren W, Lorenz S, Lawrence MS, Myklebost O, Kimby E, Pan-Hammarström Q, Steen CB, Meza-Zepeda LA, Beiske K, Smeland EB, Hovig E, Lingjærde OC, Holte H, Myklebust JH (2024)
   Multi-omics profiling of longitudinal samples reveals early genomic changes in follicular lymphoma
   Blood Cancer J, 14 (1), 147
   DOI 10.1038/s41408-024-01124-5, PubMed 39191762
8. Bjørgo E, Fagereng GL, Russnes HG, Smeland S, Taskén K, Helland Å (2024)
   Acta Oncologica Nordic Precision Cancer Medicine Symposium 2023 - merging clinical research and standard healthcare
   Acta Oncol, 63, 487-490
   DOI 10.2340/1651-226X.2024.24954, PubMed 38910311
9. Brativnyk A, Ankill J, Helland Å, Fleischer T (2024)
   Multi-omics analysis reveals epigenetically regulated processes and patient classification in lung adenocarcinoma
   Int J Cancer, 155 (2), 282-297
   DOI 10.1002/ijc.34915, PubMed 38489486
10. Bulanova D, Akimov Y, Senkowski W, Oikkonen J, Gall-Mas L, Timonen S, Elmadani M, Hynninen J, Hautaniemi S, Aittokallio T, Wennerberg K (2024)
    A synthetic lethal dependency on casein kinase 2 in response to replication-perturbing therapeutics in RB1-deficient cancer cells
    Sci Adv, 10 (21), eadj1564
    DOI 10.1126/sciadv.adj1564, PubMed 38781347
11. Chen L, Wang X, Xie N, Zhang Z, Xu X, Xue M, Yang Y, Liu L, Su L, Bjaanæs M, Karlsson A, Planck M, Staaf J, Helland Å, Esteller M, Christiani DC, Chen F, Zhang R (2024)
    A two-phase epigenome-wide four-way gene-smoking interaction study of overall survival for early-stage non-small cell lung cancer
    Mol Oncol (in press)
    DOI 10.1002/1878-0261.13766, PubMed 39630602
12. Cun HT, Bernard L, Lande KT, Lawson BC, Nesbakken AJ, Davidson B, Lindemann K, Fellman B, Sørlie T, Soliman PT, Eriksson AGZ (2024)
    Comprehensive molecular characterization of early stage grade 3 endometrioid endometrial adenocarcinoma
    Gynecol Oncol, 189, 138-145
    DOI 10.1016/j.ygyno.2024.07.677, PubMed 39126895
13. Davidson B, Teien Lande K, Nebdal D, Nesbakken AJ, Holth A, Lindemann K, Zahl Eriksson AG, Sørlie T (2024)
    Endometrial carcinomas with ambiguous histology often harbor TP53 mutations
    Virchows Arch (in press)
    DOI 10.1007/s00428-024-03912-7, PubMed 39235515
14. Demir MF, Lin YH, Costa Cruz PH, Tajima M, Honjo T, Müller E (2024)
    Blocking S100A9-signaling is detrimental to the initiation of anti-tumor immunity
    Front Immunol, 15, 1479502
    DOI 10.3389/fimmu.2024.1479502, PubMed 39497822
15. Dyrbekk APH, Warsame AA, Suhrke P, Ludahl MO, Zecic N, Moe JO, Lund-Iversen M, Brustugun OT (2024)
    Evaluation of NTRK expression and fusions in a large cohort of early-stage lung cancer
    Clin Exp Med, 24 (1), 10
    DOI 10.1007/s10238-023-01273-0, PubMed 38240952
16. Edsjö A, Russnes HG, Lehtiö J, Tamborero D, Hovig E, Stenzinger A, Rosenquist R, PCM4EU consortium (2024)
    High-throughput molecular assays for inclusion in personalised oncology trials - State-of-the-art and beyond
    J Intern Med, 295 (6), 785-803
    DOI 10.1111/joim.13785, PubMed 38698538
17. Farooqi SJ, Zhao Z, Öjlert ÅK, Thunold S, Juul HV, Bjaanæs MM, Horndalsveen H, Nymoen HMG, Helland Å, Haakensen VD (2024)
    Serum cytokines as a biomarker for immune checkpoint inhibitor toxicity in patients with pleural mesothelioma
    Front Immunol, 15, 1480183
    DOI 10.3389/fimmu.2024.1480183, PubMed 39687621
18. Fei L, Zhang K, Hautaniemi S, Sahu B (2024)
    Protocol to identify defined reprogramming factor expression using a factor-indexing single-nuclei multiome sequencing approach
    STAR Protoc, 5 (3), 103148
    DOI 10.1016/j.xpro.2024.103148, PubMed 38909361
19. Filippi AR, Bar J, Chouaid C, Christoph DC, Field JK, Fietkau R, Garassino MC, Garrido P, Haakensen VD, Kao S, Markman B, McDonald F, Mornex F, Moskovitz M, Peters S, Sibille A, Siva S, van den Heuvel M, Vercauter P, Anand S, Chander P, Licour M, de Lima AR, Qiao Y, Girard N (2024)
    Real-world outcomes with durvalumab after chemoradiotherapy in patients with unresectable stage III NSCLC: interim analysis of overall survival from PACIFIC-R
    ESMO Open, 9 (6), 103464
    DOI 10.1016/j.esmoop.2024.103464, PubMed 38833971
20. Fleischer T, Haugen MH, Ankill J, Silwal-Pandit L, Børresen-Dale AL, Hedenfalk I, Hatschek T, Tost J, Engebraaten O, Kristensen VN (2024)
    An integrated omics approach highlights how epigenetic events can explain and predict response to neoadjuvant chemotherapy and bevacizumab in breast cancer
    Mol Oncol, 18 (8), 2042-2059
    DOI 10.1002/1878-0261.13656, PubMed 38671580
21. Gullhaug A, Haakensen VD, De Ruysscher D, Simone CB, Hotca-Cho AE, Chhabra AM, Hellebust TP, Paulsen EE, Dimopoulos MP, Johansen S (2024)
    Lung cancer reirradiation: Exploring modifications to utilization, treatment modalities and factors associated with outcomes
    J Med Imaging Radiat Sci, 55 (2), 221-231
    DOI 10.1016/j.jmir.2024.02.004, PubMed 38429174
22. Hektoen HH, Tsuruda KM, Fjellbirkeland L, Nilssen Y, Brustugun OT, Andreassen BK (2024)
    Real-world evidence for pembrolizumab in non-small cell lung cancer: a nationwide cohort study
    Br J Cancer (in press)
    DOI 10.1038/s41416-024-02895-1, PubMed 39489879
23. Helland Å (2024)
    [Not Available]
    Tidsskr Nor Laegeforen, 144 (15)
    DOI 10.4045/tidsskr.24.0603, PubMed 39692664
24. Helland Å, Steinskog ESS, Blix ES, Flobak Å, Brabrand S, Puco K, Niehusmann P, Meltzer S, Oppedal IA, Haug Å, Torkildsen CF, Randen U, Gilje B, Lønning PE, Gjertsen BT, Hovland R, Russnes HG, Fagereng GL, Smeland S, Tasken K (2024)
    [Raising the quality of cancer treatment]
    Tidsskr Nor Laegeforen, 144 (1)
    DOI 10.4045/tidsskr.23.0740, PubMed 38258713
25. Haakensen VD, Öjlert ÅK, Thunold S, Farooqi S, Nowak AK, Chin WL, Grundberg O, Szejniuk WM, Cedres S, Sørensen JB, Dalen TS, Lund-Iversen M, Bjaanæs M, Helland Å (2024)
    UV1 telomerase vaccine with ipilimumab and nivolumab as second line treatment for pleural mesothelioma - A phase II randomised trial
    Eur J Cancer, 202, 113973
    DOI 10.1016/j.ejca.2024.113973, PubMed 38447379
26. Ianevski A, Kushnir A, Nader K, Miihkinen M, Xhaard H, Aittokallio T, Tanoli Z (2024)
    RepurposeDrugs: an interactive web-portal and predictive platform for repurposing mono- and combination therapies
    Brief Bioinform, 25 (4)
    DOI 10.1093/bib/bbae328, PubMed 38980370
27. Ianevski A, Nader K, Driva K, Senkowski W, Bulanova D, Moyano-Galceran L, Ruokoranta T, Kuusanmäki H, Ikonen N, Sergeev P, Vähä-Koskela M, Giri AK, Vähärautio A, Kontro M, Porkka K, Pitkänen E, Heckman CA, Wennerberg K, Aittokallio T (2024)
    Single-cell transcriptomes identify patient-tailored therapies for selective co-inhibition of cancer clones
    Nat Commun, 15 (1), 8579
    DOI 10.1038/s41467-024-52980-5, PubMed 39362905
28. Karttunen K, Patel D, Sahu B (2024)
    Transposable elements as drivers of dedifferentiation: Connections between enhancers in embryonic stem cells, placenta, and cancer
    Bioessays, 46 (10), e2400059
    DOI 10.1002/bies.202400059, PubMed 39073128
29. Mahon P, Chatzitheofilou I, Dekker A, Fernández X, Hall G, Helland A, Traverso A, Van Marcke C, Vehreschild J, Ciliberto G, Tonon G (2024)
    A federated learning system for precision oncology in Europe: DigiONE
    Nat Med, 30 (2), 334-337
    DOI 10.1038/s41591-023-02715-8, PubMed 38195748
30. Miceli R, Eriksson H, Lo Russo G, Alfieri S, Moksnes Bjaanæs M, Pietrantonio F, De Cecco L, Prelaj A, Proto C, Franzén J, McDonnell D, Berenguer Pina JJ, Beninato T, Mazzeo L, Giannatempo P, Verzoni E, Crown J, Helland Å, Eustace A (2024)
    Gender Difference in sidE eFfects of ImmuNotherapy: a possible clue to optimize cancEr tReatment (G-DEFINER): study protocol of an observational prospective multicenter study
    Acta Oncol, 63, 213-219
    DOI 10.2340/1651-226X.2024.24179, PubMed 38647024
31. Moragas N, Fernandez-Nogueira P, Recalde-Percaz L, Inman JL, López-Plana A, Bergholtz H, Noguera-Castells A, Del Burgo PJ, Chen X, Sorlie T, Gascón P, Bragado P, Bissell M, Carbó N, Fuster G (2024)
    The SEMA3F-NRP1/NRP2 axis is a key factor in the acquisition of invasive traits in in situ breast ductal carcinoma
    Breast Cancer Res, 26 (1), 122
    DOI 10.1186/s13058-024-01871-0, PubMed 39138514
32. Nader K, Tasci M, Ianevski A, Erickson A, Verschuren EW, Aittokallio T, Miihkinen M (2024)
    ScType enables fast and accurate cell type identification from spatial transcriptomics data
    Bioinformatics, 40 (7)
    DOI 10.1093/bioinformatics/btae426, PubMed 38936341
33. Niehusmann P, Leske H, Nygaard V, Russnes HG, Zhao S, Latysheva A, Straume Wiig U, Stankuniene B, Ulvmoen A (2024)
    Desmoplastic non-infantile ganglioglioma mimicking diffuse leptomeningeal glioneuronal tumor: precision diagnostics and therapeutic implications
    Acta Oncol, 63, 392-394
    DOI 10.2340/1651-226X.2024.31720, PubMed 38779936
34. Nymoen HM, Alver TN, Horndalsveen H, Eide HA, Bjaanæs MM, Brustugun OT, Grønberg BH, Haakensen VD, Helland Å (2024)
    Thoracic radiation in combination with erlotinib-results from a phase 2 randomized trial
    Front Oncol, 14, 1412716
    DOI 10.3389/fonc.2024.1412716, PubMed 39148905
35. Ohnstad HO, Blix ES, Akslen LA, Gilje B, Raj SX, Skjerven H, Borgen E, Janssen EAM, Mortensen E, Brekke MB, Falk RS, Schlichting E, Boge B, Songe-Møller S, Olsson P, Heie A, Mannsåker B, Vestlid MA, Kursetgjerde T, Gravdehaug B, Suhrke P, Sanchez E, Bublevic J, Røe OD, Geitvik GA et al. (2024)
    Impact of Prosigna test on adjuvant treatment decision in lymph node-negative early breast cancer-a prospective national multicentre study (EMIT-1)
    ESMO Open, 9 (6), 103475
    DOI 10.1016/j.esmoop.2024.103475, PubMed 38838499
36. Otterlei Fjørtoft M, Huse K, Rye IH (2024)
    The Tumor Immune Microenvironment in Breast Cancer Progression
    Acta Oncol, 63, 359-367
    DOI 10.2340/1651-226X.2024.33008, PubMed 38779867
37. Puco K, Fagereng GL, Brabrand S, Niehusmann P, Støre Blix E, Samdal Steinskog ES, Haug Å, Fredvik Torkildsen C, Oppedal IA, Meltzer S, Flobak Å, Johansson KAM, Bjørge L, Hjortland GO, Dalhaug A, Lund JÅ, Gilje B, Grønlie Cameron M, Hovland R, Falk RS, Smeland S, Giercksky Russnes HE, Taskén K, Helland Å, InPreD Consortium et al. (2024)
    IMPRESS-Norway: improving public cancer care by implementing precision medicine in Norway; inclusion rates and preliminary results
    Acta Oncol, 63, 379-384
    DOI 10.2340/1651-226X.2024.28322, PubMed 38779911
38. Pölöske D, Sorger H, Schönbichler A, de Araujo ED, Neubauer HA, Orlova A, Timonen SH, Abdallah DI, Ianevski A, Kuusanmäki H, Surbek M, Heyes E, Eder T, Wagner C, Suske T, Metzelder ML, Bergmann M, Dahlhoff M, Grebien F, Fleck R, Pirker C, Berger W, Hadzijusufovic E, Sperr WR, Kenner L et al. (2024)
    Dual specific STAT3/5 degraders effectively block acute myeloid leukemia and natural killer/T cell lymphoma
    Hemasphere, 8 (12), e70001
    DOI 10.1002/hem3.70001, PubMed 39619245
39. Rakaee M, Tafavvoghi M, Ricciuti B, Alessi JV, Cortellini A, Citarella F, Nibid L, Perrone G, Adib E, Fulgenzi CAM, Murilo Hidalgo Filho C, Di Federico A, Jabar F, Hashemi S, Houda I, Richardsen E, Rasmussen Busund LT, Donnem T, Bahce I, Pinato DJ, Helland Å, Sholl LM, Awad MM, Kwiatkowski DJ (2024)
    Deep Learning Model for Predicting Immunotherapy Response in Advanced Non-Small Cell Lung Cancer
    JAMA Oncol (in press)
    DOI 10.1001/jamaoncol.2024.5356, PubMed 39724105
40. Ringborg U, von Braun J, Celis J, Baumann M, Berns A, Eggermont A, Heard E, Heitor M, Chandy M, Chen CJ, Costa A, De Lorenzo F, De Robertis EM, Dubee FC, Ernberg I, Gabriel M, Helland Å, Henrique R, Jönsson B, Kallioniemi O, Korbel J, Krause M, Lowy DR, Michielin O, Nagy P et al. (2024)
    Strategies to decrease inequalities in cancer therapeutics, care and prevention: Proceedings on a conference organized by the Pontifical Academy of Sciences and the European Academy of Cancer Sciences, Vatican City, February 23-24, 2023
    Mol Oncol, 18 (2), 245-279
    DOI 10.1002/1878-0261.13575, PubMed 38135904
41. Schulman A, Rousu J, Aittokallio T, Tanoli Z (2024)
    Attention-based approach to predict drug-target interactions across seven target superfamilies
    Bioinformatics, 40 (8)
    DOI 10.1093/bioinformatics/btae496, PubMed 39115379
42. Shahrouzi P, Forouz F, Mathelier A, Kristensen VN, Duijf PHG (2024)
    Copy number alterations: a catastrophic orchestration of the breast cancer genome
    Trends Mol Med, 30 (8), 750-764
    DOI 10.1016/j.molmed.2024.04.017, PubMed 38772764
43. Stålberg SM, Silwal-Pandit L, Bastani NE, Nebdal DJH, Lingjærde OC, Skålhegg BS, Kure EH (2024)
    Preoperative profiles of plasma amino acids and derivatives distinguish periampullary cancer and benign disease
    BMC Cancer, 24 (1), 555
    DOI 10.1186/s12885-024-12320-8, PubMed 38702616
44. Suske T, Sorger H, Manhart G, Ruge F, Prutsch N, Zimmerman MW, Eder T, Abdallah DI, Maurer B, Wagner C, Schönefeldt S, Spirk K, Pichler A, Pemovska T, Schweicker C, Pölöske D, Hubanic E, Jungherz D, Müller TA, Aung MMK, Orlova A, Pham HTT, Zimmel K, Krausgruber T, Bock C et al. (2024)
    Hyperactive STAT5 hijacks T cell receptor signaling and drives immature T cell acute lymphoblastic leukemia
    J Clin Invest, 134 (8)
    DOI 10.1172/JCI168536, PubMed 38618957
45. Tafavvoghi M, Sildnes A, Rakaee M, Shvetsov N, Bongo LA, Busund LR, Møllersen K (2024)
    Deep learning-based classification of breast cancer molecular subtypes from H&E whole-slide images
    J Pathol Inform, 16, 100410
    DOI 10.1016/j.jpi.2024.100410, PubMed 39720418
46. Tanoli Z, Schulman A, Aittokallio T (2024)
    Validation guidelines for drug-target prediction methods
    Expert Opin Drug Discov, 1-15 (in press)
    DOI 10.1080/17460441.2024.2430955, PubMed 39568436
47. Taskén K, F Haj Mohammad S, Fagereng GL, Sørum Falk R, Helland Å, Barjesteh van Waalwijk van Doorn-Khosrovani S, Steen Carlsson K, Ryll B, Jalkanen K, Edsjö A, Russnes HG, Lassen U, Hallersjö Hult E, Lugowska I, Blay JY, Verlingue L, Abel E, Lowery MA, Krebs MG, Staal Rohrberg K, Ojamaa K, Oliveira J, Verheul HMW, Voest EE, Gelderblom H et al. (2024)
    PCM4EU and PRIME-ROSE: Collaboration for implementation of precision cancer medicine in Europe
    Acta Oncol, 63, 385-391
    DOI 10.2340/1651-226X.2024.34791, PubMed 38779910
48. Thunold S, Hernes E, Farooqi S, Öjlert ÅK, Francis RJ, Nowak AK, Szejniuk WM, Nielsen SS, Cedres S, Perdigo MS, Sørensen JB, Meltzer C, Mikalsen LTG, Helland Å, Malinen E, Haakensen VD (2024)
    Outcome prediction based on [18F]FDG PET/CT in patients with pleural mesothelioma treated with ipilimumab and nivolumab +/- UV1 telomerase vaccine
    Eur J Nucl Med Mol Imaging (in press)
    DOI 10.1007/s00259-024-06853-0, PubMed 39133306
49. Tomasova K, Seborova K, Kroupa M, Horak J, Kavec M, Vodickova L, Rob L, Hruda M, Mrhalova M, Bartakova A, Bouda J, Fleischer T, Kristensen VN, Vodicka P, Vaclavikova R (2024)
    Telomere length as a predictor of therapy response and survival in patients diagnosed with ovarian carcinoma
    Heliyon, 10 (13), e33525
    DOI 10.1016/j.heliyon.2024.e33525, PubMed 39050459
50. Ullern A, Holm K, Røssevold AH, Andresen NK, Bang C, Lingjærde OC, Naume B, Hov JR, Kyte JA (2024)
    Gut microbiota diversity is prognostic and associated with benefit from chemo-immunotherapy in metastatic triple-negative breast cancer
    Mol Oncol (in press)
    DOI 10.1002/1878-0261.13760, PubMed 39545921
51. van de Haar J, Roepman P, Andre F, Balmaña J, Castro E, Chakravarty D, Curigliano G, Czarnecka AM, Dienstmann R, Horak P, Italiano A, Marchiò C, Monkhorst K, Pritchard CC, Reardon B, Russnes HEG, Sirohi B, Sosinsky A, Spanic T, Turnbull C, Van Allen E, Westphalen CB, Tamborero D, Mateo J (2024)
    ESMO Recommendations on clinical reporting of genomic test results for solid cancers
    Ann Oncol, 35 (11), 954-967
    DOI 10.1016/j.annonc.2024.06.018, PubMed 39112111
52. von Jan J, Timonen S, Braun T, Jiang Q, Ianevski A, Peng Y, McConnell K, Sindaco P, Müller TA, Pützer S, Klepzig H, Jungherz D, Dechow A, Wahnschaffe L, Giri AK, Kankainen M, Kuusanmäki H, Neubauer HA, Moriggl R, Mazzeo P, Schmidt N, Koch R, Hallek M, Chebel A, Armisen D et al. (2024)
    Optimizing drug combinations for T-PLL: restoring DNA damage and P53-mediated apoptotic responses
    Blood, 144 (15), 1595-1610
    DOI 10.1182/blood.2023022884, PubMed 38941598
53. Zhao Z, Zobolas J, Zucknick M, Aittokallio T (2024)
    Tutorial on survival modeling with applications to omics data
    Bioinformatics, 40 (3)
    DOI 10.1093/bioinformatics/btae132, PubMed 38445722

Publications 2023

1. Athanasiadis P, Ravikumar B, Elliott RJR, Dawson JC, Carragher NO, Clemons PA, Johanssen T, Ebner D, Aittokallio T (2023)
   Chemogenomic library design strategies for precision oncology, applied to phenotypic profiling of glioblastoma patient cells
   iScience, 26 (7), 107209
   DOI 10.1016/j.isci.2023.107209, PubMed 37485377
2. Børø S, Thoresen S, Boge Brant S, Helland Å (2023)
   Initial investigation of using Norwegian health data for the purpose of external comparator arms - an example for non-small cell lung cancer
   Acta Oncol, 62 (12), 1642-1648
   DOI 10.1080/0284186X.2023.2264484, PubMed 37801361
3. Chen Y, He L, Ianevski A, Ayuda-Durán P, Potdar S, Saarela J, Miettinen JJ, Kytölä S, Miettinen S, Manninen M, Heckman CA, Enserink JM, Wennerberg K, Aittokallio T (2023)
   Robust scoring of selective drug responses for patient-tailored therapy selection
   Nat Protoc, 19 (1), 60-82
   DOI 10.1038/s41596-023-00903-x, PubMed 37996540
4. Daniel P, Balušíková K, Václavíková R, Šeborová K, Ransdorfová Š, Valeriánová M, Wei L, Jelínek M, Tlapáková T, Fleischer T, Kristensen VN, Souček P, Ojima I, Kovář J (2023)
   ABCB1 Amplicon Contains Cyclic AMP Response Element-Driven TRIP6 Gene in Taxane-Resistant MCF-7 Breast Cancer Sublines
   Genes (Basel), 14 (2)
   DOI 10.3390/genes14020296, PubMed 36833223
5. Denisova OV, Merisaari J, Huhtaniemi R, Qiao X, Yetukuri L, Jumppanen M, Kaur A, Pääkkönen M, von Schantz-Fant С, Ohlmeyer M, Wennerberg K, Kauko O, Koch R, Aittokallio T, Taipale M, Westermarck J (2023)
   PP2A-based triple-strike therapy overcomes mitochondrial apoptosis resistance in brain cancer cells
   Mol Oncol, 17 (9), 1803-1820
   DOI 10.1002/1878-0261.13488, PubMed 37458534
6. Dyrbekk APH, Warsame AA, Suhrke P, Ludahl MO, Moe JO, Eide IJZ, Lund-Iversen M, Brustugun OT (2023)
   "Evaluation of ROS1 expression and rearrangements in a large cohort of early-stage lung cancer"
   Diagn Pathol, 18 (1), 70
   DOI 10.1186/s13000-023-01357-1, PubMed 37237384
7. Figlioli G, Billaud A, Wang Q, Bolla MK, Dennis J, Lush M, Kvist A, Adank MA, Ahearn TU, Antonenkova NN, Auvinen P, Behrens S, Bermisheva M, Bogdanova NV, Bojesen SE, Bonanni B, Brüning T, Camp NJ, Campbell A, Castelao JE, Cessna MH, Nbcs Collaborators, Czene K, Devilee P, Dörk T et al. (2023)
   Spectrum and Frequency of Germline FANCM Protein-Truncating Variants in 44,803 European Female Breast Cancer Cases
   Cancers (Basel), 15 (13)
   DOI 10.3390/cancers15133313, PubMed 37444426
8. Gjelberg HK, Helgeland L, Liseth K, Micci F, Sandnes M, Russnes HG, Reikvam H (2023)
   Long-Smoldering T-prolymphocytic Leukemia: A Case Report and a Review of the Literature
   Curr Oncol, 30 (11), 10007-10018
   DOI 10.3390/curroncol30110727, PubMed 37999147
9. Halkola AS, Joki K, Mirtti T, Mäkelä MM, Aittokallio T, Laajala TD (2023)
   OSCAR: Optimal subset cardinality regression using the L0-pseudonorm with applications to prognostic modelling of prostate cancer
   PLoS Comput Biol, 19 (3), e1010333
   DOI 10.1371/journal.pcbi.1010333, PubMed 36897911
10. Haugen MH, von der Lippe Gythfeldt H, Egeland EV, Svartdal Normann L, Pandya AD, Vedin LL, Juell S, Tenstad E, Øy GF, Kristian A, Marangoni E, Sørlie T, Steffensen K, Maelandsmo GM, Engebraaten O (2023)
    Liver X receptors induce antiproliferative effects in basal-like breast cancer
    Mol Oncol, 17 (10), 2041-2055
    DOI 10.1002/1878-0261.13476, PubMed 37341140
11. Isaksen KT, Galleberg R, Mastroianni MA, Rinde M, Rusten LS, Barzenje D, Ramslien F, Fluge O, Slaaen M, Meyer P, Liestol K, Smeland EB, Lingjarde OC, Holte H, Brodtkorb M (2023)
    The Geriatric Prognostic Index: a clinical prediction model for survival of older diffuse large B-cell lymphoma patients treated with standard immunochemotherapy
    Haematologica, 108 (9), 2454-2466
    DOI 10.3324/haematol.2022.282289, PubMed 36861406
12. Johanssen T, McVeigh L, Erridge S, Higgins G, Straehla J, Frame M, Aittokallio T, Carragher NO, Ebner D (2023)
    Glioblastoma and the search for non-hypothesis driven combination therapeutics in academia
    Front Oncol, 12, 1075559
    DOI 10.3389/fonc.2022.1075559, PubMed 36733367
13. Langberg CW, Horndalsveen H, Helland Å, Haakensen VD (2023)
    Factors associated with failure to start consolidation durvalumab after definitive chemoradiation for locally advanced NSCLC
    Front Oncol, 13, 1217424
    DOI 10.3389/fonc.2023.1217424, PubMed 37476372
14. Le Tourneau C, André F, Helland Å, Mileshkin L, Minnaard W, Schiel A, Taskén K, Thomas DM, Veronese ML, Durán-Pacheco G, Leyens L, Rufibach K, Thomas M, Krämer A (2023)
    Modified study designs to expand treatment options in personalised oncology: a multistakeholder view
    Eur J Cancer, 194, 113278
    DOI 10.1016/j.ejca.2023.113278, PubMed 37820553
15. Levy-Jurgenson A, Tekpli X, Kristensen VN, Yakhini Z (2023)
    Analysis of Spatial Molecular Data
    Methods Mol Biol, 2614, 349-356
    DOI 10.1007/978-1-0716-2914-7_20, PubMed 36587134
16. Lorenzovici L, Szilberhorn L, Farkas-Ráduly S, Gasparik AI, Precup AM, Nagy AG, Niemann CU, Aittokallio T, Kaló Z, Csanádi M (2023)
    Systematic Literature Review of Economic Evaluations of Treatment Alternatives in Chronic Lymphocytic Leukemia
    BioDrugs, 37 (2), 219-233
    DOI 10.1007/s40259-023-00583-9, PubMed 36795353
17. Mo T, Brandal SHB, Geier OM, Engebråten O, Nilsen LB, Kristensen VN, Hole KH, Hompland T, Fleischer T, Seierstad T (2023)
    MRI Assessment of Changes in Tumor Vascularization during Neoadjuvant Anti-Angiogenic Treatment in Locally Advanced Breast Cancer Patients
    Cancers (Basel), 15 (18)
    DOI 10.3390/cancers15184662, PubMed 37760629
18. Nguyen HL, Geukens T, Maetens M, Aparicio S, Bassez A, Borg A, Brock J, Broeks A, Caldas C, Cardoso F, De Schepper M, Delorenzi M, Drukker CA, Glas AM, Green AR, Isnaldi E, Eyfjörð J, Khout H, Knappskog S, Krishnamurthy S, Lakhani SR, Langerod A, Martens JWM, McCart Reed AE, Murphy L et al. (2023)
    Obesity-associated changes in molecular biology of primary breast cancer
    Nat Commun, 14 (1), 4418
    DOI 10.1038/s41467-023-39996-z, PubMed 37479706
19. Nygaard V, Ree AH, Dagenborg VJ, Børresen-Dale AL, Edwin B, Fretland ÅA, Grzyb K, Haugen MH, Mælandsmo GM, Flatmark K (2023)
    A PRRX1 Signature Identifies TIM-3 and VISTA as Potential Immune Checkpoint Targets in a Subgroup of Microsatellite Stable Colorectal Cancer Liver Metastases
    Cancer Res Commun, 3 (2), 235-244
    DOI 10.1158/2767-9764.CRC-22-0295, PubMed 36968142
20. Otte M, Stachelscheid J, Glaß M, Wahnschaffe L, Jiang Q, Lone W, Ianevski A, Aittokallio T, Iqbal J, Hallek M, Hüttelmaier S, Schrader A, Braun T, Herling M (2023)
    The miR-141/200c-STAT4 Axis Contributes to Leukemogenesis by Enhancing Cell Proliferation in T-PLL
    Cancers (Basel), 15 (9)
    DOI 10.3390/cancers15092527, PubMed 37173993
21. Połeć A, Ekstrøm PO, Fougner C, Sørlie T, Norum JH (2023)
    Rapid assessment of 3-dimensional intra-tumor heterogeneity through cycling temperature capillary electrophoresis
    BMC Res Notes, 16 (1), 167
    DOI 10.1186/s13104-023-06437-5, PubMed 37568187
22. Potdar S, Ianevski F, Ianevski A, Tanoli Z, Wennerberg K, Seashore-Ludlow B, Kallioniemi O, Östling P, Aittokallio T, Saarela J (2023)
    Breeze 2.0: an interactive web-tool for visual analysis and comparison of drug response data
    Nucleic Acids Res, 51 (W1), W57-W61
    DOI 10.1093/nar/gkad390, PubMed 37178002
23. Rakaee M, Andersen S, Giannikou K, Paulsen EE, Kilvaer TK, Busund LR, Berg T, Richardsen E, Lombardi AP, Adib E, Pedersen MI, Tafavvoghi M, Wahl SGF, Petersen RH, Bondgaard AL, Yde CW, Baudet C, Licht P, Lund-Iversen M, Grønberg BH, Fjellbirkeland L, Helland Å, Pøhl M, Kwiatkowski DJ, Donnem T (2023)
    Machine learning-based immune phenotypes correlate with STK11/KEAP1 co-mutations and prognosis in resectable NSCLC: a sub-study of the TNM-I trial
    Ann Oncol, 34 (7), 578-588
    DOI 10.1016/j.annonc.2023.04.005, PubMed 37100205
24. Robsahm TE, Tsuruda KM, Hektoen HH, Storås AH, Cook MB, Hurwitz LM, Langseth H (2023)
    Applying recommended definition of aggressive prostate cancer: a validation study using high-quality data from the Cancer Registry of Norway
    Acta Oncol, 62 (1), 8-14
    DOI 10.1080/0284186X.2023.2175331, PubMed 36762472
25. Skoie IM, Skogås JG, Langø T, Myhr KM, Myhre PL, Goll R, Fretland SØ, Helland Å (2023)
    New centres to carry out more clinical trials in Norway
    Tidsskr Nor Laegeforen, 143 (2)
    DOI 10.4045/tidsskr.22.0722, PubMed 36718905
26. Stashko C, Hayward MK, Northey JJ, Pearson N, Ironside AJ, Lakins JN, Oria R, Goyette MA, Mayo L, Russnes HG, Hwang ES, Kutys ML, Polyak K, Weaver VM (2023)
    A convolutional neural network STIFMap reveals associations between stromal stiffness and EMT in breast cancer
    Nat Commun, 14 (1), 3561
    DOI 10.1038/s41467-023-39085-1, PubMed 37322009
27. van Amerongen R, Bentires-Alj M, van Boxtel AL, Clarke RB, Fre S, Suarez EG, Iggo R, Jechlinger M, Jonkers J, Mikkola ML, Koledova ZS, Sørlie T, Vivanco MD (2023)
    Imagine beyond: recent breakthroughs and next challenges in mammary gland biology and breast cancer research
    J Mammary Gland Biol Neoplasia, 28 (1), 17
    DOI 10.1007/s10911-023-09544-y, PubMed 37450065
28. Vitelli V, Fleischer T, Ankill J, Arjas E, Frigessi A, Kristensen VN, Zucknick M (2023)
    Transcriptomic pan-cancer analysis using rank-based Bayesian inference
    Mol Oncol, 17 (4), 548-563
    DOI 10.1002/1878-0261.13354, PubMed 36562628
29. Wang MM, Coupland SE, Aittokallio T, Figueiredo CR (2023)
    Resistance to immune checkpoint therapies by tumour-induced T-cell desertification and exclusion: key mechanisms, prognostication and new therapeutic opportunities
    Br J Cancer, 129 (8), 1212-1224
    DOI 10.1038/s41416-023-02361-4, PubMed 37454231
30. Wu Y, Wang Z, Zhao Z, Song X, Miao M, Zhang X (2023)
    Bile acid metabolites in early pregnancy and risk of gestational diabetes mellitus: Results from a prospective cohort study
    Diabetes Obes Metab, 25 (8), 2255-2267
    DOI 10.1111/dom.15104, PubMed 37161712

Publications 2022

1. Ahearn TU, Zhang H, Michailidou K, Milne RL, Bolla MK, Dennis J, Dunning AM, Lush M, Wang Q, Andrulis IL, Anton-Culver H, Arndt V, Aronson KJ, Auer PL, Augustinsson A, Baten A, Becher H, Behrens S, Benitez J, Bermisheva M, Blomqvist C, Bojesen SE, Bonanni B, Børresen-Dale AL, Brauch H et al. (2022)
   Common variants in breast cancer risk loci predispose to distinct tumor subtypes
   Breast Cancer Res, 24 (1), 2
   DOI 10.1186/s13058-021-01484-x, PubMed 34983606
2. Aittokallio T (2022)
   What are the current challenges for machine learning in drug discovery and repurposing?
   Expert Opin Drug Discov, 17 (5), 423-425
   DOI 10.1080/17460441.2022.2050694, PubMed 35255749
3. Alexeyenko A, Brustugun OT, Eide IJZ, Gencheva R, Kosibaty Z, Lai Y, de Petris L, Tsakonas G, Grundberg O, Franzen B, Viktorsson K, Lewensohn R, Hydbring P, Ekman S (2022)
   Plasma RNA profiling unveils transcriptional signatures associated with resistance to osimertinib in EGFR T790M positive non-small cell lung cancer patients
   Transl Lung Cancer Res, 11 (10), 2064-2078
   DOI 10.21037/tlcr-22-236, PubMed 36386450
4. Alver TN, Heintz KM, Hovig E, Bøe SL (2022)
   Cooperative induction of receptor tyrosine kinases contributes to adaptive MAPK drug resistance in melanoma through the PI3K pathway
   Cancer Rep (Hoboken), 6 (2), e1736
   DOI 10.1002/cnr2.1736, PubMed 36251678
5. Ambrosini M, Del Re M, Manca P, Hendifar A, Drilon A, Harada G, Ree AH, Klempner S, Mælandsmo GM, Flatmark K, Russnes HG, Cleary JM, Singh H, Sottotetti E, Martinetti A, Randon G, Sartore-Bianchi A, Capone I, Milione M, Di Bartolomeo M, Pietrantonio F (2022)
   ALK Inhibitors in Patients With ALK Fusion-Positive GI Cancers: An International Data Set and a Molecular Case Series
   JCO Precis Oncol, 6 (1), e2200015
   DOI 10.1200/PO.22.00015, PubMed 35476549
6. Ankill J, Aure MR, Bjørklund S, Langberg S, Oslo Breast Cancer Consortium (OSBREAC) , Kristensen VN, Vitelli V, Tekpli X, Fleischer T (2022)
   Epigenetic alterations at distal enhancers are linked to proliferation in human breast cancer
   NAR Cancer, 4 (1), zcac008
   DOI 10.1093/narcan/zcac008, PubMed 35350772
7. Athanasiadis P, Ianevski A, Skånland SS, Aittokallio T (2022)
   Computational Pipeline for Rational Drug Combination Screening in Patient-Derived Cells
   Methods Mol Biol, 2449, 327-348
   DOI 10.1007/978-1-0716-2095-3_14, PubMed 35507270
8. Ballester PJ, Stevens R, Haibe-Kains B, Huang RS, Aittokallio T (2022)
   Artificial intelligence for drug response prediction in disease models
   Brief Bioinform, 23 (1)
   DOI 10.1093/bib/bbab450, PubMed 34655289
9. Berg J, Halvorsen AR, Bengtson MB, Lindberg M, Halvorsen B, Aukrust P, Helland Å, Ueland T (2022)
   Circulating T Cell Activation and Exhaustion Markers Are Associated With Radiation Pneumonitis and Poor Survival in Non-Small-Cell Lung Cancer
   Front Immunol, 13, 875152
   DOI 10.3389/fimmu.2022.875152, PubMed 35911763
10. Berg J, Halvorsen AR, Bengtson MB, Lindberg M, Halvorsen B, Aukrust P, Helland Å, Ueland T (2022)
    Corrigendum: Circulating T cell activation and exhaustion markers are associated with radiation pneumonitis and poor survival in non-small-cell lung cancer
    Front Immunol, 13, 1051156
    DOI 10.3389/fimmu.2022.1051156, PubMed 36263024
11. Bergholtz H, Lien T, Lingaas F, Sørlie T (2022)
    Comparative analysis of the molecular subtype landscape in canine and human mammary gland tumors
    J Mammary Gland Biol Neoplasia, 27 (2), 171-183
    DOI 10.1007/s10911-022-09523-9, PubMed 35932380
12. Bjørklund SS, Aure MR, Häkkinen J, Vallon-Christersson J, Kumar S, Evensen KB, Fleischer T, Tost J, OSBREAC, Sahlberg KK, Mathelier A, Bhanot G, Ganesan S, Tekpli X, Kristensen VN (2022)
    Subtype and cell type specific expression of lncRNAs provide insight into breast cancer
    Commun Biol, 5 (1), 834
    DOI 10.1038/s42003-022-03559-7, PubMed 35982125
13. Børø S, Thoresen S, Helland Å (2022)
    Improvements in survival for patients with stage IV adenocarcinoma in the lung, diagnosed between 2010 - 2020 - A population-based registry study from Norway
    Front Oncol, 12, 1017902
    DOI 10.3389/fonc.2022.1017902, PubMed 36523970
14. Callesen LB, Hamfjord J, Boysen AK, Pallisgaard N, Guren TK, Kure EH, Spindler KG (2022)
    Circulating tumour DNA and its clinical utility in predicting treatment response or survival in patients with metastatic colorectal cancer: a systematic review and meta-analysis
    Br J Cancer, 127 (3), 500-513
    DOI 10.1038/s41416-022-01816-4, PubMed 35440666
15. Callesen LB, Takacova T, Hamfjord J, Würschmidt F, Oldhafer KJ, Brüning R, Arnold D, Spindler KG (2022)
    Circulating DNA in patients undergoing loco-regional treatment of colorectal cancer metastases: a systematic review and meta-analysis
    Ther Adv Med Oncol, 14, 17588359221133171
    DOI 10.1177/17588359221133171, PubMed 36339929
16. Castro-Mondragon JA, Aure MR, Lingjærde OC, Langerød A, Martens JWM, Børresen-Dale AL, Kristensen VN, Mathelier A (2022)
    Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of gene regulatory programs in cancers
    Nucleic Acids Res, 50 (21), 12131-12148
    DOI 10.1093/nar/gkac1143, PubMed 36477895
17. Chen J, Song Y, Li Y, Wei Y, Shen S, Zhao Y, You D, Su L, Bjaanaes MM, Karlsson A, Planck M, Staaf J, Helland Å, Esteller M, Shen H, Christiani DC, Zhang R, Chen F (2022)
    A trans-omics assessment of gene-gene interaction in early-stage NSCLC
    Mol Oncol, 17 (1), 173-187
    DOI 10.1002/1878-0261.13345, PubMed 36408734
18. Denisova OV, Merisaari J, Kaur A, Yetukuri L, Jumppanen M, von Schantz-Fant C, Ohlmeyer M, Wennerberg K, Aittokallio T, Taipale M, Westermarck J (2022)
    Development of actionable targets of multi-kinase inhibitors (AToMI) screening platform to dissect kinase targets of staurosporines in glioblastoma cells
    Sci Rep, 12 (1), 13796
    DOI 10.1038/s41598-022-18118-7, PubMed 35963891
19. Dorraji E, Borgen E, Segura-Peña D, Rawat P, Smorodina E, Dunn C, Greiff V, Sekulić N, Russnes H, Kyte JA (2022)
    Development of a High-Affinity Antibody against the Tumor-Specific and Hyperactive 611-p95HER2 Isoform
    Cancers (Basel), 14 (19)
    DOI 10.3390/cancers14194859, PubMed 36230782
20. Eide IJZ, Stensgaard S, Helland Å, Ekman S, Mellemgaard A, Hansen KH, Cicenas S, Koivunen J, Grønberg BH, Sørensen BS, Brustugun OT (2022)
    Osimertinib in non-small cell lung cancer with uncommon EGFR-mutations: a post-hoc subgroup analysis with pooled data from two phase II clinical trials
    Transl Lung Cancer Res, 11 (6), 953-963
    DOI 10.21037/tlcr-21-995, PubMed 35832438
21. Eliseussen E, Fleischer T, Vitelli V (2022)
    Rank-based Bayesian variable selection for genome-wide transcriptomic analyses
    Stat Med, 41 (23), 4532-4553
    DOI 10.1002/sim.9524, PubMed 35844145
22. Flobak Å, Skånland SS, Hovig E, Taskén K, Russnes HG (2022)
    Functional precision cancer medicine: drug sensitivity screening enabled by cell culture models
    Trends Pharmacol Sci, 43 (11), 973-985
    DOI 10.1016/j.tips.2022.08.009, PubMed 36163057
23. Girard N, Bar J, Garrido P, Garassino MC, McDonald F, Mornex F, Filippi AR, Smit HJM, Peters S, Field JK, Christoph DC, Sibille A, Fietkau R, Haakensen VD, Chouaid C, Markman B, Hiltermann TJN, Taus A, Sawyer W, Allen A, Chander P, Licour M, Solomon B (2022)
    Treatment Characteristics and Real-World Progression-Free Survival in Patients With Unresectable Stage III NSCLC Who Received Durvalumab After Chemoradiotherapy: Findings From the PACIFIC-R Study
    J Thorac Oncol, 18 (2), 181-193
    DOI 10.1016/j.jtho.2022.10.003, PubMed 36307040
24. Gulati G, Tjessem KH, Horndalsveen H, Halvorsen S, Haakensen VD (2022)
    [Checkpoint inhibitor-induced myocarditis]
    Tidsskr Nor Laegeforen, 142 (18)
    DOI 10.4045/tidsskr.21.0817, PubMed 36511752
25. Halkola AS, Aittokallio T, Parvinen K (2022)
    Tumor microenvironment as a metapopulation model: The effects of angiogenesis, emigration and treatment modalities
    J Theor Biol, 545, 111147
    DOI 10.1016/j.jtbi.2022.111147, PubMed 35489642
26. Helland Å, Andersen KK, Myklebust TÅ, Johannesen TB, Aarøe J, Enerly E (2022)
    EGFR-mutation testing and TKI treatment patterns in locally advanced and metastatic NSCLC in Norway - A nationwide retrospective cohort study
    Cancer Treat Res Commun, 33, 100636
    DOI 10.1016/j.ctarc.2022.100636, PubMed 36155129
27. 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
28. 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)
    Correction to: Improving public cancer care by implementing precision medicine in Norway: IMPRESS-Norway
    J Transl Med, 20 (1), 317
    DOI 10.1186/s12967-022-03518-0, PubMed 35841045
29. Hjerkind KV, Johansson ALV, Trewin CB, Russnes HG, Ursin G (2022)
    Incidence of breast cancer subtypes in immigrant and non-immigrant women in Norway
    Breast Cancer Res, 24 (1), 4
    DOI 10.1186/s13058-021-01498-5, PubMed 35012613
30. Horndalsveen H, Alver TN, Dalsgaard AM, Rogg LV, Helbekkmo N, Grønberg BH, Halvorsen TO, Ramberg C, Haakensen VD, Öjlert ÅK, Bjaanaes MM, Helland Å (2022)
    Atezolizumab and stereotactic body radiotherapy in patients with advanced non-small cell lung cancer: safety, clinical activity and ctDNA responses-the ComIT-1 trial
    Mol Oncol, 17 (3), 487-498
    DOI 10.1002/1878-0261.13330, PubMed 36330681
31. Ianevski A, Giri AK, Aittokallio T (2022)
    Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data
    Nat Commun, 13 (1), 1246
    DOI 10.1038/s41467-022-28803-w, PubMed 35273156
32. Ianevski A, Giri AK, Aittokallio T (2022)
    SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples
    Nucleic Acids Res, 50 (W1), W739-W743
    DOI 10.1093/nar/gkac382, PubMed 35580060
33. Ji X, Lin L, Fan J, Li Y, Wei Y, Shen S, Su L, Shafer A, Bjaanaes MM, Karlsson A, Planck M, Staaf J, Helland Å, Esteller M, Zhang R, Chen F, Christiani DC (2022)
    Epigenome-wide three-way interaction study identifies a complex pattern between TRIM27, KIAA0226, and smoking associated with overall survival of early-stage NSCLC
    Mol Oncol, 16 (3), 717-731
    DOI 10.1002/1878-0261.13167, PubMed 34932879
34. 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
35. Kong W, He L, Zhu J, Brück O, Porkka K, Heckman CA, Zhu S, Aittokallio T (2022)
    An immunity and pyroptosis gene-pair signature predicts overall survival in acute myeloid leukemia
    Leukemia, 36 (10), 2384-2395
    DOI 10.1038/s41375-022-01662-6, PubMed 35945345
36. Kong W, Midena G, Chen Y, Athanasiadis P, Wang T, Rousu J, He L, Aittokallio T (2022)
    Systematic review of computational methods for drug combination prediction
    Comput Struct Biotechnol J, 20, 2807-2814
    DOI 10.1016/j.csbj.2022.05.055, PubMed 35685365
37. Kosibaty Z, Brustugun OT, Zwicky Eide IJ, Tsakonas G, Grundberg O, De Petris L, McGowan M, Hydbring P, Ekman S (2022)
    Ras-Related Protein Rab-32 and Thrombospondin 1 Confer Resistance to the EGFR Tyrosine Kinase Inhibitor Osimertinib by Activating Focal Adhesion Kinase in Non-Small Cell Lung Cancer
    Cancers (Basel), 14 (14)
    DOI 10.3390/cancers14143430, PubMed 35884490
38. Langille E, Al-Zahrani KN, Ma Z, Liang M, Uuskula-Reimand L, Espin R, Teng K, Malik A, Bergholtz H, Ghamrasni SE, Afiuni-Zadeh S, Tsai R, Alvi S, Elia A, Lü Y, Oh RH, Kozma KJ, Trcka D, Narimatsu M, Liu JC, Nguyen T, Barutcu S, Loganathan SK, Bremner R, Bader GD et al. (2022)
    Loss of Epigenetic Regulation Disrupts Lineage Integrity, Induces Aberrant Alveogenesis, and Promotes Breast Cancer
    Cancer Discov, 12 (12), 2930-2953
    DOI 10.1158/2159-8290.CD-21-0865, PubMed 36108220
39. Lemma RB, Fleischer T, Martinsen E, Ledsaak M, Kristensen V, Eskeland R, Gabrielsen OS, Mathelier A (2022)
    Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers
    Epigenetics Chromatin, 15 (1), 13
    DOI 10.1186/s13072-022-00444-9, PubMed 35440061
40. Lobert VH, Skardal ML, Malerød L, Simensen JE, Algra HA, Andersen AN, Fleischer T, Enserink HA, Liestøl K, Heath JK, Rusten TE, Stenmark HA (2022)
    PHLPP1 regulates CFTR activity and lumen expansion through AMPK
    Development, 149 (20)
    DOI 10.1242/dev.200955, PubMed 35997536
41. Maggadóttir SM, Kvalheim G, Wernhoff P, Sæbøe-Larssen S, Revheim ME, Josefsen D, Wälchli S, Helland Å, Inderberg EM (2022)
    A phase I/II escalation trial design T-RAD: Treatment of metastatic lung cancer with mRNA-engineered T cells expressing a T cell receptor targeting human telomerase reverse transcriptase (hTERT)
    Front Oncol, 12, 1031232
    DOI 10.3389/fonc.2022.1031232, PubMed 36439452
42. Mo T, Brandal SHB, Köhn-Luque A, Engebraaten O, Kristensen VN, Fleischer T, Hompland T, Seierstad T (2022)
    Quantification of Tumor Hypoxia through Unsupervised Modelling of Consumption and Supply Hypoxia MR Imaging in Breast Cancer
    Cancers (Basel), 14 (5)
    DOI 10.3390/cancers14051326, PubMed 35267636
43. Murumägi A, Ungureanu D, Khan S, Arjama M, Välimäki K, Ianevski A, Ianevski P, Bergström R, Dini A, Kanerva A, Koivisto-Korander R, Tapper J, Lassus H, Loukovaara M, Mägi A, Hirasawa A, Aoki D, Pietiäinen V, Pellinen T, Bützow R, Aittokallio T, Kallioniemi O (2022)
    Drug response profiles in patient-derived cancer cells across histological subtypes of ovarian cancer: real-time therapy tailoring for a patient with low-grade serous carcinoma
    Br J Cancer, 128 (4), 678-690
    DOI 10.1038/s41416-022-02067-z, PubMed 36476658
44. Pedersen CA, Cao MD, Fleischer T, Rye MB, Knappskog S, Eikesdal HP, Lønning PE, Tost J, Kristensen VN, Tessem MB, Giskeødegård GF, Bathen TF (2022)
    DNA methylation changes in response to neoadjuvant chemotherapy are associated with breast cancer survival
    Breast Cancer Res, 24 (1), 43
    DOI 10.1186/s13058-022-01537-9, PubMed 35751095
45. Ravindran V, Wagoner J, Athanasiadis P, Den Hartigh AB, Sidorova JM, Ianevski A, Fink SL, Frigessi A, White J, Polyak SJ, Aittokallio T (2022)
    Discovery of host-directed modulators of virus infection by probing the SARS-CoV-2-host protein-protein interaction network
    Brief Bioinform, 23 (6)
    DOI 10.1093/bib/bbac456, PubMed 36305426
46. Ree AH, Mælandsmo GM, Flatmark K, Russnes HG, Gómez Castañeda M, Aas E (2022)
    Cost-effectiveness of molecularly matched off-label therapies for end-stage cancer - the MetAction precision medicine study
    Acta Oncol, 61 (8), 955-962
    DOI 10.1080/0284186X.2022.2098053, PubMed 35943168
47. Seborova K, Hlavac V, Holy P, Bjørklund SS, Fleischer T, Rob L, Hruda M, Bouda J, Mrhalova M, Allah MMKAO, Vodicka P, Fiala O, Soucek P, Kristensen VN, Vodickova L, Vaclavikova R (2022)
    Complex molecular profile of DNA repair genes in epithelial ovarian carcinoma patients with different sensitivity to platinum-based therapy
    Front Oncol, 12, 1016958
    DOI 10.3389/fonc.2022.1016958, PubMed 36531044
48. Silwal-Pandit L, Stålberg SM, Henrik J. Johansson, Georgios Mermelekas, Lothe IMB, Skrede ML, Dalsgaard AM, Nebdal D, Helland, Lingjærde OC, Labori KJ, Skålhegg BS, Janne Lehtiö, Kure EH (2022)
    Proteome Analysis of Pancreatic Tumors Implicates Extracellular Matrix in Patient Outcome
    Cancer Res Commun, 2 (6), 434-446
    DOI 10.1158/2767-9764.CRC-21-0100, PublikaID 411
49. Silwal-Pandit L, Stålberg SM, Johansson HJ, Mermelekas G, Lothe IMB, Skrede ML, Dalsgaard AM, Nebdal DJH, Helland Å, Lingjærde OC, Labori KJ, Skålhegg BS, Lehtiö J, Kure EH (2022)
    Proteome Analysis of Pancreatic Tumors Implicates Extracellular Matrix in Patient Outcome
    Cancer Res Commun, 2 (6), 434-446
    DOI 10.1158/2767-9764.CRC-21-0100, PubMed 36923555
50. Smirnov P, Smith I, Safikhani Z, Ba-Alawi W, Khodakarami F, Lin E, Yu Y, Martin S, Ortmann J, Aittokallio T, Hafner M, Haibe-Kains B (2022)
    Evaluation of statistical approaches for association testing in noisy drug screening data
    BMC Bioinformatics, 23 (1), 188
    DOI 10.1186/s12859-022-04693-z, PubMed 35585485
51. Staaf J, Häkkinen J, Hegardt C, Saal LH, Kimbung S, Hedenfalk I, Lien T, Sørlie T, Naume B, Russnes H, Marcone R, Ayyanan A, Brisken C, Malterling RR, Asking B, Olofsson H, Lindman H, Bendahl PO, Ehinger A, Larsson C, Loman N, Rydén L, Malmberg M, Borg Å, Vallon-Christersson J (2022)
    RNA sequencing-based single sample predictors of molecular subtype and risk of recurrence for clinical assessment of early-stage breast cancer
    NPJ Breast Cancer, 8 (1), 94
    DOI 10.1038/s41523-022-00465-3, PubMed 35974007
52. 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
53. 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
54. Wang T, Pulkkinen OI, Aittokallio T (2022)
    Target-specific compound selectivity for multi-target drug discovery and repurposing
    Front Pharmacol, 13, 1003480
    DOI 10.3389/fphar.2022.1003480, PubMed 36225560
55. Wolf J, Helland Å, Oh IJ, Migliorino MR, Dziadziuszko R, Wrona A, de Castro J, Mazieres J, Griesinger F, Chlistalla M, Cardona A, Ruf T, Trunzer K, Smoljanovic V, Novello S (2022)
    Final efficacy and safety data, and exploratory molecular profiling from the phase III ALUR study of alectinib versus chemotherapy in crizotinib-pretreated ALK-positive non-small-cell lung cancer
    ESMO Open, 7 (1), 100333
    DOI 10.1016/j.esmoop.2021.100333, PubMed 35042152
56. 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
57. Yin Y, Athanasiadis P, Karlsen L, Urban A, Xu H, Murali I, Fernandes SM, Arribas AJ, Hilli AK, Taskén K, Bertoni F, Mato AR, Normant E, Brown JR, Tjønnfjord GE, Aittokallio T, Skånland SS (2022)
    Functional Testing to Characterize and Stratify PI3K Inhibitor Responses in Chronic Lymphocytic Leukemia
    Clin Cancer Res, 28 (20), 4444-4455
    DOI 10.1158/1078-0432.CCR-22-1221, PubMed 35998013
58. Zhao Z, Wang S, Zucknick M, Aittokallio T (2022)
    Tissue-specific identification of multi-omics features for pan-cancer drug response prediction
    iScience, 25 (8), 104767
    DOI 10.1016/j.isci.2022.104767, PubMed 35992090
59. Zhao Z, Zucknick M, Aittokallio T (2022)
    EnrichIntersect: an R package for custom set enrichment analysis and interactive visualization of intersecting sets
    Bioinform Adv, 2 (1), vbac073
    DOI 10.1093/bioadv/vbac073, PubMed 36699400

Publications 2021

1. Akimov Y, Aittokallio T (2021)
   Re-defining synthetic lethality by phenotypic profiling for precision oncology
   Cell Chem Biol, 28 (3), 246-256
   DOI 10.1016/j.chembiol.2021.01.026, PubMed 33631125
2. Aure MR, Fleischer T, Bjørklund S, Ankill J, Castro-Mondragon JA, OSBREAC, Børresen-Dale AL, Tost J, Sahlberg KK, Mathelier A, Tekpli X, Kristensen VN (2021)
   Crosstalk between microRNA expression and DNA methylation drives the hormone-dependent phenotype of breast cancer
   Genome Med, 13 (1), 72
   DOI 10.1186/s13073-021-00880-4, PubMed 33926515
3. Bahrami N, Jabeen S, Tahiri A, Sauer T, Ødegård HP, Geisler SB, Gravdehaug B, Reitsma LC, Selsås K, Kristensen V, Geisler J (2021)
   Lack of cross-resistance between non-steroidal and steroidal aromatase inhibitors in breast cancer patients: the potential role of the adipokine leptin
   Breast Cancer Res Treat, 190 (3), 435-449
   DOI 10.1007/s10549-021-06399-x, PubMed 34554372
4. Baxter JS, Johnson N, Tomczyk K, Gillespie A, Maguire S, Brough R, Fachal L, Michailidou K, Bolla MK, Wang Q, Dennis J, Ahearn TU, Andrulis IL, Anton-Culver H, Antonenkova NN, Arndt V, Aronson KJ, Augustinsson A, Becher H, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Bogdanova NV, Bojesen SE et al. (2021)
   Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element
   Am J Hum Genet, 108 (7), 1190-1203
   DOI 10.1016/j.ajhg.2021.05.013, PubMed 34146516
5. Ben-Elazar S, Aure MR, Jonsdottir K, Leivonen SK, Kristensen VN, Janssen EAM, Kleivi Sahlberg K, Lingjærde OC, Yakhini Z (2021)
   miRNA normalization enables joint analysis of several datasets to increase sensitivity and to reveal novel miRNAs differentially expressed in breast cancer
   PLoS Comput Biol, 17 (2), e1008608
   DOI 10.1371/journal.pcbi.1008608, PubMed 33566819
6. Berg J, Ramberg C, Haugstvedt JOS, Bengtson MB, Gabrielsen AM, Brustugun OT, Halvorsen AR, Helland Å (2021)
   Lung Function After Stereotactic Body Radiation Therapy for Early-Stage Non-Small Cell Lung Cancer, Changes and Predictive Markers
   Front Oncol, 11, 674731
   DOI 10.3389/fonc.2021.674731, PubMed 34109123
7. Bergholtz H, Carter JM, Cesano A, Cheang MCU, Church SE, Divakar P, Fuhrman CA, Goel S, Gong J, Guerriero JL, Hoang ML, Hwang ES, Kuasne H, Lee J, Liang Y, Mittendorf EA, Perez J, Prat A, Pusztai L, Reeves JW, Riazalhosseini Y, Richer JK, Sahin Ö, Sato H, Schlam I et al. (2021)
   Best Practices for Spatial Profiling for Breast Cancer Research with the GeoMx^® Digital Spatial Profiler
   Cancers (Basel), 13 (17)
   DOI 10.3390/cancers13174456, PubMed 34503266
8. 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
9. Bjaanæs MM, Sande EPS, Loe Ø, Ramberg C, Næss TM, Ottestad A, Rogg LV, Svestad JG, Haakensen VD (2021)
   Improved adaptive radiotherapy to adjust for anatomical alterations during curative treatment for locally advanced lung cancer
   Phys Imaging Radiat Oncol, 18, 51-54
   DOI 10.1016/j.phro.2021.04.003, PubMed 34258408
10. Breast Cancer Association Consortium, Dorling L, Carvalho S, Allen J, González-Neira A, Luccarini C, Wahlström C, Pooley KA, Parsons MT, Fortuno C, Wang Q, Bolla MK, Dennis J, Keeman R, Alonso MR, Álvarez N, Herraez B, Fernandez V, Núñez-Torres R, Osorio A, Valcich J, Li M, Törngren T, Harrington PA, Baynes C et al. (2021)
    Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women
    N Engl J Med, 384 (5), 428-439
    DOI 10.1056/NEJMoa1913948, PubMed 33471991
11. Brück OE, Lallukka-Brück SE, Hohtari HR, Ianevski A, Ebeling FT, Kovanen PE, Kytölä SI, Aittokallio TA, Ramos PM, Porkka KV, Mustjoki SM (2021)
    Machine Learning of Bone Marrow Histopathology Identifies Genetic and Clinical Determinants in Patients with MDS
    Blood Cancer Discov, 2 (3), 238-249
    DOI 10.1158/2643-3230.BCD-20-0162, PubMed 34661156
12. Cichońska A, Ravikumar B, Allaway RJ, Wan F, Park S, Isayev O, Li S, Mason M, Lamb A, Tanoli Z, Jeon M, Kim S, Popova M, Capuzzi S, Zeng J, Dang K, Koytiger G, Kang J, Wells CI, Willson TM, IDG-DREAM Drug-Kinase Binding Prediction Challenge Consortium, Oprea TI, Schlessinger A, Drewry DH, Stolovitzky G et al. (2021)
    Crowdsourced mapping of unexplored target space of kinase inhibitors
    Nat Commun, 12 (1), 3307
    DOI 10.1038/s41467-021-23165-1, PubMed 34083538
13. Eide IJZ, Grut H, Helland Å, Ekman S, Sørensen JB, Hansen KH, Grønberg BH, Cicenas S, Koivunen JP, Mellemgaard A, Brustugun OT (2021)
    Intracranial effect of osimertinib in relapsed EGFR-mutated T790M-positive and -negative non-small cell lung cancer patients: results from a phase II study
    Acta Oncol, 60 (12), 1565-1571
    DOI 10.1080/0284186X.2021.1973092, PubMed 34486915
14. Erdélyi K, Ditrói T, Johansson HJ, Czikora Á, Balog N, Silwal-Pandit L, Ida T, Olasz J, Hajdú D, Mátrai Z, Csuka O, Uchida K, Tóvári J, Engebraten O, Akaike T, Børresen Dale AL, Kásler M, Lehtiö J, Nagy P (2021)
    Reprogrammed transsulfuration promotes basal-like breast tumor progression via realigning cellular cysteine persulfidation
    Proc Natl Acad Sci U S A, 118 (45)
    DOI 10.1073/pnas.2100050118, PubMed 34737229
15. Farooqi SJ, Bjaanæs MM, Helland Å, Haakensen VD (2021)
    [Immunotherapy for malignant pleural mesothelioma]
    Tidsskr Nor Laegeforen, 141
    DOI 10.4045/tidsskr.21.0503, PubMed 34505475
16. Farooqi SJ, Helland A, Haakensen VD, Bjaanaes MM (2021)
    Immunotherapy in malignant pleural mesothelioma
    Tidsskr. Nor. Laegeforen., 141 (12), 1167-1169
17. Fores-Martos J, Cervera-Vidal R, Sierra-Roca J, Lozano-Asencio C, Fedele V, Cornelissen S, Edvarsen H, Tadeo-Cervera I, Eroles P, Lluch A, Tabares-Seisdedos R, Falcó A, Van't Veer LJ, Schmidt M, Quigley DA, Børresen-Dale AL, Kristensen VN, Balmain A, Climent J (2021)
    Circadian PERformance in breast cancer: a germline and somatic genetic study of PER3^VNTR polymorphisms and gene co-expression
    NPJ Breast Cancer, 7 (1), 118
    DOI 10.1038/s41523-021-00329-2, PubMed 34508103
18. Frafjord A, Buer L, Hammarström C, Aamodt H, Woldbæk PR, Brustugun OT, Helland Å, Øynebråten I, Corthay A (2021)
    The Immune Landscape of Human Primary Lung Tumors Is Th2 Skewed
    Front Immunol, 12, 764596
    DOI 10.3389/fimmu.2021.764596, PubMed 34868011
19. Galili B, Tekpli X, Kristensen VN, Yakhini Z (2021)
    Efficient gene expression signature for a breast cancer immuno-subtype
    PLoS One, 16 (1), e0245215
    DOI 10.1371/journal.pone.0245215, PubMed 33434192
20. 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
21. Hamfjord J, Myklebust TÅ, Larsen IK, Kure EH, Glimelius B, Guren TK, Tveit KM, Guren MG (2021)
    Survival Trends of Right- and Left-Sided Colon Cancer across Four Decades: A Norwegian Population-Based Study
    Cancer Epidemiol Biomarkers Prev, 31 (2), 342-351
    DOI 10.1158/1055-9965.EPI-21-0555, PubMed 34853022
22. 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
23. He C, Micallef L, He L, Peddinti G, Aittokallio T, Jacucci G (2021)
    Characterizing the Quality of Insight by Interactions: A Case Study
    IEEE Trans Vis Comput Graph, 27 (8), 3410-3424
    DOI 10.1109/TVCG.2020.2977634, PubMed 32142444
24. Herring S, Oda JM, Wagoner J, Kirchmeier D, O'Connor A, Nelson EA, Huang Q, Liang Y, DeWald LE, Johansen LM, Glass PJ, Olinger GG, Ianevski A, Aittokallio T, Paine MF, Fink SL, White JM, Polyak SJ (2021)
    Inhibition of Arenaviruses by Combinations of Orally Available Approved Drugs
    Antimicrob Agents Chemother, 65 (4)
    DOI 10.1128/AAC.01146-20, PubMed 33468464
25. Herring S, Oda JM, Wagoner J, Kirchmeier D, O'Connor A, Nelson EA, Huang Q, Liang Y, DeWald LE, Johansen LM, Glass PJ, Olinger GG, Ianevski A, Aittokallio T, Paine MF, Fink SL, White JM, Polyak SJ (2021)
    Erratum for Herring et al., "Inhibition of Arenaviruses by Combinations of Orally Available Approved Drugs"
    Antimicrob Agents Chemother, 65 (6)
    DOI 10.1128/AAC.00653-21, PubMed 34006613
26. Haakensen VD, Nowak AK, Ellingsen EB, Farooqi SJ, Bjaanæs MM, Horndalsveen H, Mcculloch T, Grundberg O, Cedres SM, Helland Å (2021)
    NIPU: a randomised, open-label, phase II study evaluating nivolumab and ipilimumab combined with UV1 vaccination as second line treatment in patients with malignant mesothelioma
    J Transl Med, 19 (1), 232
    DOI 10.1186/s12967-021-02905-3, PubMed 34059094
27. Ianevski A, Lahtela J, Javarappa KK, Sergeev P, Ghimire BR, Gautam P, Vähä-Koskela M, Turunen L, Linnavirta N, Kuusanmäki H, Kontro M, Porkka K, Heckman CA, Mattila P, Wennerberg K, Giri AK, Aittokallio T (2021)
    Patient-tailored design for selective co-inhibition of leukemic cell subpopulations
    Sci Adv, 7 (8)
    DOI 10.1126/sciadv.abe4038, PubMed 33608276
28. Jaiswal A, Gautam P, Pietilä EA, Timonen S, Nordström N, Akimov Y, Sipari N, Tanoli Z, Fleischer T, Lehti K, Wennerberg K, Aittokallio T (2021)
    Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor
    Mol Syst Biol, 17 (3), e9526
    DOI 10.15252/msb.20209526, PubMed 33750001
29. Janiszewska M, Stein S, Metzger Filho O, Eng J, Kingston NL, Harper NW, Rye IH, Alečković M, Trinh A, Murphy KC, Marangoni E, Cristea S, Oakes B, Winer EP, Krop IE, Russnes HG, Spellman PT, Bucher E, Hu Z, Chin K, Gray JW, Michor F, Polyak K (2021)
    The impact of tumor epithelial and microenvironmental heterogeneity on treatment responses in HER2+ breast cancer
    JCI Insight, 6 (11)
    DOI 10.1172/jci.insight.147617, PubMed 33886505
30. Johannesen TB, Smeland S, Aaserud S, Buanes EA, Skog A, Ursin G, Helland Å (2021)
    COVID-19 in Cancer Patients, Risk Factors for Disease and Adverse Outcome, a Population-Based Study From Norway
    Front Oncol, 11, 652535
    DOI 10.3389/fonc.2021.652535, PubMed 33842366
31. Johansson ALV, Trewin CB, Fredriksson I, Reinertsen KV, Russnes H, Ursin G (2021)
    In modern times, how important are breast cancer stage, grade and receptor subtype for survival: a population-based cohort study
    Breast Cancer Res, 23 (1), 17
    DOI 10.1186/s13058-021-01393-z, PubMed 33526044
32. Krüger K, Silwal-Pandit L, Wik E, Straume O, Stefansson IM, Borgen E, Garred Ø, Naume B, Engebraaten O, Akslen LA (2021)
    Baseline microvessel density predicts response to neoadjuvant bevacizumab treatment of locally advanced breast cancer
    Sci Rep, 11 (1), 3388
    DOI 10.1038/s41598-021-81914-0, PubMed 33564016
33. Lai X, Taskén HA, Mo T, Funke SW, Frigessi A, Rognes ME, Köhn-Luque A (2021)
    A scalable solver for a stochastic, hybrid cellular automaton model of personalized breast cancer therapy
    Int J Numer Method Biomed Eng, 38 (1), e3542
    DOI 10.1002/cnm.3542, PubMed 34716985
34. Lehtiö J, Arslan T, Siavelis I, Pan Y, Socciarelli F, Berkovska O, Umer HM, Mermelekas G, Pirmoradian M, Jönsson M, Brunnström H, Brustugun OT, Purohit KP, Cunningham R, Foroughi Asl H, Isaksson S, Arbajian E, Aine M, Karlsson A, Kotevska M, Gram Hansen C, Drageset Haakensen V, Helland Å, Tamborero D, Johansson HJ et al. (2021)
    Proteogenomics of non-small cell lung cancer reveals molecular subtypes associated with specific therapeutic targets and immune evasion mechanisms
    Nat Cancer, 2 (11), 1224-1242
    DOI 10.1038/s43018-021-00259-9, PubMed 34870237
35. Levy-Jurgenson A, Tekpli X, Yakhini Z (2021)
    Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging
    Bioinformatics, 37 (21), 3796-3804
    DOI 10.1093/bioinformatics/btab569, PubMed 34358288
36. 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
37. Lilleborge M, Falk RS, Sørlie T, Ursin G, Hofvind S (2021)
    Can breast cancer be stopped? Modifiable risk factors of breast cancer among women with a prior benign or premalignant lesion
    Int J Cancer, 149 (6), 1247-1256
    DOI 10.1002/ijc.33680, PubMed 33990967
38. Lingjærde C, Lien TG, Borgan Ø, Bergholtz H, Glad IK (2021)
    Tailored graphical lasso for data integration in gene network reconstruction
    BMC Bioinformatics, 22 (1), 498
    DOI 10.1186/s12859-021-04413-z, PubMed 34654363
39. Malani D, Kumar A, Brück O, Kontro M, Yadav B, Hellesøy M, Kuusanmäki H, Dufva O, Kankainen M, Eldfors S, Potdar S, Saarela J, Turunen L, Parsons A, Västrik I, Kivinen K, Saarela J, Räty R, Lehto M, Wolf M, Gjertsen BT, Mustjoki S, Aittokallio T, Wennerberg K, Heckman CA et al. (2021)
    Implementing a Functional Precision Medicine Tumor Board for Acute Myeloid Leukemia
    Cancer Discov, 12 (2), 388-401
    DOI 10.1158/2159-8290.CD-21-0410, PubMed 34789538
40. Morra A, Escala-Garcia M, Beesley J, Keeman R, Canisius S, Ahearn TU, Andrulis IL, Anton-Culver H, Arndt V, Auer PL, Augustinsson A, Beane Freeman LE, Becher H, Beckmann MW, Behrens S, Bojesen SE, Bolla MK, Brenner H, Brüning T, Buys SS, Caan B, Campa D, Canzian F, Castelao JE, Chang-Claude J et al. (2021)
    Association of germline genetic variants with breast cancer-specific survival in patient subgroups defined by clinic-pathological variables related to tumor biology and type of systemic treatment
    Breast Cancer Res, 23 (1), 86
    DOI 10.1186/s13058-021-01450-7, PubMed 34407845
41. Maagdenberg H, Oosterom N, Zanen J, Gemmati D, Windsor RE, Heil SG, Esperón P, Jabeen S, Ruiz-Argüelles GJ, Zolk O, Hoerning S, Sleurs C, Lopéz-Lopéz E, Moreno-Galván M, van den Heuvel-Eibrink MM, Maitland-van der Zee AH, Carleton BC (2021)
    Genetic variants associated with methotrexate-induced mucositis in cancer treatment: A systematic review and meta-analysis
    Crit Rev Oncol Hematol, 161, 103312
    DOI 10.1016/j.critrevonc.2021.103312, PubMed 33794308
42. Oksvold MP, Berglund UW, Gad H, Bai B, Stokke T, Rein ID, Pham T, Sanjiv K, Øy GF, Norum JH, Smeland EB, Myklebust JH, Helleday T, Våtsveen TK (2021)
    Karonudib has potent anti-tumor effects in preclinical models of B-cell lymphoma
    Sci Rep, 11 (1), 6317
    DOI 10.1038/s41598-021-85613-8, PubMed 33737576
43. Park J, Choi JY, Choi J, Chung S, Song N, Park SK, Han W, Noh DY, Ahn SH, Lee JW, Kim MK, Jee SH, Wen W, Bolla MK, Wang Q, Dennis J, Michailidou K, Shah M, Conroy DM, Harrington PA, Mayes R, Czene K, Hall P, Teras LR, Patel AV et al. (2021)
    Gene-Environment Interactions Relevant to Estrogen and Risk of Breast Cancer: Can Gene-Environment Interactions Be Detected Only among Candidate SNPs from Genome-Wide Association Studies?
    Cancers (Basel), 13 (10)
    DOI 10.3390/cancers13102370, PubMed 34069208
44. 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
45. Siddiqui FA, Parkkola H, Vukic V, Oetken-Lindholm C, Jaiswal A, Kiriazis A, Pavic K, Aittokallio T, Salminen TA, Abankwa D (2021)
    Novel Small Molecule Hsp90/Cdc37 Interface Inhibitors Indirectly Target K-Ras-Signaling
    Cancers (Basel), 13 (4)
    DOI 10.3390/cancers13040927, PubMed 33672199
46. Tanoli Z, Vähä-Koskela M, Aittokallio T (2021)
    Artificial intelligence, machine learning, and drug repurposing in cancer
    Expert Opin Drug Discov, 16 (9), 977-989
    DOI 10.1080/17460441.2021.1883585, PubMed 33543671
47. Terkelsen T, Pernemalm M, Gromov P, Børresen-Dale AL, Krogh A, Haakensen VD, Lethiö J, Papaleo E, Gromova I (2021)
    High-throughput proteomics of breast cancer interstitial fluid: identification of tumor subtype-specific serologically relevant biomarkers
    Mol Oncol, 15 (2), 429-461
    DOI 10.1002/1878-0261.12850, PubMed 33176066
48. Toutah K, Nawar N, Timonen S, Sorger H, Raouf YS, Bukhari S, von Jan J, Ianevski A, Gawel JM, Olaoye OO, Geletu M, Abdeldayem A, Israelian J, Radu TB, Sedighi A, Bhatti MN, Hassan MM, Manaswiyoungkul P, Shouksmith AE, Neubauer HA, de Araujo ED, Aittokallio T, Krämer OH, Moriggl R, Mustjoki S et al. (2021)
    Development of HDAC Inhibitors Exhibiting Therapeutic Potential in T-Cell Prolymphocytic Leukemia
    J Med Chem, 64 (12), 8486-8509
    DOI 10.1021/acs.jmedchem.1c00420, PubMed 34101461
49. Wahl SGF, Dai HY, Emdal EF, Berg T, Halvorsen TO, Ottestad AL, Lund-Iversen M, Brustugun OT, Førde D, Paulsen EE, Donnem T, Andersen S, Grønberg BH, Richardsen E (2021)
    The Prognostic Effect of KRAS Mutations in Non-Small Cell Lung Carcinoma Revisited: A Norwegian Multicentre Study
    Cancers (Basel), 13 (17)
    DOI 10.3390/cancers13174294, PubMed 34503114
50. Wang T, Szedmak S, Wang H, Aittokallio T, Pahikkala T, Cichonska A, Rousu J (2021)
    Modeling drug combination effects via latent tensor reconstruction
    Bioinformatics, 37 (Suppl_1), i93-i101
    DOI 10.1093/bioinformatics/btab308, PubMed 34252952
51. White BS, Khan SA, Mason MJ, Ammad-Ud-Din M, Potdar S, Malani D, Kuusanmäki H, Druker BJ, Heckman C, Kallioniemi O, Kurtz SE, Porkka K, Tognon CE, Tyner JW, Aittokallio T, Wennerberg K, Guinney J (2021)
    Bayesian multi-source regression and monocyte-associated gene expression predict BCL-2 inhibitor resistance in acute myeloid leukemia
    NPJ Precis Oncol, 5 (1), 71
    DOI 10.1038/s41698-021-00209-9, PubMed 34302041
52. White JM, Schiffer JT, Bender Ignacio RA, Xu S, Kainov D, Ianevski A, Aittokallio T, Frieman M, Olinger GG, Polyak SJ (2021)
    Drug Combinations as a First Line of Defense against Coronaviruses and Other Emerging Viruses
    mBio, 12 (6), e0334721
    DOI 10.1128/mbio.03347-21, PubMed 34933447
53. White JM, Schiffer JT, Ignacio RAB, Xu S, Kainov D, Ianevski A, Aittokallio T, Frieman M, Olinger GG, Polyak SJ (2021)
    Drug Combinations as a First Line of Defense against Coronaviruses and Other Emerging Viruses
    mBio, 12 (6), e03347-21
54. Xu H, Lien T, Bergholtz H, Fleischer T, Djerroudi L, Vincent-Salomon A, Sørlie T, Aittokallio T (2021)
    Multi-Omics Marker Analysis Enables Early Prediction of Breast Tumor Progression
    Front Genet, 12, 670749
    DOI 10.3389/fgene.2021.670749, PubMed 34149812
55. Öjlert ÅK, Nebdal D, Snapkov I, Olsen V, Kidman J, Greiff V, Chee J, Helland Å (2021)
    Dynamic changes in the T cell receptor repertoire during treatment with radiotherapy combined with an immune checkpoint inhibitor
    Mol Oncol, 15 (11), 2958-2968
    DOI 10.1002/1878-0261.13082, PubMed 34402187
56. Aamdal E, Jacobsen KD, Straume O, Kersten C, Herlofsen O, Karlsen J, Hussain I, Amundsen A, Dalhaug A, Nyakas M, Schuster C, Hagene KT, Holmsen K, Russnes HG, Skovlund E, Kaasa S, Aamdal S, Kyte JA, Guren TK (2021)
    Ipilimumab in a real-world population: A prospective Phase IV trial with long-term follow-up
    Int J Cancer, 150 (1), 100-111
    DOI 10.1002/ijc.33768, PubMed 34449877

Publications 2020

1. Abravan A, Eide HA, Helland Å, Malinen E (2020)
   Radiotherapy-related lymphopenia in patients with advanced non-small cell lung cancer receiving palliative radiotherapy
   Clin Transl Radiat Oncol, 22, 15-21
   DOI 10.1016/j.ctro.2020.02.005, PubMed 32181373
2. Akimov Y, Bulanova D, Timonen S, Wennerberg K, Aittokallio T (2020)
   Improved detection of differentially represented DNA barcodes for high-throughput clonal phenomics
   Mol Syst Biol, 16 (3), e9195
   DOI 10.15252/msb.20199195, PubMed 32187448
3. Ask EH, Tschan-Plessl A, Gjerdingen TJ, Sætersmoen ML, Hoel HJ, Wiiger MT, Olweus J, Wahlin BE, Lingjærde OC, Horowitz A, Cashen AF, Watkins M, Fehniger TA, Holte H, Kolstad A, Malmberg KJ (2020)
   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), 180-195.e5
   DOI 10.1016/j.medj.2020.10.006, PubMed 35590201
4. Bergholtz H, Kumar S, Wärnberg F, Lüders T, Kristensen V, Sørlie T (2020)
   Comparable cancer-relevant mutation profiles in synchronous ductal carcinoma in situ and invasive breast cancer
   Cancer Rep (Hoboken), 3 (3), e1248
   DOI 10.1002/cnr2.1248, PubMed 32671987
5. Bergholtz H, Lien TG, Swanson DM, Frigessi A, Oslo Breast Cancer Research Consortium (OSBREAC), Daidone MG, Tost J, Wärnberg F, Sørlie T (2020)
   Contrasting DCIS and invasive breast cancer by subtype suggests basal-like DCIS as distinct lesions
   NPJ Breast Cancer, 6, 26
   DOI 10.1038/s41523-020-0167-x, PubMed 32577501
6. Brustugun OT, Sorhaug S, Gronberg BH, Aanerud M, Al-Zubayidy MMZ, Fjellbirkeland L, Helland A, Berg J, Andreassen B, Paulsen EE, Haram PM, Ashraf H, Wahl SGF (2020)
   Lung cancer: Improved prognosis presents capacity challenges
   Tidsskr. Nor. Laegeforen., 140 (5), 432-434
7. Chen C, Wei Y, Wei L, Chen J, Chen X, Dong X, He J, Lin L, Zhu Y, Huang H, You D, Lai L, Shen S, Duan W, Su L, Shafer A, Fleischer T, Bjaanæs MM, Karlsson A, Planck M, Wang R, Staaf J, Helland Å, Esteller M, Zhang R et al. (2020)
   Epigenome-wide gene-age interaction analysis reveals reversed effects of PRODH DNA methylation on survival between young and elderly early-stage NSCLC patients
   Aging (Albany NY), 12 (11), 10642-10662
   DOI 10.18632/aging.103284, PubMed 32511103
8. Egeland NG, Jonsdottir K, Aure MR, Sahlberg K, Kristensen VN, Cronin-Fenton D, Skaland I, Gudlaugsson E, Baak JPA, Janssen EAM (2020)
   MiR-18a and miR-18b are expressed in the stroma of oestrogen receptor alpha negative breast cancers
   BMC Cancer, 20 (1), 377
   DOI 10.1186/s12885-020-06857-7, PubMed 32370743
9. Eide IJZ, Helland Å, Ekman S, Mellemgaard A, Hansen KH, Cicenas S, Koivunen J, Grønberg BH, Brustugun OT (2020)
   Osimertinib in T790M-positive and -negative patients with EGFR-mutated advanced non-small cell lung cancer (the TREM-study)
   Lung Cancer, 143, 27-35
   DOI 10.1016/j.lungcan.2020.03.009, PubMed 32200138
10. Engelsen AST, Wnuk-Lipinska K, Bougnaud S, Pelissier Vatter FA, Tiron C, Villadsen R, Miyano M, Lotsberg ML, Madeleine N, Panahandeh P, Dhakal S, Tan TZ, Peters SD, Grøndal S, Aziz SM, Nord S, Herfindal L, Stampfer MR, Sørlie T, Brekken RA, Straume O, Halberg N, Gausdal G, Thiery JP, Akslen LA et al. (2020)
    AXL Is a Driver of Stemness in Normal Mammary Gland and Breast Cancer
    iScience, 23 (11), 101649
    DOI 10.1016/j.isci.2020.101649, PubMed 33103086
11. Escala-Garcia M, Abraham J, Andrulis IL, Anton-Culver H, Arndt V, Ashworth A, Auer PL, Auvinen P, Beckmann MW, Beesley J, Behrens S, Benitez J, Bermisheva M, Blomqvist C, Blot W, Bogdanova NV, Bojesen SE, Bolla MK, Børresen-Dale AL, Brauch H, Brenner H, Brucker SY, Burwinkel B, Caldas C, Canzian F et al. (2020)
    A network analysis to identify mediators of germline-driven differences in breast cancer prognosis
    Nat Commun, 11 (1), 312
    DOI 10.1038/s41467-019-14100-6, PubMed 31949161
12. Fachal L, Aschard H, Beesley J, Barnes DR, Allen J, Kar S, Pooley KA, Dennis J, Michailidou K, Turman C, Soucy P, Lemaçon A, Lush M, Tyrer JP, Ghoussaini M, Moradi Marjaneh M, Jiang X, Agata S, Aittomäki K, Alonso MR, Andrulis IL, Anton-Culver H, Antonenkova NN, Arason A, Arndt V et al. (2020)
    Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes
    Nat Genet, 52 (1), 56-73
    DOI 10.1038/s41588-019-0537-1, PubMed 31911677
13. Feng H, Gusev A, Pasaniuc B, Wu L, Long J, Abu-Full Z, Aittomäki K, Andrulis IL, Anton-Culver H, Antoniou AC, Arason A, Arndt V, Aronson KJ, Arun BK, Asseryanis E, Auer PL, Azzollini J, Balmaña J, Barkardottir RB, Barnes DR, Barrowdale D, Beckmann MW, Behrens S, Benitez J, Bermisheva M et al. (2020)
    Transcriptome-wide association study of breast cancer risk by estrogen-receptor status
    Genet Epidemiol, 44 (5), 442-468
    DOI 10.1002/gepi.22288, PubMed 32115800
14. Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, Modi BP, Correard S, Gheorghe M, Baranašić D, Santana-Garcia W, Tan G, Chèneby J, Ballester B, Parcy F, Sandelin A, Lenhard B, Wasserman WW, Mathelier A (2020)
    JASPAR 2020: update of the open-access database of transcription factor binding profiles
    Nucleic Acids Res, 48 (D1), D87-D92
    DOI 10.1093/nar/gkz1001, PubMed 31701148
15. Fougner C, Bergholtz H, Norum JH, Sørlie T (2020)
    Re-definition of claudin-low as a breast cancer phenotype
    Nat Commun, 11 (1), 1787
    DOI 10.1038/s41467-020-15574-5, PubMed 32286297
16. Frafjord A, Skarshaug R, Hammarström C, Stankovic B, Dorg LT, Aamodt H, Woldbaek PR, Helland Å, Brustugun OT, Øynebråten I, Corthay A (2020)
    Antibody combinations for optimized staining of macrophages in human lung tumours
    Scand J Immunol, 92 (1), e12889
    DOI 10.1111/sji.12889, PubMed 32299134
17. 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
18. 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
19. Goleva-Fjellet S, Bjurholt AM, Kure EH, Larsen IK, Støren Ø, Sæbø M (2020)
    Distribution of allele frequencies for genes associated with physical activity and/or physical capacity in a homogenous Norwegian cohort- a cross-sectional study
    BMC Genet, 21 (1), 8
    DOI 10.1186/s12863-020-0813-1, PubMed 31973699
20. Graim K, Gorenshteyn D, Robinson DG, Carriero NJ, Cahill JA, Chakrabarti R, Goldschmidt MH, Durham AC, Funk J, Storey JD, Kristensen VN, Theesfeld CL, Sorenmo KU, Troyanskaya OG (2020)
    Modeling molecular development of breast cancer in canine mammary tumors
    Genome Res, 31 (2), 337-347
    DOI 10.1101/gr.256388.119, PubMed 33361113
21. Halvorsen AR, Haugen MH, Öjlert ÅK, Lund-Iversen M, Jørgensen L, Solberg S, Mælandsmo GM, Brustugun OT, Helland Å (2020)
    Protein Kinase C Isozymes Associated With Relapse Free Survival in Non-Small Cell Lung Cancer Patients
    Front Oncol, 10, 590755
    DOI 10.3389/fonc.2020.590755, PubMed 33324562
22. Hovda T, Tsuruda K, Hoff SR, Sahlberg KK, Hofvind S (2020)
    Radiological review of prior screening mammograms of screen-detected breast cancer
    Eur Radiol, 31 (4), 2568-2579
    DOI 10.1007/s00330-020-07130-y, PubMed 33001307
23. Haakensen VD, Khadse A, Sandhu V, Halvorsen AR, Solberg SK, Jørgensen LH, Brustugun OT, Kure EH, Helland Å (2020)
    Molecular characterisation of TP53 mutated squamous cell carcinomas of the lung to identify putative targets for therapy
    Int J Cancer, 147 (10), 2957-2966
    DOI 10.1002/ijc.33121, PubMed 32468587
24. Ianevski A, Giri AK, Aittokallio T (2020)
    SynergyFinder 2.0: visual analytics of multi-drug combination synergies
    Nucleic Acids Res, 48 (W1), W488-W493
    DOI 10.1093/nar/gkaa216, PubMed 32246720
25. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020)
    Pan-cancer analysis of whole genomes
    Nature, 578 (7793), 82-93
    DOI 10.1038/s41586-020-1969-6, PubMed 32025007
26. Ji X, Lin L, Shen S, Dong X, Chen C, Li Y, Zhu Y, Huang H, Chen J, Chen X, Wei L, He J, Duan W, Su L, Jiang Y, Fan J, Guan J, You D, Shafer A, Bjaanaes MM, Karlsson A, Planck M, Staaf J, Helland Å, Esteller M et al. (2020)
    Epigenetic-smoking interaction reveals histologically heterogeneous effects of TRIM27 DNA methylation on overall survival among early-stage NSCLC patients
    Mol Oncol, 14 (11), 2759-2774
    DOI 10.1002/1878-0261.12785, PubMed 33448640
27. Julkunen H, Cichonska A, Gautam P, Szedmak S, Douat J, Pahikkala T, Aittokallio T, Rousu J (2020)
    Leveraging multi-way interactions for systematic prediction of pre-clinical drug combination effects
    Nat Commun, 11 (1), 6136
    DOI 10.1038/s41467-020-19950-z, PubMed 33262326
28. Knutsen E, Lellahi SM, Aure MR, Nord S, Fismen S, Larsen KB, Gabriel MT, Hedberg A, Bjørklund SS, Oslo Breast Cancer Research Consortium (OSBREAC), Bofin AM, Mælandsmo GM, Sørlie T, Mortensen ES, Perander M (2020)
    The expression of the long NEAT1_2 isoform is associated with human epidermal growth factor receptor 2-positive breast cancers
    Sci Rep, 10 (1), 1277
    DOI 10.1038/s41598-020-57759-4, PubMed 31992741
29. Kramer I, Hooning MJ, Mavaddat N, Hauptmann M, Keeman R, Steyerberg EW, Giardiello D, Antoniou AC, Pharoah PDP, Canisius S, Abu-Ful Z, Andrulis IL, Anton-Culver H, Aronson KJ, Augustinsson A, Becher H, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Bogdanova NV, Bojesen SE, Bolla MK, Bonanni B, Brauch H et al. (2020)
    Breast Cancer Polygenic Risk Score and Contralateral Breast Cancer Risk
    Am J Hum Genet, 107 (5), 837-848
    DOI 10.1016/j.ajhg.2020.09.001, PubMed 33022221
30. Kyte JA, Andresen NK, Russnes HG, Fretland SØ, Falk RS, Lingjærde OC, Naume B (2020)
    ICON: a randomized phase IIb study evaluating immunogenic chemotherapy combined with ipilimumab and nivolumab in patients with metastatic hormone receptor positive breast cancer
    J Transl Med, 18 (1), 269
    DOI 10.1186/s12967-020-02421-w, PubMed 32620163
31. Lampignano R, Neumann MHD, Weber S, Kloten V, Herdean A, Voss T, Groelz D, Babayan A, Tibbesma M, Schlumpberger M, Chemi F, Rothwell DG, Wikman H, Galizzi JP, Riise Bergheim I, Russnes H, Mussolin B, Bonin S, Voigt C, Musa H, Pinzani P, Lianidou E, Brady G, Speicher MR, Pantel K et al. (2020)
    Multicenter Evaluation of Circulating Cell-Free DNA Extraction and Downstream Analyses for the Development of Standardized (Pre)analytical Work Flows
    Clin Chem, 66 (1), 149-160
    DOI 10.1373/clinchem.2019.306837, PubMed 31628139
32. Levy-Jurgenson A, Tekpli X, Kristensen VN, Yakhini Z (2020)
    Spatial transcriptomics inferred from pathology whole-slide images links tumor heterogeneity to survival in breast and lung cancer
    Sci Rep, 10 (1), 18802
    DOI 10.1038/s41598-020-75708-z, PubMed 33139755
33. Malani D, Yadav B, Kumar A, Potdar S, Kontro M, Kankainen M, Javarappa KK, Porkka K, Wolf M, Aittokallio T, Wennerberg K, Heckman CA, Murumägi A, Kallioniemi O (2020)
    KIT pathway upregulation predicts dasatinib efficacy in acute myeloid leukemia
    Leukemia, 34 (10), 2780-2784
    DOI 10.1038/s41375-020-0978-7, PubMed 32678289
34. 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
35. Pulkkinen OI, Gautam P, Mustonen V, Aittokallio T (2020)
    Multiobjective optimization identifies cancer-selective combination therapies
    PLoS Comput Biol, 16 (12), e1008538
    DOI 10.1371/journal.pcbi.1008538, PubMed 33370253
36. 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
37. Riis M (2020)
    Modern surgical treatment of breast cancer
    Ann Med Surg (Lond), 56, 95-107
    DOI 10.1016/j.amsu.2020.06.016, PubMed 32637082
38. Riis M (2020)
    Future perspectives of surgical treatment of breast cancer
    Ann Med Surg (Lond), 59, 93-95
    DOI 10.1016/j.amsu.2020.09.021, PubMed 33005399
39. Russnes HG (2020)
    Clinical trials in the era of precision cancer medicine - for the few or for the many?
    Acta Oncol, 59 (7), 731-732
    DOI 10.1080/0284186X.2020.1777582, PubMed 32579040
40. Stankovic B, Aamodt H, Bjørhovde HAK, Müller E, Hammarström C, Brustugun OT, Helland Å, Øynebråten I, Corthay A (2020)
    The immune microenvironment in typical carcinoid lung tumour, a brief report of four cases
    Scand J Immunol, 92 (2), e12893
    DOI 10.1111/sji.12893, PubMed 32433774
41. Terkelsen T, Russo F, Gromov P, Haakensen VD, Brunak S, Gromova I, Krogh A, Papaleo E (2020)
    Secreted breast tumor interstitial fluid microRNAs and their target genes are associated with triple-negative breast cancer, tumor grade, and immune infiltration
    Breast Cancer Res, 22 (1), 73
    DOI 10.1186/s13058-020-01295-6, PubMed 32605588
42. Tinholt M, Stavik B, Tekpli X, Garred Ø, Borgen E, Kristensen V, Sahlberg KK, Sandset PM, Iversen N (2020)
    Coagulation factor V is a marker of tumor-infiltrating immune cells in breast cancer
    Oncoimmunology, 9 (1), 1824644
    DOI 10.1080/2162402X.2020.1824644, PubMed 33457104
43. 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
44. 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
45. Wang T, Gautam P, Rousu J, Aittokallio T (2020)
    Systematic mapping of cancer cell target dependencies using high-throughput drug screening in triple-negative breast cancer
    Comput Struct Biotechnol J, 18, 3819-3832
    DOI 10.1016/j.csbj.2020.11.001, PubMed 33335681
46. Weber S, Spiegl B, Perakis SO, Ulz CM, Abuja PM, Kashofer K, Leest PV, Azpurua MA, Tamminga M, Brudzewsky D, Rothwell DG, Mohan S, Sartori A, Lampignano R, Konigshofer Y, Sprenger-Haussels M, Wikman H, Bergheim IR, Kloten V, Schuuring E, Speicher MR, Heitzer E (2020)
    Technical Evaluation of Commercial Mutation Analysis Platforms and Reference Materials for Liquid Biopsy Profiling
    Cancers (Basel), 12 (6)
    DOI 10.3390/cancers12061588, PubMed 32560092
47. Yu H, Brustugun OT, Ekman S, Botling J, La Fleur L, Micke P, Solberg S, Berglund A, Rivard C, Hirsch FR (2020)
    Programmed Cell Death Ligand 1 Expression in Resected Non-Small Cell Lung Cancer
    Clin Lung Cancer, 22 (4), e555-e562
    DOI 10.1016/j.cllc.2020.09.018, PubMed 33214079
48. Zhang H, Ahearn TU, Lecarpentier J, Barnes D, Beesley J, Qi G, Jiang X, O'Mara TA, Zhao N, Bolla MK, Dunning AM, Dennis J, Wang Q, Ful ZA, Aittomäki K, Andrulis IL, Anton-Culver H, Arndt V, Aronson KJ, Arun BK, Auer PL, Azzollini J, Barrowdale D, Becher H, Beckmann MW et al. (2020)
    Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses
    Nat Genet, 52 (6), 572-581
    DOI 10.1038/s41588-020-0609-2, PubMed 32424353
49. Zhang R, Chen C, Dong X, Shen S, Lai L, He J, You D, Lin L, Zhu Y, Huang H, Chen J, Wei L, Chen X, Li Y, Guo Y, Duan W, Liu L, Su L, Shafer A, Fleischer T, Moksnes Bjaanæs M, Karlsson A, Planck M, Wang R, Staaf J et al. (2020)
    Independent Validation of Early-Stage Non-Small Cell Lung Cancer Prognostic Scores Incorporating Epigenetic and Transcriptional Biomarkers With Gene-Gene Interactions and Main Effects
    Chest, 158 (2), 808-819
    DOI 10.1016/j.chest.2020.01.048, PubMed 32113923
50. Zhu Q, Tekpli X, Troyanskaya OG, Kristensen VN (2020)
    Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations
    Bioinformatics, 36 (4), 994-999
    DOI 10.1093/bioinformatics/btz709, PubMed 31529022
51. Öjlert ÅK, Nebdal D, Lund-Iversen M, Åstrøm Ellefsen R, Brustugun OT, Gran JM, Halvorsen AR, Helland Å (2020)
    Immune checkpoint blockade in the treatment of advanced non-small cell lung cancer - predictors of response and impact of previous radiotherapy
    Acta Oncol, 60 (2), 149-156
    DOI 10.1080/0284186X.2020.1854851, PubMed 33356733

Publications 2019

1. Abravan A, Eide HA, Løndalen AM, Helland Å, Malinen E (2019)
   Mapping Bone Marrow Response in the Vertebral Column by Positron Emission Tomography Following Radiotherapy and Erlotinib Therapy of Lung Cancer
   Mol Imaging Biol, 21 (2), 391-398
   DOI 10.1007/s11307-018-1226-7, PubMed 29916117
2. Bergholtz H, Lien TG, Ursin G, Holmen MM, Helland Å, Sørlie T, Haakensen VD (2019)
   A Longitudinal Study of the Association between Mammographic Density and Gene Expression in Normal Breast Tissue
   J Mammary Gland Biol Neoplasia, 24 (2), 163-175
   DOI 10.1007/s10911-018-09423-x, PubMed 30613869
3. Bowitz Lothe IM, Kleive D, Pomianowska E, Cvancarova M, Kure E, Dueland S, Gladhaug IP, Labori KJ (2019)
   Clinical relevance of pancreatobiliary and intestinal subtypes of ampullary and duodenal adenocarcinoma: Pattern of recurrence, chemotherapy, and survival after pancreatoduodenectomy
   Pancreatology, 19 (2), 316-324
   DOI 10.1016/j.pan.2019.01.019, PubMed 30713128
4. Brinkman AB, Nik-Zainal S, Simmer F, Rodríguez-González FG, Smid M, Alexandrov LB, Butler A, Martin S, Davies H, Glodzik D, Zou X, Ramakrishna M, Staaf J, Ringnér M, Sieuwerts A, Ferrari A, Morganella S, Fleischer T, Kristensen V, Gut M, van de Vijver MJ, Børresen-Dale AL, Richardson AL, Thomas G, Gut IG et al. (2019)
   Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation
   Nat Commun, 10 (1), 1749
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