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Publications (original articles or review articles) published in 2022 from OUS - Computational Systems Medicine (Aittokallio)

22 publications found

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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