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Publications (original articles or review articles) published in 2024 from OUS - Computational Systems Medicine (Aittokallio)

15 publications found

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

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

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

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

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

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

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

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

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

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

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

Tanoli Z, Schulman A, Aittokallio T (2024)
Validation guidelines for drug-target prediction methods
Expert Opin Drug Discov, 20 (1), 31-45
DOI 10.1080/17460441.2024.2430955, PubMed 39568436

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

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

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