Publications | Computational Systems Medicine

Publications

List of selected and latest publications

Selected publications

Kong W, He L, Zhu J, Brück O, Porkka K, Heckman CA, Zhu S, Aittokallio T. An immunity and pyroptosis gene-pair signature predicts overall survival in acute myeloid leukemia. Leukemia (2022) doi: 10.1038/s41375-022-01662-6.
Ianevski A, Giri AK, Aittokallio T. Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data. Nat Commun 13, 1246 (2022). doi.org/10.1038/s41467-022-28803-w
Cichońska A, Ravikumar B, Allaway R.J., 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 C.I., Willson T.M., The IDG-DREAM Drug-Kinase Binding Prediction Challenge Consortium, Oprea T.I, Schlessinger A, Drewry D.H., Stolovitzky G, Wennerberg K, Guinney J, Aittokallio T. Crowdsourced mapping of unexplored target space of kinase inhibitors. Nat Commun 12, 3307 (2021). doi: 10.1038/s41467-021-23165-1
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. Patient-tailored design for selective co-inhibition of leukemic cell subpopulations. Science Advances 2020; 7: eabe4038, doi: 10.1126/sciadv.abe4038.
Julkunen H, Cichonska A, Gautam P, Szedmak S, Douat J, Pahikkala T, Aittokallio T, Rousu J. Leveraging multi-way interactions for systematic prediction of pre-clinical drug combination effects. Nat Commun. 2020. doi: 10.1038/s41467-020-19950-z.
Akimov Y, Bulanova D, Timonen S, Wennerberg K, Aittokallio T. Improved detection of differentially represented DNA barcodes for high-throughput clonal phenomics. Molecular Systems Biology 2020. doi:10.15252/msb.20199195.
Ianevski A, Giri AK, Gautam P, Kononov A, Potdar S, Saarela J, Wennerberg K, Aittokallio T. Prediction of drug combination effects with a minimal set of experiments. Nature Machine Intelligence 2019. doi: 10.1038/s42256-019-0122-4. PDF copy.
Ravikumar B, Timonen S, Alam Z, Parri E, Wennerberg K, Aittokallio T. Chemogenomic Analysis of the Druggable Kinome and Its Application to Repositioning and Lead Identification Studies. Cell Chemical Biology 2019; pii: S2451-9456(19)30272-7. doi: 10.1016/j.chembiol.2019.08.007.
He L, Tang J, Andersson EI, Timonen S, Koschmieder S, Wennerberg K, Mustjoki S, Aittokallio T. Patient-customized Drug Combination Prediction and Testing for T-cell Prolymphocytic Leukemia Patients. Cancer Research 2018; 78(9):2407-2418. doi: 10.1158/0008-5472.CAN-17-3644.
Guinney J, Wang T, Laajala TD, Winner KK, Bare JC, Neto EC, Khan SA, Peddinti G, Airola A, Pahikkala T, Mirtti T, Yu T, Bot BM, Shen L, Abdallah K, Norman T, Friend S, Stolovitzky G, Soule H, Sweeney CJ, Ryan CJ, Scher HI, Sartor O, Xie Y, Aittokallio T, Zhou FL, Costello JC. Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data. Lancet Oncol. 2017;18(1):132-142. doi: 10.1016/S1470-2045(16)30560-5.

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