List of selected and latest publications
Selected publications
- Ziaurrehman Tanoli, Adrià Fernández-Torras, Umut Onur Özcan, Aleksandr Kushnir, Kristen Michelle Nader, ... & Tero Aittokallio. Computational drug repurposing: approaches, evaluation of in silico resources and case studies. Nature reviews drug discovery (2025). doi: 10.1038/s41573-025-01164-x
- Aleksandr Ianevski, Kristen Nader, Kyriaki Driva, Wojciech Senkowski, Daria Bulanova, Lidia Moyano-Galceran, Tanja Ruokaranta, Heikki Kuusanmäki, Nemo Ikonen, Philipp Sergeev, Markus Vähä-Koskela, Anil K. Giri, Anna Vähärautio, Mika Kontro, Kimmo Porkka, Esa Pitkänen, Caroline A. Heckman, Krister Wennerberg & Tero Aittokallio. Single-cell transcriptomics identify patient-tailored therapies for selective co-inhibition of cancer clones. Nat Commun 15, 8579 (2024) doi: 10.1038/s41467-024-52980-5
- Yingjia Chen, Liye He, Aleksandr Ianevski, Pilar Ayuda-Durán, Swapnil Potdar, Jani Saarela, Juho J. Miettinen, Sari Kytölä, Susanna Miettinen, Mikko Manninen, Caroline A. Heckman, Jorrit M. Enserink, Krister Wennerberg & Tero Aittokallio. Robust scoring of selective drug responses for patient-tailored therapy selection. Nature Protocols (2023). doi: 10.1038/s41596-023-00903-x
- 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.
- 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.
Recent publications