2023
Rizzo A, Maresca C, D’Angelo C, Porru M, Di Vito S, Salvati E, Sacconi A, Berardinelli F, Sgura A, Kuznetsov S, Potdar S, Hassinen A, Stoppacciaro A, Zizza P, Biroccio A. Drug repositioning strategy for the identification of novel telomere-targeting agents: a role for NAMPT inhibitors. Aging Cell. 2023 Nov;22(11):e13944. doi: 10.1111/acel.13944
Pietiäinen V, Polso M, Migh E, Guckelsberger C, Harmati M, Diosdi A, Turunen L, Hassinen A, Potdar S, Koponen A, Sebestyen EG, Kovacs F, Kriston A, Hollandi R, Burian K, Terhes G, Visnyovszki A, Fodor E, Lacza Z, Kantele A, Kolehmainen P, Kakkola L, Strandin T, Levanov L, Kallioniemi O, Kemeny L, Julkunen I, Vapalahti O, Buzas K, Paavolainen L, Horvath P, Hepojoki J. Image-based and machine learning-guided multiplexed serology test for SARS-CoV-2. Cell Rep Methods. 2023 Aug 22;3(8):100565. doi: 10.1016/j.crmeth.2023.100565.
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, Tero Aittokallio T. Robust scoring of selective drug responses for patient-tailored therapy selection. Nature protocols. Accepted for publication.
Kuusanmäki H, Kytölä S, Vänttinen I, Ruokoranta T, Ranta A, Huuhtanen J, Suvela M, Parsons A, Holopainen A, Partanen A, Kuusisto MEL, Koskela S, Räty R, Itälä-Remes M, Västrik I, Dufva O, Siitonen S, Porkka K, Wennerberg K, Heckman CA, Ettala P, Pyörälä M, Rimpiläinen J, Siitonen T, Kontro M. Ex vivo venetoclax sensitivity testing predicts treatment response in acute myeloid leukemia. Haematologica. 2023 Jul 1;108(7):1768-1781. doi: 10.3324/haematol.2022.281692.
Potdar S, Ianevski F, Ianevski A, Tanoli Z, Wennerberg K, Seashore-Ludlow B, Kallioniemi O, Östling P, Aittokallio T, Saarela J. Breeze 2.0: an interactive web-tool for visual analysis and comparison of drug response data. Nucleic Acids Res. 2023. Jul 5;51(W1):W57-W61. doi: 10.1093/nar/gkad390.
Angori S, Banaei-Esfahani A, Mühlbauer K, Bolck HA, Kahraman A, Karakulak T, Poyet C, Feodoroff M, Potdar S, Kallioniemi O, Pietiäinen V, Schraml P, Moch H. Ex Vivo Drug Testing in Patient-derived Papillary Renal Cancer Cells Reveals EGFR and the BCL2 Family as Therapeutic Targets. Eur Urol Focus. 2023 Mar 16:S2405-4569(23)00067-6. doi: 10.1016/j.euf.2023.03.005. Online ahead of print.
Feodoroff M, Mikkonen P, Turunen L, Hassinen A, Paasonen L, Paavolainen L, Potdar S, Murumägi A, Kallioniemi O, Pietiäinen V. Comparison of two supporting matrices for patient-derived cancer cells in 3D drug sensitivity and resistance testing assay (3D-DSRT). SLAS Discov. 2023 Jun;28(4):138-148. doi: 10.1016/j.slasd.2023.03.002.
Feodoroff M, Mikkonen P, Arjama M, Murumägi A, Kallioniemi O, Potdar S, Turunen L, Pietiäinen V. Protocol for 3D Drug Sensitivity and Resistance Testing of Patient-Derived Cancer Cells in 384-Well Plates. SLAS Discov. 2023, 28(2):36-41. doi: 10.1016/j.slasd.2022.11.003.
Kuusanmäki H, Dufva O, Vähä-Koskela M, Leppä AM, Huuhtanen J, Vänttinen IM, Nygren PJ, Klievink J, Bouhlal JOV, Pölönen P, Zhang Q, Adnan Awad S, Mancebo-Pérez C, Saad J, Miettinen JJ, Javarappa KK, Aakko S, Ruokoranta T, Eldfors S, Heinäniemi M, Theilgaard-Mönch K, Wartiovaara-Kautto U, Keränen MAI, Porkka K, Konopleva M, Wennerberg K, Kontro M, Heckman CA, Mustjoki S. Erythroid/megakaryocytic differentiation confers BCL-XL dependency and venetoclax resistance in acute myeloid leukemia. Blood. 2023 Mar 30;141(13):1610-1625. doi: 10.1182/blood.2021011094.
Wang Z, Mačáková M, Bugai A, Kuznetsov SG, Hassinen A, Lenasi T, Potdar S, Friedel CC, Barborič M. P-TEFb promotes cell survival upon p53 activation by suppressing intrinsic apoptosis pathway. Nucleic Acids Res. 2023 Feb 28;51(4):1687-1706. doi: 10.1093/nar/gkad001.
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. 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. 2023 Feb;128(4):678-690. doi: 10.1038/s41416-022-02067-z.
2022
Peterziel H, Jamaladdin N, ElHarouni D, Gerloff XF, Herter S, Fiesel P, Berker Y, Blattner-Johnson M, Schramm K, Jones BC, Reuss D, Turunen L, Friedenauer A, Holland-Letz T, Sill M, Weiser L, Previti C, Balasubramanian G, Gerber NU, Gojo J, Hutter C, Øra I, Lohi O, Kattamis A, de Wilde B, Westermann F, Tippelt S, Graf N, Nathrath M, Sparber-Sauer M, Sehested A, Kramm CM, Dirksen U, Kallioniemi O, Pfister SM, van Tilburg CM, Jones DTW, Saarela J, Pietiäinen V, Jäger N, Schlesner M, Kopp-Schneider A, Oppermann S, Milde T, Witt O, Oehme I. Drug sensitivity profiling of 3D tumor tissue cultures in the pediatric precision oncology program INFORM. NPJ Precis Oncol. 2022 Dec 27;6(1):94. doi: 10.1038/s41698-022-00335-y.
Roering P, Siddiqui A, Heuser VD, Potdar S, Mikkonen P, Oikkonen J, Li Y, Pikkusaari S, Wennerberg K, Hynninen J, Grenman S, Huhtinen K, Auranen A, Carpén O, Kaipio K. Effects of Wee1 inhibitor adavosertib on patient-derived high-grade serous ovarian cancer cells are multiple and independent of homologous recombination status. Front Oncol. 2022 Aug 23;12:954430. doi: 10.3389/fonc.2022.954430.
Kainulainen V, von Schantz-Fant C, Kovanen RM, Potdar S, Laamanen K, Saarela J, Satokari R. Genome-wide siRNA screening reveals several host receptors for the binding of human gut commensal Bifidobacterium bifidum. Npj Biofilms and microbiomes. 2022, Jun 29;8(1):50. doi:10.1038/s41522-022-00312-0.
Skaga E, Kulesskiy E, Potdar S, Panagopoulos I, Micci F, Langmoen IA, Sandberg CJ, Vik-Mo EO. Functional temozolomide sensitivity testing of patient-specific glioblastoma stem cell cultures is predictive of clinical outcome. Transl Oncol. 2022 Sep 15;26:101535. doi: 10.1016/j.tranon.2022.101535. Online ahead of print.
Denisova OV, Merisaari J, Kaur A, Yetukuri L, Jumppanen M, von Schantz-Fant C, Ohlmeyer M, Wennerberg K, Aittokallio T, Taipale M, Westermarck J. Development of actionable targets of multi-kinase inhibitors (AToMI) screening platform to dissect kinase targets of staurosporines in glioblastoma cells. Sci Rep. 2022 Aug 13;12(1):13796. doi: 10.1038/s41598-022-18118-7.
Laukkanen S, Bacquelaine Veloso A, Yan C, Oksa L, Alpert EJ, Do D, Hyvärinen N, McCarthy K, Adhikari A, Yang Q, Iyer S, Garcia SP, Pello A, Ruokoranta T, Moisio S, Adhikari S, Yoder JA, Gallagher KM, Whelton L, Allen JR, Jin AH, Loontiens S, Heinäniemi M, Kelliher MA, Heckman CA, Lohi O, Langenau DM. Combination therapies to inhibit LCK tyrosine kinase and mTOR signaling in T-cell Acute Lymphoblastic Leukemia. Blood. 2022 140 (17): 1891–1906. doi: 10.1182/blood.2021015106.
Hohtari H, Kankainen M, Adnan-Awad S, Yadav B, Potdar S, Ianevski A, Dufva O, Heckman C, Sexl V, Kytölä S, Mustjoki S, Porkka K. Targeting Apoptosis Pathways With BCL2 and MDM2 Inhibitors in Adult B-cell Acute Lymphoblastic Leukemia. Hemasphere. 2022 Feb 24;6(3):e701. doi: 10.1097/HS9.0000000000000701.
Kohtamäki L, Arjama M, Mäkelä S, Ianevski P, Välimäki K, Juteau S, Ilmonen S, Ungureanu D, Kallioniemi O, Murumägi A, Hernberg M. High-throughput ex vivo drug testing identifies potential drugs and drug combinations for NRAS-positive malignant melanoma. Transl Oncol. 2022 Jan;15(1):101290. doi: 10.1016/j.tranon.2021.101290.
ElHarouni D, Berker Y, Peterziel H, Gopisetty A, Turunen L, Kreth S, Stainczyk SA, Oehme I, Pietiäinen V, Jäger N, Witt O, Schlesner M, Oppermann S. iTReX: Interactive exploration of mono- and combination therapy dose response profiling data. Pharmacol Res. 2022 Jan;175:105996. doi: 10.1016/j.phrs.2021.105996.
Malani D, Kumar A, Bruck O, Kontro M, Yadav B, Hellesoy M, Kuusanmaki H, Dufva O, Kankainen M, Eldfors S, Potdar S, Saarela J, Turunen L, Parsons A, Vastrik I, Kivinen K, Saarela J, Raty R, Lehto M, Wolf M, Gjertsen BT, Mustjoki S, Aittokallio T, Wennerberg K, Heckman CA, Kallioniemi O, Porkka K. Implementing a functional precision medicine tumor board for acute myeloid leukemia. Cancer Discovery. 2022; 12:1–14. doi: 10.1158/2159-8290.CD-21-0410.
Tanoli Z, Aldahdooh J, Alam F, Wang Y, Seemab U, Fratelli M, Pavlis P, Hajduch M, Bietrix F, Gribbon P, Zaliani A, Hall MD, Shen M, Brimacombe K, Kulesskiy E, Saarela J, Wennerberg K, Vähä-Koskela M, Tang J. Minimal information for chemosensitivity assays (MICHA): a next-generation pipeline to enable the FAIRification of drug screening experiments. Briefings in Bioinformatics. 2022, 23(1), 1–7 doi: 10.1093/bib/bbab350.
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. Bayesian multi-source regression and monocyte-associated gene expression predict BCL-2 inhibitor resistance in acute myeloid leukemia. NPJ Precis Oncol. 2021 Jul 23;5(1):71. doi: 10.1038/s41698-021-00209-9.
Talwelkar SS, Mäyränpää MI, Søraas L, Potdar S, Bao J, Hemmes A, Linnavirta N, Lømo J, Räsänen J, Knuuttila A, Wennerberg K, Verschuren EW. Functional diagnostics using fresh uncultured lung tumor cells to guide personalized treatments. Cell Rep Med. 2021 Aug 17;2(8):100373. doi: 10.1016/j.xcrm.2021.100373
Tuomainen K, Hyytiäinen A, Al-Samadi A, Ianevski P, Ianevski A, Potdar S, Turunen L, Saarela J, Kuznetsov S, Wahbi W, Risteli M, Mäkitie A, Monni O, Salo T. High-throughput compound screening identifies navitoclax combined with irradiation as a candidate therapy for HPV-negative head and neck squamous cell carcinoma. Scientific Reports. 2021 Jul 20;11(1):14755. doi: 10.1038/s41598-021-94259-5.
Jamshidi M, Fagerholm R, Muranen TA, Kaur S, Potdar S, Khan S, Netti E, Mpindi J-P, Yadav B, Kiiski JI, Aittomäki K, Heikkilä P, Saarela J, Bützow R, Blomqvist C, Nevanlinna H. High miR-30 expression associates with improved breast cancer patient survival and treatment outcome. Cancers (Basel). 2021 Jun 10;13(12):2907. doi: 10.3390/cancers13122907.
Wang L, Poque S, Laamanen K, Saarela J, Poso A, Laitinen T, Valkonen J. In vitro identification and in vivo confirmation of inhibitors for SPCSV RNA silencing suppressor, a viral RNase III. Journal of Virology. 2021 May 24;95(12):e00107-21. doi: 10.1128/JVI.00107-21.
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. Sci Adv. 2021 Feb 19;7(8):eabe4038. doi: 10.1126/sciadv.abe4038.
Adnan-Awad S, Kim D, Hohtari H, Javarappa KK, Brandstoetter T, Mayer I, Potdar S, Heckman CA, Kytölä S, Porkka K, Doma E, Sexl V, Kankainen M, Mustjoki S. Characterization of p190-Bcr-Abl chronic myeloid leukemia reveals specific signaling pathways and therapeutic targets. Leukemia. 2021 Jul;35(7):1964-1975. doi: 10.1038/s41375-020-01082-4.
Ianevski A, Yao R, Biza S, Zusinaite E, Mannik A, Kivi G, Planken A, Kurg K, Tombak EM, Ustav M Jr, Shtaida N, Kulesskiy E, Jo E, Yang J, Lysvand H, Løseth K, Oksenych V, Aas PA, Tenson T, Vitkauskienė A, Windisch MP, Fenstad MH, Nordbø SA, Ustav M, Bjørås M, Kainov DE. Identification and Tracking of Antiviral Drug Combinations. Viruses. 2020, 12(10):1178. doi: 10.3390/v12101178.
Torrente L, Maan G, Rezig AO, Quinn J, Jackson A, Grilli A, Casares L, Zhang Y, Kulesskiy E, Saarela J, Bicciato S, Edwards J, Dinkova-Kostova A, de la Vega L. High NRF2 levels correlate with poor prognosis in colorectal cancer patients and with sensitivity to the kinase inhibitor AT9283 in vitro. Biomolecules. 2020, 10(10):1365. doi: 10.3390/biom10101365.
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. KIT pathway upregulation predicts dasatinib efficacy in acute myeloid leukemia. Leukemia. 2020, 34(10):2780-2784. doi: 10.1038/s41375-020-0978-7.
Hansson K, Radke K, Aaltonen K, Saarela J, Mañas A, Sjölund J, Smith E, Wennerberg K, Gisselsson D, Bexell D. Therapeutic targeting of KSP in preclinical models of high-risk neuroblastoma. Science Translational Medicine. Accepted for publication.
Bruun J, Kryeziu K, Eide PW, Hossein Moosavi S, Eilertsen I, Langerud J, Røsok B, Totland MZ, Brunsell T, Pellinen T, Saarela J , Bergsland CH, Brudvik K, Guren T, Dienstmann R, Guren MG, Nesbakken A, Atle Bjørnbeth B, Sveen A, Lothe RA. Moderate inter-metastatic heterogeneity of drug sensitivities in organoids from patients with multiple colorectal cancer liver metastases. Clinical Cancer Research. Accepted for publication.
Kauko O, Imanishi SY, Kulesskiy E, Yetukuri L, Laajala TD, Sharma M, Pavic K, Aakula A, Rupp C, Jumppanen M, Haapaniemi P, Ruan L, Yadav B, Suni V, Varila T, Corthals GL, Reimand J, Wennerberg K, Aittokallio T, Westermarck J. Phosphoproteome and drug response effects mediated by the three Protein Phosphatase 2A inhibitor proteins CIP2A, SET and PME-1. J Biol Chem. 2020, Feb 18. pii: jbc.RA119.011265. doi: 10.1074/jbc.RA119.011265. [Epub ahead of print]
Potdar S, Ianevski A, Mpindi JP, Bychkov D, Fiere C, Ianevski P, Yadav B, Wennerberg K, Aittokallio T, Kallioniemi O, Saarela J*, Östling P*. Breeze: an integrated quality control and data analysis application for high-throughput drug screening. Bioinformatics, accepted for publication. *equal contribution. doi: 10.1093/bioinformatics/btaa138
Gupta A, Gautam P, Wennerberg K, Aittokallio T. A normalized drug response metric improves accuracy and consistency of anticancer drug sensitivity quantification in cell-based screening. Communications biology. 2020, 3:42. doi: 10.1038/s42003-020-0765-z.
Kaipio K, Chen P, Roering P, Huhtinen K, Mikkonen P, Östling P, Lehtinen L, Mansuri N, Korpela T, Potdar S, Hynninen J, Auranen A, Grénman S, Wennerberg K, Hautaniemi S, Carpén O. ALDH1A1-related stemness in high-grade serous ovarian cancer is a negative prognostic indicator but potentially targetable by EGFR/mTOR-PI3K/aurora kinase inhibitors. J Pathol. 2020, 250(2):159-169. doi: 10.1002/path.5356.
Tanoli Z, Alam Z, Ianevski A, Wennerberg K, Vähä-Koskela M, Aittokallio T. Interactive visual analysis of drug-target interaction networks using Drug Target Profiler, with applications to precision medicine and drug repurposing. Brief Bioinform. 2020, 21 (1), 211–220, https://doi.org/10.1093/bib/bby119.
Tuomainen K, Al-Samadi A, Potdar S, Turunen L, Turunen M, Karhemo PR, Bergman P, Risteli M, Åström P, Tiikkaja R, Grenman R, Wennerberg K, Monni O, Salo T. Human Tumor-Derived Matrix Improves the Predictability of Head and Neck Cancer Drug Testing. Cancers (Basel). 2019, 12(1). pii: E92. doi: 10.3390/cancers12010092.
Wang W, Malyutina A, Pessia A, Saarela J, Heckman C, Tang J. Combined gene essentiality scoring (CES) improves the prediction of cancer dependency map. EBioMedicine. 2019, 67-80. doi: 10.1016/j.ebiom.2019.10.051.
Facciotto C, Casado J, Turunen L, Leivonen S-K, Tumiati M, Rantanen V, Kauppi L, Lehtonen R, Leppä S, Wennerberg K, Hautaniemi S. Drug screening approach combines epigenetic sensitization with immunochemotherapy in cancer. Clin Epigenet. 2019, 11, 192. doi.org/10.1186/s13148-019-0781-3.
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. Nat Mach Intell 2019, 1, 568–577. doi.org/10.1038/s42256-019-0122-4.
Skaga E, Kulesskiy E, Brynjulvsen M, Sandberg CJ, Potdar S, Langmoen IA, Laakso A, Gaál-Paavola E, Perola M, Wennerberg K, Vik-Mo EO. Feasibility study of using high-throughput drug sensitivity testing to target recurrent glioblastoma stem cells for individualized treatment. Clin Transl Med. 2019, 8(1):33. doi: 10.1186/s40169-019-0253-6.
Skaga E, Kulesskiy E, Fayzullin A, Sandberg CJ, Potdar S, Kyttälä A, Langmoen IA, Laakso A, Gaál-Paavola E, Perola M, Wennerberg K, Vik-Mo EO. Intertumoral heterogeneity in patient-specific drug sensitivities in treatment-naïve glioblastoma. BMC Cancer. 2019, 19(1):628. doi: 10.1186/s12885-019-5861-4.
Talwelkar SS, Nagaraj AS, Devlin JR, Hemmes A, Potdar S, Kiss EA, Saharinen P, Salmenkivi K, Mäyränpää MI, Wennerberg K, Verschuren EW. Receptor Tyrosine Kinase Signaling Networks Define Sensitivity to ERBB Inhibition and Stratify Kras-Mutant Lung Cancers. Mol Cancer Ther. 2019, 18(10):1863-1874. doi: 10.1158/1535-7163.MCT-18-0573.
Tang J, Gautam P, Gupta A, He L, Timonen S, Akimov Y, Wang W, Szwajda A, Jaiswal A, Turei D, Yadav B, Kankainen M, Saarela J, Saez-Rodriguez J, Wennerberg K, Aittokallio T. Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer. npj systems biology and applications. 2019, 5:20. doi.org/10.1038/s41540-019-0098-z.
Ianevski A, Zusinaite E, Shtaida N, Kallio-Kokko H, Valkonen M, Kantele A, Telling K, Lutsar I, Letjuka P, Metelitsa N, Oksenych V, Dumpis U, Vitkauskiene A, Stašaitis K, Öhrmalm C, Bondeson K, Bergqvist A, Cox RJ, Tenson T, Merits A, Kainov DE. Low Temperature and Low UV Indexes Correlated with Peaks of Influenza Virus Activity in Northern Europe during 2010–2018. Viruses. 2019, 11, 207. doi: 10.3390/v11030207.
Jaiswal A, Yadav B, Wennerberg K, Aittokallio T. Integrated Analysis of Drug Sensitivity and Selectivity to Predict Synergistic Drug Combinations and Target Coaddictions in Cancer. Methods Mol Biol. 2019, 1888:205-217. doi: 10.1007/978-1-4939-8891-4_12.
Pulkka OP, Gebreyohannes YK, Wozniak A, Mpindi JP, Tynninen O, Icay K, Cervera A, Keskitalo S, Murumägi A, Kulesskiy E, Laaksonen M, Wennerberg K, Varjosalo M, Laakkonen P, Lehtonen R, Hautaniemi S, Kallioniemi O, Schöffski P, Sihto H, Joensuu H. Anagrelide for Gastrointestinal Stromal Tumor. Clin Cancer Res. 2019, 25(5):1676-1687. doi: 10.1158/1078-0432.CCR-18-0815.
Buettner R, Nguyen LXT, Kumar B, Morales C, Liu C, Chen LS, Pemovska T, Synold TW, Palmer J, Thompson R, Li L, Hoang DH, Zhang B, Ghoda L, Kowolik C, Kontro M, Leitch C, Wennerberg K, Yu X, Chen CC, Horne D, Gandhi V, Pullarkat V, Marcucci G, Rosen ST. 8-chloro-adenosine activity in FLT3-ITD acute myeloid leukemia. J Cell Physiol. 2019, 234:16295–16303. doi: 10.1002/jcp.28294.
Brodin BA, Wennerberg K, Lidbrink E, Brosjö O, Potdar S, Wilson JN, Ma L, Moens LN, Hesla A, Porovic E, Bernhardsson E, Papakonstantinou A, Bauer H, Tsagkozis P, von Sivers K, Wejde J, Östling P, Kallioniemi O, Stragliotto CL. Drug sensitivity testing on patient-derived sarcoma cells predicts patient response to treatment and identifies c-Sarc inhibitors as active drugs for translocation sarcomas. Br J Cancer. 2019, 120 (4):435-443. doi: 10.1038/s41416-018-0359-4.
Tanoli Z, Alam Z, Vähä-Koskela M, Ravikumar B, Malyutina A, Jaiswal A, Tang J, Wennerberg K, Aittokallio T. Drug Target Commons 2.0: a community platform for systematic analysis of drug-target interaction profiles. Database (Oxford). 2018, 1-13. doi: 10.1093/database/bay083.
Vaseva AV, Blake DR, Gilbert TSK, Ng S, Hostetter G, Azam SH, Ozkan-Dagliyan I, Gautam P, Bryant KL, Pearce KH, Herring LE, Han H, Graves LM, Witkiewicz AK, Knudsen ES, Pecot CV, Rashid N, Houghton PJ, Wennerberg K, Cox AD, Der CJ. KRAS Suppression-Induced Degradation of MYC Is Antagonized by a MEK5-ERK5 Compensatory Mechanism. Cancer Cell. 2018, 34(5):807-822.e7. doi: 10.1016/j.ccell.2018.10.001.
Zusinaite E, Ianevski A, Niukkanen D, Poranen MM, Bjørås M, Afset JE, Tenson T, Velagapudi V, Merits A, Kainov DE. A Systems Approach to Study Immuno- and Neuro-Modulatory Properties of Antiviral Agents. Viruses. 2018, 10(8). doi: 10.3390/v10080423. Review.
Loevenich S, Ianevski A, Oitmaa E, Kainov DE, Anthonsen MW. Single Passage of Human Metapneumovirus in LLC-MK2 Cells Does Not Affect Viral Protein-Coding Capacity. Genome Announc. 2018, 6(21). pii: e00440-18. doi: 10.1128/genomeA.00440-18.
Ianevski A, Zusinaite E, Kuivanen S, Strand M, Lysvand H, Teppor M, Kakkola L, Paavilainen H, Laajala M, Kallio-Kokko H, Valkonen M, Kantele A, Telling K, Lutsar I, Letjuka P, Metelitsa N, Oksenych V, Bjørås M, Nordbø SA, Dumpis U, Vitkauskiene A, Öhrmalm C, Bondeson K, Bergqvist A, Aittokallio T, Cox RJ, Evander M, Hukkanen V, Marjomaki V, Julkunen I, Vapalahti O, Tenson T, Merits A, Kainov D. Novel activities of safe-in-human broad-spectrum antiviral agents. Antiviral Res. 2018, 154:174-182. doi: 10.1016/j.antiviral.2018.04.016.
Kauko O, O’Connor CM, Kulesskiy E, Sangodkar J, Aakula A, Izadmehr S, Yetukuri L, Yadav B, Padzik A, Laajala TD, Haapaniemi P, Momeny M, Varila T, Ohlmeyer M, Aittokallio T, Wennerberg K, Narla G, Westermarck J. PP2A inhibition is a druggable MEK inhibitor resistance mechanism in KRAS mutant lung cancer cells. Sci Transl Med. 2018, 10(450). pii: eaaq1093. doi: 10.1126/scitranslmed.aaq1093.
Nepal C, O'Rourke CJ, Oliveira DV, Taranta A, Shema S, Gautam P, Calderaro J, Barbour A, Raggi C, Wennerberg K, Wang XW, Lautem A, Roberts LR, Andersen JB. Genomic Perturbations Reveal Distinct Regulatory Networks in Intrahepatic Cholangiocarcinoma. Hepatology. 2018, 68(3):949-963. doi: 10.1002/hep.29764.
Lepikhova T, Karhemo PR, Louhimo R, Yadav B, Murumägi A, Kulesskiy E, Kivento M, Sihto H, Grénman R, Syrjänen SM, Kallioniemi O, Aittokallio T, Wennerberg K, Joensuu H, Monni O. Drug sensitivity screening and genomic characterization of 45 HPV-negative head and neck carcinoma cell lines for novel biomarkers of drug efficacy. Mol Cancer Ther. 2018, 17(9):2060-2071. doi: 10.1158/1535-7163.MCT-17-0733.
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Härmä H, Tong-Ochoa N, van Adrichem AJ, Jelesarov I, Wennerberg K, Kopra K. Toward universal protein post-translational modification detection in high throughput format. Chem Commun (Camb). 2018, 54(23):2910-2913. doi: 10.1039/c7cc09575a.
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 Res. 2018, 78(9):2407-2418. doi: 10.1158/0008-5472.CAN-17-3644.
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Ali M, Khan SA, Wennerberg K, Aittokallio. Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach. Bioinformatics. 2018, 34(8):1353-1362. doi: 10.1093/bioinformatics/btx766.
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Cichonska A, Ravikumar B, Parri E, Timonen S, Pahikkala T, Airola A, Wennerberg K, Rousu J, Aittokallio T. Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors. PLOS Computational Biology. 2017, 13(8): e1005678. doi: 10.1371/journal.pcbi.1005678.
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Jaiswal A, Peddinti G, Akimov Y, Wennerberg K, Kuznetsov S, Tang J, Aittokallio T. Seed-effect modeling improves the consistency of genome-wide loss-of-function screens and identifies synthetic lethal vulnerabilities in cancer cells. Genome medicine. 2017, 9, 51. doi: 10.1186/s13073-017-0440-2.
Kopra K, van Adrichem AJ, Salo-Ahen OMH, Peltonen J, Wennerberg K, Harma H. High-Throughput Dual Screening Method for Ras Activities and Inhibitors. Analytical Chemistry. 2017, 89, 8, 4508-4516. doi: 10.1021/acs.analchem.6b04904.
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van Adrichem AJ, Wennerberg K. MgcRacGAP inhibition stimulates JAK-dependent STAT3 activity. FEBS Letters. 2015, 589, 24, 3859-3865. doi: 10.1016/j.febslet.2015.11.013.
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Pemovska T, Johnson E, Kontro M, Repasky GA, Chen J, Wells P, Cronin CN, McTigue M, Kallioniemi O, Porkka K, Murray BW, Wennerberg K. Axitinib effectively inhibits BCR-ABL1(T315I) with a distinct binding conformation.Nature. 2015, 519(7541):102-5. doi: 10.1038/nature14119.
He L, Wennerberg K, Aittokallio T, Tang J. TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples. Bioinformatics. 2015, 31(11):1866-8. doi: 10.1093/bioinformatics/btv067.
Tang J, Wennerberg K, Aittokallio T. What is synergy? The Saariselka agreement revisited. Frontiers in Pharmacology. 2015, 6:181. doi: 10.3389/fphar.2015.00181.
van Adrichem AJ, Fagerholm A, Turunen L, Lehto A, Saarela J, Koskinen A, Repasky GA, Wennerberg K. Discovery of MINC1, a GTPase-activating protein small molecule inhibitor, targeting MgcRacGAP. Comb Chem High Throughput Screen. 2015, 18(1):3-17. doi:10.2174/1386207318666141205112730.
Li Y, Lu W, Chen D, Boohaker RJ, Zhai L, Padmalayam I, Wennerberg K, Xu B, Zhang W. KIFC1 is a novel potential therapeutic target for breast cancer. Cancer Biology & Therapy. 2015, 16, 9, 1316-1322. doi: 10.1080/15384047.2015.1070980.
Yadav B, Wennerberg K, Aittokallio T, Tang J. Searching for Drug Synergy in Complex Dose–Response Landscapes Using an Interaction Potency Model. Computational and Structural Biotechnology Journal. 2015, 13, 504 - 513. doi: 10.1016/j.csbj.2015.09.001.
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Vidugiriene J, Leippe D, Sobol M, Vidugiris G, Zhou W, Meisenheimer P, Gautam P, Wennerberg K, Cali JJ. Bioluminescent cell-based NAD(P)/NAD(P)H assays for rapid dinucleotide measurement and inhibitor screening. Assay Drug Dev. Technol. 2014, 12(9-10):514-26. doi: 10.1089/adt.2014.605.
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