Publications by Tero Aittokallio

248 publications found

Publications 2024

1. 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, 101521 (in press)
   DOI 10.1016/j.xcrm.2024.101521, PubMed 38653245
2. 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
3. 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

Publications 2023

1. Athanasiadis P, Ravikumar B, Elliott RJR, Dawson JC, Carragher NO, Clemons PA, Johanssen T, Ebner D, Aittokallio T (2023)
   Chemogenomic library design strategies for precision oncology, applied to phenotypic profiling of glioblastoma patient cells
   iScience, 26 (7), 107209
   DOI 10.1016/j.isci.2023.107209, PubMed 37485377
2. 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, Aittokallio T (2023)
   Robust scoring of selective drug responses for patient-tailored therapy selection
   Nat Protoc, 19 (1), 60-82
   DOI 10.1038/s41596-023-00903-x, PubMed 37996540
3. Denisova OV, Merisaari J, Huhtaniemi R, Qiao X, Yetukuri L, Jumppanen M, Kaur A, Pääkkönen M, von Schantz-Fant С, Ohlmeyer M, Wennerberg K, Kauko O, Koch R, Aittokallio T, Taipale M, Westermarck J (2023)
   PP2A-based triple-strike therapy overcomes mitochondrial apoptosis resistance in brain cancer cells
   Mol Oncol, 17 (9), 1803-1820
   DOI 10.1002/1878-0261.13488, PubMed 37458534
4. Halkola AS, Joki K, Mirtti T, Mäkelä MM, Aittokallio T, Laajala TD (2023)
   OSCAR: Optimal subset cardinality regression using the L0-pseudonorm with applications to prognostic modelling of prostate cancer
   PLoS Comput Biol, 19 (3), e1010333
   DOI 10.1371/journal.pcbi.1010333, PubMed 36897911
5. Johanssen T, McVeigh L, Erridge S, Higgins G, Straehla J, Frame M, Aittokallio T, Carragher NO, Ebner D (2023)
   Glioblastoma and the search for non-hypothesis driven combination therapeutics in academia
   Front Oncol, 12, 1075559
   DOI 10.3389/fonc.2022.1075559, PubMed 36733367
6. Lorenzovici L, Szilberhorn L, Farkas-Ráduly S, Gasparik AI, Precup AM, Nagy AG, Niemann CU, Aittokallio T, Kaló Z, Csanádi M (2023)
   Systematic Literature Review of Economic Evaluations of Treatment Alternatives in Chronic Lymphocytic Leukemia
   BioDrugs, 37 (2), 219-233
   DOI 10.1007/s40259-023-00583-9, PubMed 36795353
7. Otte M, Stachelscheid J, Glaß M, Wahnschaffe L, Jiang Q, Lone W, Ianevski A, Aittokallio T, Iqbal J, Hallek M, Hüttelmaier S, Schrader A, Braun T, Herling M (2023)
   The miR-141/200c-STAT4 Axis Contributes to Leukemogenesis by Enhancing Cell Proliferation in T-PLL
   Cancers (Basel), 15 (9)
   DOI 10.3390/cancers15092527, PubMed 37173993
8. Potdar S, Ianevski F, Ianevski A, Tanoli Z, Wennerberg K, Seashore-Ludlow B, Kallioniemi O, Östling P, Aittokallio T, Saarela J (2023)
   Breeze 2.0: an interactive web-tool for visual analysis and comparison of drug response data
   Nucleic Acids Res, 51 (W1), W57-W61
   DOI 10.1093/nar/gkad390, PubMed 37178002
9. Wang MM, Coupland SE, Aittokallio T, Figueiredo CR (2023)
   Resistance to immune checkpoint therapies by tumour-induced T-cell desertification and exclusion: key mechanisms, prognostication and new therapeutic opportunities
   Br J Cancer, 129 (8), 1212-1224
   DOI 10.1038/s41416-023-02361-4, PubMed 37454231

Publications 2022

1. Aittokallio T (2022)
   What are the current challenges for machine learning in drug discovery and repurposing?
   Expert Opin Drug Discov, 17 (5), 423-425
   DOI 10.1080/17460441.2022.2050694, PubMed 35255749
2. 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
3. Ballester PJ, Stevens R, Haibe-Kains B, Huang RS, Aittokallio T (2022)
   Artificial intelligence for drug response prediction in disease models
   Brief Bioinform, 23 (1)
   DOI 10.1093/bib/bbab450, PubMed 34655289
4. 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
5. 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
6. Huhtaniemi R, Sipilä P, Junnila A, Oksala R, Knuuttila M, Mehmood A, Aho E, Laajala TD, Aittokallio T, Laiho A, Elo L, Ohlsson C, Thulin MH, Kallio P, Mäkelä S, Mustonen MVJ, Poutanen M (2022)
   High intratumoral dihydrotestosterone is associated with antiandrogen resistance in VCaP prostate cancer xenografts in castrated mice
   iScience, 25 (5), 104287
   DOI 10.1016/j.isci.2022.104287, PubMed 35573198
7. 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
8. 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
9. 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
10. 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
11. 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
12. 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
13. 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
14. Wagoner J, Herring S, Hsiang TY, Ianevski A, Biering SB, Xu S, Hoffmann M, Pöhlmann S, Gale M, Aittokallio T, Schiffer JT, White JM, Polyak SJ (2022)
    Combinations of Host- and Virus-Targeting Antiviral Drugs Confer Synergistic Suppression of SARS-CoV-2
    Microbiol Spectr, 10 (5), e0333122
    DOI 10.1128/spectrum.03331-22, PubMed 36190406
15. 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
16. 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
17. 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
18. 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

Publications 2021

1. Akimov Y, Aittokallio T (2021)
   Re-defining synthetic lethality by phenotypic profiling for precision oncology
   Cell Chem Biol, 28 (3), 246-256
   DOI 10.1016/j.chembiol.2021.01.026, PubMed 33631125
2. Cichońska A, Ravikumar B, Allaway RJ, 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 CI, Willson TM, IDG-DREAM Drug-Kinase Binding Prediction Challenge Consortium, Oprea TI, Schlessinger A, Drewry DH, Stolovitzky G et al. (2021)
   Crowdsourced mapping of unexplored target space of kinase inhibitors
   Nat Commun, 12 (1), 3307
   DOI 10.1038/s41467-021-23165-1, PubMed 34083538
3. He C, Micallef L, He L, Peddinti G, Aittokallio T, Jacucci G (2021)
   Characterizing the Quality of Insight by Interactions: A Case Study
   IEEE Trans Vis Comput Graph, 27 (8), 3410-3424
   DOI 10.1109/TVCG.2020.2977634, PubMed 32142444
4. He L, Bulanova D, Oikkonen J, Häkkinen A, Zhang K, Zheng S, Wang W, Erkan EP, Carpén O, Joutsiniemi T, Hietanen S, Hynninen J, Huhtinen K, Hautaniemi S, Vähärautio A, Tang J, Wennerberg K, Aittokallio T (2021)
   Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer
   Brief Bioinform, 22 (6)
   DOI 10.1093/bib/bbab272, PubMed 34343245
5. Herring S, Oda JM, Wagoner J, Kirchmeier D, O'Connor A, Nelson EA, Huang Q, Liang Y, DeWald LE, Johansen LM, Glass PJ, Olinger GG, Ianevski A, Aittokallio T, Paine MF, Fink SL, White JM, Polyak SJ (2021)
   Inhibition of Arenaviruses by Combinations of Orally Available Approved Drugs
   Antimicrob Agents Chemother, 65 (4)
   DOI 10.1128/AAC.01146-20, PubMed 33468464
6. Herring S, Oda JM, Wagoner J, Kirchmeier D, O'Connor A, Nelson EA, Huang Q, Liang Y, DeWald LE, Johansen LM, Glass PJ, Olinger GG, Ianevski A, Aittokallio T, Paine MF, Fink SL, White JM, Polyak SJ (2021)
   Erratum for Herring et al., "Inhibition of Arenaviruses by Combinations of Orally Available Approved Drugs"
   Antimicrob Agents Chemother, 65 (6)
   DOI 10.1128/AAC.00653-21, PubMed 34006613
7. 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 (2021)
   Patient-tailored design for selective co-inhibition of leukemic cell subpopulations
   Sci Adv, 7 (8)
   DOI 10.1126/sciadv.abe4038, PubMed 33608276
8. Jaiswal A, Gautam P, Pietilä EA, Timonen S, Nordström N, Akimov Y, Sipari N, Tanoli Z, Fleischer T, Lehti K, Wennerberg K, Aittokallio T (2021)
   Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor
   Mol Syst Biol, 17 (3), e9526
   DOI 10.15252/msb.20209526, PubMed 33750001
9. Malani D, Kumar A, Brück O, Kontro M, Yadav B, Hellesøy M, Kuusanmäki H, Dufva O, Kankainen M, Eldfors S, Potdar S, Saarela J, Turunen L, Parsons A, Västrik I, Kivinen K, Saarela J, Räty R, Lehto M, Wolf M, Gjertsen BT, Mustjoki S, Aittokallio T, Wennerberg K, Heckman CA et al. (2021)
   Implementing a Functional Precision Medicine Tumor Board for Acute Myeloid Leukemia
   Cancer Discov, 12 (2), 388-401
   DOI 10.1158/2159-8290.CD-21-0410, PubMed 34789538
10. Pützer S, Varghese L, von Jan J, Braun T, Giri AK, Mayer P, Riet N, Timonen S, Oberbeck S, Kuusanmäki H, Mustjoki S, Stern MH, Aittokallio T, Newrzela S, Schrader A, Herling M (2021)
    Corrections: Reinstated p53 response and high anti-T-cell leukemia activity by the novel alkylating deacetylase inhibitor tinostamustine
    Leukemia, 35 (1), 293
    DOI 10.1038/s41375-020-01067-3, PubMed 33097839
11. Siddiqui FA, Parkkola H, Vukic V, Oetken-Lindholm C, Jaiswal A, Kiriazis A, Pavic K, Aittokallio T, Salminen TA, Abankwa D (2021)
    Novel Small Molecule Hsp90/Cdc37 Interface Inhibitors Indirectly Target K-Ras-Signaling
    Cancers (Basel), 13 (4)
    DOI 10.3390/cancers13040927, PubMed 33672199
12. Tanoli Z, Vähä-Koskela M, Aittokallio T (2021)
    Artificial intelligence, machine learning, and drug repurposing in cancer
    Expert Opin Drug Discov, 16 (9), 977-989
    DOI 10.1080/17460441.2021.1883585, PubMed 33543671
13. Toutah K, Nawar N, Timonen S, Sorger H, Raouf YS, Bukhari S, von Jan J, Ianevski A, Gawel JM, Olaoye OO, Geletu M, Abdeldayem A, Israelian J, Radu TB, Sedighi A, Bhatti MN, Hassan MM, Manaswiyoungkul P, Shouksmith AE, Neubauer HA, de Araujo ED, Aittokallio T, Krämer OH, Moriggl R, Mustjoki S et al. (2021)
    Development of HDAC Inhibitors Exhibiting Therapeutic Potential in T-Cell Prolymphocytic Leukemia
    J Med Chem, 64 (12), 8486-8509
    DOI 10.1021/acs.jmedchem.1c00420, PubMed 34101461
14. Wang T, Szedmak S, Wang H, Aittokallio T, Pahikkala T, Cichonska A, Rousu J (2021)
    Modeling drug combination effects via latent tensor reconstruction
    Bioinformatics, 37 (Suppl_1), i93-i101
    DOI 10.1093/bioinformatics/btab308, PubMed 34252952
15. 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 (2021)
    Bayesian multi-source regression and monocyte-associated gene expression predict BCL-2 inhibitor resistance in acute myeloid leukemia
    NPJ Precis Oncol, 5 (1), 71
    DOI 10.1038/s41698-021-00209-9, PubMed 34302041
16. White JM, Schiffer JT, Bender Ignacio RA, Xu S, Kainov D, Ianevski A, Aittokallio T, Frieman M, Olinger GG, Polyak SJ (2021)
    Drug Combinations as a First Line of Defense against Coronaviruses and Other Emerging Viruses
    mBio, 12 (6), e0334721
    DOI 10.1128/mbio.03347-21, PubMed 34933447
17. White JM, Schiffer JT, Ignacio RAB, Xu S, Kainov D, Ianevski A, Aittokallio T, Frieman M, Olinger GG, Polyak SJ (2021)
    Drug Combinations as a First Line of Defense against Coronaviruses and Other Emerging Viruses
    mBio, 12 (6), e03347-21
18. Xu H, Lien T, Bergholtz H, Fleischer T, Djerroudi L, Vincent-Salomon A, Sørlie T, Aittokallio T (2021)
    Multi-Omics Marker Analysis Enables Early Prediction of Breast Tumor Progression
    Front Genet, 12, 670749
    DOI 10.3389/fgene.2021.670749, PubMed 34149812

Publications 2020

1. Adnan Awad S, Dufva O, Ianevski A, Ghimire B, Koski J, Maliniemi P, Thomson D, Schreiber A, Heckman CA, Koskenvesa P, Korhonen M, Porkka K, Branford S, Aittokallio T, Kankainen M, Mustjoki S (2020)
   RUNX1 mutations in blast-phase chronic myeloid leukemia associate with distinct phenotypes, transcriptional profiles, and drug responses
   Leukemia, 35 (4), 1087-1099
   DOI 10.1038/s41375-020-01011-5, PubMed 32782381
2. Akimov Y, Bulanova D, Timonen S, Wennerberg K, Aittokallio T (2020)
   Improved detection of differentially represented DNA barcodes for high-throughput clonal phenomics
   Mol Syst Biol, 16 (3), e9195
   DOI 10.15252/msb.20199195, PubMed 32187448
3. Dufva O, Koski J, Maliniemi P, Ianevski A, Klievink J, Leitner J, Pölönen P, Hohtari H, Saeed K, Hannunen T, Ellonen P, Steinberger P, Kankainen M, Aittokallio T, Keränen MAI, Korhonen M, Mustjoki S (2020)
   Integrated drug profiling and CRISPR screening identify essential pathways for CAR T-cell cytotoxicity
   Blood, 135 (9), 597-609
   DOI 10.1182/blood.2019002121, PubMed 31830245
4. Gabriel M, Fey V, Heinosalo T, Adhikari P, Rytkönen K, Komulainen T, Huhtinen K, Laajala TD, Siitari H, Virkki A, Suvitie P, Kujari H, Aittokallio T, Perheentupa A, Poutanen M (2020)
   A relational database to identify differentially expressed genes in the endometrium and endometriosis lesions
   Sci Data, 7 (1), 284
   DOI 10.1038/s41597-020-00623-x, PubMed 32859947
5. Gupta A, Gautam P, Wennerberg K, Aittokallio T (2020)
   A normalized drug response metric improves accuracy and consistency of anticancer drug sensitivity quantification in cell-based screening
   Commun Biol, 3 (1), 42
   DOI 10.1038/s42003-020-0765-z, PubMed 31974521
6. Ianevski A, Giri AK, Aittokallio T (2020)
   SynergyFinder 2.0: visual analytics of multi-drug combination synergies
   Nucleic Acids Res, 48 (W1), W488-W493
   DOI 10.1093/nar/gkaa216, PubMed 32246720
7. Ianevski A, He L, Aittokallio T, Tang J (2020)
   SynergyFinder: a web application for analyzing drug combination dose-response matrix data
   Bioinformatics, 36 (8), 2645
   DOI 10.1093/bioinformatics/btaa102, PubMed 32118251
8. Ianevski A, Timonen S, Kononov A, Aittokallio T, Giri AK (2020)
   SynToxProfiler: An interactive analysis of drug combination synergy, toxicity and efficacy
   PLoS Comput Biol, 16 (2), e1007604
   DOI 10.1371/journal.pcbi.1007604, PubMed 32012154
9. Julkunen H, Cichonska A, Gautam P, Szedmak S, Douat J, Pahikkala T, Aittokallio T, Rousu J (2020)
   Leveraging multi-way interactions for systematic prediction of pre-clinical drug combination effects
   Nat Commun, 11 (1), 6136
   DOI 10.1038/s41467-020-19950-z, PubMed 33262326
10. 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 (2020)
    Phosphoproteome and drug-response effects mediated by the three protein phosphatase 2A inhibitor proteins CIP2A, SET, and PME-1
    J Biol Chem, 295 (13), 4194-4211
    DOI 10.1074/jbc.RA119.011265, PubMed 32071079
11. 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 (2020)
    KIT pathway upregulation predicts dasatinib efficacy in acute myeloid leukemia
    Leukemia, 34 (10), 2780-2784
    DOI 10.1038/s41375-020-0978-7, PubMed 32678289
12. Oberbeck S, Schrader A, Warner K, Jungherz D, Crispatzu G, von Jan J, Chmielewski M, Ianevski A, Diebner HH, Mayer P, Kondo Ados A, Wahnschaffe L, Braun T, Müller TA, Wagle P, Bouska A, Neumann T, Pützer S, Varghese L, Pflug N, Thelen M, Makalowski J, Riet N, Göx HJM, Rappl G et al. (2020)
    Noncanonical effector functions of the T-memory-like T-PLL cell are shaped by cooperative TCL1A and TCR signaling
    Blood, 136 (24), 2786-2802
    DOI 10.1182/blood.2019003348, PubMed 33301031
13. Potdar S, Ianevski A, Mpindi JP, Bychkov D, Fiere C, Ianevski P, Yadav B, Wennerberg K, Aittokallio T, Kallioniemi O, Saarela J, Östling P (2020)
    Breeze: an integrated quality control and data analysis application for high-throughput drug screening
    Bioinformatics, 36 (11), 3602-3604
    DOI 10.1093/bioinformatics/btaa138, PubMed 32119072
14. Pulkkinen OI, Gautam P, Mustonen V, Aittokallio T (2020)
    Multiobjective optimization identifies cancer-selective combination therapies
    PLoS Comput Biol, 16 (12), e1008538
    DOI 10.1371/journal.pcbi.1008538, PubMed 33370253
15. Pützer S, Varghese L, von Jan J, Braun T, Giri AK, Mayer P, Riet N, Timonen S, Oberbeck S, Kuusanmäki H, Mustjoki S, Stern MH, Aittokallio T, Newrzela S, Schrader A, Herling M (2020)
    Reinstated p53 response and high anti-T-cell leukemia activity by the novel alkylating deacetylase inhibitor tinostamustine
    Leukemia, 34 (9), 2513-2518
    DOI 10.1038/s41375-020-0772-6, PubMed 32099034
16. Qiao X, Liu Y, Prada ML, Mohan AK, Gupta A, Jaiswal A, Sharma M, Merisaari J, Haikala HM, Talvinen K, Yetukuri L, Pylvänäinen JW, Klefström J, Kronqvist P, Meinander A, Aittokallio T, Hietakangas V, Eilers M, Westermarck J (2020)
    UBR5 Is Coamplified with MYC in Breast Tumors and Encodes an Ubiquitin Ligase That Limits MYC-Dependent Apoptosis
    Cancer Res, 80 (7), 1414-1427
    DOI 10.1158/0008-5472.CAN-19-1647, PubMed 32029551
17. Tanoli Z, Alam Z, Ianevski A, Wennerberg K, Vähä-Koskela M, Aittokallio T (2020)
    Interactive visual analysis of drug-target interaction networks using Drug Target Profiler, with applications to precision medicine and drug repurposing
    Brief Bioinform, 21 (1), 211-220
    DOI 10.1093/bib/bby119, PubMed 30566623
18. Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, Warner JL, Rieke DT, Aittokallio T, Cerami E, Ritter DI, Schriml LM, Freimuth RR, Haendel M, Raca G, Madhavan S et al. (2020)
    A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer
    Nat Genet, 52 (4), 448-457
    DOI 10.1038/s41588-020-0603-8, PubMed 32246132
19. Wang T, Gautam P, Rousu J, Aittokallio T (2020)
    Systematic mapping of cancer cell target dependencies using high-throughput drug screening in triple-negative breast cancer
    Comput Struct Biotechnol J, 18, 3819-3832
    DOI 10.1016/j.csbj.2020.11.001, PubMed 33335681

Publications 2019

1. Elmadani M, Khan S, Tenhunen O, Magga J, Aittokallio T, Wennerberg K, Kerkelä R (2019)
   Novel Screening Method Identifies PI3Kα, mTOR, and IGF1R as Key Kinases Regulating Cardiomyocyte Survival
   J Am Heart Assoc, 8 (21), e013018
   DOI 10.1161/JAHA.119.013018, PubMed 31617439
2. Gautam P, Jaiswal A, Aittokallio T, Al-Ali H, Wennerberg K (2019)
   Phenotypic Screening Combined with Machine Learning for Efficient Identification of Breast Cancer-Selective Therapeutic Targets
   Cell Chem Biol, 26 (7), 970-979.e4
   DOI 10.1016/j.chembiol.2019.03.011, PubMed 31056464
3. Giri AK, Aittokallio T (2019)
   DNMT Inhibitors Increase Methylation in the Cancer Genome
   Front Pharmacol, 10, 385
   DOI 10.3389/fphar.2019.00385, PubMed 31068808
4. Giri AK, Ianevski A, Aittokallio T (2019)
   Genome-wide off-targets of drugs: risks and opportunities
   Cell Biol Toxicol, 35 (6), 485-487
   DOI 10.1007/s10565-019-09491-7, PubMed 31432301
5. Haikala HM, Anttila JM, Marques E, Raatikainen T, Ilander M, Hakanen H, Ala-Hongisto H, Savelius M, Balboa D, Von Eyss B, Eskelinen V, Munne P, Nieminen AI, Otonkoski T, Schüler J, Laajala TD, Aittokallio T, Sihto H, Mattson J, Heikkilä P, Leidenius M, Joensuu H, Mustjoki S, Kovanen P, Eilers M et al. (2019)
   Pharmacological reactivation of MYC-dependent apoptosis induces susceptibility to anti-PD-1 immunotherapy
   Nat Commun, 10 (1), 620
   DOI 10.1038/s41467-019-08541-2, PubMed 30728358
6. Haikala HM, Anttila JM, Marques E, Raatikainen T, Ilander M, Hakanen H, Ala-Hongisto H, Savelius M, Balboa D, Von Eyss B, Eskelinen V, Munne P, Nieminen AI, Otonkoski T, Schüler J, Laajala TD, Aittokallio T, Sihto H, Mattson J, Heikkilä P, Leidenius M, Joensuu H, Mustjoki S, Kovanen P, Eilers M et al. (2019)
   Publisher Correction: Pharmacological reactivation of MYC-dependent apoptosis induces susceptibility to anti-PD-1 immunotherapy
   Nat Commun, 10 (1), 932
   DOI 10.1038/s41467-019-08956-x, PubMed 30787321
7. Halkola AS, Parvinen K, Kasanen H, Mustjoki S, Aittokallio T (2019)
   Modelling of killer T-cell and cancer cell subpopulation dynamics under immuno- and chemotherapies
   J Theor Biol, 488, 110136
   DOI 10.1016/j.jtbi.2019.110136, PubMed 31887273
8. Heliste J, Chheda H, Paatero I, Salminen TA, Akimov Y, Paavola J, Elenius K, Aittokallio T (2019)
   Genetic and functional implications of an exonic TRIM55 variant in heart failure
   J Mol Cell Cardiol, 138, 222-233
   DOI 10.1016/j.yjmcc.2019.12.008, PubMed 31866377
9. Ianevski A, Giri AK, Gautam P, Kononov A, Potdar S, Saarela J, Wennerberg K, Aittokallio T (2019)
   Prediction of drug combination effects with a minimal set of experiments
   Nat Mach Intell, 1 (12), 568-577
   DOI 10.1038/s42256-019-0122-4, PubMed 32368721
10. Jaiswal A, Yadav B, Wennerberg K, Aittokallio T (2019)
    Integrated Analysis of Drug Sensitivity and Selectivity to Predict Synergistic Drug Combinations and Target Coaddictions in Cancer
    Methods Mol Biol, 1888, 205-217
    DOI 10.1007/978-1-4939-8891-4_12, PubMed 30519949
11. Murtojärvi M, Halkola AS, Airola A, Laajala TD, Mirtti T, Aittokallio T, Pahikkala T (2019)
    Cost-effective survival prediction for patients with advanced prostate cancer using clinical trial and real-world hospital registry datasets
    Int J Med Inform, 133, 104014
    DOI 10.1016/j.ijmedinf.2019.104014, PubMed 31783311
12. Ravikumar B, Timonen S, Alam Z, Parri E, Wennerberg K, Aittokallio T (2019)
    Chemogenomic Analysis of the Druggable Kinome and Its Application to Repositioning and Lead Identification Studies
    Cell Chem Biol, 26 (11), 1608-1622.e6
    DOI 10.1016/j.chembiol.2019.08.007, PubMed 31521622
13. 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 (2019)
    Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer
    NPJ Syst Biol Appl, 5, 20
    DOI 10.1038/s41540-019-0098-z, PubMed 31312514
14. Wahnschaffe L, Braun T, Timonen S, Giri AK, Schrader A, Wagle P, Almusa H, Johansson P, Bellanger D, López C, Haferlach C, Stern MH, Dürig J, Siebert R, Mustjoki S, Aittokallio T, Herling M (2019)
    JAK/STAT-Activating Genomic Alterations Are a Hallmark of T-PLL
    Cancers (Basel), 11 (12)
    DOI 10.3390/cancers11121833, PubMed 31766351

Publications 2018

1. Ali M, Aittokallio T (2018)
   Machine learning and feature selection for drug response prediction in precision oncology applications
   Biophys Rev, 11 (1), 31-39
   DOI 10.1007/s12551-018-0446-z, PubMed 30097794
2. Ali M, Khan SA, Wennerberg K, Aittokallio T (2018)
   Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach
   Bioinformatics, 34 (8), 1353-1362
   DOI 10.1093/bioinformatics/btx766, PubMed 29186355
3. Brück O, Blom S, Dufva O, Turkki R, Chheda H, Ribeiro A, Kovanen P, Aittokallio T, Koskenvesa P, Kallioniemi O, Porkka K, Pellinen T, Mustjoki S (2018)
   Immune cell contexture in the bone marrow tumor microenvironment impacts therapy response in CML
   Leukemia, 32 (7), 1643-1656
   DOI 10.1038/s41375-018-0175-0, PubMed 29925907
4. Cichonska A, Pahikkala T, Szedmak S, Julkunen H, Airola A, Heinonen M, Aittokallio T, Rousu J (2018)
   Learning with multiple pairwise kernels for drug bioactivity prediction
   Bioinformatics, 34 (13), i509-i518
   DOI 10.1093/bioinformatics/bty277, PubMed 29949975
5. Dufva O, Kankainen M, Kelkka T, Sekiguchi N, Awad SA, Eldfors S, Yadav B, Kuusanmäki H, Malani D, Andersson EI, Pietarinen P, Saikko L, Kovanen PE, Ojala T, Lee DA, Loughran TP, Nakazawa H, Suzumiya J, Suzuki R, Ko YH, Kim WS, Chuang SS, Aittokallio T, Chan WC, Ohshima K et al. (2018)
   Aggressive natural killer-cell leukemia mutational landscape and drug profiling highlight JAK-STAT signaling as therapeutic target
   Nat Commun, 9 (1), 1567
   DOI 10.1038/s41467-018-03987-2, PubMed 29674644
6. He L, Kulesskiy E, Saarela J, Turunen L, Wennerberg K, Aittokallio T, Tang J (2018)
   Methods for High-throughput Drug Combination Screening and Synergy Scoring
   Methods Mol Biol, 1711, 351-398
   DOI 10.1007/978-1-4939-7493-1_17, PubMed 29344898
7. He L, Tang J, Andersson EI, Timonen S, Koschmieder S, Wennerberg K, Mustjoki S, Aittokallio T (2018)
   Patient-Customized Drug Combination Prediction and Testing for T-cell Prolymphocytic Leukemia Patients
   Cancer Res, 78 (9), 2407-2418
   DOI 10.1158/0008-5472.CAN-17-3644, PubMed 29483097
8. Heinosalo T, Gabriel M, Kallio L, Adhikari P, Huhtinen K, Laajala TD, Kaikkonen E, Mehmood A, Suvitie P, Kujari H, Aittokallio T, Perheentupa A, Poutanen M (2018)
   Secreted frizzled-related protein 2 (SFRP2) expression promotes lesion proliferation via canonical WNT signaling and indicates lesion borders in extraovarian endometriosis
   Hum Reprod, 33 (5), 817-831
   DOI 10.1093/humrep/dey026, PubMed 29462326
9. Huhtaniemi R, Oksala R, Knuuttila M, Mehmood A, Aho E, Laajala TD, Nicorici D, Aittokallio T, Laiho A, Elo L, Ohlsson C, Kallio P, Mäkelä S, Mustonen MVJ, Sipilä P, Poutanen M (2018)
   Adrenals Contribute to Growth of Castration-Resistant VCaP Prostate Cancer Xenografts
   Am J Pathol, 188 (12), 2890-2901
   DOI 10.1016/j.ajpath.2018.07.029, PubMed 30273606
10. Huvila J, Laajala TD, Edqvist PH, Mardinoglu A, Talve L, Pontén F, Grénman S, Carpén O, Aittokallio T, Auranen A (2018)
    Combined ASRGL1 and p53 immunohistochemistry as an independent predictor of survival in endometrioid endometrial carcinoma
    Gynecol Oncol, 149 (1), 173-180
    DOI 10.1016/j.ygyno.2018.02.016, PubMed 29486992
11. 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 et al. (2018)
    Novel activities of safe-in-human broad-spectrum antiviral agents
    Antiviral Res, 154, 174-182
    DOI 10.1016/j.antiviral.2018.04.016, PubMed 29698664
12. 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 (2018)
    PP2A inhibition is a druggable MEK inhibitor resistance mechanism in KRAS-mutant lung cancer cells
    Sci Transl Med, 10 (450)
    DOI 10.1126/scitranslmed.aaq1093, PubMed 30021885
13. 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 (2018)
    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, 17 (9), 2060-2071
    DOI 10.1158/1535-7163.MCT-17-0733, PubMed 29970484
14. Laajala TD, Murtojärvi M, Virkki A, Aittokallio T (2018)
    ePCR: an R-package for survival and time-to-event prediction in advanced prostate cancer, applied to real-world patient cohorts
    Bioinformatics, 34 (22), 3957-3959
    DOI 10.1093/bioinformatics/bty477, PubMed 29912284
15. Ruuth M, Nguyen SD, Vihervaara T, Hilvo M, Laajala TD, Kondadi PK, Gisterå A, Lähteenmäki H, Kittilä T, Huusko J, Uusitupa M, Schwab U, Savolainen MJ, Sinisalo J, Lokki ML, Nieminen MS, Jula A, Perola M, Ylä-Herttula S, Rudel L, Öörni A, Baumann M, Baruch A, Laaksonen R, Ketelhuth DFJ et al. (2018)
    Susceptibility of low-density lipoprotein particles to aggregate depends on particle lipidome, is modifiable, and associates with future cardiovascular deaths
    Eur Heart J, 39 (27), 2562-2573
    DOI 10.1093/eurheartj/ehy319, PubMed 29982602
16. Tanoli Z, Alam Z, Vähä-Koskela M, Ravikumar B, Malyutina A, Jaiswal A, Tang J, Wennerberg K, Aittokallio T (2018)
    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, PubMed 30219839

Publications 2017

1. Aittokallio T, Scherer A, Poutanen M, Freedman LP (2017)
   Matched preclinical designs for improved translatability
   Sci Transl Med, 9 (389)
   DOI 10.1126/scitranslmed.aal4101, PubMed 28490671
2. Ammad-Ud-Din M, Khan SA, Wennerberg K, Aittokallio T (2017)
   Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression
   Bioinformatics, 33 (14), i359-i368
   DOI 10.1093/bioinformatics/btx266, PubMed 28881998
3. Andersson EI, Pützer S, Yadav B, Dufva O, Khan S, He L, Sellner L, Schrader A, Crispatzu G, Oleś M, Zhang H, Adnan-Awad S, Lagström S, Bellanger D, Mpindi JP, Eldfors S, Pemovska T, Pietarinen P, Lauhio A, Tomska K, Cuesta-Mateos C, Faber E, Koschmieder S, Brümmendorf TH, Kytölä S et al. (2017)
   Discovery of novel drug sensitivities in T-PLL by high-throughput ex vivo drug testing and mutation profiling
   Leukemia, 32 (3), 774-787
   DOI 10.1038/leu.2017.252, PubMed 28804127
4. Azencott CA, Aittokallio T, Roy S, DREAM Idea Challenge Consortium, Norman T, Friend S, Stolovitzky G, Goldenberg A (2017)
   The inconvenience of data of convenience: computational research beyond post-mortem analyses
   Nat Methods, 14 (10), 937-938
   DOI 10.1038/nmeth.4457, PubMed 28960198
5. Bulanova D, Ianevski A, Bugai A, Akimov Y, Kuivanen S, Paavilainen H, Kakkola L, Nandania J, Turunen L, Ohman T, Ala-Hongisto H, Pesonen HM, Kuisma MS, Honkimaa A, Walton EL, Oksenych V, Lorey MB, Guschin D, Shim J, Kim J, Than TT, Chang SY, Hukkanen V, Kulesskiy E, Marjomaki VS et al. (2017)
   Antiviral Properties of Chemical Inhibitors of Cellular Anti-Apoptotic Bcl-2 Proteins
   Viruses, 9 (10)
   DOI 10.3390/v9100271, PubMed 28946654
6. Bulanova DR, Akimov YA, Rokka A, Laajala TD, Aittokallio T, Kouvonen P, Pellinen T, Kuznetsov SG (2017)
   Orphan G protein-coupled receptor GPRC5A modulates integrin β1-mediated epithelial cell adhesion
   Cell Adh Migr, 11 (5-6), 434-446
   DOI 10.1080/19336918.2016.1245264, PubMed 27715394
7. Chheda H, Palta P, Pirinen M, McCarthy S, Walter K, Koskinen S, Salomaa V, Daly M, Durbin R, Palotie A, Aittokallio T, Ripatti S (2017)
   Whole-genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom
   Eur J Hum Genet, 25 (4), 477-484
   DOI 10.1038/ejhg.2016.205, PubMed 28145424
8. Cichonska A, Ravikumar B, Parri E, Timonen S, Pahikkala T, Airola A, Wennerberg K, Rousu J, Aittokallio T (2017)
   Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors
   PLoS Comput Biol, 13 (8), e1005678
   DOI 10.1371/journal.pcbi.1005678, PubMed 28787438
9. Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, Bivol A, Bunte K, Carlin D, Chopra S, Deran A, Ellrott K, Gopalacharyulu P, Graim K, Kaski S, Khan SA et al. (2017)
   A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines
   Cell Syst, 5 (5), 485-497.e3
   DOI 10.1016/j.cels.2017.09.004, PubMed 28988802
10. Haltia UM, Andersson N, Yadav B, Färkkilä A, Kulesskiy E, Kankainen M, Tang J, Bützow R, Riska A, Leminen A, Heikinheimo M, Kallioniemi O, Unkila-Kallio L, Wennerberg K, Aittokallio T, Anttonen M (2017)
    Systematic drug sensitivity testing reveals synergistic growth inhibition by dasatinib or mTOR inhibitors with paclitaxel in ovarian granulosa cell tumor cells
    Gynecol Oncol, 144 (3), 621-630
    DOI 10.1016/j.ygyno.2016.12.016, PubMed 28104295
11. He C, Micallef L, Tanoli ZU, Kaski S, Aittokallio T, Jacucci G (2017)
    MediSyn: uncertainty-aware visualization of multiple biomedical datasets to support drug treatment selection
    BMC Bioinformatics, 18 (Suppl 10), 393
    DOI 10.1186/s12859-017-1785-7, PubMed 28929971
12. Ianevski A, He L, Aittokallio T, Tang J (2017)
    SynergyFinder: a web application for analyzing drug combination dose-response matrix data
    Bioinformatics, 33 (15), 2413-2415
    DOI 10.1093/bioinformatics/btx162, PubMed 28379339
13. Jaiswal A, Peddinti G, Akimov Y, Wennerberg K, Kuznetsov S, Tang J, Aittokallio T (2017)
    Seed-effect modeling improves the consistency of genome-wide loss-of-function screens and identifies synthetic lethal vulnerabilities in cancer cells
    Genome Med, 9 (1), 51
    DOI 10.1186/s13073-017-0440-2, PubMed 28569207
14. Karjalainen R, Pemovska T, Popa M, Liu M, Javarappa KK, Majumder MM, Yadav B, Tamborero D, Tang J, Bychkov D, Kontro M, Parsons A, Suvela M, Mayoral Safont M, Porkka K, Aittokallio T, Kallioniemi O, McCormack E, Gjertsen BT, Wennerberg K, Knowles J, Heckman CA (2017)
    JAK1/2 and BCL2 inhibitors synergize to counteract bone marrow stromal cell-induced protection of AML
    Blood, 130 (6), 789-802
    DOI 10.1182/blood-2016-02-699363, PubMed 28619982
15. Knuuttila M, Mehmood A, Huhtaniemi R, Yatkin E, Häkkinen MR, Oksala R, Laajala TD, Ryberg H, Handelsman DJ, Aittokallio T, Auriola S, Ohlsson C, Laiho A, Elo LL, Sipilä P, Mäkelä SI, Poutanen M (2017)
    Antiandrogens Reduce Intratumoral Androgen Concentrations and Induce Androgen Receptor Expression in Castration-Resistant Prostate Cancer Xenografts
    Am J Pathol, 188 (1), 216-228
    DOI 10.1016/j.ajpath.2017.08.036, PubMed 29126837
16. Mirtti T, Aittokallio T (2017)
    Re: Fatemeh Seyednasrollah, Mehrad Mahmoudian, Liisa Rautakorpi, et al. How Reliable are Trial-based Prognostic Models in Real-world Patients with Metastatic Castration-resistant Prostate Cancer? Eur Urol. 2017;71:838-40
    Eur Urol, 72 (3), e68-e69
    DOI 10.1016/j.eururo.2017.04.030, PubMed 28499620
17. Peddinti G, Cobb J, Yengo L, Froguel P, Kravić J, Balkau B, Tuomi T, Aittokallio T, Groop L (2017)
    Early metabolic markers identify potential targets for the prevention of type 2 diabetes
    Diabetologia, 60 (9), 1740-1750
    DOI 10.1007/s00125-017-4325-0, PubMed 28597074
18. Posada IMD, Lectez B, Sharma M, Oetken-Lindholm C, Yetukuri L, Zhou Y, Aittokallio T, Abankwa D (2017)
    Rapalogs can promote cancer cell stemness in vitro in a Galectin-1 and H-ras-dependent manner
    Oncotarget, 8 (27), 44550-44566
    DOI 10.18632/oncotarget.17819, PubMed 28562352
19. Ravikumar B, Aittokallio T (2017)
    Improving the efficacy-safety balance of polypharmacology in multi-target drug discovery
    Expert Opin Drug Discov, 13 (2), 179-192
    DOI 10.1080/17460441.2018.1413089, PubMed 29233023
20. Ravikumar B, Alam Z, Peddinti G, Aittokallio T (2017)
    C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms
    Nucleic Acids Res, 45 (W1), W495-W500
    DOI 10.1093/nar/gkx384, PubMed 28472495
21. Tang J, Tanoli ZU, Ravikumar B, Alam Z, Rebane A, Vähä-Koskela M, Peddinti G, van Adrichem AJ, Wakkinen J, Jaiswal A, Karjalainen E, Gautam P, He L, Parri E, Khan S, Gupta A, Ali M, Yetukuri L, Gustavsson AL, Seashore-Ludlow B, Hersey A, Leach AR, Overington JP, Repasky G, Wennerberg K et al. (2017)
    Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions
    Cell Chem Biol, 25 (2), 224-229.e2
    DOI 10.1016/j.chembiol.2017.11.009, PubMed 29276046
22. Ussi AE, de Kort M, Coussens NP, Aittokallio T, Hajduch M (2017)
    In Search of System-Wide Productivity Gains - The Role of Global Collaborations in Preclinical Translation
    Clin Transl Sci, 10 (6), 423-425
    DOI 10.1111/cts.12498, PubMed 28929592
23. Yadav B, Wennerberg K, Aittokallio T, Tang J (2017)
    Corrigendum to "Searching for drug synergy in complex dose-response landscapes using an interaction potency model" [Comput. Struct. Biotechnol. J. 13 (2015) 504-513]
    Comput Struct Biotechnol J, 15, 387
    DOI 10.1016/j.csbj.2017.07.003, PubMed 29991977

Publications 2016

1. Ammad-Ud-Din M, Khan SA, Malani D, Murumägi A, Kallioniemi O, Aittokallio T, Kaski S (2016)
   Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization
   Bioinformatics, 32 (17), i455-i463
   DOI 10.1093/bioinformatics/btw433, PubMed 27587662
2. Côme C, Cvrljevic A, Khan MM, Treise I, Adler T, Aguilar-Pimentel JA, Au-Yeung B, Sittig E, Laajala TD, Chen Y, Oeder S, Calzada-Wack J, Horsch M, Aittokallio T, Busch DH, Ollert MW, Neff F, Beckers J, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Chen Z, Lahesmaa R, Westermarck J (2016)
   CIP2A Promotes T-Cell Activation and Immune Response to Listeria monocytogenes Infection
   PLoS One, 11 (4), e0152996
   DOI 10.1371/journal.pone.0152996, PubMed 27100879
3. Gautam P, Karhinen L, Szwajda A, Jha SK, Yadav B, Aittokallio T, Wennerberg K (2016)
   Identification of selective cytotoxic and synthetic lethal drug responses in triple negative breast cancer cells
   Mol Cancer, 15 (1), 34
   DOI 10.1186/s12943-016-0517-3, PubMed 27165605
4. 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 et al. (2016)
   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, 18 (1), 132-142
   DOI 10.1016/S1470-2045(16)30560-5, PubMed 27864015
5. Kangaspeska S, Hultsch S, Jaiswal A, Edgren H, Mpindi JP, Eldfors S, Brück O, Aittokallio T, Kallioniemi O (2016)
   Systematic drug screening reveals specific vulnerabilities and co-resistance patterns in endocrine-resistant breast cancer
   BMC Cancer, 16, 378
   DOI 10.1186/s12885-016-2452-5, PubMed 27378269
6. Kemiläinen H, Adam M, Mäki-Jouppila J, Damdimopoulou P, Damdimopoulos AE, Kere J, Hovatta O, Laajala TD, Aittokallio T, Adamski J, Ryberg H, Ohlsson C, Strauss L, Poutanen M (2016)
   The Hydroxysteroid (17β) Dehydrogenase Family Gene HSD17B12 Is Involved in the Prostaglandin Synthesis Pathway, the Ovarian Function, and Regulation of Fertility
   Endocrinology, 157 (10), 3719-3730
   DOI 10.1210/en.2016-1252, PubMed 27490311
7. Kibble M, Khan SA, Saarinen N, Iorio F, Saez-Rodriguez J, Mäkelä S, Aittokallio T (2016)
   Transcriptional response networks for elucidating mechanisms of action of multitargeted agents
   Drug Discov Today, 21 (7), 1063-75
   DOI 10.1016/j.drudis.2016.03.001, PubMed 26979547
8. Laajala TD, Jumppanen M, Huhtaniemi R, Fey V, Kaur A, Knuuttila M, Aho E, Oksala R, Westermarck J, Mäkelä S, Poutanen M, Aittokallio T (2016)
   Optimized design and analysis of preclinical intervention studies in vivo
   Sci Rep, 6, 30723
   DOI 10.1038/srep30723, PubMed 27480578
9. Malani D, Murumägi A, Yadav B, Kontro M, Eldfors S, Kumar A, Karjalainen R, Majumder MM, Ojamies P, Pemovska T, Wennerberg K, Heckman C, Porkka K, Wolf M, Aittokallio T, Kallioniemi O (2016)
   Enhanced sensitivity to glucocorticoids in cytarabine-resistant AML
   Leukemia, 31 (5), 1187-1195
   DOI 10.1038/leu.2016.314, PubMed 27833094
10. Mpindi JP, Yadav B, Östling P, Gautam P, Malani D, Murumägi A, Hirasawa A, Kangaspeska S, Wennerberg K, Kallioniemi O, Aittokallio T (2016)
    Consistency in drug response profiling
    Nature, 540 (7631), E5-E6
    DOI 10.1038/nature20171, PubMed 27905421
11. Najumudeen AK, Jaiswal A, Lectez B, Oetken-Lindholm C, Guzmán C, Siljamäki E, Posada IM, Lacey E, Aittokallio T, Abankwa D (2016)
    Cancer stem cell drugs target K-ras signaling in a stemness context
    Oncogene, 35 (40), 5248-5262
    DOI 10.1038/onc.2016.59, PubMed 26973241
12. Saeed K, Rahkama V, Eldfors S, Bychkov D, Mpindi JP, Yadav B, Paavolainen L, Aittokallio T, Heckman C, Wennerberg K, Peehl DM, Horvath P, Mirtti T, Rannikko A, Kallioniemi O, Östling P, Af Hällström TM (2016)
    Comprehensive Drug Testing of Patient-derived Conditionally Reprogrammed Cells from Castration-resistant Prostate Cancer
    Eur Urol, 71 (3), 319-327
    DOI 10.1016/j.eururo.2016.04.019, PubMed 27160946
13. Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VSK, Dillenberger D, Neto EC et al. (2016)
    Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis
    Nat Commun, 7, 12460
    DOI 10.1038/ncomms12460, PubMed 27549343
14. Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VSK, Dillenberger D, Neto EC et al. (2016)
    Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis
    Nat Commun, 7, 13205
    DOI 10.1038/ncomms13205, PubMed 27721464
15. Söderholm S, Fu Y, Gaelings L, Belanov S, Yetukuri L, Berlinkov M, Cheltsov AV, Anders S, Aittokallio T, Nyman TA, Matikainen S, Kainov DE (2016)
    Multi-Omics Studies towards Novel Modulators of Influenza A Virus-Host Interaction
    Viruses, 8 (10)
    DOI 10.3390/v8100269, PubMed 27690086
16. Söderholm S, Kainov DE, Öhman T, Denisova OV, Schepens B, Kulesskiy E, Imanishi SY, Corthals G, Hintsanen P, Aittokallio T, Saelens X, Matikainen S, Nyman TA (2016)
    Phosphoproteomics to Characterize Host Response During Influenza A Virus Infection of Human Macrophages
    Mol Cell Proteomics, 15 (10), 3203-3219
    DOI 10.1074/mcp.M116.057984, PubMed 27486199

Publications 2015

1. Cichonska A, Rousu J, Aittokallio T (2015)
   Identification of drug candidates and repurposing opportunities through compound-target interaction networks
   Expert Opin Drug Discov, 10 (12), 1333-45
   DOI 10.1517/17460441.2015.1096926, PubMed 26429153
2. He L, Wennerberg K, Aittokallio T, Tang J (2015)
   TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples
   Bioinformatics, 31 (11), 1866-8
   DOI 10.1093/bioinformatics/btv067, PubMed 25638808
3. Hilvo M, de Santiago I, Gopalacharyulu P, Schmitt WD, Budczies J, Kuhberg M, Dietel M, Aittokallio T, Markowetz F, Denkert C, Sehouli J, Frezza C, Darb-Esfahani S, Braicu EI (2015)
   Accumulated Metabolites of Hydroxybutyric Acid Serve as Diagnostic and Prognostic Biomarkers of Ovarian High-Grade Serous Carcinomas
   Cancer Res, 76 (4), 796-804
   DOI 10.1158/0008-5472.CAN-15-2298, PubMed 26685161
4. Kauko O, Laajala TD, Jumppanen M, Hintsanen P, Suni V, Haapaniemi P, Corthals G, Aittokallio T, Westermarck J, Imanishi SY (2015)
   Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling
   Sci Rep, 5, 13099
   DOI 10.1038/srep13099, PubMed 26278961
5. Kibble M, Saarinen N, Tang J, Wennerberg K, Mäkelä S, Aittokallio T (2015)
   Network pharmacology applications to map the unexplored target space and therapeutic potential of natural products
   Nat Prod Rep, 32 (8), 1249-66
   DOI 10.1039/c5np00005j, PubMed 26030402
6. Mpindi JP, Swapnil P, Dmitrii B, Jani S, Saeed K, Wennerberg K, Aittokallio T, Östling P, Kallioniemi O (2015)
   Impact of normalization methods on high-throughput screening data with high hit rates and drug testing with dose-response data
   Bioinformatics, 31 (23), 3815-21
   DOI 10.1093/bioinformatics/btv455, PubMed 26254433
7. Pokharel YR, Saarela J, Szwajda A, Rupp C, Rokka A, Lal Kumar Karna S, Teittinen K, Corthals G, Kallioniemi O, Wennerberg K, Aittokallio T, Westermarck J (2015)
   Relevance Rank Platform (RRP) for Functional Filtering of High Content Protein-Protein Interaction Data
   Mol Cell Proteomics, 14 (12), 3274-83
   DOI 10.1074/mcp.M115.050773, PubMed 26499835
8. Šolman M, Ligabue A, Blaževitš O, Jaiswal A, Zhou Y, Liang H, Lectez B, Kopra K, Guzmán C, Härmä H, Hancock JF, Aittokallio T, Abankwa D (2015)
   Specific cancer-associated mutations in the switch III region of Ras increase tumorigenicity by nanocluster augmentation
   Elife, 4, e08905
   DOI 10.7554/eLife.08905, PubMed 26274561
9. Szwajda A, Gautam P, Karhinen L, Jha SK, Saarela J, Shakyawar S, Turunen L, Yadav B, Tang J, Wennerberg K, Aittokallio T (2015)
   Systematic Mapping of Kinase Addiction Combinations in Breast Cancer Cells by Integrating Drug Sensitivity and Selectivity Profiles
   Chem Biol, 22 (8), 1144-55
   DOI 10.1016/j.chembiol.2015.06.021, PubMed 26211361
10. Tang J, Wennerberg K, Aittokallio T (2015)
    What is synergy? The Saariselkä agreement revisited
    Front Pharmacol, 6, 181
    DOI 10.3389/fphar.2015.00181, PubMed 26388771
11. Vehmas AP, Adam M, Laajala TD, Kastenmüller G, Prehn C, Rozman J, Ohlsson C, Fuchs H, Hrabě de Angelis M, Gailus-Durner V, Elo LL, Aittokallio T, Adamski J, Corthals G, Poutanen M, Strauss L (2015)
    Liver lipid metabolism is altered by increased circulating estrogen to androgen ratio in male mouse
    J Proteomics, 133, 66-75
    DOI 10.1016/j.jprot.2015.12.009, PubMed 26691839
12. Yadav B, Gopalacharyulu P, Pemovska T, Khan SA, Szwajda A, Tang J, Wennerberg K, Aittokallio T (2015)
    From drug response profiling to target addiction scoring in cancer cell models
    Dis Model Mech, 8 (10), 1255-64
    DOI 10.1242/dmm.021105, PubMed 26438695
13. Yadav B, Wennerberg K, Aittokallio T, Tang J (2015)
    Searching for Drug Synergy in Complex Dose-Response Landscapes Using an Interaction Potency Model
    Comput Struct Biotechnol J, 13, 504-13
    DOI 10.1016/j.csbj.2015.09.001, PubMed 26949479
14. Aakula A, Kohonen P, Leivonen SK, Mäkelä R, Hintsanen P, Mpindi JP, Martens-Uzunova E, Aittokallio T, Jenster G, Perälä M, Kallioniemi O, Östling P (2015)
    Systematic Identification of MicroRNAs That Impact on Proliferation of Prostate Cancer Cells and Display Changed Expression in Tumor Tissue
    Eur Urol, 69 (6), 1120-8
    DOI 10.1016/j.eururo.2015.09.019, PubMed 26489476
15. Aakula A, Leivonen SK, Hintsanen P, Aittokallio T, Ceder Y, Børresen-Dale AL, Perälä M, Östling P, Kallioniemi O (2015)
    MicroRNA-135b regulates ERα, AR and HIF1AN and affects breast and prostate cancer cell growth
    Mol Oncol, 9 (7), 1287-300
    DOI 10.1016/j.molonc.2015.03.001, PubMed 25907805

Publications 2014

1. Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G (2014)
   A community effort to assess and improve drug sensitivity prediction algorithms
   Nat Biotechnol, 32 (12), 1202-12
   DOI 10.1038/nbt.2877, PubMed 24880487
2. Elo LL, Karjalainen R, Ohman T, Hintsanen P, Nyman TA, Heckman CA, Aittokallio T (2014)
   Statistical detection of quantitative protein biomarkers provides insights into signaling networks deregulated in acute myeloid leukemia
   Proteomics, 14 (21-22), 2443-53
   DOI 10.1002/pmic.201300460, PubMed 25211154
3. Huhtinen K, Saloniemi-Heinonen T, Keski-Rahkonen P, Desai R, Laajala D, Ståhle M, Häkkinen MR, Awosanya M, Suvitie P, Kujari H, Aittokallio T, Handelsman DJ, Auriola S, Perheentupa A, Poutanen M (2014)
   Intra-tissue steroid profiling indicates differential progesterone and testosterone metabolism in the endometrium and endometriosis lesions
   J Clin Endocrinol Metab, 99 (11), E2188-97
   DOI 10.1210/jc.2014-1913, PubMed 25137424
4. Knuuttila M, Yatkin E, Kallio J, Savolainen S, Laajala TD, Aittokallio T, Oksala R, Häkkinen M, Keski-Rahkonen P, Auriola S, Poutanen M, Mäkelä S (2014)
   Castration induces up-regulation of intratumoral androgen biosynthesis and androgen receptor expression in an orthotopic VCaP human prostate cancer xenograft model
   Am J Pathol, 184 (8), 2163-73
   DOI 10.1016/j.ajpath.2014.04.010, PubMed 24949550
5. Okser S, Pahikkala T, Airola A, Salakoski T, Ripatti S, Aittokallio T (2014)
   Regularized machine learning in the genetic prediction of complex traits
   PLoS Genet, 10 (11), e1004754
   DOI 10.1371/journal.pgen.1004754, PubMed 25393026
6. Pahikkala T, Airola A, Pietilä S, Shakyawar S, Szwajda A, Tang J, Aittokallio T (2014)
   Toward more realistic drug-target interaction predictions
   Brief Bioinform, 16 (2), 325-37
   DOI 10.1093/bib/bbu010, PubMed 24723570
7. Söderholm S, Hintsanen P, Öhman T, Aittokallio T, Nyman TA (2014)
   PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data
   Proteome Sci, 12, 36
   DOI 10.1186/1477-5956-12-36, PubMed 25028575
8. Tang J, Aittokallio T (2014)
   Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles
   Curr Pharm Des, 20 (1), 23-36
   DOI 10.2174/13816128113199990470, PubMed 23530504
9. Tang J, Szwajda A, Shakyawar S, Xu T, Hintsanen P, Wennerberg K, Aittokallio T (2014)
   Making sense of large-scale kinase inhibitor bioactivity data sets: a comparative and integrative analysis
   J Chem Inf Model, 54 (3), 735-43
   DOI 10.1021/ci400709d, PubMed 24521231
10. Vehmas AP, Muth-Pawlak D, Huhtinen K, Saloniemi-Heinonen T, Jaakkola K, Laajala TD, Kaprio H, Suvitie PA, Aittokallio T, Siitari H, Perheentupa A, Poutanen M, Corthals GL (2014)
    Ovarian endometriosis signatures established through discovery and directed mass spectrometry analysis
    J Proteome Res, 13 (11), 4983-94
    DOI 10.1021/pr500384n, PubMed 25099244
11. Yadav B, Pemovska T, Szwajda A, Kulesskiy E, Kontro M, Karjalainen R, Majumder MM, Malani D, Murumägi A, Knowles J, Porkka K, Heckman C, Kallioniemi O, Wennerberg K, Aittokallio T (2014)
    Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies
    Sci Rep, 4, 5193
    DOI 10.1038/srep05193, PubMed 24898935
12. Yatkin E, Polari L, Laajala TD, Smeds A, Eckerman C, Holmbom B, Saarinen NM, Aittokallio T, Mäkelä SI (2014)
    Novel Lignan and stilbenoid mixture shows anticarcinogenic efficacy in preclinical PC-3M-luc2 prostate cancer model
    PLoS One, 9 (4), e93764
    DOI 10.1371/journal.pone.0093764, PubMed 24699425
13. Öhman T, Söderholm S, Hintsanen P, Välimäki E, Lietzén N, MacKintosh C, Aittokallio T, Matikainen S, Nyman TA (2014)
    Phosphoproteomics combined with quantitative 14-3-3-affinity capture identifies SIRT1 and RAI as novel regulators of cytosolic double-stranded RNA recognition pathway
    Mol Cell Proteomics, 13 (10), 2604-17
    DOI 10.1074/mcp.M114.038968, PubMed 24997996

Publications 2013

1. Heiskanen MA, Aittokallio T (2013)
   Predicting drug-target interactions through integrative analysis of chemogenetic assays in yeast
   Mol Biosyst, 9 (4), 768-79
   DOI 10.1039/c3mb25591c, PubMed 23420501
2. Kakkola L, Denisova OV, Tynell J, Viiliäinen J, Ysenbaert T, Matos RC, Nagaraj A, Ohman T, Kuivanen S, Paavilainen H, Feng L, Yadav B, Julkunen I, Vapalahti O, Hukkanen V, Stenman J, Aittokallio T, Verschuren EW, Ojala PM, Nyman T, Saelens X, Dzeyk K, Kainov DE (2013)
   Anticancer compound ABT-263 accelerates apoptosis in virus-infected cells and imbalances cytokine production and lowers survival rates of infected mice
   Cell Death Dis, 4 (7), e742
   DOI 10.1038/cddis.2013.267, PubMed 23887633
3. Khanna A, Kauko O, Böckelman C, Laine A, Schreck I, Partanen JI, Szwajda A, Bormann S, Bilgen T, Helenius M, Pokharel YR, Pimanda J, Russel MR, Haglund C, Cole KA, Klefström J, Aittokallio T, Weiss C, Ristimäki A, Visakorpi T, Westermarck J (2013)
   Chk1 targeting reactivates PP2A tumor suppressor activity in cancer cells
   Cancer Res, 73 (22), 6757-69
   DOI 10.1158/0008-5472.CAN-13-1002, PubMed 24072747
4. Okser S, Pahikkala T, Aittokallio T (2013)
   Genetic variants and their interactions in disease risk prediction - machine learning and network perspectives
   BioData Min, 6 (1), 5
   DOI 10.1186/1756-0381-6-5, PubMed 23448398
5. Pemovska T, Kontro M, Yadav B, Edgren H, Eldfors S, Szwajda A, Almusa H, Bespalov MM, Ellonen P, Elonen E, Gjertsen BT, Karjalainen R, Kulesskiy E, Lagström S, Lehto A, Lepistö M, Lundán T, Majumder MM, Marti JM, Mattila P, Murumägi A, Mustjoki S, Palva A, Parsons A, Pirttinen T et al. (2013)
   Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia
   Cancer Discov, 3 (12), 1416-29
   DOI 10.1158/2159-8290.CD-13-0350, PubMed 24056683
6. Tang J, Karhinen L, Xu T, Szwajda A, Yadav B, Wennerberg K, Aittokallio T (2013)
   Target inhibition networks: predicting selective combinations of druggable targets to block cancer survival pathways
   PLoS Comput Biol, 9 (9), e1003226
   DOI 10.1371/journal.pcbi.1003226, PubMed 24068907

Publications 2012

1. Corander J, Aittokallio T, Ripatti S, Kaski S (2012)
   The rocky road to personalized medicine: computational and statistical challenges
   Per Med, 9 (2), 109-114
   DOI 10.2217/pme.12.1, PubMed 29758814
2. Denisova OV, Kakkola L, Feng L, Stenman J, Nagaraj A, Lampe J, Yadav B, Aittokallio T, Kaukinen P, Ahola T, Kuivanen S, Vapalahti O, Kantele A, Tynell J, Julkunen I, Kallio-Kokko H, Paavilainen H, Hukkanen V, Elliott RM, De Brabander JK, Saelens X, Kainov DE (2012)
   Obatoclax, saliphenylhalamide, and gemcitabine inhibit influenza a virus infection
   J Biol Chem, 287 (42), 35324-35332
   DOI 10.1074/jbc.M112.392142, PubMed 22910914
3. Kiviniemi TO, Yegutkin GG, Toikka JO, Paul S, Aittokallio T, Janatuinen T, Knuuti J, Rönnemaa T, Koskenvuo JW, Hartiala JJ, Jalkanen S, Raitakari OT (2012)
   Pravastatin-induced improvement in coronary reactivity and circulating ATP and ADP levels in young adults with type 1 diabetes
   Front Physiol, 3, 338
   DOI 10.3389/fphys.2012.00338, PubMed 22934084
4. Laajala TD, Corander J, Saarinen NM, Mäkelä K, Savolainen S, Suominen MI, Alhoniemi E, Mäkelä S, Poutanen M, Aittokallio T (2012)
   Improved statistical modeling of tumor growth and treatment effect in preclinical animal studies with highly heterogeneous responses in vivo
   Clin Cancer Res, 18 (16), 4385-96
   DOI 10.1158/1078-0432.CCR-11-3215, PubMed 22745104
5. Pahikkala T, Okser S, Airola A, Salakoski T, Aittokallio T (2012)
   Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations
   Algorithms Mol Biol, 7 (1), 11
   DOI 10.1186/1748-7188-7-11, PubMed 22551170
6. Tuikkala J, Vähämaa H, Salmela P, Nevalainen OS, Aittokallio T (2012)
   A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization
   BioData Min, 5, 2
   DOI 10.1186/1756-0381-5-2, PubMed 22448851

Publications 2011

1. Elo LL, Kallio A, Laajala TD, Hawkins RD, Korpelainen E, Aittokallio T (2011)
   Optimized detection of transcription factor-binding sites in ChIP-seq experiments
   Nucleic Acids Res, 40 (1), e1
   DOI 10.1093/nar/gkr839, PubMed 22009681
2. Lahti L, Elo LL, Aittokallio T, Kaski S (2011)
   Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays
   IEEE/ACM Trans Comput Biol Bioinform, 8 (1), 217-25
   DOI 10.1109/TCBB.2009.38, PubMed 21071809
3. Lietzén N, Ohman T, Rintahaka J, Julkunen I, Aittokallio T, Matikainen S, Nyman TA (2011)
   Quantitative subcellular proteome and secretome profiling of influenza A virus-infected human primary macrophages
   PLoS Pathog, 7 (5), e1001340
   DOI 10.1371/journal.ppat.1001340, PubMed 21589892
4. Lindén RO, Eronen VP, Aittokallio T (2011)
   Quantitative maps of genetic interactions in yeast - comparative evaluation and integrative analysis
   BMC Syst Biol, 5, 45
   DOI 10.1186/1752-0509-5-45, PubMed 21435228
5. Vähämaa H, Koskinen VR, Hosia W, Moulder R, Nevalainen OS, Lahesmaa R, Aittokallio T, Salmi J (2011)
   PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use
   Int J Proteomics, 2011, 450290
   DOI 10.1155/2011/450290, PubMed 22084688

Publications 2010

1. Codrea MC, Hakala-Yatkin M, Kårlund-Marttila A, Nedbal L, Aittokallio T, Nevalainen OS, Tyystjärvi E (2010)
   Mahalanobis distance screening of Arabidopsis mutants with chlorophyll fluorescence
   Photosynth Res, 105 (3), 273-83
   DOI 10.1007/s11120-010-9578-0, PubMed 20730565
2. Elo LL, Järvenpää H, Tuomela S, Raghav S, Ahlfors H, Laurila K, Gupta B, Lund RJ, Tahvanainen J, Hawkins RD, Oresic M, Lähdesmäki H, Rasool O, Rao KV, Aittokallio T, Lahesmaa R (2010)
   Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming
   Immunity, 32 (6), 852-62
   DOI 10.1016/j.immuni.2010.06.011, PubMed 20620947
3. Elo LL, Mykkänen J, Nikula T, Järvenpää H, Simell S, Aittokallio T, Hyöty H, Ilonen J, Veijola R, Simell T, Knip M, Simell O, Lahesmaa R (2010)
   Early suppression of immune response pathways characterizes children with prediabetes in genome-wide gene expression profiling
   J Autoimmun, 35 (1), 70-6
   DOI 10.1016/j.jaut.2010.03.001, PubMed 20356713
4. Eronen VP, Lindén RO, Lindroos A, Kanerva M, Aittokallio T (2010)
   Genome-wide scoring of positive and negative epistasis through decomposition of quantitative genetic interaction fitness matrices
   PLoS One, 5 (7), e11611
   DOI 10.1371/journal.pone.0011611, PubMed 20657656
5. Moulder R, Lönnberg T, Elo LL, Filén JJ, Rainio E, Corthals G, Oresic M, Nyman TA, Aittokallio T, Lahesmaa R (2010)
   Quantitative proteomics analysis of the nuclear fraction of human CD4+ cells in the early phases of IL-4-induced Th2 differentiation
   Mol Cell Proteomics, 9 (9), 1937-53
   DOI 10.1074/mcp.M900483-MCP200, PubMed 20467038
6. Okser S, Lehtimäki T, Elo LL, Mononen N, Peltonen N, Kähönen M, Juonala M, Fan YM, Hernesniemi JA, Laitinen T, Lyytikäinen LP, Rontu R, Eklund C, Hutri-Kähönen N, Taittonen L, Hurme M, Viikari JS, Raitakari OT, Aittokallio T (2010)
   Genetic variants and their interactions in the prediction of increased pre-clinical carotid atherosclerosis: the cardiovascular risk in young Finns study
   PLoS Genet, 6 (9), e1001146
   DOI 10.1371/journal.pgen.1001146, PubMed 20941391

Publications 2009

1. Aittokallio J, Hiissa J, Saaresranta T, Polo-Kantola P, Aittokallio T, Polo O (2009)
   Nocturnal transcutaneous carbon dioxide tension in postmenopausal estrogen users and non-users
   Menopause Int, 15 (3), 107-12
   DOI 10.1258/mi.2009.009028, PubMed 19723680
2. Aittokallio J, Saaresranta T, Virkki A, Karppinen N, Heinonen OJ, Aittokallio T, Polo O (2009)
   Transcutaneous carbon dioxide profile during sleep reveals metabolic risk factors in post-menopausal females
   Eur Respir J, 34 (5), 1132-9
   DOI 10.1183/09031936.00017909, PubMed 19574334
3. Aittokallio T (2009)
   Dealing with missing values in large-scale studies: microarray data imputation and beyond
   Brief Bioinform, 11 (2), 253-64
   DOI 10.1093/bib/bbp059, PubMed 19965979
4. Aittokallio T, Virkki A, Polo O (2009)
   Understanding sleep-disordered breathing through mathematical modelling
   Sleep Med Rev, 13 (5), 333-43
   DOI 10.1016/j.smrv.2008.09.008, PubMed 19285884
5. Clément-Ziza M, Malabat C, Weber C, Moszer I, Aittokallio T, Letondal C, Rousseau S (2009)
   Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks
   Bioinformatics, 25 (19), 2617-8
   DOI 10.1093/bioinformatics/btp464, PubMed 19654116
6. Elo LL, Hiissa J, Tuimala J, Kallio A, Korpelainen E, Aittokallio T (2009)
   Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets
   Brief Bioinform, 10 (5), 547-55
   DOI 10.1093/bib/bbp033, PubMed 19549804
7. Hiissa J, Elo LL, Huhtinen K, Perheentupa A, Poutanen M, Aittokallio T (2009)
   Resampling reveals sample-level differential expression in clinical genome-wide studies
   OMICS, 13 (5), 381-96
   DOI 10.1089/omi.2009.0027, PubMed 19663710
8. Korolainen MA, Nyman TA, Aittokallio T, Pirttilä T (2009)
   An update on clinical proteomics in Alzheimer's research
   J Neurochem, 112 (6), 1386-414
   DOI 10.1111/j.1471-4159.2009.06558.x, PubMed 20050976
9. Laajala E, Aittokallio T, Lahesmaa R, Elo LL (2009)
   Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies
   Genome Biol, 10 (7), R77
   DOI 10.1186/gb-2009-10-7-r77, PubMed 19607685
10. Laajala TD, Raghav S, Tuomela S, Lahesmaa R, Aittokallio T, Elo LL (2009)
    A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments
    BMC Genomics, 10, 618
    DOI 10.1186/1471-2164-10-618, PubMed 20017957
11. Salmi J, Nyman TA, Nevalainen OS, Aittokallio T (2009)
    Filtering strategies for improving protein identification in high-throughput MS/MS studies
    Proteomics, 9 (4), 848-60
    DOI 10.1002/pmic.200800517, PubMed 19160393

Publications 2008

1. Ahola V, Aittokallio T, Vihinen M, Uusipaikka E (2008)
   Model-based prediction of sequence alignment quality
   Bioinformatics, 24 (19), 2165-71
   DOI 10.1093/bioinformatics/btn414, PubMed 18678587
2. Aittokallio J, Polo O, Hiissa J, Virkki A, Toikka J, Raitakari O, Saaresranta T, Aittokallio T (2008)
   Overnight variability in transcutaneous carbon dioxide predicts vascular impairment in women
   Exp Physiol, 93 (7), 880-91
   DOI 10.1113/expphysiol.2007.041277, PubMed 18296495
3. Elo LL, Filen S, Lahesmaa R, Aittokallio T (2008)
   Reproducibility-optimized test statistic for ranking genes in microarray studies
   IEEE/ACM Trans Comput Biol Bioinform, 5 (3), 423-431
   DOI 10.1109/tcbb.2007.1078, PubMed 18670045
4. Järvinen AP, Hiissa J, Elo LL, Aittokallio T (2008)
   Predicting quantitative genetic interactions by means of sequential matrix approximation
   PLoS One, 3 (9), e3284
   DOI 10.1371/journal.pone.0003284, PubMed 18818762
5. Tuikkala J, Elo LL, Nevalainen OS, Aittokallio T (2008)
   Missing value imputation improves clustering and interpretation of gene expression microarray data
   BMC Bioinformatics, 9, 202
   DOI 10.1186/1471-2105-9-202, PubMed 18423022
6. Vandenbogaert M, Li-Thiao-Té S, Kaltenbach HM, Zhang R, Aittokallio T, Schwikowski B (2008)
   Alignment of LC-MS images, with applications to biomarker discovery and protein identification
   Proteomics, 8 (4), 650-72
   DOI 10.1002/pmic.200700791, PubMed 18297649

Publications 2007

1. Elo LL, Järvenpää H, Oresic M, Lahesmaa R, Aittokallio T (2007)
   Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process
   Bioinformatics, 23 (16), 2096-103
   DOI 10.1093/bioinformatics/btm309, PubMed 17553854
2. Virkki A, Polo O, Gyllenberg M, Aittokallio T (2007)
   Can carotid body perfusion act as a respiratory controller?
   J Theor Biol, 249 (4), 737-48
   DOI 10.1016/j.jtbi.2007.09.010, PubMed 17936799
3. Virkki A, Polo O, Saaresranta T, Laapotti-Salo A, Gyllenberg M, Aittokallio T (2007)
   Overnight features of transcutaneous carbon dioxide measurement as predictors of metabolic status
   Artif Intell Med, 42 (1), 55-65
   DOI 10.1016/j.artmed.2007.09.001, PubMed 17981017
4. Vähämaa H, Ojala P, Pahikkala T, Nevalainen OS, Lahesmaa R, Aittokallio T (2007)
   Computer-assisted identification of multitrace electrophoretic patterns in differential display experiments
   Electrophoresis, 28 (6), 879-93
   DOI 10.1002/elps.200600424, PubMed 17309051

Publications 2006

1. Ahola V, Aittokallio T, Vihinen M, Uusipaikka E (2006)
   A statistical score for assessing the quality of multiple sequence alignments
   BMC Bioinformatics, 7, 484
   DOI 10.1186/1471-2105-7-484, PubMed 17081313
2. Aittokallio T, Gyllenberg M, Polo O, Toivonen J, Virkki A (2006)
   Model-based analysis of mechanisms responsible for sleep-induced carbon dioxide differences
   Bull Math Biol, 68 (2), 315-41
   DOI 10.1007/s11538-005-9059-3, PubMed 16794933
3. Aittokallio T, Gyllenberg M, Polo O, Virkki A (2006)
   Parameter estimation of a respiratory control model from noninvasive carbon dioxide measurements during sleep
   Math Med Biol, 24 (2), 225-49
   DOI 10.1093/imammb/dql031, PubMed 17164471
4. Aittokallio T, Malminen JS, Pahikkala T, Polo O, Nevalainen OS (2006)
   Inspiratory flow shape clustering: an automated method to monitor upper airway performance during sleep
   Comput Methods Programs Biomed, 85 (1), 8-18
   DOI 10.1016/j.cmpb.2006.09.012, PubMed 17084481
5. Aittokallio T, Ojala P, Nevalainen TJ, Nevalainen OS (2006)
   Automated pattern ranking in differential display data analysis
   Methods Mol Biol, 317, 111-22
   DOI 10.1385/1-59259-968-0:111, PubMed 16264225
6. Aittokallio T, Schwikowski B (2006)
   Graph-based methods for analysing networks in cell biology
   Brief Bioinform, 7 (3), 243-55
   DOI 10.1093/bib/bbl022, PubMed 16880171
7. Elo LL, Katajamaa M, Lund R, Oresic M, Lahesmaa R, Aittokallio T (2006)
   Improving identification of differentially expressed genes by integrative analysis of Affymetrix and Illumina arrays
   OMICS, 10 (3), 369-80
   DOI 10.1089/omi.2006.10.369, PubMed 17069514
8. Garcia O, Saveanu C, Cline M, Fromont-Racine M, Jacquier A, Schwikowski B, Aittokallio T (2006)
   GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring
   Bioinformatics, 23 (3), 394-6
   DOI 10.1093/bioinformatics/btl605, PubMed 17127678
9. Hahtola S, Tuomela S, Elo L, Häkkinen T, Karenko L, Nedoszytko B, Heikkilä H, Saarialho-Kere U, Roszkiewicz J, Aittokallio T, Lahesmaa R, Ranki A (2006)
   Th1 response and cytotoxicity genes are down-regulated in cutaneous T-cell lymphoma
   Clin Cancer Res, 12 (16), 4812-21
   DOI 10.1158/1078-0432.CCR-06-0532, PubMed 16914566
10. Talvinen K, Tuikkala J, Grönroos J, Huhtinen H, Kronqvist P, Aittokallio T, Nevalainen O, Hiekkanen H, Nevalainen T, Sundström J (2006)
    Biochemical and clinical approaches in evaluating the prognosis of colon cancer
    Anticancer Res, 26 (6C), 4745-51
    PubMed 17214335

Publications 2005

1. Aittokallio J, Virkki A, Aittokallio T, Saaresranta T, Polo-Kantola P, Polo O (2005)
   Non-invasive respiratory monitoring during wakefulness and sleep in pre- and postmenopausal women
   Respir Physiol Neurobiol, 150 (1), 66-74
   DOI 10.1016/j.resp.2005.03.012, PubMed 15927542
2. Aittokallio T, Salmi J, Nyman TA, Nevalainen OS (2005)
   Geometrical distortions in two-dimensional gels: applicable correction methods
   J Chromatogr B Analyt Technol Biomed Life Sci, 815 (1-2), 25-37
   DOI 10.1016/j.jchromb.2004.07.037, PubMed 15652796
3. Elo LL, Lahti L, Skottman H, Kyläniemi M, Lahesmaa R, Aittokallio T (2005)
   Integrating probe-level expression changes across generations of Affymetrix arrays
   Nucleic Acids Res, 33 (22), e193
   DOI 10.1093/nar/gni193, PubMed 16356924
4. Moulder R, Filén JJ, Salmi J, Katajamaa M, Nevalainen OS, Oresic M, Aittokallio T, Lahesmaa R, Nyman TA (2005)
   A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments
   Proteomics, 5 (11), 2748-60
   DOI 10.1002/pmic.200401187, PubMed 15952233
5. Nikula T, West A, Katajamaa M, Lönnberg T, Sara R, Aittokallio T, Nevalainen OS, Lahesmaa R (2005)
   A human ImmunoChip cDNA microarray provides a comprehensive tool to study immune responses
   J Immunol Methods, 303 (1-2), 122-34
   DOI 10.1016/j.jim.2005.06.004, PubMed 16054160
6. Salmi J, Moulder R, Filén JJ, Nevalainen OS, Nyman TA, Lahesmaa R, Aittokallio T (2005)
   Quality classification of tandem mass spectrometry data
   Bioinformatics, 22 (4), 400-6
   DOI 10.1093/bioinformatics/bti829, PubMed 16352652
7. Saaresranta T, Aittokallio T, Utriainen K, Polo O (2005)
   Medroxyprogesterone improves nocturnal breathing in postmenopausal women with chronic obstructive pulmonary disease
   Respir Res, 6 (1), 28
   DOI 10.1186/1465-9921-6-28, PubMed 15807890
8. Saaresranta T, Irjala K, Aittokallio T, Polo O (2005)
   Sleep quality, daytime sleepiness and fasting insulin levels in women with chronic obstructive pulmonary disease
   Respir Med, 99 (7), 856-63
   DOI 10.1016/j.rmed.2004.11.017, PubMed 15939247
9. Tuikkala J, Elo L, Nevalainen OS, Aittokallio T (2005)
   Improving missing value estimation in microarray data with gene ontology
   Bioinformatics, 22 (5), 566-72
   DOI 10.1093/bioinformatics/btk019, PubMed 16377613

Publications 2004

1. Ahola V, Aittokallio T, Uusipaikka E, Vihinen M (2004)
   Statistical methods for identifying conserved residues in multiple sequence alignment
   Stat Appl Genet Mol Biol, 3, Article28
   DOI 10.2202/1544-6115.1074, PubMed 16646807

Publications 2003

1. Ahola V, Aittokallio T, Uusipaikka E, Vihinen M (2003)
   Efficient estimation of emission probabilities in profile hidden Markov models
   Bioinformatics, 19 (18), 2359-68
   DOI 10.1093/bioinformatics/btg328, PubMed 14668219
2. Aittokallio T, Gyllenberg M, Saaresranta T, Polo O (2003)
   Prediction of inspiratory flow shapes during sleep with a mathematic model of upper airway forces
   Sleep, 26 (7), 857-63
   DOI 10.1093/sleep/26.7.857, PubMed 14655920
3. Aittokallio T, Kurki M, Nevalainen O, Nikula T, West A, Lahesmaa R (2003)
   Computational strategies for analyzing data in gene expression microarray experiments
   J Bioinform Comput Biol, 1 (3), 541-86
   DOI 10.1142/s0219720003000319, PubMed 15290769
4. Aittokallio T, Pahikkala T, Ojala P, Nevalainen TJ, Nevalainen O (2003)
   Electrophoretic signal comparison applied to mRNA differential display analysis
   Biotechniques, 34 (1), 116-22
   DOI 10.2144/03341rr02, PubMed 12545548
5. Chen Z, Lund R, Aittokallio T, Kosonen M, Nevalainen O, Lahesmaa R (2003)
   Identification of novel IL-4/Stat6-regulated genes in T lymphocytes
   J Immunol, 171 (7), 3627-35
   DOI 10.4049/jimmunol.171.7.3627, PubMed 14500660
6. Lund R, Aittokallio T, Nevalainen O, Lahesmaa R (2003)
   Identification of novel genes regulated by IL-12, IL-4, or TGF-beta during the early polarization of CD4+ lymphocytes
   J Immunol, 171 (10), 5328-36
   DOI 10.4049/jimmunol.171.10.5328, PubMed 14607935
7. Lund RJ, Ylikoski EK, Aittokallio T, Nevalainen O, Lahesmaa R (2003)
   Kinetics and STAT4- or STAT6-mediated regulation of genes involved in lymphocyte polarization to Th1 and Th2 cells
   Eur J Immunol, 33 (4), 1105-16
   DOI 10.1002/eji.200323899, PubMed 12672077
8. Rosengren AT, Salmi JM, Aittokallio T, Westerholm J, Lahesmaa R, Nyman TA, Nevalainen OS (2003)
   Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels
   Proteomics, 3 (10), 1936-46
   DOI 10.1002/pmic.200300544, PubMed 14625856
9. Saaresranta T, Aittokallio T, Polo-Kantola P, Helenius H, Polo O (2003)
   Effect of medroxyprogesterone on inspiratory flow shapes during sleep in postmenopausal women
   Respir Physiol Neurobiol, 134 (2), 131-43
   DOI 10.1016/s1569-9048(02)00208-2, PubMed 12609480
10. Virtanen I, Ekholm E, Aittokallio T, Tähtinen J, Salmi J, Järvi J, Polo-Kantola P, Polo O (2003)
    State of vigilance, oestrogen replacement therapy, and lipid profile as modifiers of nocturnal movement-induced heart rate responses
    Clin Physiol Funct Imaging, 23 (5), 293-9
    DOI 10.1046/j.1475-097x.2003.00513.x, PubMed 12950328

Publications 2002

1. Aittokallio T, Gyllenberg M, Polo O (2002)
   Adjustment of the human respiratory system to increased upper airway resistance during sleep
   Bull Math Biol, 64 (1), 3-28
   DOI 10.1006/bulm.2001.0264, PubMed 11868337
2. Salmi J, Aittokallio T, Westerholm J, Griese M, Rosengren A, Nyman TA, Lahesmaa R, Nevalainen O (2002)
   Hierarchical grid transformation for image warping in the analysis of two-dimensional electrophoresis gels
   Proteomics, 2 (11), 1504-15
   DOI 10.1002/1615-9861(200211)2:11<1504::AID-PROT1504>3.0.CO;2-B, PubMed 12442250

Publications 2001

1. Aittokallio T, Gyllenberg M, Polo O (2001)
   A model of a snorer's upper airway
   Math Biosci, 170 (1), 79-90
   DOI 10.1016/s0025-5564(00)00062-6, PubMed 11259804
2. Aittokallio T, Ojala P, Nevalainen TJ, Nevalainen O (2001)
   Automated detection of differently expressed fragments in mRNA differential display
   Electrophoresis, 22 (10), 1935-45
   DOI 10.1002/1522-2683(200106)22:10<1935::AID-ELPS1935>3.0.CO;2-5, PubMed 11465492
3. Aittokallio T, Saaresranta T, Polo-Kantola P, Nevalainen O, Polo O (2001)
   Analysis of inspiratory flow shapes in patients with partial upper-airway obstruction during sleep
   Chest, 119 (1), 37-44
   DOI 10.1378/chest.119.1.37, PubMed 11157582
4. Polo-Kantola P, Rauhala E, Saaresranta T, Aittokallio T, Erkkola R, Polo O (2001)
   Climacteric vasomotor symptoms do not predict nocturnal breathing abnormalities in postmenopausal women
   Maturitas, 39 (1), 29-37
   DOI 10.1016/s0378-5122(01)00172-4, PubMed 11451618

Publications 2000

1. Aittokallio T, Gyllenberg M, Järvi J, Nevalainen O, Polo O (2000)
   Detection of high-frequency respiratory movements during sleep
   Comput Methods Programs Biomed, 61 (3), 171-85
   DOI 10.1016/s0169-2607(99)00043-7, PubMed 10710180
2. Aittokallio T, Ojala P, Nevalainen TJ, Nevalainen O (2000)
   Analysis of similarity of electrophoretic patterns in mRNA differential display
   Electrophoresis, 21 (14), 2947-56
   DOI 10.1002/1522-2683(20000801)21:14<2947::AID-ELPS2947>3.0.CO;2-N, PubMed 11001309

Publications 1999

1. Aittokallio T, Gyllenberg M, Hietarinta J, Kuusela T, Multamäki T (1999)
   Improving the false nearest neighbors method with graphical analysis
   Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics, 60 (1), 416-21
   DOI 10.1103/physreve.60.416, PubMed 11969777
2. Aittokallio T, Nevalainen O, Pursiheimo U, Saaresranta T, Polo O (1999)
   Classification of nasal inspiratory flow shapes by attributed finite automata
   Comput Biomed Res, 32 (1), 34-55
   DOI 10.1006/cbmr.1998.1499, PubMed 10066354