Publications 2024

Adnan Awad S, Dufva O, Klievink J, Karjalainen E, Ianevski A, Pietarinen P, Kim D, Potdar S, Wolf M, Lotfi K, Aittokallio T, Wennerberg K, Porkka K, Mustjoki S (2024)
Integrated drug profiling and CRISPR screening identify BCR::ABL1-independent vulnerabilities in chronic myeloid leukemia
Cell Rep Med, 5 (5), 101521
DOI 10.1016/j.xcrm.2024.101521, PubMed 38653245

Aittokallio T, Fang EF (2024)
Editorial overview-Artificial intelligence methodologies in structural biology: Bridging the gap to medical applications
Curr Opin Struct Biol, 87, 102862
DOI 10.1016/j.sbi.2024.102862, PubMed 38870638

Bulanova D, Akimov Y, Senkowski W, Oikkonen J, Gall-Mas L, Timonen S, Elmadani M, Hynninen J, Hautaniemi S, Aittokallio T, Wennerberg K (2024)
A synthetic lethal dependency on casein kinase 2 in response to replication-perturbing therapeutics in RB1-deficient cancer cells
Sci Adv, 10 (21), eadj1564
DOI 10.1126/sciadv.adj1564, PubMed 38781347

Ianevski A, Kushnir A, Nader K, Miihkinen M, Xhaard H, Aittokallio T, Tanoli Z (2024)
RepurposeDrugs: an interactive web-portal and predictive platform for repurposing mono- and combination therapies
Brief Bioinform, 25 (4)
DOI 10.1093/bib/bbae328, PubMed 38980370

Ianevski A, Nader K, Driva K, Senkowski W, Bulanova D, Moyano-Galceran L, Ruokoranta T, Kuusanmäki H, Ikonen N, Sergeev P, Vähä-Koskela M, Giri AK, Vähärautio A, Kontro M, Porkka K, Pitkänen E, Heckman CA, Wennerberg K, Aittokallio T (2024)
Single-cell transcriptomes identify patient-tailored therapies for selective co-inhibition of cancer clones
Nat Commun, 15 (1), 8579
DOI 10.1038/s41467-024-52980-5, PubMed 39362905

Nader K, Tasci M, Ianevski A, Erickson A, Verschuren EW, Aittokallio T, Miihkinen M (2024)
ScType enables fast and accurate cell type identification from spatial transcriptomics data
Bioinformatics, 40 (7)
DOI 10.1093/bioinformatics/btae426, PubMed 38936341

Schulman A, Rousu J, Aittokallio T, Tanoli Z (2024)
Attention-based approach to predict drug-target interactions across seven target superfamilies
Bioinformatics, 40 (8)
DOI 10.1093/bioinformatics/btae496, PubMed 39115379

Suske T, Sorger H, Manhart G, Ruge F, Prutsch N, Zimmerman MW, Eder T, Abdallah DI, Maurer B, Wagner C, Schönefeldt S, Spirk K, Pichler A, Pemovska T, Schweicker C, Pölöske D, Hubanic E, Jungherz D, Müller TA, Aung MMK, Orlova A, Pham HTT, Zimmel K, Krausgruber T, Bock C et al. (2024)
Hyperactive STAT5 hijacks T cell receptor signaling and drives immature T cell acute lymphoblastic leukemia
J Clin Invest, 134 (8)
DOI 10.1172/JCI168536, PubMed 38618957

von Jan J, Timonen S, Braun T, Jiang Q, Ianevski A, Peng Y, McConnell K, Sindaco P, Müller TA, Pützer S, Klepzig H, Jungherz D, Dechow A, Wahnschaffe L, Giri AK, Kankainen M, Kuusanmäki H, Neubauer HA, Moriggl R, Mazzeo P, Schmidt N, Koch R, Hallek M, Chebel A, Armisen D et al. (2024)
Optimizing drug combinations for T-PLL: restoring DNA damage and P53-mediated apoptotic responses
Blood, 144 (15), 1595-1610
DOI 10.1182/blood.2023022884, PubMed 38941598

Zhao Z, Zobolas J, Zucknick M, Aittokallio T (2024)
Tutorial on survival modeling with applications to omics data
Bioinformatics, 40 (3)
DOI 10.1093/bioinformatics/btae132, PubMed 38445722

Publications 2023

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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