Tero Aittokallio

  • Group leader; PhD
  • +47 22 78 13 75
 

Original articles

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 (in press)
DOI 10.1074/jbc.RA119.011265, PubMed 32071079

Qiao X, Liu Y, Llamazares Prada M, 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 co-amplified with MYC in breast tumors and encodes an ubiquitin ligase that limits MYC-dependent apoptosis
Cancer Res (in press)
DOI 10.1158/0008-5472.CAN-19-1647, PubMed 32029551

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

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

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

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 (2019)
Integrated drug profiling and CRISPR screening identify essential pathways for CAR T cell cytotoxicity
Blood (in press)
DOI 10.1182/blood.2019002121, PubMed 31830245

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

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

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

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

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

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

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

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

Tanoli Z, Alam Z, Ianevski A, Wennerberg K, Vähä-Koskela M, Aittokallio T (2018)
Interactive visual analysis of drug-target interaction networks using Drug Target Profiler, with applications to precision medicine and drug repurposing
Brief Bioinform (in press)
DOI 10.1093/bib/bby119, PubMed 30566623

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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, 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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, e742
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Heiskanen MA, Aittokallio T (2013)
Predicting drug-target interactions through integrative analysis of chemogenetic assays in yeast
Mol Biosyst, 9 (4), 768-79
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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
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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
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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
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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), 35324-32
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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
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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
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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
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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
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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
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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
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Lindén RO, Eronen VP, Aittokallio T (2011)
Quantitative maps of genetic interactions in yeast - comparative evaluation and integrative analysis
BMC Syst Biol, 5, 45
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Järvinen AP, Hiissa J, Elo LL, Aittokallio T (2008)
Predicting quantitative genetic interactions by means of sequential matrix approximation
PLoS One, 3 (9), e3284
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Ahola V, Aittokallio T, Vihinen M, Uusipaikka E (2008)
Model-based prediction of sequence alignment quality
Bioinformatics, 24 (19), 2165-71
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Elo LL, Filén S, Lahesmaa R, Aittokallio T (2008)
Reproducibility-optimized test statistic for ranking genes in microarray studies
IEEE/ACM Trans Comput Biol Bioinform, 5 (3), 423-31
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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
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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
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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
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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
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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
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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
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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
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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
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Ahola V, Aittokallio T, Vihinen M, Uusipaikka E (2006)
A statistical score for assessing the quality of multiple sequence alignments
BMC Bioinformatics, 7, 484
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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
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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
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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
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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
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Aittokallio T, Ojala P, Nevalainen TJ, Nevalainen OS (2006)
Automated pattern ranking in differential display data analysis
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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
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Tuikkala J, Elo L, Nevalainen OS, Aittokallio T (2005)
Improving missing value estimation in microarray data with gene ontology
Bioinformatics, 22 (5), 566-72
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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
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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

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

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

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

Saaresranta T, Aittokallio T, Utriainen K, Polo O (2005)
Medroxyprogesterone improves nocturnal breathing in postmenopausal women with chronic obstructive pulmonary disease
Respir Res, 6, 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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, 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, 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

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

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, 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

Review articles

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Other articles

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

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

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

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

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

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