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Department: Any ÅAU / Department of Information Technologies UTU / Department of Information Technology UTU / Department of Mathematics and Statistics UTU / Turku School of Economics, Institute of Information Systems Sciences

Research Unit: Any Algorithmics and Computational Intelligence Group (ACI) Biomathematics Research Unit (BIOMATH) Communication Systems (ComSys) Computational Biomodeling Laboratory (Combio Lab) Data Mining and Knowledge Management Laboratory Distributed Systems Laboratory (DS Lab) Embedded Computer and Electronic Systems (ECES) Embedded Systems Laboratory (ESLAB) FUNDIM, Fundamentals of Computing and Discrete Mathematics Institute for Advanced Management Systems Research (IAMSR) Learning and Reasoning Lab Software Construction Laboratorium Software Development Laboratory (SwDev) Software Engineering Laboratory (SE Lab) Turku BioNLP Group Turku Optimization Group (TOpGroup) UTU Information Systems Science (ISS)

Publication type: Any Monographs Edited books Edited special issues of journals Edited proceedings Articles in journals Articles in proceedings Chapters in edited books Ph.D. thesis Lic. thesis Technical reports

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Articles in journals (111):

• Anna Aakula, Pekka Kohonen, Suvi-Katri Leivonen, Rami Mäkelä, Petteri Hintsanen, John Patrick Mpindi, Elena Martens-Uzunova, Tero Aittokallio, Guido Jenster, Merja Perälä, Olli Kallioniemi, Päivi Östling, Systematic Identification of MicroRNAs That Impact on Proliferation of Prostate Cancer Cells and Display Changed Expression in Tumor Tissue. European Urology Epub ahead of print, , 2015.
• Anna Aakula, Suvi-Katri Leivonen, Petteri Hintsanen, Tero Aittokallio, Yvonne Ceder, Anne-Lise Børresen-Dale, Merja Perälä, Päivi Östling, Olli Kallioniemi, MicroRNA-135b Regulates ERα, AR and HIF1AN and Affects Breast and Prostate Cancer Cell Growth. Molecular Oncology 9(7), 1287–1300, 2015.
• Anna Cichonska, Juho Rousu, Tero Aittokallio, Identification of Drug Candidates and Repurposing Opportunities Through Compound-Target Interaction Networks. Expert Opinion on Drug Discovery In Press, 1–13, 2015.
• Liye He, Krister Wennerberg, Tero Aittokallio, Jing Tang, 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, 2015.
• Otto Kauko, Teemu D. Laajala, Mikael Jumppanen, Petteri Hintsanen, Veronika Suni, Pekka Haapaniemi, Garry Corthals, Tero Aittokallio, Jukka Westermarck, Susumu Y. Imanishi, Label-Free Quantitative Phosphoproteomics with Novel Pairwise Abundance Normalization Reveals Synergistic RAS and CIP2A Signaling. Scientific Reports 5(13099), , 2015.
• Milla Kibble, Niina Saarinen, Jing Tang, Krister Wennerberg, Sari Mäkelä, Tero Aittokallio, Network Pharmacology Applications to Map the Unexplored Target Space and Therapeutic Potential of Natural Products. Natural Product Reports 32, 1249–1266, 2015.
• John-Patrick Mpindi, Swapnil Potdar, Dmitrii Bychkov, Jani Saarela, Khalid Saeed, Krister Wennerberg, Tero Aittokallio, Päivi Östling, Olli Kallioniemi, 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, 2015.
• Tapio Pahikkala, Antti Airola, Sami Pietilä, Sushil Shakyawar, Agnieszka Szwajda, Jing Tang, Tero Aittokallio, Toward More Realistic Drug-Target Interaction Predictions. Briefings in Bioinformatics 16(2), 325–37, 2015.
• Pokharel Yuba R., Jani Saarela, Agnieszka Szwajda, Christian Rupp, Anne Rokka, Shibendra K. L. Karna, Kaisa Teittinen, Garry Corthals, Olli Kallioniemi, Krister Wennerberg, Tero Aittokallio, Jukka Westermarck, Relevance Rank Platform (RRP) for Functional Filtering of High Content Protein-Protein Interaction Data. Molecular and Cellular Proteomics mcp-M115, , 2015.
• Maja Šolman, Alessio Ligabue, Olga Blaževitš, Alok Jaiswal, Yong Zhou, Hong Liang, Benoit Lectez, Kari Kopra, Camilo Guzmán, Harri Härmä, John F. Hancock, Tero Aittokallio, Daniel Abankwa, Specific Cancer-Associated Mutations in the Switch III Region of Ras Increase Tumorigenicity by Nanocluster Augmentation. Elife 4, e08905, 2015.
• Agnieszka Szwajda, Prson Gautam, Leena Karhinen, Sawan Kumar Jha, Jani Saarela, Sushil Shakyawar, Laura Turunen, Bhagwan Yadav, Jing Tang, Krister Wennerberg, Tero Aittokallio, Systematic Mapping of Kinase Addiction Combinations in Breast Cancer Cells by Integrating Drug Sensitivity and Selectivity Profiles. Chemistry and Biology 22(8), 1144–1155, 2015.
• Jing Tang, Krister Wennerberg, Tero Aittokallio, What Is Synergy? The Saariselkä Agreement Revisited. Frontiers in Pharmacology 6(181), 1–5 , 2015.
• Bhagwan Yadav, Peddinti Gopalacharyulu, Tea Pemovska, Suleiman A. Khan, Agnieszka Szwajda, Jing Tang, Krister Wennerberg, Tero Aittokallio, From Drug Response Profiling to Target Addiction Scoring in Cancer Cell Models. Disease Models and Mechanisms 8(10), 1255–1264, 2015.
• Bhagwan Yadav, Krister Wennerberg, Tero Aittokallio, Jing Tang, Searching for Drug Synergy in Complex Dose-Response Landscapes Using an Interaction Potency Model. Computational and Structural Biotechnology Journal 13, 504–513, 2015.
• James C. Costello, Laura M. Heiser, Elisabeth Georgii, Mehmet Gönen, Michael P. Menden, Nicholas J. Wang, Mukesh Bansal, Muhammad Ammad-ud-din, Petteri Hintsanen, Suleiman A. Khan, John-Patrick Mpindi, Olli Kallioniemi, Antti Honkela, Tero Aittokallio, Krister Wennerberg, NCI DREAM Community, James J. Collins, Dan Gallahan, Dinah Singer, Julio Saez-Rodriguez, Samuel Kaski, Joe W. Gray, Gustavo Stolovitzky, A Community Effort to Assess and Improve Drug Sensitivity Prediction Algorithms. Nature Biotechnology 32, 1202–1212, 2014.
• Laura L. Elo, Riikka Karjalainen, Tiina Öhman, Petteri Hintsanen, Tuula A. Nyman, Caroline A. Heckman, Tero Aittokallio, Statistical Detection of Quantitative Protein Biomarkers Provides Insights Into Signaling Networks Deregulated in Acute Myeloid Leukemia. Proteomics 14(21-22), 2443–53, 2014.
• Kaisa Huhtinen, Taija Saloniemi-Heinonen, Pekka Keski-Rahkonen, Reena Desai, Teemu D. Laajala, Mia Ståhle, Merja R. Häkkinen, Michael Awosanya, Pia Suvitie, Harry Kujari, Tero Aittokallio, David J. Handelsman, Seppo Auriola, Antti Perheentupa, Matti Poutanen, Intra-Tissue Steroid Profiling Indicates Differential Progesterone and Testosterone Metabolism in the Endometrium and Endometriosis Lesions. Journal of Clinical Endocrinology and Metabolism 99, E2188–97, 2014.
• Matias Knuuttila, Emrah Yatkin, Jenny Kallio, Saija Savolainen, Teemu D. Laajala, Tero Aittokallio, Riikka Oksala, Merja Häkkinen, Pekka Keski-Rahkonen, Seppo Auriola, Matti Poutanen, Sari Mäkelä, Castration Induces Up-Regulation of Intratumoral Androgen Biosynthesis and Androgen Receptor Expression in an Orthotopic VCaP Human Prostate Cancer Xenograft Model. American Journal of Pathology 184(8), 2163–2173, 2014.
• Tiina Öhman, Sandra Söderholm, Petteri Hintsanen, Elina Välimäki, Niina Lietzén, Carol MacKintosh, Tero Aittokallio, Sampsa Matikainen, Tuula A. Nyman, Phosphoproteomics Combined with Quantitative 14-3-3-Affinity Capture Identifies SIRT1 and RAI as Novel Regulators of Cytosolic Double-Stranded RNA Recognition Pathway. Molecular and Cellular Proteomics 13(10), 2604–17, 2014.
• Sebastian Okser, Tapio Pahikkala, Antti Airola, Tapio Salakoski, Samuli Ripatti, Tero Aittokallio, Regularized Machine Learning in the Genetic Prediction of Complex Traits. Plos Genetics 10(11), e1004754, 2014.
• Sandra Söderholm, Petteri Hintsanen, Tiina Öhman, Tero Aittokallio, Tuula A. Nyman, PhosFox: A Bioinformatics Tool for Peptide-Level Processing of LC-MS/MS-Based Phosphoproteomic Data. Proteome Science 12, 36, 2014.
• Jing Tang, Tero Aittokallio, Network Pharmacology Strategies Toward Multi-Target Anticancer Therapies: From Computational Models to Experimental Design Principles. Current Pharmaceutical Design 20(1), 23–36, 2014.
• Jing Tang, Agnieszka Szwajda, Sushil Shakyawar, Tao Xu, Petteri Hintsanen, Krister Wennerberg, Tero Aittokallio, Making Sense of Large-Scale Kinase Inhibitor Bioactivity Data Sets: A Comparative and Integrative Analysis. Journal of Chemical Information and Modeling 54(3), 735–743, 2014.
• Anni P. Vehmas, Dorota Muth-Pawlak, Kaisa Huhtinen, Taija Saloniemi-Heinonen, Kimmo Jaakkola, Teemu D. Laajala, Heidi Kaprio, Pia A. Suvitie, Tero Aittokallio, Harri Siitari, Antti Perheentupa, Matti Poutanen, Garry L. Corthals, Ovarian Endometriosis Signatures Established Through Discovery and Directed Mass Spectrometry Analysis. Journal of Proteome Research 13, 4983–4994, 2014.
• Bhagwan Yadav, Tea Pemovska, Agnieszka Szwajda, Evgeny Kulesskiy, Mika Kontro, Riikka Karjalainen, Muntasir Mamun Majumder, Disha Malani, Astrid Murumägi, Jonathan Knowles, Kimmo Porkka, Caroline Heckman, Olli Kallioniemi, Krister Wennerberg, Tero Aittokallio, Quantitative Scoring of Differential Drug Sensitivity for Individually Optimized Anticancer Therapies. Scientific Reports 4(5193), , 2014.
• Emrah Yatkin, Lauri Polari, Teemu D. Laajala, Annika Smeds, Christer Eckerman, Bjarne Holmbom, Niina M. Saarinen, Tero Aittokallio, Sari I. Mäkelä, Novel Lignan and Stilbenoid Mixture Shows Anticarcinogenic Efficacy in Preclinical PC-3M-luc2 Prostate Cancer Model. Plos One 9(4), e93764, 2014.
• Marja A. Heiskanen, Tero Aittokallio, Predicting Drug-Target Interactions Through Integrative Analysis of Chemogenetic Assays in Yeast. Molecular Biosystems 9(4), 768–779, 2013.
• Laura Kakkola, Oxana V. Denisova, Janne Tynell, Johanna Viiliäinen, Tine Ysenbaert, Rita C. Matos, Ashwini Nagaraj, Tiina Öhman, Suvi Kuivanen, Henrik Paavilainen, L Feng, Bhagwan Yadav, Ilkka Julkunen, Olli Vapalahti, Veijo Hukkanen, Veijo Hukkanen, Jakob Stenman, Tero Aittokallio, Emmy W. Verschuren, Päivi Ojala, Tuula Nyman, Xavier Saelens, K. Dzeyk, Denis Kainov, Anticancer Compound ABT-263 Accelerates Apoptosis in Virus-Infected Cells and Imbalances Cytokine Production and Lowers Survival Rates of Infected Mice. Cell Death and Disease 4, 1–13, 2013.
• Anchit Khanna, Otto Kauko, Camilla Böckelman, Anni Laine, Ilona Schreck, Johanna I. Partanen, Agnieszka Szwajda, Stefanie Bormann, Turker Bilgen, Merja Helenius, Yuba R. Pokharel, John Pimanda, Mike R. Russel, Caj Haglund, Kristina A. Cole, Juha Klefström, Tero Aittokallio, Carsten Weiss, Ari Ristimäki, Tapio Visakorpi, Jukka Westermarck, Chk1 Targeting Reactivates PP2A Tumor Suppressor Activity in Cancer Cells. Cancer Research 73, 6757–6769, 2013.
• Sebastian Okser, Tapio Pahikkala, Tero Aittokallio, Genetic Variants and Their Interactions in Disease Risk Prediction - Machine Learning and Network Perspectives. Biodata Mining 6, 1–15, 2013.
• Tea Pemovska, Mika Kontro, Bhagwan Yadav, Henrik Edgren, Samuli Eldfors, Agnieszka Szwajda, Henrikki Almusa, Maxim M. Bespalov, Pekka Ellonen, Erkki Elonen, Bjørn T. Gjertsen, Riikka Karjalainen, Evgeny Kulesskiy, Sonja Lagström, Anna Lehto, Maija Lepistö, Tuija Lundán, Muntasir Mamun Majumder, Jesus M. Lopez Marti, Pirkko Mattila, Astrid Murumägi, Satu Mustjoki, Aino Palva, Alun Parsons, Tero Pirttinen, Maria E. Rämet, Minna Suvela, Laura Turunen, Imre Västrik, Maija Wolf, Jonathan Knowles, Tero Aittokallio, Caroline A. Heckman, Kimmo Porkka, Olli Kallioniemi, Krister Wennerberg, Individualized Systems Medicine Strategy to Tailor Treatments for Patients with Chemorefractory Acute Myeloid Leukemia. Cancer Discovery 3(12), 1416–1429, 2013.
• Jing Tang, Leena Karhinen, Tao Xu, Agnieszka Szwajda, Bhagwan Yadav, Krister Wennerberg, Tero Aittokallio, Target Inhibition Networks: Predicting Selective Combinations of Druggable Targets to Block Cancer Survival Pathways. Plos Computational Biology 9, e1003226, 2013.
• Jukka Corander, Tero Aittokallio, Samuli Ripatti, Samuel Kaski, The Rocky Road to Personalized Medicine: Computational and Statistical Challenges. Personalized Medicine 9(2), 109–114, 2012.
• Oxana V. Denisova, Laura Kakkola, Lin Feng, Jakob Stenman, Ashwini Nagaraj, Johanna Lampe, Bhagwan Yadav, Tero Aittokallio, Pasi Kaukinen, Tero Ahola, Suvi Kuivanen, Olli Vapalahti, Anu Kantele, Janne Tynell, Ilkka Julkunen, Hannimari Kallio-Kokko, Henrik Paavilainen, Veijo Hukkanen, Richard M. Elliott, Jef K. De Brabande, Xavier Saelens, Denis E. Kainov, Obatoclax, Saliphenylhalamide, and Gemcitabine Inhibit Influenza a Virus Infection. Journal of Biological Chemistry 287, 35324–35332, 2012.
• Marja A. Heiskanen, Tero Aittokallio, Mining High-Throughput Screens for Cancer Drug Targets—Lessons from Yeast Chemical-Genomic Profiling and Synthetic Lethality. Data Mining and Knowledge Discovery 2, 263–272, 2012.
• Tuomas O. Kiviniemi, Gennady G. Yegutkin, Jyri O. Toikka, Subhadeep Paul, Tero Aittokallio, Tuula Janatuinen, Juhani Knuuti, Tapani Rönnemaa, Juha W. Koskenvuo, Jaakko J. Hartiala, Sirpa Jalkanen, Olli T. Raitakari, Pravastatin-Induced Improvement in Coronary Reactivity and Circulating ATP and ADP Levels in Young Adults with Type 1 Diabetes. Frontiers in Physiology 3(338), , 2012.
• Teemu D. Laajala, Jukka Corander, Niina M. Saarinen, Katja Mäkelä, Saija Savolainen, Mari I. Suominen, Esa Alhoniemi, Sari Mäkelä, Matti Poutanen, Tero Aittokallio, Improved Statistical Modeling of Tumor Growth and Treatment Effect in Preclinical Animal Studies with Highly Heterogeneous Responses in Vivo. Clinical Cancer Research 18(16), 4385–96, 2012.
• Tapio Pahikkala, Sebastian Okser, Antti Airola, Tapio Salakoski, Tero Aittokallio, Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations. Algorithms for Molecular Biology 7, 1–11, 2012.
• Johannes Tuikkala, Heidi Vähämaa, Pekka Salmela, Olli S. Nevalainen, Tero Aittokallio, A Multilevel Layout Algorithm for Visualizing Physical and Genetic Interaction Networks, with Emphasis on Their Modular Organization. Biodata Mining 5(2), , 2012.
• Laura L. Elo, Aleksi Kallio, Teemu D. Laajala, R. David Hawkins, Eija Korpelainen, Tero Aittokallio, Optimized Detection of Transcription Factor-Binding Sites in ChIP-Seq Experiments. Nucleic Acids Research 40(1), e1, 2011.
• Leo Lahti, Laura L. Elo, Tero Aittokallio, Samuel Kaski, Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays. IEEE-ACM Transactions on Computational Biology and Bioinformatics 8(1), 217–225, 2011.
• Niina Lietzén, Tiina Öhman, Johanna Rintahaka, Ilkka Julkunen, Tero Aittokallio, Sampsa Matikainen, Tuula A. Nyman, Quantitative Subcellular Proteome and Secretome Profiling of Influenza A Virus-Infected Human Primary Macrophages. Plos Pathogens 7, e1001340, 2011.
• Rolf Lindén, Ville-Pekka Eronen, Tero Aittokallio, Quantitative Maps of Genetic Interactions in Yeast - Comparative Evaluation and Integrative Analysis. BMC Systems Biology , 1–14, 2011.
• Heidi Vähämaa, Ville R. Koskinen, Waltteri Hosia, Robert Moulder, Olli S. Nevalainen, Riitta Lahesmaa, Tero Aittokallio, Jussi Salmi, PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use. International Journal of Proteomics Vol. 2011 , 9, 2011.
• Tero Aittokallio, Dealing with Missing Values in Large-Scale Studies – Microarray Data Imputation and Beyond. Briefings in Bioinformatics 11(2), 253–264, 2010.
• Marius C. Codrea, Marja Hakala-Yatkin, Anna Kårlund-Marttila, Ladislav Nedbal, Tero Aittokallio, Olli S. Nevalainen, Esa Tyystjärvi, Mahalanobis Distance Screening of Arabidopsis Mutans with Chlorophyll Fluorescence. Photosynthesis Research 105, 273–283, 2010.
• Laura L. Elo, Henna Järvenpää, Soile Tuomela, Sunil Raghav, Helena Ahlfors, Kirsti Laurila, Bhawna Gupta, Riikka J. Lund, Johanna Tahvanainen, R. David Hawkins, Matej Orešič, Harri Lähdesmäki, Omid Rasool, Kanury V. S. Rao, Tero Aittokallio, Riitta Lahesmaa, Genome-Wide Profiling of Interleukin-4 and STAT6 Transcription Factor Regulation of Human Th2 Cell Programming. Immunity 32(6), 852–862, 2010.
• Laura L. Elo, Juha Mykkänen, Tuomas Nikula, Henna Järvenpää, Satu Simell, Tero Aittokallio, Heikki Hyöty, Jorma Ilonen, Riitta Veijola, Tuula Simell, Mikael Knip, Olli Simell, Riitta Lahesmaaa, Early Suppression of Immune Response Pathways Characterizes Children with Prediabetes in Genome-Wide Gene Expression Profiling. Journal of Autoimmunity 35(1), 70–76, 2010.
• Ville-Pekka Eronen, Rolf Lindén, Anna Lindroos, Mirella Kanerva, Tero Aittokallio, Genome-Wide Scoring of Positive and Negative Epistasis through Decomposition of Quantitative Genetic Interaction Fitness Matrices. Plos One , 1–13, 2010.
• Minna A. Korolainen, Tuula A. Nyman, Tero Aittokallio, Tuula Pirttilä, An Update on Clinical Proteomics in Alzheimer's Research. Journal of Neurochemistry 112(6), 1386–1414, 2010.