Tero Aittokallio

72 papers Journal 67Unranked 5

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	From library to landscape: integrative annotation workflows for compound libraries in drug repurposing. Database J. Biol. Databases Curation Jeanette Reinshagen, Brinton Seashore-Ludlow, Yojana Gadiya, Anna-Lena Gustavsson, ZiaurRehman Tanoli, Tero Aittokallio, Johanna Huchting, Annika Jenmalm-Jensen, Philip Gribbon, Andrea Zaliani, Flavio Ballante
2025	J	`jnl`	Optimizing Prognostic Biomarker Discovery in Pancreatic Cancer Through Hybrid Ensemble Feature Selection and Multi-Omics Data. CoRR John Zobolas, Anne-Marie George, Alberto López, Sebastian Fischer, Marc Becker, Tero Aittokallio
2025	J	`jnl`	Scaling up drug combination surface prediction. Briefings Bioinform. Riikka Huusari, Tianduanyi Wang, Sándor Szedmák, Diogo Dias, Tero Aittokallio, Juho Rousu
2024	J	`jnl`	Attention-based approach to predict drug-target interactions across seven target superfamilies. Bioinform. Aron Schulman, Juho Rousu, Tero Aittokallio, ZiaurRehman Tanoli
2024	J	`jnl`	RepurposeDrugs: an interactive web-portal and predictive platform for repurposing mono- and combination therapies. Briefings Bioinform. Aleksandr Ianevski, Aleksandr Kushnir, Kristen Nader, Mitro Miihkinen, Henri Xhaard, Tero Aittokallio, ZiaurRehman Tanoli
2024	J	`jnl`	ScType enables fast and accurate cell type identification from spatial transcriptomics data. Bioinform. Kristen Nader, Misra Tasci, Aleksandr Ianevski, Andrew Erickson, Emmy W. Verschuren, Tero Aittokallio, Mitro Miihkinen
2024	J	`jnl`	Tutorial on survival modeling with applications to omics data. Bioinform. Zhi Zhao, John Zobolas, Manuela Zucknick, Tero Aittokallio
2023	J	`jnl`	Breeze 2.0: an interactive web-tool for visual analysis and comparison of drug response data. Nucleic Acids Res. Potdar Swapnil, Filipp Ianevski, Aleksandr Ianevski, ZiaurRehman Tanoli, Krister Wennerberg, Brinton Seashore-Ludlow, Olli-P. Kallioniemi, Päivi Östling, Tero Aittokallio, Saarela Jani
2023	J	`jnl`	OSCAR: Optimal subset cardinality regression using the L0-pseudonorm with applications to prognostic modelling of prostate cancer. PLoS Comput. Biol. Anni S. Halkola, Kaisa Joki, Tuomas Mirtti, Marko M. Mäkelä, Tero Aittokallio, Teemu D. Laajala
2022	J	`jnl`	Discovery of host-directed modulators of virus infection by probing the SARS-CoV-2-host protein-protein interaction network. Briefings Bioinform. Vandana Ravindran, Jessica Wagoner, Paschalis Athanasiadis, Andreas B. Den Hartigh, Julia M. Sidorova, Aleksandr Ianevski, Susan L. Fink, Arnoldo Frigessi, Judith White, Stephen J. Polyak, Tero Aittokallio
2022	J	`jnl`	Evaluation of statistical approaches for association testing in noisy drug screening data. BMC Bioinform. Petr Smirnov, Ian Smith, Zhaleh Safikhani, Wail Ba-alawi, Farnoosh Khodakarami, Eva Lin, Yihong Yu, Scott Martin, Janosch Ortmann, Tero Aittokallio, Marc Hafner, Benjamin Haibe-Kains
2022	J	`jnl`	SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples. Nucleic Acids Res. Aleksandr Ianevski, Anil K. Giri, Tero Aittokallio
2021	J	`jnl`	Characterizing the Quality of Insight by Interactions: A Case Study. IEEE Trans. Vis. Comput. Graph. Chen He, Luana Micallef, Liye He, Gopal Peddinti, Tero Aittokallio, Giulio Jacucci
2021	J	`jnl`	Modeling drug combination effects via latent tensor reconstruction. Bioinform. Tianduanyi Wang, Sándor Szedmák, Haishan Wang, Tero Aittokallio, Tapio Pahikkala, Anna Cichonska, Juho Rousu
2021	J	`jnl`	Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer. Briefings Bioinform. Liye He, Daria Bulanova, Jaana Oikkonen, Antti Häkkinen, Kaiyang Zhang, Shuyu Zheng, Wenyu Wang, Erdogan Pekcan Erkan, Olli Carpén, Titta Joutsiniemi, Sakari Hietanen, Johanna Hynninen, Kaisa Huhtinen, Sampsa Hautaniemi, Anna Vähärautio, Jing Tang, Krister Wennerberg, Tero Aittokallio
2020	J	`jnl`	Breeze: an integrated quality control and data analysis application for high-throughput drug screening. Bioinform. Potdar Swapnil, Aleksandr Ianevski, John-Patrick Mpindi, Dmitrii Bychkov, Clément Fiere, Philipp Ianevski, Bhagwan Yadav, Krister Wennerberg, Tero Aittokallio, Olli-P. Kallioniemi, Saarela Jani, Päivi Östling
2020	J	`jnl`	Characterizing the Quality of Insight by Interactions: A Case Study. CoRR Chen He, Luana Micallef, Liye He, Gopal Peddinti, Tero Aittokallio, Giulio Jacucci
2020	J	`jnl`	Cost-effective survival prediction for patients with advanced prostate cancer using clinical trial and real-world hospital registry datasets. Int. J. Medical Informatics Mika Murtojärvi, Anni S. Halkola, Antti Airola, Teemu D. Laajala, Tuomas Mirtti, Tero Aittokallio, Tapio Pahikkala
2020	J	`jnl`	Interactive visual analysis of drug-target interaction networks using Drug Target Profiler, with applications to precision medicine and drug repurposing. Briefings Bioinform. ZiaurRehman Tanoli, Zaid Alam, Aleksandr Ianevski, Krister Wennerberg, Markus Vähä-Koskela, Tero Aittokallio
2020	J	`jnl`	Multiobjective optimization identifies cancer-selective combination therapies. PLoS Comput. Biol. Otto Pulkkinen, Prson Gautam, Ville Mustonen, Tero Aittokallio
2020	J	`jnl`	SynToxProfiler: An interactive analysis of drug combination synergy, toxicity and efficacy. PLoS Comput. Biol. Aleksandr Ianevski, Sanna Timonen, Alexander Kononov, Tero Aittokallio, Anil K. Giri
2020	J	`jnl`	SynergyFinder 2.0: visual analytics of multi-drug combination synergies. Nucleic Acids Res. Aleksandr Ianevski, Anil K. Giri, Tero Aittokallio
2020	J	`jnl`	SynergyFinder: a web application for analyzing drug combination dose-response matrix data. Bioinform. Aleksandr Ianevski, Liye He, Tero Aittokallio, Jing Tang
2019	J	`jnl`	Prediction of drug combination effects with a minimal set of experiments. Nat. Mach. Intell. Aleksandr Ianevski, Anil K. Giri, Prson Gautam, Alexander Kononov, Potdar Swapnil, Saarela Jani, Krister Wennerberg, Tero Aittokallio
2018	J	`jnl`	Drug Target Commons 2.0: a community platform for systematic analysis of drug-target interaction profiles. Database J. Biol. Databases Curation ZiaurRehman Tanoli, Zaid Alam, Markus Vähä-Koskela, Balaguru Ravikumar, Alina Malyutina, Alok Jaiswal, Jing Tang, Krister Wennerberg, Tero Aittokallio
2018	J	`jnl`	Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach. Bioinform. Mehreen Ali, Suleiman A. Khan, Krister Wennerberg, Tero Aittokallio
2018	J	`jnl`	Learning with multiple pairwise kernels for drug bioactivity prediction. Bioinform. Anna Cichonska, Tapio Pahikkala, Sándor Szedmák, Heli Julkunen, Antti Airola, Markus Heinonen, Tero Aittokallio, Juho Rousu
2018	J	`jnl`	ePCR: an R-package for survival and time-to-event prediction in advanced prostate cancer, applied to real-world patient cohorts. Bioinform. Teemu D. Laajala, Mika Murtojärvi, Arho Virkki, Tero Aittokallio
2017	J	`jnl`	C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms. Nucleic Acids Res. Balaguru Ravikumar, Zaid Alam, Gopal Peddinti, Tero Aittokallio
2017	J	`jnl`	Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors. PLoS Comput. Biol. Anna Cichonska, Balaguru Ravikumar, Elina Parri, Sanna Timonen, Tapio Pahikkala, Antti Airola, Krister Wennerberg, Juho Rousu, Tero Aittokallio
2017	J	`jnl`	MediSyn: uncertainty-aware visualization of multiple biomedical datasets to support drug treatment selection. BMC Bioinform. Chen He, Luana Micallef, ZiaurRehman Tanoli, Samuel Kaski, Tero Aittokallio, Giulio Jacucci
2017	J	`jnl`	SynergyFinder: a web application for analyzing drug combination dose-response matrix data. Bioinform. Aleksandr Ianevski, Liye He, Tero Aittokallio, Jing Tang
2017	J	`jnl`	Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression. Bioinform. Muhammad Ammad-ud-din, Suleiman A. Khan, Krister Wennerberg, Tero Aittokallio
2016	J	`jnl`	Drug response prediction by inferring pathway-response associations with Kernelized Bayesian Matrix Factorization. CoRR Muhammad Ammad-ud-din, Suleiman A. Khan, Disha Malani, Astrid Murumägi, Olli-P. Kallioniemi, Tero Aittokallio, Samuel Kaski
2016	J	`jnl`	Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization. Bioinform. Muhammad Ammad-ud-din, Suleiman A. Khan, Disha Malani, Astrid Murumägi, Olli-P. Kallioniemi, Tero Aittokallio, Samuel Kaski
2015	J	`jnl`	Impact of normalization methods on high-throughput screening data with high hit rates and drug testing with dose-response data. Bioinform. John-Patrick Mpindi, Potdar Swapnil, Dmitrii Bychkov, Saarela Jani, Khalid Saeed, Krister Wennerberg, Tero Aittokallio, Päivi Östling, Olli-P. Kallioniemi
2015	J	`jnl`	TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples. Bioinform. Liye He, Krister Wennerberg, Tero Aittokallio, Jing Tang
2015	J	`jnl`	Toward more realistic drug-target interaction predictions. Briefings Bioinform. Tapio Pahikkala, Antti Airola, Sami Pietilä, Sushil Kumar Shakyawar, Agnieszka Szwajda, Jing Tang, Tero Aittokallio
2014	—	`conf`	A Two-Step Learning Approach for Solving Full and Almost Full Cold Start Problems in Dyadic Prediction. ECML/PKDD (2) Tapio Pahikkala, Michiel Stock, Antti Airola, Tero Aittokallio, Bernard De Baets, Willem Waegeman
2014	J	`jnl`	A two-step learning approach for solving full and almost full cold start problems in dyadic prediction. CoRR Tapio Pahikkala, Michiel Stock, Antti Airola, Tero Aittokallio, Bernard De Baets, Willem Waegeman
2014	J	`jnl`	Making Sense of Large-Scale Kinase Inhibitor Bioactivity Data Sets: A Comparative and Integrative Analysis. J. Chem. Inf. Model. Jing Tang, Agnieszka Szwajda, Sushil Kumar Shakyawar, Tao Xu, Petteri Hintsanen, Krister Wennerberg, Tero Aittokallio
2013	J	`jnl`	Genetic variants and their interactions in disease risk prediction - machine learning and network perspectives. BioData Min. Sebastian Okser, Tapio Pahikkala, Tero Aittokallio
2013	J	`jnl`	Target Inhibition Networks: Predicting Selective Combinations of Druggable Targets to Block Cancer Survival Pathways. PLoS Comput. Biol. Jing Tang, Leena Karhinen, Tao Xu, Agnieszka Szwajda, Bhagwan Yadav, Krister Wennerberg, Tero Aittokallio
2012	J	`jnl`	A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization. BioData Min. Johannes Tuikkala, Heidi Vähämaa, Pekka Salmela, Olli Nevalainen, Tero Aittokallio
2012	J	`jnl`	Mining high-throughput screens for cancer drug targets - lessons from yeast chemical-genomic profiling and synthetic lethality. WIREs Data Mining Knowl. Discov. Marja A. Heiskanen, Tero Aittokallio
2012	—	`conf`	Parallel Feature Selection for Regularized Least-Squares. PARA Sebastian Okser, Antti Airola, Tero Aittokallio, Tapio Salakoski, Tapio Pahikkala
2012	J	`jnl`	Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations. Algorithms Mol. Biol. Tapio Pahikkala, Sebastian Okser, Antti Airola, Tapio Salakoski, Tero Aittokallio
2011	—	`conf`	Fast and parallelized greedy forward selection of genetic variants in Genome-wide association studies. GENSiPS Sebastian Okser, Tapio Pahikkala, Antti Airola, Tero Aittokallio, Tapio Salakoski
2011	J	`jnl`	Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays. IEEE ACM Trans. Comput. Biol. Bioinform. Leo Lahti, Laura Elo, Tero Aittokallio, Samuel Kaski
2011	J	`jnl`	Quantitative maps of genetic interactions in yeast - Comparative evaluation and integrative analysis. BMC Syst. Biol. Rolf Lindén, Ville-Pekka Eronen, Tero Aittokallio
2010	J	`jnl`	Dealing with missing values in large-scale studies: microarray data imputation and beyond. Briefings Bioinform. Tero Aittokallio
2009	J	`jnl`	Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks. Bioinform. Mathieu Clément-Ziza, Christophe Malabat, Christian Weber, Ivan Moszer, Tero Aittokallio, Catherine Letondal, Sandrine Rousseau
2009	J	`jnl`	Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets. Briefings Bioinform. Laura Elo, Jukka Hiissa, Jarno Tuimala, Aleksi Kallio, Eija Korpelainen, Tero Aittokallio
2008	J	`jnl`	Missing value imputation improves clustering and interpretation of gene expression microarray data. BMC Bioinform. Johannes Tuikkala, Laura Elo, Olli Nevalainen, Tero Aittokallio
2008	J	`jnl`	Model-based prediction of sequence alignment quality. Bioinform. Virpi Ahola, Tero Aittokallio, Mauno Vihinen, Esa Uusipaikka
2008	J	`jnl`	Overnight features of transcutaneous carbon dioxide measurement as predictors of metabolic status. Artif. Intell. Medicine Arho Virkki, Olli Polo, Tarja Saaresranta, Anne Laapotti-Salo, Mats Gyllenberg, Tero Aittokallio
2008	J	`jnl`	Reproducibility-Optimized Test Statistic for Ranking Genes in Microarray Studies. IEEE ACM Trans. Comput. Biol. Bioinform. Laura Elo, Sanna Filen, Riitta Lahesmaa, Tero Aittokallio
2007	J	`jnl`	GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinform. Olivier Garcia, Cosmin Saveanu, Melissa S. Cline, Micheline Fromont-Racine, Alain Jacquier, Benno Schwikowski, Tero Aittokallio
2007	J	`jnl`	Inspiratory flow shape clustering: An automated method to monitor upper airway performance during sleep. Comput. Methods Programs Biomed. Tero Aittokallio, Jani S. Malminen, Tapio Pahikkala, Olli Polo, Olli Nevalainen
2007	J	`jnl`	Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. Bioinform. Laura Elo, Henna Järvenpää, Matej Oresic, Riitta Lahesmaa, Tero Aittokallio
2006	J	`jnl`	A statistical score for assessing the quality of multiple sequence alignments. BMC Bioinform. Virpi Ahola, Tero Aittokallio, Mauno Vihinen, Esa Uusipaikka
2006	J	`jnl`	Graph-based methods for analysing networks in cell biology. Briefings Bioinform. Tero Aittokallio, Benno Schwikowski
2006	J	`jnl`	Improving missing value estimation in microarray data with gene ontology. Bioinform. Johannes Tuikkala, Laura Elo, Olli Nevalainen, Tero Aittokallio
2006	J	`jnl`	Inference of Gene Coexpression Networks by Integrative Analysis across Microarray Experiments. J. Integr. Bioinform. Laura Elo, Riitta Lahesmaa, Tero Aittokallio
2006	J	`jnl`	Quality classification of tandem mass spectrometry data. Bioinform. Jussi Salmi, Robert Moulder, Jan-Jonas Filén, Olli Nevalainen, Tuula A. Nyman, Riitta Lahesmaa, Tero Aittokallio
2005	—	`conf`	On the Robustness of Fluorescence Fingerprinting of Plants. Artificial Intelligence and Applications Marius C. Codrea, Tero Aittokallio, Mika Keränen, Esa Tyystjärvi, Olli Nevalainen
2003	J	`jnl`	Computational Strategies for Analyzing Data in Gene Expression Microarray Experiments. J. Bioinform. Comput. Biol. Tero Aittokallio, Markus Kurki, Olli Nevalainen, Tuomas Nikula, Anne West, Riitta Lahesmaa
2003	J	`jnl`	Efficient estimation of emission probabilities in profile hidden Markov models. Bioinform. Virpi Ahola, Tero Aittokallio, Esa Uusipaikka, Mauno Vihinen
2003	J	`jnl`	Feature learning with a genetic algorithm for fluorescence fingerprinting of plant species. Pattern Recognit. Lett. Marius C. Codrea, Tero Aittokallio, Mika Keränen, Esa Tyystjärvi, Olli Nevalainen
2003	—	`conf`	Genetic Feature Learning Algorithm for Fluorescence Fingerprinting of Plants. Artificial Evolution Marius C. Codrea, Tero Aittokallio, Mika Keränen, Esa Tyystjärvi, Olli Nevalainen
2000	J	`jnl`	Detection of high-frequency respiratory movements during sleep. Comput. Methods Programs Biomed. Tero Aittokallio, Mats Gyllenberg, J. Järvi, Olli Nevalainen, Olli Polo
1999	J	`jnl`	Classification of Nasal Inspiratory Flow Shapes by Attributed Finite Automata. Comput. Biomed. Res. Tero Aittokallio, Olli Nevalainen, U. Pursiheimo, Tarja Saaresranta, Olli Polo