Tero Aittokallio

Publication Activity (10 Years)

Years Active: 1999-2024
Publications (10 Years): 29

Top Topics

Visual Analytics

Biomedical Data

Matrix Factorization

Prostate Cancer

Top Venues

Briefings Bioinform.

Nucleic Acids Res.

PLoS Comput. Biol.

Publications

Aleksandr Ianevski, Aleksandr Kushnir, Kristen Nader, Mitro Miihkinen, Henri Xhaard, Tero Aittokallio, ZiaurRehman Tanoli
RepurposeDrugs: an interactive web-portal and predictive platform for repurposing mono- and combination therapies. Briefings Bioinform. 25 (4) (2024)
Potdar Swapnil, Filipp Ianevski, Aleksandr Ianevski, ZiaurRehman Tanoli, Krister Wennerberg, Brinton Seashore-Ludlow, Olli-P. Kallioniemi, Päivi Östling, Tero Aittokallio, Saarela Jani
Breeze 2.0: an interactive web-tool for visual analysis and comparison of drug response data. Nucleic Acids Res. 51 (W1) (2023)
Anni S. Halkola, Kaisa Joki, Tuomas Mirtti, Marko M. Mäkelä, Tero Aittokallio, Teemu D. Laajala
OSCAR: Optimal subset cardinality regression using the L0-pseudonorm with applications to prognostic modelling of prostate cancer. PLoS Comput. Biol. 19 (3) (2023)
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
Discovery of host-directed modulators of virus infection by probing the SARS-CoV-2-host protein-protein interaction network. Briefings Bioinform. 23 (6) (2022)
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
Evaluation of statistical approaches for association testing in noisy drug screening data. BMC Bioinform. 23 (1) (2022)
Aleksandr Ianevski, Anil K. Giri, Tero Aittokallio
SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples. Nucleic Acids Res. 50 (W1) (2022)
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
Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer. Briefings Bioinform. 22 (6) (2021)
Tianduanyi Wang, Sándor Szedmák, Haishan Wang, Tero Aittokallio, Tapio Pahikkala, Anna Cichonska, Juho Rousu
Modeling drug combination effects via latent tensor reconstruction. Bioinform. 37 (Supplement) (2021)
Chen He, Luana Micallef, Liye He, Gopal Peddinti, Tero Aittokallio, Giulio Jacucci
Characterizing the Quality of Insight by Interactions: A Case Study. IEEE Trans. Vis. Comput. Graph. 27 (8) (2021)
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
Breeze: an integrated quality control and data analysis application for high-throughput drug screening. Bioinform. 36 (11) (2020)
Aleksandr Ianevski, Anil K. Giri, Tero Aittokallio
SynergyFinder 2.0: visual analytics of multi-drug combination synergies. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Aleksandr Ianevski, Sanna Timonen, Alexander Kononov, Tero Aittokallio, Anil K. Giri
SynToxProfiler: An interactive analysis of drug combination synergy, toxicity and efficacy. PLoS Comput. Biol. 16 (2) (2020)
Otto Pulkkinen, Prson Gautam, Ville Mustonen, Tero Aittokallio
Multiobjective optimization identifies cancer-selective combination therapies. PLoS Comput. Biol. 16 (12) (2020)
Aleksandr Ianevski, Liye He, Tero Aittokallio, Jing Tang
SynergyFinder: a web application for analyzing drug combination dose-response matrix data. Bioinform. 36 (8) (2020)
ZiaurRehman Tanoli, Zaid Alam, Aleksandr Ianevski, Krister Wennerberg, Markus Vähä-Koskela, Tero Aittokallio
Interactive visual analysis of drug-target interaction networks using Drug Target Profiler, with applications to precision medicine and drug repurposing. Briefings Bioinform. 21 (1) (2020)
Mika Murtojärvi, Anni S. Halkola, Antti Airola, Teemu D. Laajala, Tuomas Mirtti, Tero Aittokallio, Tapio Pahikkala
Cost-effective survival prediction for patients with advanced prostate cancer using clinical trial and real-world hospital registry datasets. Int. J. Medical Informatics 133 (2020)
Chen He, Luana Micallef, Liye He, Gopal Peddinti, Tero Aittokallio, Giulio Jacucci
Characterizing the Quality of Insight by Interactions: A Case Study. CoRR (2020)
Aleksandr Ianevski, Anil K. Giri, Prson Gautam, Alexander Kononov, Potdar Swapnil, Saarela Jani, Krister Wennerberg, Tero Aittokallio
Prediction of drug combination effects with a minimal set of experiments. Nat. Mach. Intell. 1 (12) (2019)
Anna Cichonska, Tapio Pahikkala, Sándor Szedmák, Heli Julkunen, Antti Airola, Markus Heinonen, Tero Aittokallio, Juho Rousu
Learning with multiple pairwise kernels for drug bioactivity prediction. Bioinform. 34 (13) (2018)
ZiaurRehman Tanoli, Zaid Alam, Markus Vähä-Koskela, Balaguru Ravikumar, Alina Malyutina, Alok Jaiswal, Jing Tang, Krister Wennerberg, Tero Aittokallio
Drug Target Commons 2.0: a community platform for systematic analysis of drug-target interaction profiles. Database J. Biol. Databases Curation 2018 (2018)
Teemu D. Laajala, Mika Murtojärvi, Arho Virkki, Tero Aittokallio
ePCR: an R-package for survival and time-to-event prediction in advanced prostate cancer, applied to real-world patient cohorts. Bioinform. 34 (22) (2018)
Mehreen Ali, Suleiman A. Khan, Krister Wennerberg, Tero Aittokallio
Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach. Bioinform. 34 (8) (2018)
Chen He, Luana Micallef, ZiaurRehman Tanoli, Samuel Kaski, Tero Aittokallio, Giulio Jacucci
MediSyn: uncertainty-aware visualization of multiple biomedical datasets to support drug treatment selection. BMC Bioinform. 18 (S-10) (2017)
Aleksandr Ianevski, Liye He, Tero Aittokallio, Jing Tang
SynergyFinder: a web application for analyzing drug combination dose-response matrix data. Bioinform. 33 (15) (2017)
Balaguru Ravikumar, Zaid Alam, Gopal Peddinti, Tero Aittokallio
C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Anna Cichonska, Balaguru Ravikumar, Elina Parri, Sanna Timonen, Tapio Pahikkala, Antti Airola, Krister Wennerberg, Juho Rousu, Tero Aittokallio
Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors. PLoS Comput. Biol. 13 (8) (2017)
Muhammad Ammad-ud-din, Suleiman A. Khan, Krister Wennerberg, Tero Aittokallio
Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression. Bioinform. 33 (14) (2017)
Muhammad Ammad-ud-din, Suleiman A. Khan, Disha Malani, Astrid Murumägi, Olli-P. Kallioniemi, Tero Aittokallio, Samuel Kaski
Drug response prediction by inferring pathway-response associations with Kernelized Bayesian Matrix Factorization. CoRR (2016)
Muhammad Ammad-ud-din, Suleiman A. Khan, Disha Malani, Astrid Murumägi, Olli-P. Kallioniemi, Tero Aittokallio, Samuel Kaski
Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization. Bioinform. 32 (17) (2016)
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. Bioinform. 31 (11) (2015)
Tapio Pahikkala, Antti Airola, Sami Pietilä, Sushil Shakyawar, Agnieszka Szwajda, Jing Tang, Tero Aittokallio
Toward more realistic drug-target interaction predictions. Briefings Bioinform. 16 (2) (2015)
John-Patrick Mpindi, Potdar Swapnil, Dmitrii Bychkov, Saarela Jani, Khalid Saeed, Krister Wennerberg, Tero Aittokallio, Päivi Östling, Olli-P. Kallioniemi
Impact of normalization methods on high-throughput screening data with high hit rates and drug testing with dose-response data. Bioinform. 31 (23) (2015)
Tapio Pahikkala, Michiel Stock, Antti Airola, Tero Aittokallio, Bernard De Baets, Willem Waegeman
A Two-Step Learning Approach for Solving Full and Almost Full Cold Start Problems in Dyadic Prediction. ECML/PKDD (2) (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. J. Chem. Inf. Model. 54 (3) (2014)
Tapio Pahikkala, Michiel Stock, Antti Airola, Tero Aittokallio, Bernard De Baets, Willem Waegeman
A two-step learning approach for solving full and almost full cold start problems in dyadic prediction. CoRR (2014)
Sebastian Okser, Tapio Pahikkala, Tero Aittokallio
Genetic variants and their interactions in disease risk prediction - machine learning and network perspectives. BioData Min. 6 (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 Comput. Biol. 9 (9) (2013)
Johannes Tuikkala, Heidi Vähämaa, Pekka Salmela, Olli Nevalainen, Tero Aittokallio
A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization. BioData Min. 5 (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 Mol. Biol. 7 (2012)
Sebastian Okser, Antti Airola, Tero Aittokallio, Tapio Salakoski, Tapio Pahikkala
Parallel Feature Selection for Regularized Least-Squares. PARA (2012)
Marja A. Heiskanen, Tero Aittokallio
Mining high-throughput screens for cancer drug targets - lessons from yeast chemical-genomic profiling and synthetic lethality. WIREs Data Mining Knowl. Discov. 2 (3) (2012)
Sebastian Okser, Tapio Pahikkala, Antti Airola, Tero Aittokallio, Tapio Salakoski
Fast and parallelized greedy forward selection of genetic variants in Genome-wide association studies. GENSiPS (2011)
Rolf Lindén, Ville-Pekka Eronen, Tero Aittokallio
Quantitative maps of genetic interactions in yeast - Comparative evaluation and integrative analysis. BMC Syst. Biol. 5 (2011)
Leo Lahti, Laura Elo, Tero Aittokallio, Samuel Kaski
Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (1) (2011)
Tero Aittokallio
Dealing with missing values in large-scale studies: microarray data imputation and beyond. Briefings Bioinform. 11 (2) (2010)
Mathieu Clément-Ziza, Christophe Malabat, Christian Weber, Ivan Moszer, Tero Aittokallio, Catherine Letondal, Sandrine Rousseau
Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks. Bioinform. 25 (19) (2009)
Laura Elo, Jukka Hiissa, Jarno Tuimala, Aleksi Kallio, Eija Korpelainen, Tero Aittokallio
Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets. Briefings Bioinform. 10 (5) (2009)
Laura Elo, Sanna Filen, Riitta Lahesmaa, Tero Aittokallio
Reproducibility-Optimized Test Statistic for Ranking Genes in Microarray Studies. IEEE ACM Trans. Comput. Biol. Bioinform. 5 (3) (2008)
Arho Virkki, Olli Polo, Tarja Saaresranta, Anne Laapotti-Salo, Mats Gyllenberg, Tero Aittokallio
Overnight features of transcutaneous carbon dioxide measurement as predictors of metabolic status. Artif. Intell. Medicine 42 (1) (2008)
Johannes Tuikkala, Laura Elo, Olli Nevalainen, Tero Aittokallio
Missing value imputation improves clustering and interpretation of gene expression microarray data. BMC Bioinform. 9 (2008)
Virpi Ahola, Tero Aittokallio, Mauno Vihinen, Esa Uusipaikka
Model-based prediction of sequence alignment quality. Bioinform. 24 (19) (2008)
Olivier Garcia, Cosmin Saveanu, Melissa S. Cline, Micheline Fromont-Racine, Alain Jacquier, Benno Schwikowski, Tero Aittokallio
GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinform. 23 (3) (2007)
Tero Aittokallio, Jani S. Malminen, Tapio Pahikkala, Olli Polo, Olli Nevalainen
Inspiratory flow shape clustering: An automated method to monitor upper airway performance during sleep. Comput. Methods Programs Biomed. 85 (1) (2007)
Laura Elo, Henna Järvenpää, Matej Oresic, Riitta Lahesmaa, Tero Aittokallio
Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. Bioinform. 23 (16) (2007)
Jussi Salmi, Robert Moulder, Jan-Jonas Filén, Olli Nevalainen, Tuula A. Nyman, Riitta Lahesmaa, Tero Aittokallio
Quality classification of tandem mass spectrometry data. Bioinform. 22 (4) (2006)
Johannes Tuikkala, Laura Elo, Olli Nevalainen, Tero Aittokallio
Improving missing value estimation in microarray data with gene ontology. Bioinform. 22 (5) (2006)
Tero Aittokallio, Benno Schwikowski
Graph-based methods for analysing networks in cell biology. Briefings Bioinform. 7 (3) (2006)
Virpi Ahola, Tero Aittokallio, Mauno Vihinen, Esa Uusipaikka
A statistical score for assessing the quality of multiple sequence alignments. BMC Bioinform. 7 (2006)
Laura Elo, Riitta Lahesmaa, Tero Aittokallio
Inference of Gene Coexpression Networks by Integrative Analysis across Microarray Experiments. J. Integr. Bioinform. 3 (2) (2006)
Marius C. Codrea, Tero Aittokallio, Mika Keränen, Esa Tyystjärvi, Olli Nevalainen
On the Robustness of Fluorescence Fingerprinting of Plants. Artificial Intelligence and Applications (2005)
Marius C. Codrea, Tero Aittokallio, Mika Keränen, Esa Tyystjärvi, Olli Nevalainen
Feature learning with a genetic algorithm for fluorescence fingerprinting of plant species. Pattern Recognit. Lett. 24 (15) (2003)
Tero Aittokallio, Markus Kurki, Olli Nevalainen, Tuomas Nikula, Anne West, Riitta Lahesmaa
Computational Strategies for Analyzing Data in Gene Expression Microarray Experiments. J. Bioinform. Comput. Biol. 1 (3) (2003)
Marius C. Codrea, Tero Aittokallio, Mika Keränen, Esa Tyystjärvi, Olli Nevalainen
Genetic Feature Learning Algorithm for Fluorescence Fingerprinting of Plants. Artificial Evolution (2003)
Virpi Ahola, Tero Aittokallio, Esa Uusipaikka, Mauno Vihinen
Efficient estimation of emission probabilities in profile hidden Markov models. Bioinform. 19 (18) (2003)
Tero Aittokallio, Mats Gyllenberg, J. Järvi, Olli Nevalainen, Olli Polo
Detection of high-frequency respiratory movements during sleep. Comput. Methods Programs Biomed. 61 (3) (2000)
Tero Aittokallio, Olli Nevalainen, U. Pursiheimo, Tarja Saaresranta, Olli Polo
Classification of Nasal Inspiratory Flow Shapes by Attributed Finite Automata. Comput. Biomed. Res. 32 (1) (1999)