Classification of Nasal Inspiratory Flow Shapes by Attributed Finite Automata. - Tero Aittokallio; Olli Nevalainen; U. Pursiheimo; Tarja Saaresranta; Olli Polo (Comput. Biomed. Res., 1999)

Detection of high-frequency respiratory movements during sleep. - Tero Aittokallio; Mats Gyllenberg; J. Järvi; Olli Nevalainen; Olli Polo (Comput. Methods Programs Biomed., 2000)

Genetic Feature Learning Algorithm for Fluorescence Fingerprinting of Plants. - Marius C. Codrea; Tero Aittokallio; Mika Keränen; Esa Tyystjärvi; Olli Nevalainen (Artificial Evolution, 2003)

Efficient estimation of emission probabilities in profile hidden Markov models. - Virpi Ahola; Tero Aittokallio; Esa Uusipaikka; Mauno Vihinen (Bioinform., 2003)

Computational Strategies for Analyzing Data in Gene Expression Microarray Experiments. - Tero Aittokallio; Markus Kurki; Olli Nevalainen; Tuomas Nikula; Anne West; Riitta Lahesmaa (J. Bioinform. Comput. Biol., 2003)

Feature learning with a genetic algorithm for fluorescence fingerprinting of plant species. - Marius C. Codrea; Tero Aittokallio; Mika Keränen; Esa Tyystjärvi; Olli Nevalainen (Pattern Recognit. Lett., 2003)

On the Robustness of Fluorescence Fingerprinting of Plants. - Marius C. Codrea; Tero Aittokallio; Mika Keränen; Esa Tyystjärvi; Olli Nevalainen (Artificial Intelligence and Applications, 2005)

Graph-based methods for analysing networks in cell biology. - Tero Aittokallio; Benno Schwikowski (Briefings Bioinform., 2006)

Quality classification of tandem mass spectrometry data. - Jussi Salmi; Robert Moulder; Jan-Jonas Filén; Olli Nevalainen; Tuula A. Nyman; Riitta Lahesmaa; Tero Aittokallio (Bioinform., 2006)

Improving missing value estimation in microarray data with gene ontology. - Johannes Tuikkala; Laura Elo; Olli Nevalainen; Tero Aittokallio (Bioinform., 2006)

A statistical score for assessing the quality of multiple sequence alignments. - Virpi Ahola; Tero Aittokallio; Mauno Vihinen; Esa Uusipaikka (BMC Bioinform., 2006)

Inference of Gene Coexpression Networks by Integrative Analysis across Microarray Experiments. - Laura Elo; Riitta Lahesmaa; Tero Aittokallio (J. Integr. Bioinform., 2006)

Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. - Laura Elo; Henna Järvenpää; Matej Oresic; Riitta Lahesmaa; Tero Aittokallio (Bioinform., 2007)

GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. - Olivier Garcia; Cosmin Saveanu; Melissa S. Cline; Micheline Fromont-Racine; Alain Jacquier; Benno Schwikowski; Tero Aittokallio (Bioinform., 2007)

Inspiratory flow shape clustering: An automated method to monitor upper airway performance during sleep. - Tero Aittokallio; Jani S. Malminen; Tapio Pahikkala; Olli Polo; Olli Nevalainen (Comput. Methods Programs Biomed., 2007)

Overnight features of transcutaneous carbon dioxide measurement as predictors of metabolic status. - Arho Virkki; Olli Polo; Tarja Saaresranta; Anne Laapotti-Salo; Mats Gyllenberg; Tero Aittokallio (Artif. Intell. Medicine, 2008)

Model-based prediction of sequence alignment quality. - Virpi Ahola; Tero Aittokallio; Mauno Vihinen; Esa Uusipaikka (Bioinform., 2008)

Missing value imputation improves clustering and interpretation of gene expression microarray data. - Johannes Tuikkala; Laura Elo; Olli Nevalainen; Tero Aittokallio (BMC Bioinform., 2008)

Reproducibility-Optimized Test Statistic for Ranking Genes in Microarray Studies. - Laura Elo; Sanna Filen; Riitta Lahesmaa; Tero Aittokallio (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets. - Laura Elo; Jukka Hiissa; Jarno Tuimala; Aleksi Kallio; Eija Korpelainen; Tero Aittokallio (Briefings Bioinform., 2009)

Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks. - Mathieu Clément-Ziza; Christophe Malabat; Christian Weber; Ivan Moszer; Tero Aittokallio; Catherine Letondal; Sandrine Rousseau (Bioinform., 2009)

Dealing with missing values in large-scale studies: microarray data imputation and beyond. - Tero Aittokallio (Briefings Bioinform., 2010)

Fast and parallelized greedy forward selection of genetic variants in Genome-wide association studies. - Sebastian Okser; Tapio Pahikkala; Antti Airola; Tero Aittokallio; Tapio Salakoski (GENSiPS, 2011)

Quantitative maps of genetic interactions in yeast - Comparative evaluation and integrative analysis. - Rolf Lindén; Ville-Pekka Eronen; Tero Aittokallio (BMC Syst. Biol., 2011)

Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays. - Leo Lahti; Laura Elo; Tero Aittokallio; Samuel Kaski (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Parallel Feature Selection for Regularized Least-Squares. - Sebastian Okser; Antti Airola; Tero Aittokallio; Tapio Salakoski; Tapio Pahikkala (PARA, 2012)

Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations. - Tapio Pahikkala; Sebastian Okser; Antti Airola; Tapio Salakoski; Tero Aittokallio (Algorithms Mol. Biol., 2012)

A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization. - Johannes Tuikkala; Heidi Vähämaa; Pekka Salmela; Olli Nevalainen; Tero Aittokallio (BioData Min., 2012)

Mining high-throughput screens for cancer drug targets - lessons from yeast chemical-genomic profiling and synthetic lethality. - Marja A. Heiskanen; Tero Aittokallio (WIREs Data Mining Knowl. Discov., 2012)

Genetic variants and their interactions in disease risk prediction - machine learning and network perspectives. - Sebastian Okser; Tapio Pahikkala; Tero Aittokallio (BioData Min., 2013)

Target Inhibition Networks: Predicting Selective Combinations of Druggable Targets to Block Cancer Survival Pathways. - Jing Tang 002; Leena Karhinen; Tao Xu; Agnieszka Szwajda; Bhagwan Yadav; Krister Wennerberg; Tero Aittokallio (PLoS Comput. Biol., 2013)

A Two-Step Learning Approach for Solving Full and Almost Full Cold Start Problems in Dyadic Prediction. - Tapio Pahikkala; Michiel Stock; Antti Airola; Tero Aittokallio; Bernard De Baets; Willem Waegeman (ECML/PKDD (2), 2014)

Making Sense of Large-Scale Kinase Inhibitor Bioactivity Data Sets: A Comparative and Integrative Analysis. - Jing Tang 002; Agnieszka Szwajda; Sushil Kumar Shakyawar; Tao Xu; Petteri Hintsanen; Krister Wennerberg; Tero Aittokallio (J. Chem. Inf. Model., 2014)

Toward more realistic drug-target interaction predictions. - Tapio Pahikkala; Antti Airola; Sami Pietilä; Sushil Kumar Shakyawar; Agnieszka Szwajda; Jing Tang 002; Tero Aittokallio (Briefings Bioinform., 2015)

TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples. - Liye He; Krister Wennerberg; Tero Aittokallio; Jing Tang 002 (Bioinform., 2015)

Impact of normalization methods on high-throughput screening data with high hit rates and drug testing with dose-response data. - John-Patrick Mpindi; Potdar Swapnil; Dmitrii Bychkov; Saarela Jani; Khalid Saeed 002; Krister Wennerberg; Tero Aittokallio; Päivi Östling; Olli-P. Kallioniemi (Bioinform., 2015)

Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization. - Muhammad Ammad-ud-din; Suleiman A. Khan; Disha Malani; Astrid Murumägi; Olli-P. Kallioniemi; Tero Aittokallio; Samuel Kaski (Bioinform., 2016)

Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression. - Muhammad Ammad-ud-din; Suleiman A. Khan; Krister Wennerberg; Tero Aittokallio (Bioinform., 2017)

MediSyn: uncertainty-aware visualization of multiple biomedical datasets to support drug treatment selection. - Chen He 003; Luana Micallef; ZiaurRehman Tanoli; Samuel Kaski; Tero Aittokallio; Giulio Jacucci (BMC Bioinform., 2017)

C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms. - Balaguru Ravikumar; Zaid Alam; Gopal Peddinti; Tero Aittokallio (Nucleic Acids Res., 2017)

Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors. - Anna Cichonska; Balaguru Ravikumar; Elina Parri; Sanna Timonen; Tapio Pahikkala; Antti Airola; Krister Wennerberg; Juho Rousu; Tero Aittokallio (PLoS Comput. Biol., 2017)

Drug Target Commons 2.0: a community platform for systematic analysis of drug-target interaction profiles. - ZiaurRehman Tanoli; Zaid Alam; Markus Vähä-Koskela; Balaguru Ravikumar; Alina Malyutina; Alok Jaiswal; Jing Tang 002; Krister Wennerberg; Tero Aittokallio (Database J. Biol. Databases Curation, 2018)

Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach. - Mehreen Ali; Suleiman A. Khan; Krister Wennerberg; Tero Aittokallio (Bioinform., 2018)

Learning with multiple pairwise kernels for drug bioactivity prediction. - Anna Cichonska; Tapio Pahikkala; Sándor Szedmák; Heli Julkunen; Antti Airola; Markus Heinonen; Tero Aittokallio; Juho Rousu (Bioinform., 2018)

ePCR: an R-package for survival and time-to-event prediction in advanced prostate cancer, applied to real-world patient cohorts. - Teemu D. Laajala; Mika Murtojärvi; Arho Virkki; Tero Aittokallio (Bioinform., 2018)

Prediction of drug combination effects with a minimal set of experiments. - Aleksandr Ianevski; Anil K. Giri; Prson Gautam; Alexander Kononov; Potdar Swapnil; Saarela Jani; Krister Wennerberg; Tero Aittokallio (Nat. Mach. Intell., 2019)

Interactive visual analysis of drug-target interaction networks using Drug Target Profiler, with applications to precision medicine and drug repurposing. - ZiaurRehman Tanoli; Zaid Alam; Aleksandr Ianevski; Krister Wennerberg; Markus Vähä-Koskela; Tero Aittokallio (Briefings Bioinform., 2020)

SynergyFinder: a web application for analyzing drug combination dose-response matrix data. - Aleksandr Ianevski; Liye He; Tero Aittokallio; Jing Tang 002 (Bioinform., 2020)

Breeze: an integrated quality control and data analysis application for high-throughput drug screening. - 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 (Bioinform., 2020)

Cost-effective survival prediction for patients with advanced prostate cancer using clinical trial and real-world hospital registry datasets. - Mika Murtojärvi; Anni S. Halkola; Antti Airola; Teemu D. Laajala; Tuomas Mirtti; Tero Aittokallio; Tapio Pahikkala (Int. J. Medical Informatics, 2020)

SynergyFinder 2.0: visual analytics of multi-drug combination synergies. - Aleksandr Ianevski; Anil K. Giri; Tero Aittokallio (Nucleic Acids Res., 2020)

SynToxProfiler: An interactive analysis of drug combination synergy, toxicity and efficacy. - Aleksandr Ianevski; Sanna Timonen; Alexander Kononov; Tero Aittokallio; Anil K. Giri (PLoS Comput. Biol., 2020)

Multiobjective optimization identifies cancer-selective combination therapies. - Otto Pulkkinen; Prson Gautam; Ville Mustonen; Tero Aittokallio (PLoS Comput. Biol., 2020)

Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer. - 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; et al. (Briefings Bioinform., 2021)

Modeling drug combination effects via latent tensor reconstruction. - Tianduanyi Wang; Sándor Szedmák; Haishan Wang; Tero Aittokallio; Tapio Pahikkala; Anna Cichonska; Juho Rousu (Bioinform., 2021)

Characterizing the Quality of Insight by Interactions: A Case Study. - Chen He 003; Luana Micallef; Liye He; Gopal Peddinti; Tero Aittokallio; Giulio Jacucci (IEEE Trans. Vis. Comput. Graph., 2021)

Evaluation of statistical approaches for association testing in noisy drug screening data. - 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 (BMC Bioinform., 2022)

SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples. - Aleksandr Ianevski; Anil K. Giri; Tero Aittokallio (Nucleic Acids Res., 2022)

Discovery of host-directed modulators of virus infection by probing the SARS-CoV-2-host protein-protein interaction network. - 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 (Briefings Bioinform., 2022)

OSCAR: Optimal subset cardinality regression using the L0-pseudonorm with applications to prognostic modelling of prostate cancer. - Anni S. Halkola; Kaisa Joki; Tuomas Mirtti; Marko M. Mäkelä; Tero Aittokallio; Teemu D. Laajala (PLoS Comput. Biol., 2023)

Breeze 2.0: an interactive web-tool for visual analysis and comparison of drug response data. - Potdar Swapnil; Filipp Ianevski; Aleksandr Ianevski; ZiaurRehman Tanoli; Krister Wennerberg; Brinton Seashore-Ludlow; Olli-P. Kallioniemi; Päivi Östling; Tero Aittokallio; Saarela Jani (Nucleic Acids Res., 2023)

RepurposeDrugs: an interactive web-portal and predictive platform for repurposing mono- and combination therapies. - Aleksandr Ianevski; Aleksandr Kushnir; Kristen Nader; Mitro Miihkinen; Henri Xhaard; Tero Aittokallio; ZiaurRehman Tanoli (Briefings Bioinform., 2024)

Scaling up drug combination surface prediction. - Riikka Huusari; Tianduanyi Wang; Sándor Szedmák; Diogo Dias; Tero Aittokallio; Juho Rousu (Briefings Bioinform., 2025)