Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs. - Suleiman A. Khan; Ali Faisal; John Mpindi; Juuso A. Parkkinen; Tuomo Kalliokoski; Antti Poso; Olli-P. Kallioniemi; Krister Wennerberg; Samuel Kaski (BMC Bioinform., 2012)

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)

Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis. - Suleiman A. Khan; Seppo Virtanen; Olli-P. Kallioniemi; Krister Wennerberg; Antti Poso; Samuel Kaski (Bioinform., 2014)

Integrative and Personalized QSAR Analysis in Cancer by Kernelized Bayesian Matrix Factorization. - Muhammad Ammad-ud-din; Elisabeth Georgii; Mehmet Gönen; Tuomo Laitinen; Olli-P. Kallioniemi; Krister Wennerberg; Antti Poso; Samuel Kaski (J. Chem. Inf. Model., 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)

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)

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)

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)

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)

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)

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)

Exploration of databases and methods supporting drug repurposing: a comprehensive survey. - ZiaurRehman Tanoli; Umair Seemab; Andreas Scherer; Krister Wennerberg; Jing Tang 002; Markus Vähä-Koskela (Briefings Bioinform., 2021)

Minimal information for chemosensitivity assays (MICHA): a next-generation pipeline to enable the FAIRification of drug screening experiments. - ZiaurRehman Tanoli; Jehad Aldahdooh; Farhan Alam; Yinyin Wang; Umair Seemab; Maddalena Fratelli; Petr Pavlis; Marián Hajdúch; Florence Bietrix; Philip Gribbon; Andrea Zaliani; Matthew D. Hall; et al. (Briefings Bioinform., 2022)

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)