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)

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)

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)

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 (CoRR, 2016)

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; Krister Wennerberg; Tero Aittokallio; Päivi Östling; Olli-P. Kallioniemi (Bioinform., 2015)

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)

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)

Delivering ICT infrastructure for biomedical research - Tommi H. Nyrönen; Jarno Laitinen; Olli Tourunen; Danny Sternkopf; Risto Laurikainen; Per Öster; Pekka T. Lehtovuori; Timo A. Miettinen; Tomi Simonen; Teemu Perheentupa; Imre Vastrik; Olli-P. Kallioniemi; et al. (2012 Joint Working IEEE/IFIP Conference on Software Architecture and European Conference on Software Architecture, WICSA/ECSA 2012, Helsinki, Finland, August 20-24, 2012 - Companion Volume, 2012)

Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data - Sami Kilpinen; Kalle A. Ojala; Olli-P. Kallioniemi (BioData Min., 2011)

On the organization of bioinformatics core services in biology-based research institutes - Olli-P. Kallioniemi; Lodewyk F. A. Wessels; Alfonso Valencia (Bioinform., 2011)

Comparison of Affymetrix data normalization methods using 6, 926 experiments across five array generations - Reija Autio; Sami Kilpinen; Matti Saarela; Olli-P. Kallioniemi; Sampsa Hautaniemi; Jaakko Astola (BMC Bioinform., 2009)

Comparison of structure fingerprint and molecular interaction field based methods in explaining biological similarity of small molecules in cell-based screens - Pekka Tiikkainen; Antti Poso; Olli-P. Kallioniemi (J. Comput. Aided Mol. Des., 2009)

Critical Comparison of Virtual Screening Methods against the MUV Data Set - Pekka Tiikkainen; Patrick Markt; Gerhard Wolber; Johannes Kirchmair; Simona Distinto; Antti Poso; Olli-P. Kallioniemi (J. Chem. Inf. Model., 2009)

A strategy for identifying putative causes of gene expression variation in human cancers - Sampsa Hautaniemi; Markus Ringnér; Päivikki Kauraniemi; Reija Autio; Henrik Edgren; Olli Yli-Harja; Jaakko Astola; Anne Kallioniemi; Olli-Pekka Kallioniemi (J. Frankl. Inst., 2004)

A novel strategy for microarray quality control using Bayesian networks - Sampsa Hautaniemi; Henrik Edgren; Petri Vesanen; Maija Wolf; Anna-Kaarina Järvinen; Olli Yli-Harja; Jaakko Astola; Olli-P. Kallioniemi; Outi Monni (Bioinform., 2003)

Analysis and Visualization of Gene Expression Microarray Data in Human Cancer Using Self-Organizing Maps - Sampsa Hautaniemi; Olli Yli-Harja; Jaakko Astola; Päivikki Kauraniemi; Anne Kallioniemi; Maija Wolf; Jimmy Ruiz; Spyro Mousses; Olli-P. Kallioniemi (Mach. Learn., 2003)

Simulation Toolbox for 3D-FISH Spot-Counting Algorithms - Artyom M. Grigoryan; Galen Hostetter; Olli-P. Kallioniemi; Edward R. Dougherty (Real Time Imaging, 2002)

Distance-Based Reconstruction of Tree Models for Oncogenesis - Richard Desper; Feng Jiang; Olli-P. Kallioniemi; Holger Moch; Christos H. Papadimitriou; Alejandro A. Schäffer (J. Comput. Biol., 2000)

Inferring Tree Models for Oncogenesis from Comparative Genome Hybridization Data - Richard Desper; Feng Jiang; Olli-P. Kallioniemi; Holger Moch; Christos H. Papadimitriou; Alejandro A. Schäffer (J. Comput. Biol., 1999)