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

Breeze: an integrated quality control and data analysis application for high-throughput drug screening. - Swapnil, Potdar; Ianevski, Aleksandr; Mpindi, John-Patrick; Bychkov, Dmitrii; Fiere, Clément; Ianevski, Philipp; Yadav, Bhagwan; Wennerberg, Krister; Aittokallio, Tero; Kallioniemi, Olli-P.; Jani, Saarela; Östling, Päivi (Bioinform., 2020)

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

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

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

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

Integrative and Personalized QSAR Analysis in Cancer by Kernelized Bayesian Matrix Factorization. - Ammad-ud-din, Muhammad; Georgii, Elisabeth; Gönen, Mehmet; Laitinen, Tuomo; Kallioniemi, Olli-P.; Wennerberg, Krister; Poso, Antti; Kaski, Samuel (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. - Khan, Suleiman A.; Faisal, Ali; Mpindi, John; Parkkinen, Juuso A.; Kalliokoski, Tuomo; Poso, Antti; Kallioniemi, Olli-P.; Wennerberg, Krister; Kaski, Samuel (BMC Bioinform., 2012)

Delivering ICT infrastructure for biomedical research. - Nyrönen, Tommi H.; Laitinen, Jarno; Tourunen, Olli; Sternkopf, Danny; Laurikainen, Risto; Öster, Per; Lehtovuori, Pekka T.; Miettinen, Timo A.; Simonen, Tomi; Perheentupa, Teemu; Vastrik, Imre; Kallioniemi, Olli-P.; et al. (2012)

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

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

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

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

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

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

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

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

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

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

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