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Journal Articles
- 2023
[j18]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): 57-61 (2023)- 2020
- [j17]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): 3602-3604 (2020) - 2016
- [j16]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): 455-463 (2016) - 2015
- [j15]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): 3815-3821 (2015) - 2014
- [j14]Suleiman A. Khan, Seppo Virtanen, Olli-P. Kallioniemi, Krister Wennerberg, Antti Poso, Samuel Kaski:
Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis. Bioinform. 30(17): 497-504 (2014) - [j13]Muhammad Ammad-ud-din, Elisabeth Georgii, Mehmet Gönen, Tuomo Laitinen, Olli-P. Kallioniemi, Krister Wennerberg, Antti Poso, Samuel Kaski:
Integrative and Personalized QSAR Analysis in Cancer by Kernelized Bayesian Matrix Factorization. J. Chem. Inf. Model. 54(8): 2347-2359 (2014) - 2012
- [j12]Suleiman A. Khan, Ali Faisal, John Mpindi, Juuso A. Parkkinen, Tuomo Kalliokoski, Antti Poso, Olli-P. Kallioniemi, Krister Wennerberg, Samuel Kaski:
Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs. BMC Bioinform. 13: 112 (2012) - 2011
- [j11]Sami Kilpinen, Kalle A. Ojala, Olli-P. Kallioniemi:
Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data. BioData Min. 4: 5 (2011) - [j10]Olli-P. Kallioniemi, Lodewyk F. A. Wessels, Alfonso Valencia:
On the organization of bioinformatics core services in biology-based research institutes. Bioinform. 27(10): 1345 (2011) - 2009
- [j9]Reija Autio, Sami Kilpinen, Matti Saarela, Olli-P. Kallioniemi, Sampsa Hautaniemi, Jaakko Astola:
Comparison of Affymetrix data normalization methods using 6, 926 experiments across five array generations. BMC Bioinform. 10(S-1) (2009) - [j8]Pekka Tiikkainen, Antti Poso, Olli-P. Kallioniemi:
Comparison of structure fingerprint and molecular interaction field based methods in explaining biological similarity of small molecules in cell-based screens. J. Comput. Aided Mol. Des. 23(4): 227-239 (2009) - [j7]Pekka Tiikkainen, Patrick Markt, Gerhard Wolber, Johannes Kirchmair, Simona Distinto, Antti Poso, Olli-P. Kallioniemi:
Critical Comparison of Virtual Screening Methods against the MUV Data Set. J. Chem. Inf. Model. 49(10): 2168-2178 (2009) - 2004
- [j6]Sampsa Hautaniemi, Markus Ringnér, Päivikki Kauraniemi, Reija Autio, Henrik Edgren, Olli Yli-Harja, Jaakko Astola, Anne Kallioniemi, Olli-Pekka Kallioniemi:
A strategy for identifying putative causes of gene expression variation in human cancers. J. Frankl. Inst. 341(1-2): 77-88 (2004) - 2003
- [j5]Sampsa Hautaniemi, Henrik Edgren, Petri Vesanen, Maija Wolf, Anna-Kaarina Järvinen, Olli Yli-Harja, Jaakko Astola, Olli-P. Kallioniemi, Outi Monni:
A novel strategy for microarray quality control using Bayesian networks. Bioinform. 19(16): 2031-2038 (2003) - [j4]Sampsa Hautaniemi, Olli Yli-Harja, Jaakko Astola, Päivikki Kauraniemi, Anne Kallioniemi, Maija Wolf, Jimmy Ruiz, Spyro Mousses, Olli-P. Kallioniemi:
Analysis and Visualization of Gene Expression Microarray Data in Human Cancer Using Self-Organizing Maps. Mach. Learn. 52(1-2): 45-66 (2003) - 2002
- [j3]Artyom M. Grigoryan, Galen Hostetter, Olli-P. Kallioniemi, Edward R. Dougherty:
Simulation Toolbox for 3D-FISH Spot-Counting Algorithms. Real Time Imaging 8(3): 203-212 (2002) - 2000
- [j2]Richard Desper, Feng Jiang, Olli-P. Kallioniemi, Holger Moch, Christos H. Papadimitriou, Alejandro A. Schäffer:
Distance-Based Reconstruction of Tree Models for Oncogenesis. J. Comput. Biol. 7(6): 789-803 (2000) - 1999
- [j1]Richard Desper, Feng Jiang, Olli-P. Kallioniemi, Holger Moch, Christos H. Papadimitriou, Alejandro A. Schäffer:
Inferring Tree Models for Oncogenesis from Comparative Genome Hybridization Data. J. Comput. Biol. 6(1): 37-51 (1999)
Conference and Workshop Papers
- 2012
- [c1]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, Andrew Lyall, Janet M. Thornton:
Delivering ICT infrastructure for biomedical research. WICSA/ECSA Companion Volume 2012: 37-44
Informal and Other Publications
- 2016
- [i1]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 abs/1606.03623 (2016)
Coauthor Index
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