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ORCIDBibTeX records: Olli-P. Kallioniemi
@article{DBLP:journals/nar/SwapnilIITWSKOAJ23,
author = {Potdar Swapnil and
Filipp Ianevski and
Aleksandr Ianevski and
ZiaurRehman Tanoli and
Krister Wennerberg and
Brinton Seashore{-}Ludlow and
Olli{-}P. Kallioniemi and
P{\"{a}}ivi {\"{O}}stling and
Tero Aittokallio and
Saarela Jani},
title = {Breeze 2.0: an interactive web-tool for visual analysis and comparison
of drug response data},
journal = {Nucleic Acids Res.},
volume = {51},
number = {{W1}},
pages = {57--61},
year = {2023},
url = {https://doi.org/10.1093/nar/gkad390},
doi = {10.1093/NAR/GKAD390},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SwapnilIITWSKOAJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SwapnilIMBFIYWA20,
author = {Potdar Swapnil and
Aleksandr Ianevski and
John{-}Patrick Mpindi and
Dmitrii Bychkov and
Cl{\'{e}}ment Fiere and
Philipp Ianevski and
Bhagwan Yadav and
Krister Wennerberg and
Tero Aittokallio and
Olli{-}P. Kallioniemi and
Saarela Jani and
P{\"{a}}ivi {\"{O}}stling},
title = {Breeze: an integrated quality control and data analysis application
for high-throughput drug screening},
journal = {Bioinform.},
volume = {36},
number = {11},
pages = {3602--3604},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa138},
doi = {10.1093/BIOINFORMATICS/BTAA138},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SwapnilIMBFIYWA20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Ammad-ud-dinKMM16,
author = {Muhammad Ammad{-}ud{-}din and
Suleiman A. Khan and
Disha Malani and
Astrid Murum{\"{a}}gi and
Olli{-}P. Kallioniemi and
Tero Aittokallio and
Samuel Kaski},
title = {Drug response prediction by inferring pathway-response associations
with kernelized Bayesian matrix factorization},
journal = {Bioinform.},
volume = {32},
number = {17},
pages = {455--463},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw433},
doi = {10.1093/BIOINFORMATICS/BTW433},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Ammad-ud-dinKMM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/Ammad-ud-dinKMM16,
author = {Muhammad Ammad{-}ud{-}din and
Suleiman A. Khan and
Disha Malani and
Astrid Murum{\"{a}}gi and
Olli{-}P. Kallioniemi and
Tero Aittokallio and
Samuel Kaski},
title = {Drug response prediction by inferring pathway-response associations
with Kernelized Bayesian Matrix Factorization},
journal = {CoRR},
volume = {abs/1606.03623},
year = {2016},
url = {http://arxiv.org/abs/1606.03623},
eprinttype = {arXiv},
eprint = {1606.03623},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/Ammad-ud-dinKMM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MpindiSDJSWAOK15,
author = {John{-}Patrick Mpindi and
Potdar Swapnil and
Dmitrii Bychkov and
Saarela Jani and
Khalid Saeed and
Krister Wennerberg and
Tero Aittokallio and
P{\"{a}}ivi {\"{O}}stling and
Olli{-}P. Kallioniemi},
title = {Impact of normalization methods on high-throughput screening data
with high hit rates and drug testing with dose-response data},
journal = {Bioinform.},
volume = {31},
number = {23},
pages = {3815--3821},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv455},
doi = {10.1093/BIOINFORMATICS/BTV455},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MpindiSDJSWAOK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KhanVKWPK14,
author = {Suleiman A. Khan and
Seppo Virtanen and
Olli{-}P. Kallioniemi and
Krister Wennerberg and
Antti Poso and
Samuel Kaski},
title = {Identification of structural features in chemicals associated with
cancer drug response: a systematic data-driven analysis},
journal = {Bioinform.},
volume = {30},
number = {17},
pages = {497--504},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu456},
doi = {10.1093/BIOINFORMATICS/BTU456},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KhanVKWPK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/Ammad-ud-dinGGLKWPK14,
author = {Muhammad Ammad{-}ud{-}din and
Elisabeth Georgii and
Mehmet G{\"{o}}nen and
Tuomo Laitinen and
Olli{-}P. Kallioniemi and
Krister Wennerberg and
Antti Poso and
Samuel Kaski},
title = {Integrative and Personalized {QSAR} Analysis in Cancer by Kernelized
Bayesian Matrix Factorization},
journal = {J. Chem. Inf. Model.},
volume = {54},
number = {8},
pages = {2347--2359},
year = {2014},
url = {https://doi.org/10.1021/ci500152b},
doi = {10.1021/CI500152B},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/Ammad-ud-dinGGLKWPK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KhanFMPKPKWK12,
author = {Suleiman A. Khan and
Ali Faisal and
John Mpindi and
Juuso A. Parkkinen and
Tuomo Kalliokoski and
Antti Poso and
Olli{-}P. Kallioniemi and
Krister Wennerberg and
Samuel Kaski},
title = {Comprehensive data-driven analysis of the impact of chemoinformatic
structure on the genome-wide biological response profiles of cancer
cells to 1159 drugs},
journal = {{BMC} Bioinform.},
volume = {13},
pages = {112},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-112},
doi = {10.1186/1471-2105-13-112},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KhanFMPKPKWK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wicsa/NyronenLTSLOLMSPVKLT12,
author = {Tommi H. Nyr{\"{o}}nen and
Jarno Laitinen and
Olli Tourunen and
Danny Sternkopf and
Risto Laurikainen and
Per {\"{O}}ster and
Pekka T. Lehtovuori and
Timo A. Miettinen and
Tomi Simonen and
Teemu Perheentupa and
Imre Vastrik and
Olli{-}P. Kallioniemi and
Andrew Lyall and
Janet M. Thornton},
editor = {Tomi M{\"{a}}nnist{\"{o}} and
Muhammad Ali Babar and
Carlos E. Cuesta and
Juha Erik Savolainen},
title = {Delivering {ICT} infrastructure for biomedical research},
booktitle = {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},
series = {{ACM} International Conference Proceeding Series},
volume = {704},
pages = {37--44},
publisher = {{ACM}},
year = {2012},
url = {https://doi.org/10.1145/2361999.2362006},
doi = {10.1145/2361999.2362006},
timestamp = {Fri, 14 Apr 2023 23:05:46 +0200},
biburl = {https://dblp.org/rec/conf/wicsa/NyronenLTSLOLMSPVKLT12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodatamining/KilpinenOK11,
author = {Sami Kilpinen and
Kalle A. Ojala and
Olli{-}P. Kallioniemi},
title = {Alignment of gene expression profiles from test samples against a
reference database: New method for context-specific interpretation
of microarray data},
journal = {BioData Min.},
volume = {4},
pages = {5},
year = {2011},
url = {https://doi.org/10.1186/1756-0381-4-5},
doi = {10.1186/1756-0381-4-5},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodatamining/KilpinenOK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KallioniemiWV11,
author = {Olli{-}P. Kallioniemi and
Lodewyk F. A. Wessels and
Alfonso Valencia},
title = {On the organization of bioinformatics core services in biology-based
research institutes},
journal = {Bioinform.},
volume = {27},
number = {10},
pages = {1345},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr125},
doi = {10.1093/BIOINFORMATICS/BTR125},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KallioniemiWV11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AutioKSKHA09,
author = {Reija Autio and
Sami Kilpinen and
Matti Saarela and
Olli{-}P. Kallioniemi and
Sampsa Hautaniemi and
Jaakko Astola},
title = {Comparison of Affymetrix data normalization methods using 6, 926 experiments
across five array generations},
journal = {{BMC} Bioinform.},
volume = {10},
number = {{S-1}},
year = {2009},
url = {https://doi.org/10.1186/1471-2105-10-S1-S24},
doi = {10.1186/1471-2105-10-S1-S24},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AutioKSKHA09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TiikkainenPK09,
author = {Pekka Tiikkainen and
Antti Poso and
Olli{-}P. Kallioniemi},
title = {Comparison of structure fingerprint and molecular interaction field
based methods in explaining biological similarity of small molecules
in cell-based screens},
journal = {J. Comput. Aided Mol. Des.},
volume = {23},
number = {4},
pages = {227--239},
year = {2009},
url = {https://doi.org/10.1007/s10822-008-9253-0},
doi = {10.1007/S10822-008-9253-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TiikkainenPK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/TiikkainenMWKDPK09,
author = {Pekka Tiikkainen and
Patrick Markt and
Gerhard Wolber and
Johannes Kirchmair and
Simona Distinto and
Antti Poso and
Olli{-}P. Kallioniemi},
title = {Critical Comparison of Virtual Screening Methods against the {MUV}
Data Set},
journal = {J. Chem. Inf. Model.},
volume = {49},
number = {10},
pages = {2168--2178},
year = {2009},
url = {https://doi.org/10.1021/ci900249b},
doi = {10.1021/CI900249B},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/TiikkainenMWKDPK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jfi/HautaniemiRKAEY04,
author = {Sampsa Hautaniemi and
Markus Ringn{\'{e}}r and
P{\"{a}}ivikki Kauraniemi and
Reija Autio and
Henrik Edgren and
Olli Yli{-}Harja and
Jaakko Astola and
Anne Kallioniemi and
Olli{-}Pekka Kallioniemi},
title = {A strategy for identifying putative causes of gene expression variation
in human cancers},
journal = {J. Frankl. Inst.},
volume = {341},
number = {1-2},
pages = {77--88},
year = {2004},
url = {https://doi.org/10.1016/j.jfranklin.2003.12.005},
doi = {10.1016/J.JFRANKLIN.2003.12.005},
timestamp = {Mon, 24 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jfi/HautaniemiRKAEY04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HautaniemiEVWJYAKM03,
author = {Sampsa Hautaniemi and
Henrik Edgren and
Petri Vesanen and
Maija Wolf and
Anna{-}Kaarina J{\"{a}}rvinen and
Olli Yli{-}Harja and
Jaakko Astola and
Olli{-}P. Kallioniemi and
Outi Monni},
title = {A novel strategy for microarray quality control using Bayesian networks},
journal = {Bioinform.},
volume = {19},
number = {16},
pages = {2031--2038},
year = {2003},
url = {https://doi.org/10.1093/bioinformatics/btg275},
doi = {10.1093/BIOINFORMATICS/BTG275},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HautaniemiEVWJYAKM03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ml/HautaniemiYAKKWRMK03,
author = {Sampsa Hautaniemi and
Olli Yli{-}Harja and
Jaakko Astola and
P{\"{a}}ivikki Kauraniemi and
Anne Kallioniemi and
Maija Wolf and
Jimmy Ruiz and
Spyro Mousses and
Olli{-}P. Kallioniemi},
title = {Analysis and Visualization of Gene Expression Microarray Data in Human
Cancer Using Self-Organizing Maps},
journal = {Mach. Learn.},
volume = {52},
number = {1-2},
pages = {45--66},
year = {2003},
url = {https://doi.org/10.1023/A:1023941307670},
doi = {10.1023/A:1023941307670},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ml/HautaniemiYAKKWRMK03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/rti/GrigoryanHKD02,
author = {Artyom M. Grigoryan and
Galen Hostetter and
Olli{-}P. Kallioniemi and
Edward R. Dougherty},
title = {Simulation Toolbox for 3D-FISH Spot-Counting Algorithms},
journal = {Real Time Imaging},
volume = {8},
number = {3},
pages = {203--212},
year = {2002},
url = {https://doi.org/10.1006/rtim.2001.0280},
doi = {10.1006/RTIM.2001.0280},
timestamp = {Thu, 21 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/rti/GrigoryanHKD02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/DesperJKMPS00,
author = {Richard Desper and
Feng Jiang and
Olli{-}P. Kallioniemi and
Holger Moch and
Christos H. Papadimitriou and
Alejandro A. Sch{\"{a}}ffer},
title = {Distance-Based Reconstruction of Tree Models for Oncogenesis},
journal = {J. Comput. Biol.},
volume = {7},
number = {6},
pages = {789--803},
year = {2000},
url = {https://doi.org/10.1089/10665270050514936},
doi = {10.1089/10665270050514936},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/DesperJKMPS00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/DesperJKMPS99,
author = {Richard Desper and
Feng Jiang and
Olli{-}P. Kallioniemi and
Holger Moch and
Christos H. Papadimitriou and
Alejandro A. Sch{\"{a}}ffer},
title = {Inferring Tree Models for Oncogenesis from Comparative Genome Hybridization
Data},
journal = {J. Comput. Biol.},
volume = {6},
number = {1},
pages = {37--51},
year = {1999},
url = {https://doi.org/10.1089/cmb.1999.6.37},
doi = {10.1089/CMB.1999.6.37},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/DesperJKMPS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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