Olli P Kallioniemi

Olli P Kallioniemi

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Olli P Kallioniemi

Olli P Kallioniemi

Publications by authors named "Olli P Kallioniemi"

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Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis.

Bioinformatics 2014 Sep;30(17):i497-504

Department of Information and Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, 00076 Espoo, Institute for Molecular Medicine Finland FIMM, University of Helsinki, 00014 Helsinki, School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio and Department of Computer Science, Helsinki Institute for Information Technology HIIT, University Of Helsinki, 00014 Helsinki, Finland Department of Information and Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, 00076 Espoo, Institute for Molecular Medicine Finland FIMM, University of Helsinki, 00014 Helsinki, School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio and Department of Computer Science, Helsinki Institute for Information Technology HIIT, University Of Helsinki, 00014 Helsinki, Finland.

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http://dx.doi.org/10.1093/bioinformatics/btu456DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147909PMC
September 2014

Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs.

BMC Bioinformatics 2012 May 30;13:112. Epub 2012 May 30.

Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University, PO Box 15400, Espoo, 00076, Finland.

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http://dx.doi.org/10.1186/1471-2105-13-112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3532323PMC
May 2012

Classification of unknown primary tumors with a data-driven method based on a large microarray reference database.

Genome Med 2011 Oct 17;3(9):63. Epub 2011 Oct 17.

Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 00140 Helsinki, Finland.

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http://dx.doi.org/10.1186/gm279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3239238PMC
October 2011

The miR-15a-miR-16-1 locus is homozygously deleted in a subset of prostate cancers.

Genes Chromosomes Cancer 2011 Jul 31;50(7):499-509. Epub 2011 Mar 31.

Institute of Medical Technology, University of Tampere, Tampere University Hospital, Finland.

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http://dx.doi.org/10.1002/gcc.20873DOI Listing
July 2011

Androgen regulation of micro-RNAs in prostate cancer.

Prostate 2011 May 13;71(6):604-14. Epub 2010 Oct 13.

Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland.

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http://dx.doi.org/10.1002/pros.21276DOI Listing
May 2011

Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data.

BioData Min 2011 Mar 31;4. Epub 2011 Mar 31.

Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, Helsinki, Finland.

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http://dx.doi.org/10.1186/1756-0381-4-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080808PMC
March 2011

International network of cancer genome projects.

Authors:
Thomas J Hudson Warwick Anderson Axel Artez Anna D Barker Cindy Bell Rosa R Bernabé M K Bhan Fabien Calvo Iiro Eerola Daniela S Gerhard Alan Guttmacher Mark Guyer Fiona M Hemsley Jennifer L Jennings David Kerr Peter Klatt Patrik Kolar Jun Kusada David P Lane Frank Laplace Lu Youyong Gerd Nettekoven Brad Ozenberger Jane Peterson T S Rao Jacques Remacle Alan J Schafer Tatsuhiro Shibata Michael R Stratton Joseph G Vockley Koichi Watanabe Huanming Yang Matthew M F Yuen Bartha M Knoppers Martin Bobrow Anne Cambon-Thomsen Lynn G Dressler Stephanie O M Dyke Yann Joly Kazuto Kato Karen L Kennedy Pilar Nicolás Michael J Parker Emmanuelle Rial-Sebbag Carlos M Romeo-Casabona Kenna M Shaw Susan Wallace Georgia L Wiesner Nikolajs Zeps Peter Lichter Andrew V Biankin Christian Chabannon Lynda Chin Bruno Clément Enrique de Alava Françoise Degos Martin L Ferguson Peter Geary D Neil Hayes Thomas J Hudson Amber L Johns Arek Kasprzyk Hidewaki Nakagawa Robert Penny Miguel A Piris Rajiv Sarin Aldo Scarpa Tatsuhiro Shibata Marc van de Vijver P Andrew Futreal Hiroyuki Aburatani Mónica Bayés David D L Botwell Peter J Campbell Xavier Estivill Daniela S Gerhard Sean M Grimmond Ivo Gut Martin Hirst Carlos López-Otín Partha Majumder Marco Marra John D McPherson Hidewaki Nakagawa Zemin Ning Xose S Puente Yijun Ruan Tatsuhiro Shibata Michael R Stratton Hendrik G Stunnenberg Harold Swerdlow Victor E Velculescu Richard K Wilson Hong H Xue Liu Yang Paul T Spellman Gary D Bader Paul C Boutros Peter J Campbell Paul Flicek Gad Getz Roderic Guigó Guangwu Guo David Haussler Simon Heath Tim J Hubbard Tao Jiang Steven M Jones Qibin Li Nuria López-Bigas Ruibang Luo Lakshmi Muthuswamy B F Francis Ouellette John V Pearson Xose S Puente Victor Quesada Benjamin J Raphael Chris Sander Tatsuhiro Shibata Terence P Speed Lincoln D Stein Joshua M Stuart Jon W Teague Yasushi Totoki Tatsuhiko Tsunoda Alfonso Valencia David A Wheeler Honglong Wu Shancen Zhao Guangyu Zhou Lincoln D Stein Roderic Guigó Tim J Hubbard Yann Joly Steven M Jones Arek Kasprzyk Mark Lathrop Nuria López-Bigas B F Francis Ouellette Paul T Spellman Jon W Teague Gilles Thomas Alfonso Valencia Teruhiko Yoshida Karen L Kennedy Myles Axton Stephanie O M Dyke P Andrew Futreal Daniela S Gerhard Chris Gunter Mark Guyer Thomas J Hudson John D McPherson Linda J Miller Brad Ozenberger Kenna M Shaw Arek Kasprzyk Lincoln D Stein Junjun Zhang Syed A Haider Jianxin Wang Christina K Yung Anthony Cros Anthony Cross Yong Liang Saravanamuttu Gnaneshan Jonathan Guberman Jack Hsu Martin Bobrow Don R C Chalmers Karl W Hasel Yann Joly Terry S H Kaan Karen L Kennedy Bartha M Knoppers William W Lowrance Tohru Masui Pilar Nicolás Emmanuelle Rial-Sebbag Laura Lyman Rodriguez Catherine Vergely Teruhiko Yoshida Sean M Grimmond Andrew V Biankin David D L Bowtell Nicole Cloonan Anna deFazio James R Eshleman Dariush Etemadmoghadam Brooke B Gardiner Brooke A Gardiner James G Kench Aldo Scarpa Robert L Sutherland Margaret A Tempero Nicola J Waddell Peter J Wilson John D McPherson Steve Gallinger Ming-Sound Tsao Patricia A Shaw Gloria M Petersen Debabrata Mukhopadhyay Lynda Chin Ronald A DePinho Sarah Thayer Lakshmi Muthuswamy Kamran Shazand Timothy Beck Michelle Sam Lee Timms Vanessa Ballin Youyong Lu Jiafu Ji Xiuqing Zhang Feng Chen Xueda Hu Guangyu Zhou Qi Yang Geng Tian Lianhai Zhang Xiaofang Xing Xianghong Li Zhenggang Zhu Yingyan Yu Jun Yu Huanming Yang Mark Lathrop Jörg Tost Paul Brennan Ivana Holcatova David Zaridze Alvis Brazma Lars Egevard Egor Prokhortchouk Rosamonde Elizabeth Banks Mathias Uhlén Anne Cambon-Thomsen Juris Viksna Fredrik Ponten Konstantin Skryabin Michael R Stratton P Andrew Futreal Ewan Birney Ake Borg Anne-Lise Børresen-Dale Carlos Caldas John A Foekens Sancha Martin Jorge S Reis-Filho Andrea L Richardson Christos Sotiriou Hendrik G Stunnenberg Giles Thoms Marc van de Vijver Laura van't Veer Fabien Calvo Daniel Birnbaum Hélène Blanche Pascal Boucher Sandrine Boyault Christian Chabannon Ivo Gut Jocelyne D Masson-Jacquemier Mark Lathrop Iris Pauporté Xavier Pivot Anne Vincent-Salomon Eric Tabone Charles Theillet Gilles Thomas Jörg Tost Isabelle Treilleux Fabien Calvo Paulette Bioulac-Sage Bruno Clément Thomas Decaens Françoise Degos Dominique Franco Ivo Gut Marta Gut Simon Heath Mark Lathrop Didier Samuel Gilles Thomas Jessica Zucman-Rossi Peter Lichter Roland Eils Benedikt Brors Jan O Korbel Andrey Korshunov Pablo Landgraf Hans Lehrach Stefan Pfister Bernhard Radlwimmer Guido Reifenberger Michael D Taylor Christof von Kalle Partha P Majumder Rajiv Sarin T S Rao M K Bhan Aldo Scarpa Paolo Pederzoli Rita A Lawlor Massimo Delledonne Alberto Bardelli Andrew V Biankin Sean M Grimmond Thomas Gress David Klimstra Giuseppe Zamboni Tatsuhiro Shibata Yusuke Nakamura Hidewaki Nakagawa Jun Kusada Tatsuhiko Tsunoda Satoru Miyano Hiroyuki Aburatani Kazuto Kato Akihiro Fujimoto Teruhiko Yoshida Elias Campo Carlos López-Otín Xavier Estivill Roderic Guigó Silvia de Sanjosé Miguel A Piris Emili Montserrat Marcos González-Díaz Xose S Puente Pedro Jares Alfonso Valencia Heinz Himmelbauer Heinz Himmelbaue Victor Quesada Silvia Bea Michael R Stratton P Andrew Futreal Peter J Campbell Anne Vincent-Salomon Andrea L Richardson Jorge S Reis-Filho Marc van de Vijver Gilles Thomas Jocelyne D Masson-Jacquemier Samuel Aparicio Ake Borg Anne-Lise Børresen-Dale Carlos Caldas John A Foekens Hendrik G Stunnenberg Laura van't Veer Douglas F Easton Paul T Spellman Sancha Martin Anna D Barker Lynda Chin Francis S Collins Carolyn C Compton Martin L Ferguson Daniela S Gerhard Gad Getz Chris Gunter Alan Guttmacher Mark Guyer D Neil Hayes Eric S Lander Brad Ozenberger Robert Penny Jane Peterson Chris Sander Kenna M Shaw Terence P Speed Paul T Spellman Joseph G Vockley David A Wheeler Richard K Wilson Thomas J Hudson Lynda Chin Bartha M Knoppers Eric S Lander Peter Lichter Lincoln D Stein Michael R Stratton Warwick Anderson Anna D Barker Cindy Bell Martin Bobrow Wylie Burke Francis S Collins Carolyn C Compton Ronald A DePinho Douglas F Easton P Andrew Futreal Daniela S Gerhard Anthony R Green Mark Guyer Stanley R Hamilton Tim J Hubbard Olli P Kallioniemi Karen L Kennedy Timothy J Ley Edison T Liu Youyong Lu Partha Majumder Marco Marra Brad Ozenberger Jane Peterson Alan J Schafer Paul T Spellman Hendrik G Stunnenberg Brandon J Wainwright Richard K Wilson Huanming Yang

Nature 2010 Apr;464(7291):993-8

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http://dx.doi.org/10.1038/nature08987DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902243PMC
April 2010

Defining the molecular action of HDAC inhibitors and synergism with androgen deprivation in ERG-positive prostate cancer.

Int J Cancer 2008 Dec;123(12):2774-81

Medical Biotechnology, VTT Technical Research Centre of Finland, Institute for Molecular Medicine Finland and University of Turku, Turku, Finland.

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http://dx.doi.org/10.1002/ijc.23885DOI Listing
December 2008

BRCA2 mutations in 154 finnish male breast cancer patients.

Neoplasia 2004 Sep-Oct;6(5):541-5

Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere, Tampere University Hospital, Tampere, Finland.

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http://dx.doi.org/10.1593/neo.04193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1531658PMC
April 2005

Are data from different gene expression microarray platforms comparable?

Genomics 2004 Jun;83(6):1164-8

Biomedicum Biochip Center, University of Helsinki, P.O. Box 63, Room A415b, 00014 University of Helsinki, Finland.

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http://dx.doi.org/10.1016/j.ygeno.2004.01.004DOI Listing
June 2004

Prognostic impact of ANX7-GTPase in metastatic and HER2-negative breast cancer patients.

Clin Cancer Res 2004 Apr;10(7):2344-50

Department of Anatomy, Physiology and Genetics and Institute for Molecular Medicine, Uniformed Services University School of Medicine, Bethesda, Maryland 20814, USA.

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http://dx.doi.org/10.1158/1078-0432.ccr-03-0278DOI Listing
April 2004

CHEK2 1100delC is not a risk factor for male breast cancer population.

Int J Cancer 2004 Jan;108(3):475-6

Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland.

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http://dx.doi.org/10.1002/ijc.11384DOI Listing
January 2004

Thymidylate synthase expression predicts the response to 5-fluorouracil-based adjuvant therapy in pancreatic cancer.

Clin Cancer Res 2003 Sep;9(11):4165-71

Department of Surgery, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA.

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September 2003

Loss of the tight junction protein claudin-7 correlates with histological grade in both ductal carcinoma in situ and invasive ductal carcinoma of the breast.

Oncogene 2003 Apr;22(13):2021-33

Breast Cancer Program, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.

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http://dx.doi.org/10.1038/sj.onc.1206199DOI Listing
April 2003

Androgen receptor gene alterations in Finnish male breast cancer.

Breast Cancer Res Treat 2003 Jan;77(2):167-70

Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere, Tampere University Hospital, Tampere, Finland.

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http://dx.doi.org/10.1023/a:1021369508561DOI Listing
January 2003

Cloning of BCAS3 (17q23) and BCAS4 (20q13) genes that undergo amplification, overexpression, and fusion in breast cancer.

Genes Chromosomes Cancer 2002 Dec;35(4):311-7

Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland.

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http://dx.doi.org/10.1002/gcc.10121DOI Listing
December 2002

Impact of DNA amplification on gene expression patterns in breast cancer.

Cancer Res 2002 Nov;62(21):6240-5

Howard Hughes Medical Institute-NIH Research Scholar, Bethesda, Maryland 20892, USA.

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November 2002

A CHEK2 genetic variant contributing to a substantial fraction of familial breast cancer.

Am J Hum Genet 2002 Aug 28;71(2):432-8. Epub 2002 Jul 28.

Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Haartmaninkatu 8, FIN-00029 HUS, Helsinki, Finland.

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http://dx.doi.org/10.1086/341943DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC379177PMC
August 2002

Androgen receptor CAG polymorphism and prostate cancer risk.

Hum Genet 2002 Aug 3;111(2):166-71. Epub 2002 Jul 3.

Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Lenkkeilijankatu 6, 33520 Tampere, Finland.

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http://dx.doi.org/10.1007/s00439-002-0776-5DOI Listing
August 2002

New insights into testicular germ cell tumorigenesis from gene expression profiling.

Cancer Res 2002 Apr;62(8):2359-64

Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, N-0310 Oslo, Norway.

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April 2002

Clinical and functional target validation using tissue and cell microarrays.

Curr Opin Chem Biol 2002 Feb;6(1):97-101

Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-8000, USA.

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http://dx.doi.org/10.1016/s1367-5931(01)00283-6DOI Listing
February 2002