Olli-Pekka Kallioniemi

Om mig
Publikationer
Populärvetenskap och samverkan

Om mig

Professor i precisionsmedicin. Director för Science for Life Laboratory

Artiklar

Article: COMMUNICATIONS BIOLOGY. 2024;7(1):1355
Distinct molecular profiles and shared drug vulnerabilities in pancreatic metastases of renal cell carcinoma
Roos-Mattila M; Kallio P; Luck TJ; Polso M; Kumari R; Mikkonen P; Valimaki K; Malmstedt M; Ellonen P; Pellinen T; Heckman CA; Mustonen H; Puolakkainen PA; Alitalo K; Kallioniemi O; Mirtti T; Rannikko AS; Pietiainen VM; Seppanen HE
Article: BLOOD CANCER DISCOVERY. 2024;5(3):180-201
Acquired Multidrug Resistance in AML Is Caused by Low Apoptotic Priming in Relapsed Myeloblasts
Olesinski EA; Bhatia KS; Wang C; Pioso MS; Lin XX; Mamdouh AM; Ng SX; Sandhu V; Jasdanwala SS; Yilma B; Bohl S; Ryan JA; Malani D; Luskin MR; Kallioniemi O; Porkka K; Adamia S; Chng WJ; Osato M; Weinstock DM; Garcia JS; Letai A; Bhatt S
Article: ANTIVIRAL RESEARCH. 2024;223:105813
Drug repurposing platform for deciphering the druggable SARS-CoV-2 interactome
Bogacheva MS; Kuivanen S; Potdar S; Hassinen A; Huuskonen S; Pohner I; Luck TJ; Turunen L; Feodoroff M; Szirovicza L; Savijoki K; Saarela J; Tammela P; Paavolainen L; Poso A; Varjosalo M; Kallioniemi O; Pietiainen V; Vapalahti O
Article: NPJ PRECISION ONCOLOGY. 2024;8(1):38
Delineating functional and molecular impact of ex vivo sample handling in precision medicine
Struyf N; Osterroos A; Vesterlund M; Arnroth C; James T; Sunandar S; Mermelekas G; Bohlin A; Hamberg Levedahl K; Bengtzen S; Jafari R; Orre LM; Lehtio J; Lehmann S; Ostling P; Kallioniemi O; Seashore-Ludlow B; Erkers T
Article: MOLECULAR ONCOLOGY. 2024;18(2):245-279
Strategies to decrease inequalities in cancer therapeutics, care and preventionProceedings on a conference organized by the Pontifical Academy of Sciences and the European Academy of Cancer Sciences, Vatican City, February 23-24, 2023
Ringborg U; von Braun J; Celis J; Baumann M; Berns A; Eggermont A; Heard E; Heitor M; Chandy M; Chen C-J; Costa A; De Lorenzo F; De Robertis EM; Dubee FC; Ernberg I; Gabriel M; Helland A; Henrique R; Joensson B; Kallioniemi O; Korbel J; Krause M; Lowy DR; Michielin O; Nagy P; Oberst S; Paglia V; Parker MI; Ryan K; Sawyers CL; Schuz J; Silkaitis K; Solary E; Thomas D; Turkson P; Weiderpass E; Yang H
Article: NPJ PRECISION ONCOLOGY. 2023;7(1):111
The drug efficacy testing in 3D cultures platform identifies effective drugs for ovarian cancer patients
Akerlund E; Gudoityte G; Moussaud-Lamodiere E; Lind O; Bwanika HC; Lehti K; Salehi S; Carlson J; Wallin E; Fernebro J; Ostling P; Kallioniemi O; Joneborg U; Seashore-Ludlow B
Article: EUROPEAN UROLOGY FOCUS. 2023;9(5):751-759
Ex Vivo Drug Testing in Patient-derived Papillary Renal Cancer Cells Reveals EGFR and the BCL2 Family as Therapeutic Targets
Angori S; Banaei-Esfahani A; Muhlbauer K; Bolck HA; Kahraman A; Karakulak T; Poyet C; Feodoroff M; Potdar S; Kallioniemi O; Pietiainen V; Schraml P; Moch H
Article: CELL REPORTS: METHODS. 2023;3(8):100565
Image-based and machine learning-guided multiplexed serology test for SARS-CoV-2
Pietiainen V; Polso M; Migh E; Guckelsberger C; Harmati M; Diosdi A; Turunen L; Hassinen A; Potdar S; Koponen A; Sebestyen EG; Kovacs F; Kriston A; Hollandi R; Burian K; Terhes G; Visnyovszki A; Fodor E; Lacza Z; Kantele A; Kolehmainen P; Kakkola L; Strandin T; Levanov L; Kallioniemi O; Kemeny L; Julkunen I; Vapalahti O; Buzas K; Paavolainen L; Horvath P; Hepojoki J
Article: NUCLEIC ACIDS RESEARCH (NAR). 2023;51(W1):W57-W61
Breeze 2.0: an interactive web-tool for visual analysis and comparison of drug response data
Potdar S; Ianevski F; Ianevski A; Tanoli Z; Wennerberg K; Seashore-Ludlow B; Kallioniemi O; Ostling P; Aittokallio T; Saarela J
Article: SLAS DISCOVERY. 2023;28(4):138-148
Comparison of two supporting matrices for patient-derived cancer cells in 3D drug sensitivity and resistance testing assay (3D-DSRT)
Feoforoff M; Mikkonen P; Turunen L; Hassinen A; Paasonen L; Paavolainen L; Potdar S; Murumagi A; Kallioniemi O; Pietiainen V
Article: LUNG CANCER. 2023;178:213-219
Novel therapeutic approaches for pleural mesothelioma identified by functional ex vivo drug sensitivity testing
Ollila-Raj H; Murumagi A; Pellinen T; Arjama M; Sutinen E; Volmonen K; Haikala HM; Kallioniemi O; Mayranpaa MI; Ilonen I
Article: NPJ PRECISION ONCOLOGY. 2023;7(1):32
Prediction model for drug response of acute myeloid leukemia patients
Trac QT; Pawitan Y; Mou T; Erkers T; Ostling P; Bohlin A; Osterroos A; Vesterlund M; Jafari R; Siavelis I; Backvall H; Kiviluoto S; Orre LM; Rantalainen M; Lehtio J; Lehmann S; Kallioniemi O; Vu TN
Article: SLAS DISCOVERY. 2023;28(2):36-41
Protocol for 3D drug sensitivity and resistance testing of patient-derived cancer cells in 384-well plates
Feodoroff M; Mikkonen P; Arjama M; Murumagi A; Kallioniemi O; Potdar S; Turunen L; Pietiainen V
Article: BRITISH JOURNAL OF CANCER. 2023;128(4):678-690
Drug response profiles in patient-derived cancer cells across histological subtypes of ovarian cancer: real-time therapy tailoring for a patient with low-grade serous carcinoma
Murumagi A; Ungureanu D; Khan S; Arjama M; Valimaki K; Ianevski A; Ianevski P; Bergstrom R; Dini A; Kanerva A; Koivisto-Korander R; Tapper J; Lassus H; Loukovaara M; Magi A; Hirasawa A; Aoki D; Pietiainen V; Pellinen T; Butzow R; Aittokallio T; Kallioniemi O
Article: JOURNAL OF THE NATIONAL CANCER INSTITUTE. 2023;115(1):71-82
Fibroblast subsets in non-small cell lung cancer: Associations with survival, mutations, and immune features
Pellinen T; Paavolainen L; Martin-Bernabe A; Araujo RP; Strell C; Mezheyeuski A; Backman M; La Fleur L; Bruck O; Sjolund J; Holmberg E; Valimaki K; Brunnstrom H; Botling J; Moreno-Ruiz P; Kallioniemi O; Micke P; Ostman A
Article: NPJ PRECISION ONCOLOGY. 2022;6(1):94
Drug sensitivity profiling of 3D tumor tissue cultures in the pediatric precision oncology program INFORM
Peterziel H; Jamaladdin N; ElHarouni D; Gerloff XF; Herter S; Fiesel P; Berker Y; Blattner-Johnson M; Schramm K; Jones BC; Reuss D; Turunen L; Friedenauer A; Holland-Letz T; Sill M; Weiser L; Previti C; Balasubramanian G; Gerber NU; Gojo J; Hutter C; Ora I; Lohi O; Kattamis A; de Wilde B; Westermann F; Tippelt S; Graf N; Nathrath M; Sparber-Sauer M; Sehested A; Kramm CM; Dirksen U; Kallioniemi O; Pfister SM; van Tilburg CM; Jones DTW; Saarela J; Pietiaeinen V; Jaeger N; Schlesner M; Kopp-Schneider A; Oppermann S; Milde T; Witt O; Oehme I
Article: CELL DEATH AND DISEASE. 2022;13(8):714
Multiomics characterization implicates PTK7 in ovarian cancer EMT and cell plasticity and offers strategies for therapeutic intervention
Raivola J; Dini A; Karvonen H; Piki E; Salokas K; Niininen W; Kaleva L; Zhang K; Arjama M; Gudoityte G; Seashore-Ludlow B; Varjosalo M; Kallioniemi O; Hautaniemi S; Murumagi A; Ungureanu D
Article: MOLECULAR ONCOLOGY. 2022;16(12):2312-2329
E-cadherin is a robust prognostic biomarker in colorectal cancer and low expression is associated with sensitivity to inhibitors of topoisomerase, aurora, and HSP90 in preclinical models
Bruun J; Eide PW; Bergsland CH; Bruck O; Svindland A; Arjama M; Valimaki K; Bjornslett M; Guren MG; Kallioniemi O; Nesbakken A; Lothe RA; Pellinen T
Article: NATURE COMMUNICATIONS. 2022;13(1):1691
Integrative multi-omics and drug response profiling of childhood acute lymphoblastic leukemia cell lines
Leo IR; Aswad L; Stahl M; Kunold E; Post F; Erkers T; Struyf N; Mermelekas G; Joshi RN; Gracia-Villacampa E; Ostling P; Kallioniemi OP; Tamm KP; Siavelis I; Lehtio J; Vesterlund M; Jafari R
Article: CANCER RESEARCH COMMUNICATIONS. 2022;2(3):172-181
Stromal FAP Expression is Associated with MRI Visibility and Patient Survival in Prostate Cancer
Pellinen T; Sandeman K; Blom S; Turkki R; Hemmes A; Vaelimaeki K; Eineluoto J; Kenttaemies A; Nordling S; Kallioniemi O; Rannikko A; Mirtti T
Article: CELL SYSTEMS. 2022;13(3):241-255.e7
Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health
Marabita F; James T; Karhu A; Virtanen H; Kettunen K; Stenlund H; Boulund F; Hellstrom C; Neiman M; Mills R; Perheentupa T; Laivuori H; Helkkula P; Byrne M; Jokinen I; Honko H; Kallonen A; Ermes M; Simila H; Lindholm M; Widen E; Ripatti S; Perala-Heape M; Engstrand L; Nilsson P; Moritz T; Miettinen T; Sallinen R; Kallioniemi O
Article: CANCER DISCOVERY. 2022;12(2):388-401
Implementing a Functional Precision Medicine Tumor Board for Acute Myeloid Leukemia
Malani D; Kumar A; Bruck O; Kontro M; Yadav B; Hellesoy M; Kuusanmaki H; Dufva O; Kankainen M; Eldfors S; Potdar S; Saarela J; Turunen L; Parsons A; Vastrik I; Kivinen K; Saarela J; Raty R; Lehto M; Wolf M; Gjertsen BT; Mustjoki S; Aittokallio T; Wennerberg K; Heckman CA; Kallioniemi O; Porkka K
Article: FRONTIERS IN ONCOLOGY. 2022;12:870352
Prognostic Role of Tumor Immune Microenvironment in Pleural Epithelioid Mesothelioma.
Ollila H; Mäyränpää MI; Paavolainen L; Paajanen J; Välimäki K; Sutinen E; Wolff H; Räsänen J; Kallioniemi O; Myllärniemi M; Ilonen I; Pellinen T
Article: TRANSLATIONAL ONCOLOGY. 2022;15(1):101290
High-throughput ex vivo drug testing identifies potential drugs and drug combinations for NRAS-positive malignant melanoma
Kohtamaki L; Arjama M; Makela S; Ianevski P; Valimaki K; Juteau S; Ilmonen S; Ungureanu D; Kallioniemi O; Murumagi A; Hernberg M
Article: SCIENTIFIC REPORTS. 2021;11(1):23565
FLT3-ITD allelic ratio and HLF expression predict FLT3 inhibitor efficacy in adult AML
Kivioja J; Malani D; Kumar A; Kontro M; Parsons A; Kallioniemi O; Heckman CA
Article: MOLECULAR ONCOLOGY. 2021;15(10):2507-2543
The Porto European Cancer Research Summit 2021
Ringborg U; Berns A; Celis JE; Heitor M; Tabernero J; Schuz J; Baumann M; Henrique R; Aapro M; Basu P; Beets-Tan R; Besse B; Cardoso F; Carneiro F; van den Eede G; Eggermont A; Froehling S; Galbraith S; Garralda E; Hanahan D; Hofmarcher T; Joensson B; Kallioniemi O; Kasler M; Kondorosi E; Korbel J; Lacombe D; Machado JC; Martin-Moreno JM; Meunier F; Nagy P; Nuciforo P; Oberst S; Oliveiera J; Papatriantafyllou M; Ricciardi W; Roediger A; Ryll B; Schilsky R; Scocca G; Seruca R; Soares M; Steindorf K; Valentini V; Voest E; Weiderpass E; Wilking N; Wren A; Zitvogel L
Article: THE JOURNAL OF PATHOLOGY: CLINICAL RESEARCH. 2021;7(5):482-494
High tumor cell platelet-derived growth factor receptor beta expression is associated with shorter survival in malignant pleural epithelioid mesothelioma
Ollila H; Paajanen J; Wolff H; Ilonen I; Sutinen E; Valimaki K; ostman A; Anttila S; Kettunen E; Rasanen J; Kallioniemi O; Myllarniemi M; Mayranpaa MI; Pellinen T
Article: NPJ PRECISION ONCOLOGY. 2021;5(1):71
Bayesian multi-source regression and monocyte-associated gene expression predict BCL-2 inhibitor resistance in acute myeloid leukemia
White BS; Khan SA; Mason MJ; Ammad-ud-din M; Potdar S; Malani D; Kuusanmaki H; Druker BJ; Heckman C; Kallioniemi O; Kurtz SE; Porkka K; Tognon CE; Tyner JW; Aittokallio T; Wennerberg K; Guinney J
Article: AMERICAN JOURNAL OF HEMATOLOGY. 2021;96(5):580-588
The transcriptome-wide landscape of molecular subtype-specific mRNA expression profiles in acute myeloid leukemia
Mou T; Pawitan Y; Stahl M; Vesterlund M; Deng W; Jafari R; Bohlin A; Osterroos A; Siavelis L; Backvall H; Erkers T; Kiviluoto S; Seashore-Ludlow B; Ostling P; Orre LM; Kallioniemi O; Lehmann S; Lehtio J; Trung NV
Article: TRANSLATIONAL ONCOLOGY. 2021;14(4):101027
STRN-ALK rearranged pediatric malignant peritoneal mesothelioma - Functional testing of 527 cancer drugs in patient-derived cancer cells
Murumagi A; Ungureanu D; Arjama M; Butzow R; Lohi J; Sariola H; Kanerva J; Koskenvuo M; Kallioniemi O
Article: JOURNAL OF NUTRITION. 2021;151(2):281-292
Genetic Risk Score for Serum 25-Hydroxyvitamin D Concentration Helps to Guide Personalized Vitamin D Supplementation in Healthy Finnish Adults
Sallinen RJ; Dethlefsen O; Ruotsalainen S; Mills RD; Miettinen TA; Jaaskelainen TE; Lundqvist A; Kyllonen E; Kroger H; Karppinen JI; Lamberg-Allardt C; Viljakainen H; Kaunisto MA; Kallioniemi O
Article: CELL DEATH AND DISEASE. 2020;11(9):790
Glucocorticoids induce differentiation and chemoresistance in ovarian cancer by promoting ROR1-mediated stemness
Karvonen H; Arjama M; Kaleva L; Niininen W; Barker H; Koivisto-Korander R; Tapper J; Pakarinen P; Lassus H; Loukovaara M; Butzow R; Kallioniemi O; Murumagi A; Ungureanu D
Article: HAEMATOLOGICA. 2020;105(6):1527-1538
Multi-parametric single cell evaluation defines distinct drug responses in healthy hematologic cells that are retained in corresponding malignant cell types
Majumder MM; Leppa A-M; Hellesoy M; Dowling P; Malyutina A; Kopperud R; Bazou D; Andersson E; Parsons A; Tang J; Kallioniemi O; Mustjoki S; O'Gorman P; Wennerberg K; Porkka K; Gjertsen BT; Heckman CA
Article: BIOINFORMATICS. 2020;36(11):3602-3604
Breeze: an integrated quality control and data analysis application for high-throughput drug screening
Potdar S; Ianevski A; Mpindi J-P; Bychkov D; Fiere C; Ianevski P; Yadav B; Wennerberg K; Aittokallio T; Kallioniemi O; Saarela J; Ostling P
Article: BLOOD ADVANCES. 2020;4(2):274-286
Immune profiles in acute myeloid leukemia bone marrow associate with patient age, T-cell receptor clonality, and survival
Bruck O; Dufva O; Hohtari H; Blom S; Turkki R; Ilander M; Kovanen P; Pallaud C; Ramos PM; Lahteenmaki H; Valimaki K; El Missiry M; Ribeiro A; Kallioniemi O; Porkka K; Pellinen T; Mustjoki S
Article: PROSTATE. 2019;79(13):1505-1513
Fibroblast as a critical stromal cell type determining prognosis in prostate cancer
Blom S; Erickson A; Ostman A; Rannikko A; Mirtti T; Kallioniemi O; Pellinen T
Article: LEUKEMIA. 2019;33(7):1570-1582
Immune cell constitution in bone marrow microenvironment predicts outcome in adult ALL
Hohtari H; Bruck O; Blom S; Turkki R; Sinisalo M; Kovanen PE; Kallioniemi O; Pellinen T; Porkka K; Mustjoki S
Article: INTERNATIONAL JOURNAL OF CANCER. 2019;144(6):1356-1366
Clonal heterogeneity influences drug responsiveness in renal cancer assessed by ex vivo drug testing of multiple patient-derived cancer cells
Saeed K; Ojamies P; Pellinen T; Eldfors S; Turkki R; Lundin J; Jarvinen P; Nisen H; Taari K; af Hallstrom TM; Rannikko A; Mirtti T; Kallioniemi O; Ostling P
Article: CLINICAL CANCER RESEARCH. 2019;25(5):1676-1687
Anagrelide for Gastrointestinal Stromal Tumor.
Pulkka O-P; Gebreyohannes YK; Wozniak A; Mpindi J-P; Tynninen O; Icay K; Cervera A; Keskitalo S; Murumägi A; Kulesskiy E; Laaksonen M; Wennerberg K; Varjosalo M; Laakkonen P; Lehtonen R; Hautaniemi S; Kallioniemi O; Schöffski P; Sihto H; Joensuu H
Article: BRITISH JOURNAL OF CANCER. 2019;120(4):435-443
Drug sensitivity testing on patient-derived sarcoma cells predicts patient response to treatment and identifies c-Sarc inhibitors as active drugs for translocation sarcomas
Brodin BA; Wennerberg K; Lidbrink E; Brosjo O; Potdar S; Wilson JN; Ma L; Moens LN; Hesla A; Porovic E; Bernhardsson E; Papakonstantinou A; Bauer H; Tsagkozis P; von Sivers K; Wejde J; Ostling P; Kallioniemi O; Stragliotto CL
Article: HAEMATOLOGICA. 2019;104(2):338-346
T-cell inflamed tumor microenvironment predicts favorable prognosis in primary testicular lymphoma
Leivonen S-K; Pollari M; Bruck O; Pellinen T; Autio M; Karjalainen-Lindsberg M-L; Mannisto S; Kellokumpu-Lehtinen P-L; Kallioniemi O; Mustjoki S; Leppa S
Article: AUTOIMMUNITY. 2019;52(1):1-11
Individual and stable autoantibody repertoires in healthy individuals
Neiman M; Hellstrom C; Just D; Mattsson C; Fagerberg L; Schuppe-Koistinen I; Gummesson A; Bergstrom G; Kallioniemi O; Achour A; Sallinen R; Uhlen M; Nilsson P
Article: PERSONALIZED MEDICINE. 2019;16(1):51-65
Characterization of farnesyl diphosphate farnesyl transferase 1 (FDFT1) expression in cancer.
Tüzmen Ş; Hostetter G; Watanabe A; Ekmekçi C; Carrigan PE; Shechter I; Kallioniemi O; Miller LJ; Mousses S
Article: THE JOURNAL OF PATHOLOGY: CLINICAL RESEARCH. 2019;5(1):63-78
Combined epithelial marker analysis of tumour budding in stage II colorectal cancer
Silk K; Blom S; Turkki R; Valimaki K; Kurki S; Mustonen H; Haglund C; Carpen O; Kallioniemi O; Korkeila E; Sundstrom J; Pellinen T
Article: HAEMATOLOGICA. 2018;103(11):1908-1914
PD-L1⁺ tumor-associated macrophages and PD-1⁺ tumor-infiltrating lymphocytes predict survival in primary testicular lymphoma
Pollari M; Bruck O; Pellinen T; Vahamurto P; Karjalainen-Lindsberg M-L; Mannisto S; Kallioniemi O; Kellokumpu-Lehtinen P-L; Mustjoki S; Leivonen S-K; Leppa S
Article: MOLECULAR CANCER THERAPEUTICS. 2018;17(9):2060-2071
Drug-Sensitivity Screening and Genomic Characterization of 45 HPV-Negative Head and Neck Carcinoma Cell Lines for Novel Biomarkers of Drug Efficacy.
Lepikhova T; Karhemo P-R; Louhimo R; Yadav B; Murumägi A; Kulesskiy E; Kivento M; Sihto H; Grénman R; Syrjänen SM; Kallioniemi O; Aittokallio T; Wennerberg K; Joensuu H; Monni O
Article: MOLECULAR ONCOLOGY. 2018;12(9):1639-1655
Prognostic, predictive, and pharmacogenomic assessments of CDX2 refine stratification of colorectal cancer
Bruun J; Sveen A; Barros R; Eide PW; Eilertsen I; Kolberg M; Pellinen T; David L; Svindland A; Kallioniemi O; Guren MG; Nesbakken A; Almeida R; Lothe RA
Article: BMC CANCER. 2018;18(1):850
Association of tamoxifen resistance and lipid reprogramming in breast cancer
Hultsch S; Kankainen M; Paavolainen L; Kovanen R-M; Ikonen E; Kangaspeska S; Pietiainen V; Kallioniemi O
Article: LEUKEMIA. 2018;32(7):1643-1656
Immune cell contexture in the bone marrow tumor microenvironment impacts therapy response in CML
Bruck O; Blom S; Dufva O; Turkki R; Chheda H; Ribeiro A; Kovanen P; Aittokallio T; Koskenvesa P; Kallioniemi O; Porkka K; Pellinen T; Mustjoki S
Article: JOURNAL OF PATHOLOGY. 2018;245(1):101-113
Spatial aspects of oncogenic signalling determine the response to combination therapy in slice explants from Kras-driven lung tumours
Narhi K; Nagaraj AS; Parri E; Turkki R; van Duijn PW; Hemmes A; Lahtela J; Uotinen V; Mayranpaa MI; Salmenkivi K; Rasanen J; Linder N; Trapman J; Rannikko A; Kallioniemi O; Af Hallstrom TM; Lundin J; Sommergruber W; Anders S; Verschuren EW
Article: JOURNAL OF CELLULAR AND MOLECULAR MEDICINE. 2018;22(4):2220-2230
Clinical relevance of integrin alpha 4 in gastrointestinal stromal tumours
Pulkka O-P; Mpindi J-P; Tynninen O; Nilsson B; Kallioniemi O; Sihto H; Joensuu H
Article: LEUKEMIA. 2018;32(3):774-787
Discovery of novel drug sensitivities in T-PLL by high-throughput ex vivo drug testing and mutation profiling.
Andersson EI; Pützer S; Yadav B; Dufva O; Khan S; He L; Sellner L; Schrader A; Crispatzu G; Oleś M; Zhang H; Adnan-Awad S; Lagström S; Bellanger D; Mpindi JP; Eldfors S; Pemovska T; Pietarinen P; Lauhio A; Tomska K; Cuesta-Mateos C; Faber E; Koschmieder S; Brümmendorf TH; Kytölä S; Savolainen E-R; Siitonen T; Ellonen P; Kallioniemi O; Wennerberg K; Ding W; Stern M-H; Huber W; Anders S; Tang J; Aittokallio T; Zenz T; Herling M; Mustjoki S
Article: CLINICAL CANCER RESEARCH. 2018;24(4):794-806
Colorectal Cancer Consensus Molecular Subtypes Translated to Preclinical Models Uncover Potentially Targetable Cancer Cell Dependencies.
Sveen A; Bruun J; Eide PW; Eilertsen IA; Ramirez L; Murumägi A; Arjama M; Danielsen SA; Kryeziu K; Elez E; Tabernero J; Guinney J; Palmer HG; Nesbakken A; Kallioniemi O; Dienstmann R; Lothe RA
Article: SCIENTIFIC REPORTS. 2018;8(1):2338
ITGB1-dependent upregulation of Caveolin-1 switches TGFβ signalling from tumour-suppressive to oncogenic in prostate cancer
Pellinen T; Blom S; Sanchez S; Valimaki K; Mpindi J-P; Azegrouz H; Strippoli R; Nieto R; Viton M; Palacios I; Turkki R; Wang Y; Sanchez-Alvarez M; Nordling S; Butzow A; Mirtti T; Rannikko A; Montoya MC; Kallioniemi O; del Pozo MA
Article: SCIENTIFIC REPORTS. 2017;7(1):15580
Systems pathology by multiplexed immunohistochemistry and whole-slide digital image analysis
Blom S; Paavolainen L; Bychkov D; Turkki R; Maki-Teeri P; Hemmes A; Valimaki K; Lundin J; Kallioniemi O; Pellinen T
Article: BLOOD ADVANCES. 2017;1(24):2257-2268
Crosstalk between ROR1 and BCR pathways defines novel treatment strategies in mantle cell lymphoma
Karvonen H; Chiron D; Niininen W; Ek S; Jerkeman M; Moradi E; Nykter M; Heckman CA; Kallioniemi O; Murumagi A; Ungureanu D
Article: MOLECULAR ONCOLOGY. 2017;11(9):1156-1171
Drug sensitivity and resistance testing identifies PLK1 inhibitors and gemcitabine as potent drugs for malignant peripheral nerve sheath tumors
Kolberg M; Bruun J; Murumagi A; Mpindi JP; Bergsland CH; Holand M; Eilertsen IA; Danielsen SA; Kallioniemi O; Lothe RA
Article: BMC GENOMICS. 2017;18(1):629
The impact of RNA sequence library construction protocols on transcriptomic profiling of leukemia
Kumar A; Kankainen M; Parsons A; Kallioniemi O; Mattila P; Heckman CA
Article: BLOOD. 2017;130(6):789-802
JAK1/2 and BCL2 inhibitors synergize to counteract bone marrow stromal cell-induced protection of AML.
Karjalainen R; Pemovska T; Popa M; Liu M; Javarappa KK; Majumder MM; Yadav B; Tamborero D; Tang J; Bychkov D; Kontro M; Parsons A; Suvela M; Mayoral Safont M; Porkka K; Aittokallio T; Kallioniemi O; McCormack E; Gjertsen BT; Wennerberg K; Knowles J; Heckman CA
Article: LEUKEMIA. 2017;31(5):1187-1195
Enhanced sensitivity to glucocorticoids in cytarabine-resistant AML
Malani D; Murumagi A; Yadav B; Kontro M; Eldfors S; Kumar A; Karjalainen R; Majumder MM; Ojamies P; Pemovska T; Wennerberg K; Heckman C; Porkka K; Wolf M; Aittokallio T; Kallioniemi O
Article: LEUKEMIA. 2017;31(5):1048-1058
Monitoring therapy responses at the leukemic subclone level by ultra-deep amplicon resequencing in acute myeloid leukemia
Ojamies P; Kontro M; Edgren H; Ellonen P; Lagstrom S; Almusa H; Miettinen T; Eldfors S; Tamborero D; Wennerberg K; Heckman C; Porkka K; Wolf M; Kallioniemi O
Article: ONCOTARGET. 2017;8(14):22606-22615
Differentiation status of primary chronic myeloid leukemia cells affects sensitivity to BCR-ABL1 inhibitors.
Pietarinen PO; Eide CA; Ayuda-Durán P; Potdar S; Kuusanmäki H; Andersson EI; Mpindi JP; Pemovska T; Kontro M; Heckman CA; Kallioniemi O; Wennerberg K; Hjorth-Hansen H; Druker BJ; Enserink JM; Tyner JW; Mustjoki S; Porkka K
Article: THE JOURNAL OF PATHOLOGY: CLINICAL RESEARCH. 2017;3(2):123-138
PLA2G7 associates with hormone receptor negativity in clinical breast cancer samples and regulates epithelial-mesenchymal transition in cultured breast cancer cells
Lehtinen L; Vainio P; Wikman H; Huhtala H; Mueller V; Kallioniemi A; Pantel K; Kronqvist P; Kallioniemi O; Carpen O; Iljin K
Article: EUROPEAN UROLOGY. 2017;71(3):319-327
Comprehensive Drug Testing of Patient-derived Conditionally Reprogrammed Cells from Castration-resistant Prostate Cancer
Saeed K; Rahkama V; Eldfors S; Bychkov D; Mpindi JP; Yadav B; Paavolainen L; Aittokallio T; Heckman C; Wennerberg K; Peehl DM; Horvath P; Mirtti T; Rannikko A; Kallioniemi O; Ostling P; af Hallstrom TM
Article: GYNECOLOGIC ONCOLOGY. 2017;144(3):621-630
Systematic drug sensitivity testing reveals synergistic growth inhibition by dasatinib or mTOR inhibitors with paclitaxel in ovarian granulosa cell tumor cells.
Haltia U-M; Andersson N; Yadav B; Färkkilä A; Kulesskiy E; Kankainen M; Tang J; Bützow R; Riska A; Leminen A; Heikinheimo M; Kallioniemi O; Unkila-Kallio L; Wennerberg K; Aittokallio T; Anttonen M
Article: EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES. 2017;98:30-39
KeepEX, a simple dilution protocol for improving extracellular vesicle yields from urine.
Puhka M; Nordberg M-E; Valkonen S; Rannikko A; Kallioniemi O; Siljander P; Af Hällström TM
Article: LEUKEMIA. 2017;31(2):301-309
HOX gene expression predicts response to BCL-2 inhibition in acute myeloid leukemia.
Kontro M; Kumar A; Majumder MM; Eldfors S; Parsons A; Pemovska T; Saarela J; Yadav B; Malani D; Fløisand Y; Höglund M; Remes K; Gjertsen BT; Kallioniemi O; Wennerberg K; Heckman CA; Porkka K
Article: CELL REPORTS. 2017;18(3):673-684
Cell of Origin Links Histotype Spectrum to Immune Microenvironment Diversity in Non-small-Cell Lung Cancer Driven by Mutant Kras and Loss of Lkb1
Nagaraj AS; Lahtela J; Hemmes A; Pellinen T; Blom S; Devlin JR; Salmenkivi K; Kallioniemi O; Mayranpaa MI; Narhi K; Verschuren EW
Article: LEUKEMIA. 2017;31(1):51-57
Idelalisib sensitivity and mechanisms of disease progression in relapsed TCF3-PBX1 acute lymphoblastic leukemia.
Eldfors S; Kuusanmäki H; Kontro M; Majumder MM; Parsons A; Edgren H; Pemovska T; Kallioniemi O; Wennerberg K; Gökbuget N; Burmeister T; Porkka K; Heckman CA
Article: THERANOSTICS. 2017;7(16):3824-3841
Metabolomic Profiling of Extracellular Vesicles and Alternative Normalization Methods Reveal Enriched Metabolites and Strategies to Study Prostate Cancer-Related Changes
Puhka M; Takatalo M; Nordberg M-E; Valkonen S; Nandania J; Aatonen M; Yliperttula M; Laitinen S; Velagapudi V; Mirtti T; Kallioniemi O; Rannikko A; Siljander PR-M; Af Hallstrom TM
Article: BREAST CANCER: TARGETS AND THERAPY. 2017;9:185-198
Drug-screening and genomic analyses of HER2-positive breast cancer cell lines reveal predictors for treatment response.
Jernström S; Hongisto V; Leivonen S-K; Due EU; Tadele DS; Edgren H; Kallioniemi O; Perälä M; Mælandsmo GM; Sahlberg KK
Article: BMC CANCER. 2016;16:378
Systematic drug screening reveals specific vulnerabilities and co-resistance patterns in endocrine-resistant breast cancer
Kangaspeska S; Hultsch S; Jaiswal A; Edgren H; Mpindi J-P; Eldfors S; Bruck O; Aittokallio T; Kallioniemi O
Article: ONCOTARGET. 2016;7(25):37407-37419
Intrinsic resistance to PIM kinase inhibition in AML through p38α-mediated feedback activation of mTOR signaling.
Brunen D; García-Barchino MJ; Malani D; Jagalur Basheer N; Lieftink C; Beijersbergen RL; Murumägi A; Porkka K; Wolf M; Zwaan CM; Fornerod M; Kallioniemi O; Martínez-Climent JÁ; Bernards R
Article: EUROPEAN UROLOGY. 2016;69(6):1120-1128
Systematic Identification of MicroRNAs That Impact on Proliferation of Prostate Cancer Cells and Display Changed Expression in Tumor Tissue
Aakula A; Kohonen P; Leivonen S-K; Makela R; Hintsanen P; Mpindi JP; Martens-Uzunova E; Aittokallio T; Jenster G; Perala M; Kallioniemi O; Ostling P
Article: ONCOTARGET. 2016;7(19):28510-28522
A loss-of-function genetic screening identifies novel mediators of thyroid cancer cell viability.
Cantisani MC; Parascandolo A; Perälä M; Allocca C; Fey V; Sahlberg N; Merolla F; Basolo F; Laukkanen MO; Kallioniemi OP; Santoro M; Castellone MD
Article: JOURNAL OF MOLECULAR BIOCHEMISTRY. 2016;5(1):12-22
High-throughput cell-based compound screen identifies pinosylvin methyl ether and tanshinone IIA as inhibitors of castration-resistant prostate cancer.
Ketola K; Viitala M; Kohonen P; Fey V; Culig Z; Kallioniemi O; Iljin K
Article: PLOS PATHOGENS. 2016;12(2):e1005424
Oncogenic Herpesvirus Utilizes Stress-Induced Cell Cycle Checkpoints for Efficient Lytic Replication.
Balistreri G; Viiliäinen J; Turunen M; Diaz R; Lyly L; Pekkonen P; Rantala J; Ojala K; Sarek G; Teesalu M; Denisova O; Peltonen K; Julkunen I; Varjosalo M; Kainov D; Kallioniemi O; Laiho M; Taipale J; Hautaniemi S; Ojala PM
Article: MOLECULAR & CELLULAR PROTEOMICS. 2015;14(12):3274-3283
Relevance Rank Platform (RRP) for Functional Filtering of High Content Protein-Protein Interaction Data.
Pokharel YR; Saarela J; Szwajda A; Rupp C; Rokka A; Lal Kumar Karna S; Teittinen K; Corthals G; Kallioniemi O; Wennerberg K; Aittokallio T; Westermarck J
Article: BIOINFORMATICS. 2015;31(23):3815-3821
Impact of normalization methods on high-throughput screening data with high hit rates and drug testing with dose-response data
Mpindi J-P; Swapnil P; Dmitrii B; Jani S; Saeed K; Wennerberg K; Aittokallio T; Ostling P; Kallioniemi O
Article: EUROPEAN UROLOGY. 2015;68(4):581-588
miR-183 in Prostate Cancer Cells Positively Regulates Synthesis and Serum Levels of Prostate-specific Antigen
Larne O; Ostling P; Haflidadottir BS; Hagman Z; Aakula A; Kohonen P; Kallioniemi O; Edsjo A; Bjartell A; Lilja H; Lundwall A; Ceder Y
Article: MOLECULAR ONCOLOGY. 2015;9(7):1287-1300
MicroRNA-135b regulates ERα, AR and HIF1AN and affects breast and prostate cancer cell growth
Aakula A; Leivonen S-K; Hintsanen P; Aittokallio T; Ceder Y; Borresen-Dale A-L; Perala M; Ostling P; Kallioniemi O
Article: INTERNATIONAL JOURNAL OF CANCER. 2015;136(11):2535-2545
Androgen receptor-interacting protein HSPBAP1 facilitates growth of prostate cancer cells in androgen-deficient conditions
Saeed K; Ostling P; Bjorkman M; Mirtti T; Alanen K; Vesterinen T; Sankila A; Lundin J; Lundin M; Rannikko A; Nordling S; Mpindi J-P; Kohonen P; Iljin K; Kallioniemi O; Rantala JK
Article: NATURE GENETICS. 2015;47(6):589-597
The impact of low-frequency and rare variants on lipid levels
Surakka I; Horikoshi M; Magi R; Sarin A-P; Mahajan A; Lagou V; Marullo L; Ferreira T; Miraglio B; Timonen S; Kettunen J; Pirinen M; Karjalainen J; Thorleifsson G; Hagg S; Hottenga J-J; Isaacs A; Ladenvall C; Beekman M; Esko T; Ried JS; Nelson CP; Willenborg C; Gustafsson S; Westra H-J; Blades M; de Craen AJM; de Geus EJ; Deelen J; Grallert H; Hamsten A; Havulinna AS; Hengstenberg C; Houwing-Duistermaat JJ; Hypponen E; Karssen LC; Lehtimaki T; Lyssenko V; Magnusson PKE; Mihailov E; Muller-Nurasyid M; Mpindi J-P; Pedersen NL; Penninx BWJH; Perola M; Pers TH; Peters A; Rung J; Smit JH; Steinthorsdottir V; Tobin MD; Tsernikova N; van Leeuwen EM; Viikari JS; Willems SM; Willemsen G; Schunkert H; Erdmann J; Samani NJ; Kaprio J; Lind L; Gieger C; Metspalu A; Slagboom PE; Groop L; van Duijn CM; Eriksson JG; Jula A; Salomaa V; Boomsma DI; Power C; Raitakari OT; Ingelsson E; Jarvelin M-R; Thorsteinsdottir U; Franke L; Ikonen E; Kallioniemi O; Pietiainen V; Lindgren CM; Stefansson K; Palotie A; McCarthy MI; Morris AP; Prokopenko I; Ripatti S
Article: BLOOD CANCER JOURNAL. 2015;5(5):e309
Novel drug candidates for blast phase chronic myeloid leukemia from high-throughput drug sensitivity and resistance testing.
Pietarinen PO; Pemovska T; Kontro M; Yadav B; Mpindi JP; Andersson EI; Majumder MM; Kuusanmäki H; Koskenvesa P; Kallioniemi O; Wennerberg K; Heckman CA; Mustjoki S; Porkka K
Article: NATURE. 2015;519(7541):102-105
Axitinib effectively inhibits BCR-ABL1(T315I) with a distinct binding conformation.
Pemovska T; Johnson E; Kontro M; Repasky GA; Chen J; Wells P; Cronin CN; McTigue M; Kallioniemi O; Porkka K; Murray BW; Wennerberg K
Article: NATURE BIOTECHNOLOGY. 2014;32(12):1213-1222
A community computational challenge to predict the activity of pairs of compounds.
Bansal M; Yang J; Karan C; Menden MP; Costello JC; Tang H; Xiao G; Li Y; Allen J; Zhong R; Chen B; Kim M; Wang T; Heiser LM; Realubit R; Mattioli M; Alvarez MJ; Shen Y; NCI-DREAM Community; Gallahan D; Singer D; Saez-Rodriguez J; Xie Y; Stolovitzky G; Califano A; NCI-DREAM Community
Article: NATURE BIOTECHNOLOGY. 2014;32(12):1202-1212
A community effort to assess and improve drug sensitivity prediction algorithms.
Costello JC; Heiser LM; Georgii E; Gönen M; Menden MP; Wang NJ; Bansal M; Ammad-ud-din M; Hintsanen P; Khan SA; Mpindi J-P; Kallioniemi O; Honkela A; Aittokallio T; Wennerberg K; NCI DREAM Community; Collins JJ; Gallahan D; Singer D; Saez-Rodriguez J; Kaski S; Gray JW; Stolovitzky G
Article: INTERNATIONAL JOURNAL OF CANCER. 2014;135(9):2077-2084
A novel transcript, VNN1-AB, as a biomarker for colorectal cancer.
Løvf M; Nome T; Bruun J; Eknaes M; Bakken AC; Mpindi JP; Kilpinen S; Rognum TO; Nesbakken A; Kallioniemi O; Lothe RA; Skotheim RI
Article: MICROBIOLOGY RESOURCE ANNOUNCEMENTS. 2014;2(5):e00841-e00814
Genetic Instability of Influenza pH1N1 Viruses.
Jalovaara P; Bychkov D; Ahtiainen L; Kallio-Kokko H; Valkonen M; Kantele A; Mattila P; Almusa H; Kallioniemi O; Kainov D
Article: JOURNAL OF CHEMICAL INFORMATION AND MODELING. 2014;54(8):2347-2359
Integrative and personalized QSAR analysis in cancer by kernelized Bayesian matrix factorization.
Ammad-ud-din M; Georgii E; Gönen M; Laitinen T; Kallioniemi O; Wennerberg K; Poso A; Kaski S
Article: ONCOGENE. 2014;33(27):3538-3549
Inhibition of the mitochondrial pyrimidine biosynthesis enzyme dihydroorotate dehydrogenase by doxorubicin and brequinar sensitizes cancer cells to TRAIL-induced apoptosis
He T; Haapa-Paananen S; Kaminskyy VO; Kohonen P; Fey V; Zhivotovsky B; Kallioniemi O; Perala M
Article: ANTIMICROBIAL AGENTS AND CHEMOTHERAPY. 2014;58(7):3689-3696
Akt inhibitor MK2206 prevents influenza pH1N1 virus infection in vitro.
Denisova OV; Söderholm S; Virtanen S; Von Schantz C; Bychkov D; Vashchinkina E; Desloovere J; Tynell J; Ikonen N; Theisen LL; Nyman TA; Matikainen S; Kallioniemi O; Julkunen I; Muller CP; Saelens X; Verkhusha VV; Kainov DE
Article: SCIENTIFIC REPORTS. 2014;4:5193
Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies.
Yadav B; Pemovska T; Szwajda A; Kulesskiy E; Kontro M; Karjalainen R; Majumder MM; Malani D; Murumägi A; Knowles J; Porkka K; Heckman C; Kallioniemi O; Wennerberg K; Aittokallio T
Article: MOLECULAR ONCOLOGY. 2014;8(1):93-104
High-throughput screens identify microRNAs essential for HER2 positive breast cancer cell growth.
Leivonen S-K; Sahlberg KK; Mäkelä R; Due EU; Kallioniemi O; Børresen-Dale A-L; Perälä M
Article: CELL DEATH AND DISEASE. 2014;5(1):e1043
Plasminogen activator urokinase expression reveals TRAIL responsiveness and supports fractional survival of cancer cells
Pavet V; Shlyakhtina Y; He T; Ceschin DG; Kohonen P; Perala M; Kallioniemi O; Gronemeyer H
Article: SCIENCE. 2014;343(6166):88-91
Break-Induced Replication Repair of Damaged Forks Induces Genomic Duplications in Human Cells
Costantino L; Sotiriou SK; Rantala JK; Magin S; Mladenov E; Helleday T; Haber JE; Iliakis G; Kallioniemi OP; Halazonetis TD
Article: PLOS ONE. 2014;9(6):e96767
Functional screening identifies miRNAs influencing apoptosis and proliferation in colorectal cancer.
Christensen LL; Holm A; Rantala J; Kallioniemi O; Rasmussen MH; Ostenfeld MS; Dagnaes-Hansen F; Øster B; Schepeler T; Tobiasen H; Thorsen K; Sieber OM; Gibbs P; Lamy P; Hansen TF; Jakobsen A; Riising EM; Helin K; Lubinski J; Hagemann-Madsen R; Laurberg S; Ørntoft TF; Andersen CL
Article: BLOOD CANCER JOURNAL. 2013;3(12):e168
Novel somatic mutations in large granular lymphocytic leukemia affecting the STAT-pathway and T-cell activation.
Andersson EI; Rajala HLM; Eldfors S; Ellonen P; Olson T; Jerez A; Clemente MJ; Kallioniemi O; Porkka K; Heckman C; Loughran TP; Maciejewski JP; Mustjoki S
Article: CANCER DISCOVERY. 2013;3(12):1416-1429
Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia.
Pemovska T; Kontro M; Yadav B; Edgren H; Eldfors S; Szwajda A; Almusa H; Bespalov MM; Ellonen P; Elonen E; Gjertsen BT; Karjalainen R; Kulesskiy E; Lagström S; Lehto A; Lepistö M; Lundán T; Majumder MM; Marti JML; Mattila P; Murumägi A; Mustjoki S; Palva A; Parsons A; Pirttinen T; Rämet ME; Suvela M; Turunen L; Västrik I; Wolf M; Knowles J; Aittokallio T; Heckman CA; Porkka K; Kallioniemi O; Wennerberg K
Article: ONCOGENE. 2013;32(41):4892-4902
Non-canonical Notch signaling activates IL-6/JAK/STAT signaling in breast tumor cells and is controlled by p53 and IKKα/IKKb
Jin S; Mutvei AP; Chivukula IV; Andersson ER; Ramskold D; Sandberg R; Lee KL; Kronqvist P; Mamaeva V; Ostling P; Mpindi J-P; Kallioniemi O; Screpanti I; Poellinger L; Sahlgren C; Lendahl U
Article: CARCINOGENESIS. 2013;34(9):2000-2009
Aneuploidy facilitates oncogenic transformation via specific genetic alterations, including Twist2 upregulation.
Högnäs G; Hämälistö S; Rilla K; Laine JO; Vilkki V; Murumägi A; Edgren H; Kallioniemi O; Ivaska J
Article: MOLECULAR ONCOLOGY. 2013;7(3):392-401
The HER2 amplicon includes several genes required for the growth and survival of HER2 positive breast cancer cells.
Sahlberg KK; Hongisto V; Edgren H; Mäkelä R; Hellström K; Due EU; Moen Vollan HK; Sahlberg N; Wolf M; Børresen-Dale A-L; Perälä M; Kallioniemi O
Article: BLOOD. 2013;121(22):4541-4550
Discovery of somatic STAT5b mutations in large granular lymphocytic leukemia.
Rajala HLM; Eldfors S; Kuusanmäki H; van Adrichem AJ; Olson T; Lagström S; Andersson EI; Jerez A; Clemente MJ; Yan Y; Zhang D; Awwad A; Ellonen P; Kallioniemi O; Wennerberg K; Porkka K; Maciejewski JP; Loughran TP; Heckman C; Mustjoki S
Article: ONCOTARGET. 2013;4(1):48-63
High-throughput RNAi screening for novel modulators of vimentin expression identifies MTHFD2 as a regulator of breast cancer cell migration and invasion.
Lehtinen L; Ketola K; Mäkelä R; Mpindi J-P; Viitala M; Kallioniemi O; Iljin K
Article: PLOS ONE. 2013;8(10):e77232
High-throughput 3D screening reveals differences in drug sensitivities between culture models of JIMT1 breast cancer cells.
Hongisto V; Jernström S; Fey V; Mpindi J-P; Kleivi Sahlberg K; Kallioniemi O; Perälä M
Article: PLOS ONE. 2013;8(9):e74293
Plasticity of blood- and lymphatic endothelial cells and marker identification.
Keuschnigg J; Karinen S; Auvinen K; Irjala H; Mpindi J-P; Kallioniemi O; Hautaniemi S; Jalkanen S; Salmi M
Article: PLOS ONE. 2013;8(8):e72040
ARLTS1 and prostate cancer risk--analysis of expression and regulation.
Siltanen S; Fischer D; Rantapero T; Laitinen V; Mpindi JP; Kallioniemi O; Wahlfors T; Schleutker J
Article: PLOS ONE. 2013;8(4):e60930
Functional Profiling of Precursor MicroRNAs Identifies MicroRNAs Essential for Glioma Proliferation
Haapa-Paananen S; Chen P; Hellstrom K; Kohonen P; Hautaniemi S; Kallioniemi O; Perala M
Article: ONCOGENE. 2012;31(39):4266-4278
CIP2A signature reveals the MYC dependency of CIP2A-regulated phenotypes and its clinical association with breast cancer subtypes.
Niemelä M; Kauko O; Sihto H; Mpindi J-P; Nicorici D; Pernilä P; Kallioniemi O-P; Joensuu H; Hautaniemi S; Westermarck J
Article: MOLECULAR AND CELLULAR BIOLOGY. 2012;32(17):3513-3526
c-Jun N-terminal kinase phosphorylation of MARCKSL1 determines actin stability and migration in neurons and in cancer cells.
Björkblom B; Padzik A; Mohammad H; Westerlund N; Komulainen E; Hollos P; Parviainen L; Papageorgiou AC; Iljin K; Kallioniemi O; Kallajoki M; Courtney MJ; Mågård M; James P; Coffey ET
Article: NEOPLASIA: AN INTERNATIONAL JOURNAL FOR ONCOLOGY RESEARCH. 2012;14(9):868-879
MiR-9, -31, and -182 deregulation promote proliferation and tumor cell survival in colon cancer.
Cekaite L; Rantala JK; Bruun J; Guriby M; Agesen TH; Danielsen SA; Lind GE; Nesbakken A; Kallioniemi O; Lothe RA; Skotheim RI
Article: ONCOGENE. 2012;31(31):3597-3606
Cytokinesis failure due to derailed integrin traffic induces aneuploidy and oncogenic transformation in vitro and in vivo.
Högnäs G; Tuomi S; Veltel S; Mattila E; Murumägi A; Edgren H; Kallioniemi O; Ivaska J
Article: BREAST CANCER RESEARCH. 2012;14(4):R113
The gene expression landscape of breast cancer is shaped by tumor protein p53 status and epithelial-mesenchymal transition.
Fredlund E; Staaf J; Rantala JK; Kallioniemi O; Borg A; Ringnér M
Article: ONCOGENE. 2012;31(29):3444-3456
Systematic knockdown of epigenetic enzymes identifies a novel histone demethylase PHF8 overexpressed in prostate cancer with an impact on cell proliferation, migration and invasion
Bjorkman M; Ostling P; Harma V; Virtanen J; Mpindi J-P; Rantala J; Mirtti T; Vesterinen T; Lundin M; Sankila A; Rannikko A; Kaivanto E; Kohonen P; Kallioniemi O; Nees M
Article: BMC BIOINFORMATICS. 2012;13:112
Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs.
Khan SA; Faisal A; Mpindi JP; Parkkinen JA; Kalliokoski T; Poso A; Kallioniemi OP; Wennerberg K; Kaski S
Article: NEW ENGLAND JOURNAL OF MEDICINE. 2012;366(20):1905-1913
Somatic STAT3 mutations in large granular lymphocytic leukemia.
Koskela HLM; Eldfors S; Ellonen P; van Adrichem AJ; Kuusanmäki H; Andersson EI; Lagström S; Clemente MJ; Olson T; Jalkanen SE; Majumder MM; Almusa H; Edgren H; Lepistö M; Mattila P; Guinta K; Koistinen P; Kuittinen T; Penttinen K; Parsons A; Knowles J; Saarela J; Wennerberg K; Kallioniemi O; Porkka K; Loughran TP; Heckman CA; Maciejewski JP; Mustjoki S
Article: PROSTATE. 2012;72(7):789-802
Integrative genomic, transcriptomic, and RNAi analysis indicates a potential oncogenic role for FAM110B in castration-resistant prostate cancer
Vainio P; Wolf M; Edgren H; He T; Kohonen P; Mpindi J-P; Smit F; Verhaegh G; Schalken J; Perala M; Iljin K; Kallioniemi O
Article: MOLECULAR CANCER RESEARCH. 2012;10(5):597-604
Heparin-like polysaccharides reduce osteolytic bone destruction and tumor growth in a mouse model of breast cancer bone metastasis.
Pollari S; Käkönen RS; Mohammad KS; Rissanen JP; Halleen JM; Wärri A; Nissinen L; Pihlavisto M; Marjamäki A; Perälä M; Guise TA; Kallioniemi O; Käkönen S-M
Article: ONCOGENE. 2012;31(16):2090-2100
An integrated genomic approach identifies ARID1A as a candidate tumor-suppressor gene in breast cancer.
Mamo A; Cavallone L; Tuzmen S; Chabot C; Ferrario C; Hassan S; Edgren H; Kallioniemi O; Aleynikova O; Przybytkowski E; Malcolm K; Mousses S; Tonin PN; Basik M
Article: ONCOGENE. 2012;31(16):2075-2089
Lysophosphatidic acid and sphingosine-1-phosphate promote morphogenesis and block invasion of prostate cancer cells in three-dimensional organotypic models
Harma V; Knuuttila M; Virtanen J; Mirtti T; Kohonen P; Kovanen P; Happonen A; Kaewphan S; Ahonen I; Kallioniemi O; Grafstrom R; Lotjonen J; Nees M
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 2012;287(13):9659-9671
Interaction with ErbB4 promotes hypoxia-inducible factor-1α signaling.
Paatero I; Jokilammi A; Heikkinen PT; Iljin K; Kallioniemi O-P; Jones FE; Jaakkola PM; Elenius K
Article: ONCOGENE. 2012;31(10):1299-1310
HES6 gene is selectively overexpressed in glioma and represents an important transcriptional regulator of glioma proliferation
Haapa-Paananen S; Kiviluoto S; Waltari M; Puputti M; Mpindi JP; Kohonen P; Tynninen O; Haapasalo H; Joensuu H; Perala M; Kallioniemi O
Article: JOURNAL OF PATHOLOGY. 2012;226(4):674-686
15-Hydroxyprostaglandin dehydrogenase associates with poor prognosis in breast cancer, induces epithelial-mesenchymal transition, and promotes cell migration in cultured breast cancer cells.
Lehtinen L; Vainio P; Wikman H; Reemts J; Hilvo M; Issa R; Pollari S; Brandt B; Oresic M; Pantel K; Kallioniemi O; Iljin K
Article: JOURNAL OF PROTEOME RESEARCH. 2012;11(2):850-860
Integration of metabolomics and expression of glycerol-3-phosphate acyltransferase (GPAM) in breast cancer-link to patient survival, hormone receptor status, and metabolic profiling.
Brockmöller SF; Bucher E; Müller BM; Budczies J; Hilvo M; Griffin JL; Orešič M; Kallioniemi O; Iljin K; Loibl S; Darb-Esfahani S; Sinn BV; Klauschen F; Prinzler J; Bangemann N; Ismaeel F; Fiehn O; Dietel M; Denkert C
Article: JOURNAL OF CELL SCIENCE. 2012;125(Pt 3):649-661
A functional genetic screen reveals new regulators of β1-integrin activity.
Pellinen T; Rantala JK; Arjonen A; Mpindi J-P; Kallioniemi O; Ivaska J
Article: BRITISH JOURNAL OF CANCER. 2012;106(1):99-106
Salinomycin inhibits prostate cancer growth and migration via induction of oxidative stress.
Ketola K; Hilvo M; Hyötyläinen T; Vuoristo A; Ruskeepää A-L; Orešič M; Kallioniemi O; Iljin K
Article: PLOS ONE. 2012;7(6):e39801
High-throughput transcriptomic and RNAi analysis identifies AIM1, ERGIC1, TMED3 and TPX2 as potential drug targets in prostate cancer.
Vainio P; Mpindi J-P; Kohonen P; Fey V; Mirtti T; Alanen KA; Perälä M; Kallioniemi O; Iljin K
Article: PLOS ONE. 2012;7(12):e50819
Systemic analysis of gene expression profiles identifies ErbB3 as a potential drug target in pediatric alveolar rhabdomyosarcoma.
Nordberg J; Mpindi JP; Iljin K; Pulliainen AT; Kallajoki M; Kallioniemi O; Elenius K; Elenius V
Article: PLOS ONE. 2012;7(12):e51470
Chemical biology drug sensitivity screen identifies sunitinib as synergistic agent with disulfiram in prostate cancer cells.
Ketola K; Kallioniemi O; Iljin K
Article: PLOS ONE. 2012;7(10):e48745
Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms.
Kangaspeska S; Hultsch S; Edgren H; Nicorici D; Murumägi A; Kallioniemi O
Article: PLOS ONE. 2012;7(5):e37361
Identification of microRNAs inhibiting TGF-β-induced IL-11 production in bone metastatic breast cancer cells.
Pollari S; Leivonen S-K; Perälä M; Fey V; Käkönen S-M; Kallioniemi O
Article: ONCOTARGET. 2011;2(12):1176-1190
Phospholipase PLA2G7, associated with aggressive prostate cancer, promotes prostate cancer cell migration and invasion and is inhibited by statins
Vainio P; Lehtinen L; Mirtti T; Hilvo M; Seppanen-Laakso T; Virtanen J; Sankila A; Nordling S; Lundin J; Rannikko A; Oresic M; Kallioniemi O; Iljin K
Article: GENOME MEDICINE. 2011;3(9):63
Classification of unknown primary tumors with a data-driven method based on a large microarray reference database.
Ojala KA; Kilpinen SK; Kallioniemi OP
Article: NATURE CELL BIOLOGY. 2011;13(11):1315-1324
SHARPIN is an endogenous inhibitor of β1-integrin activation.
Rantala JK; Pouwels J; Pellinen T; Veltel S; Laasola P; Mattila E; Potter CS; Duffy T; Sundberg JP; Kallioniemi O; Askari JA; Humphries MJ; Parsons M; Salmi M; Ivaska J
Article: EMBO JOURNAL. 2011;30(19):3962-3976
Dual role of FoxA1 in androgen receptor binding to chromatin, androgen signalling and prostate cancer
Sahu B; Laakso M; Ovaska K; Mirtti T; Lundin J; Rannikko A; Sankila A; Turunen J-P; Lundin M; Konsti J; Vesterinen T; Nordling S; Kallioniemi O; Hautaniemi S; Janne OA
Article: AMERICAN JOURNAL OF SURGICAL PATHOLOGY. 2011;35(7):937-948
SATB2 in Combination With Cytokeratin 20 Identifies Over 95% of all Colorectal Carcinomas
Magnusson K; de Wit M; Brennan DJ; Johnson LB; Mcgee SF; Lundberg E; Naicker K; Klinger R; Kampf C; Asplund A; Wester K; Gry M; Bjartell A; Gallagher WM; Rexhepaj E; Kilpinen S; Kallioniemi O-P; Belt E; Goos J; Meijer G; Birgisson H; Glimelius B; Borrebaeck CAK; Navani S; Uhlen M; O'Connor DP; Jirstrom K; Ponten F
Article: GENES CHROMOSOMES AND CANCER. 2011;50(7):499-509
The miR-15a-miR-16-1 locus is homozygously deleted in a subset of prostate cancers.
Porkka KP; Ogg E-L; Saramäki OR; Vessella RL; Pukkila H; Lähdesmäki H; van Weerden WM; Wolf M; Kallioniemi OP; Jenster G; Visakorpi T
Article: MOLECULAR & CELLULAR PROTEOMICS. 2011;10(7):M110.005322
Identification of miR-193b Targets in Breast Cancer Cells and Systems Biological Analysis of Their Functional Impact
Leivonen S-K; Rokka A; Ostling P; Kohonen P; Corthals GL; Kallioniemi O; Perala M
Article: CANCER RESEARCH. 2011;71(9):3236-3245
Novel theranostic opportunities offered by characterization of altered membrane lipid metabolism in breast cancer progression.
Hilvo M; Denkert C; Lehtinen L; Müller B; Brockmöller S; Seppänen-Laakso T; Budczies J; Bucher E; Yetukuri L; Castillo S; Berg E; Nygren H; Sysi-Aho M; Griffin JL; Fiehn O; Loibl S; Richter-Ehrenstein C; Radke C; Hyötyläinen T; Kallioniemi O; Iljin K; Oresic M
Article: PROSTATE. 2011;71(6):604-614
Androgen Regulation of micro-RNAs in Prostate Cancer
Waltering KK; Porkka KP; Jalava SE; Urbanucci A; Kohonen PJ; Latonen LM; Kallioniemi OP; Jenster G; Visakorpi T
Article: BIODATA MINING. 2011;4:5
Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data.
Kilpinen SK; Ojala KA; Kallioniemi OP
Article: BMC GENOMICS. 2011;12:162
A cell spot microarray method for production of high density siRNA transfection microarrays.
Rantala JK; Mäkelä R; Aaltola A-R; Laasola P; Mpindi J-P; Nees M; Saviranta P; Kallioniemi O
Article: CANCER RESEARCH. 2011;71(5):1956-1967
Systematic Analysis of MicroRNAs Targeting the Androgen Receptor in Prostate Cancer Cells
Ostling P; Leivonen S-K; Aakula A; Kohonen P; Makela R; Hagman Z; Edsjo A; Kangaspeska S; Edgren H; Nicorici D; Bjartell A; Ceder Y; Perala M; Kallioniemi O
Article: PLOS ONE. 2011;6(2):e16915
miRNA-mRNA integrated analysis reveals roles for miRNAs in primary breast tumors.
Enerly E; Steinfeld I; Kleivi K; Leivonen S-K; Aure MR; Russnes HG; Rønneberg JA; Johnsen H; Navon R; Rødland E; Mäkelä R; Naume B; Perälä M; Kallioniemi O; Kristensen VN; Yakhini Z; Børresen-Dale A-L
Article: PLOS ONE. 2011;6(2):e17259
GTI: A Novel Algorithm for Identifying Outlier Gene Expression Profiles from Integrated Microarray Datasets
Mpindi JP; Sara H; Haapa-Paananen S; Kilpinen S; Pisto T; Bucher E; Ojala K; Iljin K; Vainio P; Bjorkman M; Gupta S; Kohonen P; Nees M; Kallioniemi O
Article: AMERICAN JOURNAL OF PATHOLOGY. 2011;178(2):525-536
Arachidonic Acid Pathway Members PLA2G7, HPGD, EPHX2, and CYP4F8 Identified as Putative Novel Therapeutic Targets in Prostate Cancer
Vainio P; Gupta S; Ketola K; Mirtti T; Mpindi J-P; Kohonen P; Fey V; Perala M; Smit F; Verhaegh G; Schalken J; Alanen KA; Kallioniemi O; Iljin K
Article: PLOS ONE. 2011;6(10):e26595
Contribution of ARLTS1 Cys148Arg (T442C) variant with prostate cancer risk and ARLTS1 function in prostate cancer cells.
Siltanen S; Wahlfors T; Schindler M; Saramäki OR; Mpindi JP; Latonen L; Vessella RL; Tammela TLJ; Kallioniemi O; Visakorpi T; Schleutker J
Article: GENOME BIOLOGY. 2011;12(1):R6
Identification of fusion genes in breast cancer by paired-end RNA-sequencing.
Edgren H; Murumagi A; Kangaspeska S; Nicorici D; Hongisto V; Kleivi K; Rye IH; Nyberg S; Wolf M; Borresen-Dale A-L; Kallioniemi O
Article: BREAST CANCER RESEARCH AND TREATMENT. 2011;125(2):421-430
Enhanced serine production by bone metastatic breast cancer cells stimulates osteoclastogenesis
Pollari S; Kakonen S-M; Edgren H; Wolf M; Kohonen P; Sara H; Guise T; Nees M; Kallioniemi O
Article: PLOS ONE. 2010;5(12):e15068
Analysis of kinase gene expression patterns across 5681 human tissue samples reveals functional genomic taxonomy of the kinome.
Kilpinen S; Ojala K; Kallioniemi O
Article: MOLECULAR CANCER THERAPEUTICS. 2010;9(12):3175-3185
Monensin is a potent inducer of oxidative stress and inhibitor of androgen signaling leading to apoptosis in prostate cancer cells.
Ketola K; Vainio P; Fey V; Kallioniemi O; Iljin K
Article: GENES CHROMOSOMES AND CANCER. 2010;49(11):1062-1069
Use of cancer-specific genomic rearrangements to quantify disease burden in plasma from patients with solid tumors.
McBride DJ; Orpana AK; Sotiriou C; Joensuu H; Stephens PJ; Mudie LJ; Hämäläinen E; Stebbings LA; Andersson LC; Flanagan AM; Durbecq V; Ignatiadis M; Kallioniemi O; Heckman CA; Alitalo K; Edgren H; Futreal PA; Stratton MR; Campbell PJ
Article: NEOPLASIA: AN INTERNATIONAL JOURNAL FOR ONCOLOGY RESEARCH. 2010;12(11):877-888
Integrative functional genomics analysis of sustained polyploidy phenotypes in breast cancer cells identifies an oncogenic profile for GINS2.
Rantala JK; Edgren H; Lehtinen L; Wolf M; Kleivi K; Vollan HKM; Aaltola A-R; Laasola P; Kilpinen S; Saviranta P; Iljin K; Kallioniemi O
Article: CANCER RESEARCH. 2010;70(20):7851-7861
Fibroblast Growth Factor Receptor 4 Regulates Tumor Invasion by Coupling Fibroblast Growth Factor Signaling to Extracellular Matrix Degradation
Sugiyama N; Varjosalo M; Meller P; Lohi J; Hyytiainen M; Kilpinen S; Kallioniemi O; Ingvarsen S; Engelholm LH; Taipale J; Alitalo K; Keski-Oja J; Lehti K
Article: EPIGENOMICS. 2010;2(5):683-689
Epigenetics of prostate cancer and the prospect of identification of novel drug targets by RNAi screening of epigenetic enzymes.
Björkman M; Rantala J; Nees M; Kallioniemi O
Article: CANCER RESEARCH. 2010;70(17):6735-6745
FZD4 as a mediator of ERG oncogene-induced WNT signaling and epithelial-to-mesenchymal transition in human prostate cancer cells.
Gupta S; Iljin K; Sara H; Mpindi JP; Mirtti T; Vainio P; Rantala J; Alanen K; Nees M; Kallioniemi O
Article: EXPERIMENTAL CELL RESEARCH. 2010;316(9):1610-1624
Interactions between Notch- and hypoxia-induced transcriptomes in embryonic stem cells
Main H; Lee KL; Yang H; Haapa-Paananen S; Edgren H; Jin S; Sahlgren C; Kallioniemi O; Poellinger L; Lim B; Lendahl U
Article: PLOS ONE. 2010;5(5):e10431
A Comprehensive Panel of Three-Dimensional Models for Studies of Prostate Cancer Growth, Invasion and Drug Responses
Harma V; Virtanen J; Makela R; Happonen A; Mpindi J-P; Knuuttila M; Kohonen P; Lotjonen J; Kallioniemi O; Nees M
Article: NATURE. 2010;464(7291):993-998
International network of cancer genome projects
Hudson TJ; Anderson W; Aretz A; Barker AD; Bell C; Bernabe RR; Bhan MK; Calvo F; Eerola I; Gerhard DS; Guttmacher A; Guyer M; Hemsley FM; Jennings JL; Kerr D; Klatt P; Kolar P; Kusuda J; Lane DP; Laplace F; Lu Y; Nettekoven G; Ozenberger B; Peterson J; Rao TS; Remacle J; Schafer AJ; Shibata T; Stratton MR; Vockley JG; Watanabe K; Yang H; Yuen MMF; Knoppers M; Bobrow M; Cambon-Thomsen A; Dressler LG; Dyke SOM; Joly Y; Kato K; Kennedy KL; Nicolas P; Parker MJ; Rial-Sebbag E; Romeo-Casabona CM; Shaw KM; Wallace S; Wiesner GL; Zeps N; Lichter P; Biankin AV; Chabannon C; Chin L; Clement B; de Alava E; Degos F; Ferguson ML; Geary P; Hayes DN; Johns AL; Nakagawa H; Penny R; Piris MA; Sarin R; Scarpa A; van de Vijver M; Futreal PA; Aburatani H; Bayes M; Bowtell DDL; Campbell PJ; Estivill X; Grimmond SM; Gut I; Hirst M; Lopez-Otin C; Majumder P; Marra M; Ning Z; Puente XS; Ruan Y; Stunnenberg HG; Swerdlow H; Velculescu VE; Wilson RK; Xue HH; Yang L; Spellman PT; Bader GD; Boutros PC; Flicek P; Getz G; Guigo R; Guo G; Haussler D; Heath S; Hubbard TJ; Jiang T; Jones SM; Li Q; Lopez-Bigas N; Luo R; Pearson JV; Quesada V; Raphael BJ; Sander C; Speed TP; Stuart JM; Teague JW; Totoki Y; Tsunoda T; Valencia A; Wheeler DA; Wu H; Zhao S; Zhou G; Stein LD; Lathrop M; Ouellette BFF; Thomas G; Yoshida T; Axton M; Gunter C; McPherson JD; Miller LJ; Kasprzyk A; Zhang J; Haider SA; Wang J; Yung CK; Cross A; Liang Y; Gnaneshan S; Guberman J; Hsu J; Chalmers DRC; Hasel KW; Kaan TSH; Knoppers BM; Lowrance WW; Masui T; Rodriguez LL; Vergely C; Cloonan N; Defazio A; Eshleman JR; Etemadmoghadam D; Gardiner BA; Kench JG; Sutherland RL; Tempero MA; Waddell NJ; Wilson PJ; Gallinger S; Tsao M-S; Shaw PA; Petersen GM; Mukhopadhyay D; DePinho RA; Thayer S; Muthuswamy L; Shazand K; Beck T; Sam M; Timms L; Ballin V; Ji J; Zhang X; Chen F; Hu X; Yang Q; Tian G; Zhang L; Xing X; Li X; Zhu Z; Yu Y; Yu J; Tost J; Brennan P; Holcatova I; Zaridze D; Brazma A; Egevad L; Prokhortchouk E; Banks RE; Uhlen M; Viksna J; Ponten F; Skryabin K; Birney E; Borg A; Borresen-Dale A-L; Caldas C; Foekens JA; Martin S; Reis-Filho JS; Richardson AL; Sotiriou C; van't Veer L; Birnbaum D; Blanche H; Boucher P; Boyault S; Masson-Jacquemier JD; Pauporte I; Pivot X; Vincent-Salomon A; Tabone E; Theillet C; Treilleux I; Bioulac-Sage P; Decaens T; Franco D; Gut M; Samuel D; Zucman-Rossi J; Eils R; Brors B; Korbel JO; Korshunov A; Landgraf P; Lehrach H; Pfister S; Radlwimmer B; Reifenberger G; Taylor MD; von Kalle C; Majumder PP; Pederzoli P; Lawlor RT; Delledonne M; Bardelli A; Gress T; Klimstra D; Zamboni G; Nakamura Y; Miyano S; Fujimoto A; Campo E; de Sanjose S; Montserrat E; Gonzalez-Diaz M; Jares P; Himmelbaue H; Bea S; Aparicio S; Easton DF; Collins FS; Compton CC; Lander ES; Burke W; Green AR; Hamilton SR; Kallioniemi OP; Ley TJ; Liu ET; Wainwright BJ
Article: ONCOGENE. 2009;28(44):3926-3936
Protein lysate microarray analysis to identify microRNAs regulating estrogen receptor signaling in breast cancer cell lines
Leivonen S-K; Makela R; Ostling P; Kohonen P; Haapa-Paananen S; Kleivi K; Enerly E; Aakula A; Hellstrom K; Sahlberg N; Kristensen VN; Borresen-Dale A-L; Saviranta P; Perala M; Kallioniemi O
Article: CLINICAL CANCER RESEARCH. 2009;15(21):6570-6581
Mammary-derived growth inhibitor alters traffic of EGFR and induces a novel form of cetuximab resistance.
Nevo J; Mattila E; Pellinen T; Yamamoto DL; Sara H; Iljin K; Kallioniemi O; Bono P; Heikkilä P; Joensuu H; Wärri A; Ivaska J
Article: JOURNAL OF CHEMICAL INFORMATION AND MODELING. 2009;49(10):2168-2178
Critical comparison of virtual screening methods against the MUV data set.
Tiikkainen P; Markt P; Wolber G; Kirchmair J; Distinto S; Poso A; Kallioniemi O
Article: CLINICAL CANCER RESEARCH. 2009;15(19):6070-6078
High-Throughput Cell-Based Screening of 4910 Known Drugs and Drug-like Small Molecules Identifies Disulfiram as an Inhibitor of Prostate Cancer Cell Growth
Iljin K; Ketola K; Vainio P; Halonen P; Kohonen P; Fey V; Grafstrom RC; Perala M; Kallioniemi O
Article: CLINICAL CANCER RESEARCH. 2009;15(16):5092-5100
CIP2A is associated with human breast cancer aggressivity.
Côme C; Laine A; Chanrion M; Edgren H; Mattila E; Liu X; Jonkers J; Ivaska J; Isola J; Darbon J-M; Kallioniemi O; Thézenas S; Westermarck J
Article: CARCINOGENESIS. 2009;30(6):1032-1040
Dietary flavonoid fisetin induces a forced exit from mitosis by targeting the mitotic spindle checkpoint.
Salmela A-L; Pouwels J; Varis A; Kukkonen AM; Toivonen P; Halonen PK; Perälä M; Kallioniemi O; Gorbsky GJ; Kallio MJ
Article: BMC MEDICAL GENOMICS. 2009;2:26
Data integration from two microarray platforms identifies bi-allelic genetic inactivation of RIC8A in a breast cancer cell line.
Muggerud AA; Edgren H; Wolf M; Kleivi K; Dejeux E; Tost J; Sørlie T; Kallioniemi O
Article: EUROPEAN JOURNAL OF CANCER. 2009;45(8):1510-1517
The transcription factor Sox11 is a prognostic factor for improved recurrence-free survival in epithelial ovarian cancer.
Brennan DJ; Ek S; Doyle E; Drew T; Foley M; Flannelly G; O'Connor DP; Gallagher WM; Kilpinen S; Kallioniemi O-P; Jirstrom K; O'Herlihy C; Borrebaeck CAK
Article: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN. 2009;23(4):227-239
Comparison of structure fingerprint and molecular interaction field based methods in explaining biological similarity of small molecules in cell-based screens.
Tiikkainen P; Poso A; Kallioniemi O
Article: INTERNATIONAL JOURNAL OF CANCER. 2008;123(12):2774-2781
Defining the molecular action of HDAC inhibitors and synergism with androgen deprivation in ERG-positive prostate cancer.
Björkman M; Iljin K; Halonen P; Sara H; Kaivanto E; Nees M; Kallioniemi OP
Article: DEVELOPMENTAL CELL. 2008;15(3):371-385
Integrin trafficking regulated by Rab21 is necessary for cytokinesis.
Pellinen T; Tuomi S; Arjonen A; Wolf M; Edgren H; Meyer H; Grosse R; Kitzing T; Rantala JK; Kallioniemi O; Fässler R; Kallio M; Ivaska J
Article: INTERNATIONAL JOURNAL OF CANCER. 2008;123(2):330-339
Functional evidence implicating S100P in prostate cancer progression.
Basu GD; Azorsa DO; Kiefer JA; Rojas AM; Tuzmen S; Barrett MT; Trent JM; Kallioniemi O; Mousses S
Article: JOURNAL OF MAMMARY GLAND BIOLOGY AND NEOPLASIA. 2008;13(2):259-268
Role of ErbB4 in breast cancer.
Sundvall M; Iljin K; Kilpinen S; Sara H; Kallioniemi O-P; Elenius K
Article: CELL. 2008;133(3):537-548
Application of active and kinase-deficient kinome collection for identification of kinases regulating hedgehog signaling.
Varjosalo M; Björklund M; Cheng F; Syvänen H; Kivioja T; Kilpinen S; Sun Z; Kallioniemi O; Stunnenberg HG; He W-W; Ojala P; Taipale J
Article: BRITISH JOURNAL OF CANCER. 2008;98(8):1457-1466
The BOADICEA model of genetic susceptibility to breast and ovarian cancers: updates and extensions.
Antoniou AC; Cunningham AP; Peto J; Evans DG; Lalloo F; Narod SA; Risch HA; Eyfjord JE; Hopper JL; Southey MC; Olsson H; Johannsson O; Borg A; Pasini B; Radice P; Manoukian S; Eccles DM; Tang N; Olah E; Anton-Culver H; Warner E; Lubinski J; Gronwald J; Gorski B; Tryggvadottir L; Syrjakoski K; Kallioniemi O-P; Eerola H; Nevanlinna H; Pharoah PDP; Easton DF
Article: GENOME BIOLOGY. 2008;9(9):R139
Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues.
Kilpinen S; Autio R; Ojala K; Iljin K; Bucher E; Sara H; Pisto T; Saarela M; Skotheim RI; Björkman M; Mpindi J-P; Haapa-Paananen S; Vainio P; Edgren H; Wolf M; Astola J; Nees M; Hautaniemi S; Kallioniemi O
Article: ONCOGENE. 2007;26(26):3846-3856
Claudin-1 overexpression in melanoma is regulated by PKC and contributes to melanoma cell motility.
Leotlela PD; Wade MS; Duray PH; Rhode MJ; Brown HF; Rosenthal DT; Dissanayake SK; Earley R; Indig FE; Nickoloff BJ; Taub DD; Kallioniemi OP; Meltzer P; Morin PJ; Weeraratna AT
Article: CARCINOGENESIS. 2007;28(5):1040-1045
Evaluation of the role of Finnish ataxia-telangiectasia mutations in hereditary predisposition to breast cancer
Pylkas K; Tommiska J; Syrjakoski K; Kere J; Gatei M; Waddell N; Allinen M; Karppinen S-M; Rapakko K; Kaariainen H; Aittomaki K; Blomqvist C; Mustonen A; Holli K; Khanna KK; Kallioniemi O-P; Nevanlinna H; Winqvist R
Article: BMC GENOMICS. 2007;8:84
A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH.
Wicker N; Carles A; Mills IG; Wolf M; Veerakumarasivam A; Edgren H; Boileau F; Wasylyk B; Schalken JA; Neal DE; Kallioniemi O; Poch O
Article: NATURE METHODS. 2007;4(1):13-17
ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome.
Taussig MJ; Stoevesandt O; Borrebaeck CAK; Bradbury AR; Cahill D; Cambillau C; de Daruvar A; Dübel S; Eichler J; Frank R; Gibson TJ; Gloriam D; Gold L; Herberg FW; Hermjakob H; Hoheisel JD; Joos TO; Kallioniemi O; Koegl M; Konthur Z; Korn B; Kremmer E; Krobitsch S; Landegren U; van der Maarel S; McCafferty J; Muyldermans S; Nygren P-A; Palcy S; Plückthun A; Polic B; Przybylski M; Saviranta P; Sawyer A; Sherman DJ; Skerra A; Templin M; Ueffing M; Uhlén M
Article: ONCOGENE. 2006;25(52):6997-7008
Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses.
Järvinen A-K; Autio R; Haapa-Paananen S; Wolf M; Saarela M; Grénman R; Leivo I; Kallioniemi O; Mäkitie AA; Monni O
Article: CANCER RESEARCH. 2006;66(21):10242-10246
TMPRSS2 fusions with oncogenic ETS factors in prostate cancer involve unbalanced genomic rearrangements and are associated with HDAC1 and epigenetic reprogramming.
Iljin K; Wolf M; Edgren H; Gupta S; Kilpinen S; Skotheim RI; Peltola M; Smit F; Verhaegh G; Schalken J; Nees M; Kallioniemi O
Article: EUROPEAN JOURNAL OF HUMAN GENETICS. 2006;14(2):167-172
BARD1 variants Cys557Ser and Val507Met in breast cancer predisposition.
Vahteristo P; Syrjäkoski K; Heikkinen T; Eerola H; Aittomäki K; von Smitten K; Holli K; Blomqvist C; Kallioniemi O-P; Nevanlinna H
Article: CANCER RESEARCH. 2006;66(2):743-747
Profiling genetic variation along the androgen biosynthesis and metabolism pathways implicates several single nucleotide polymorphisms and their combinations as prostate cancer risk factors.
Mononen N; Seppälä EH; Duggal P; Autio V; Ikonen T; Ellonen P; Saharinen J; Saarela J; Vihinen M; Tammela TLJ; Kallioniemi O; Bailey-Wilson JE; Schleutker J
Article: CELLULAR ONCOLOGY (DORDRECHT). 2006;28(5-6):315-326
Novel genomic aberrations in testicular germ cell tumors by array-CGH, and associated gene expression changes.
Skotheim RI; Autio R; Lind GE; Kraggerud SM; Andrews PW; Monni O; Kallioniemi O; Lothe RA
Article: CLINICAL CANCER RESEARCH. 2005;11(18):6450-6458
EphB2 expression across 138 human tumor types in a tissue microarray: high levels of expression in gastrointestinal cancers.
Lugli A; Spichtin H; Maurer R; Mirlacher M; Kiefer J; Huusko P; Azorsa D; Terracciano L; Sauter G; Kallioniemi O-P; Mousses S; Tornillo L
Article: HUMAN GENETICS. 2005;117(4):307-316
A major locus for hereditary prostate cancer in Finland: localization by linkage disequilibrium of a haplotype in the HPCX region.
Baffoe-Bonnie AB; Smith JR; Stephan DA; Schleutker J; Carpten JD; Kainu T; Gillanders EM; Matikainen M; Teslovich TM; Tammela T; Sood R; Balshem AM; Scarborough SD; Xu J; Isaacs WB; Trent JM; Kallioniemi O-P; Bailey-Wilson JE
Article: JOURNAL OF MEDICAL GENETICS. 2005;42(7):602-603
Breast and ovarian cancer risks to carriers of the BRCA1 5382insC and 185delAG and BRCA2 6174delT mutations: a combined analysis of 22 population based studies.
Antoniou AC; Pharoah PDP; Narod S; Risch HA; Eyfjord JE; Hopper JL; Olsson H; Johannsson O; Borg A; Pasini B; Radice P; Manoukian S; Eccles DM; Tang N; Olah E; Anton-Culver H; Warner E; Lubinski J; Gronwald J; Gorski B; Tulinius H; Thorlacius S; Eerola H; Nevanlinna H; Syrjäkoski K; Kallioniemi O-P; Thompson D; Evans C; Peto J; Lalloo F; Evans DG; Easton DF
Article: INTERNATIONAL JOURNAL OF CANCER. 2005;113(4):575-580
Correlation of CHEK2 protein expression and c.1100delC mutation status with tumor characteristics among unselected breast cancer patients.
Kilpivaara O; Bartkova J; Eerola H; Syrjäkoski K; Vahteristo P; Lukas J; Blomqvist C; Holli K; Heikkilä P; Sauter G; Kallioniemi O-P; Bartek J; Nevanlinna H
Article: HUMAN GENETICS. 2005;116(1-2):43-50
Hereditary prostate cancer in Finland: fine-mapping validates 3p26 as a major predisposition locus.
Rökman A; Baffoe-Bonnie AB; Gillanders E; Fredriksson H; Autio V; Ikonen T; Gibbs KD; Jones M; Gildea D; Freas-Lutz D; Markey C; Matikainen MP; Koivisto PA; Tammela TLJ; Kallioniemi OP; Trent J; Bailey-Wilson JE; Schleutker J
Article: INTERNATIONAL JOURNAL OF CANCER. 2004;111(4):543-547
CHEK2 variant I157T may be associated with increased breast cancer risk.
Kilpivaara O; Vahteristo P; Falck J; Syrjäkoski K; Eerola H; Easton D; Bartkova J; Lukas J; Heikkilä P; Aittomäki K; Holli K; Blomqvist C; Kallioniemi O-P; Bartek J; Nevanlinna H
Article: NATURE GENETICS. 2004;36(9):979-983
Nonsense-mediated decay microarray analysis identifies mutations of EPHB2 in human prostate cancer.
Huusko P; Ponciano-Jackson D; Wolf M; Kiefer JA; Azorsa DO; Tuzmen S; Weaver D; Robbins C; Moses T; Allinen M; Hautaniemi S; Chen Y; Elkahloun A; Basik M; Bova GS; Bubendorf L; Lugli A; Sauter G; Schleutker J; Ozcelik H; Elowe S; Pawson T; Trent JM; Carpten JD; Kallioniemi O-P; Mousses S
Article: NEOPLASIA: AN INTERNATIONAL JOURNAL FOR ONCOLOGY RESEARCH. 2004;6(5):541-545
BRCA2 mutations in 154 finnish male breast cancer patients.
Syrjäkoski K; Kuukasjärvi T; Waltering K; Haraldsson K; Auvinen A; Borg A; Kainu T; Kallioniemi O-P; Koivisto PA
Article: GENOMICS. 2004;83(6):1164-1168
Are data from different gene expression microarray platforms comparable?
Järvinen A-K; Hautaniemi S; Edgren H; Auvinen P; Saarela J; Kallioniemi O-P; Monni O
Article: AMERICAN JOURNAL OF HUMAN GENETICS. 2004;74(6):1175-1182
CHEK2*1100delC and susceptibility to breast cancer: a collaborative analysis involving 10,860 breast cancer cases and 9,065 controls from 10 studies.
CHEK2 Breast Cancer Case-Control Consortium
Article: NEOPLASIA: AN INTERNATIONAL JOURNAL FOR ONCOLOGY RESEARCH. 2004;6(3):240-247
High-resolution analysis of gene copy number alterations in human prostate cancer using CGH on cDNA microarrays: impact of copy number on gene expression.
Wolf M; Mousses S; Hautaniemi S; Karhu R; Huusko P; Allinen M; Elkahloun A; Monni O; Chen Y; Kallioniemi A; Kallioniemi O-P
Article: CLINICAL CANCER RESEARCH. 2004;10(7):2344-2350
Prognostic impact of ANX7-GTPase in metastatic and HER2-negative breast cancer patients.
Srivastava M; Bubendorf L; Raffeld M; Bucher C; Torhorst J; Sauter G; Olsen C; Kallioniemi OP; Eidelman O; Pollard HB
Article: ONCOGENE. 2004;23(12):2264-2274
Generation and analysis of melanoma SAGE libraries: SAGE advice on the melanoma transcriptome.
Weeraratna AT; Becker D; Carr KM; Duray PH; Rosenblatt KP; Yang S; Chen Y; Bittner M; Strausberg RL; Riggins GJ; Wagner U; Kallioniemi OP; Trent JM; Morin PJ; Meltzer PS
Article: EUROPEAN JOURNAL OF HUMAN GENETICS. 2004;12(2):98-104
Genome-wide scanning for linkage in Finnish breast cancer families.
Huusko P; Juo S-HH; Gillanders E; Sarantaus L; Kainu T; Vahteristo P; Allinen M; Jones M; Rapakko K; Eerola H; Markey C; Vehmanen P; Gildea D; Freas-Lutz D; Blomqvist C; Leisti J; Blanco G; Puistola U; Trent J; Bailey-Wilson J; Winqvist R; Nevanlinna H; Kallioniemi O-P
Article: INTERNATIONAL JOURNAL OF CANCER. 2004;108(3):475-476
CHEK2 1100delC is not a risk factor for male breast cancer population.
Syrjäkoski K; Kuukasjärvi T; Auvinen A; Kallioniemi O-P
Article: JOURNAL OF CLINICAL ONCOLOGY. 2003;21(24):4586-4591
Topoisomerase-II alpha is upregulated in malignant peripheral nerve sheath tumors and associated with clinical outcome.
Skotheim RI; Kallioniemi A; Bjerkhagen B; Mertens F; Brekke HR; Monni O; Mousses S; Mandahl N; Soeter G; Nesland JM; Smeland S; Kallioniemi O-P; Lothe RA
Article: PROSTATE. 2003;57(4):280-289
Genome-wide scan for linkage in finnish hereditary prostate cancer (HPC) families identifies novel susceptibility loci at 11q14 and 3p25-26.
Schleutker J; Baffoe-Bonnie AB; Gillanders E; Kainu T; Jones M-P; Freas-Lutz D; Markey C; Gildea D; Riedesel E; Albertus J; Gibbs KD; Matikainen M; Koivisto PA; Tammela T; Bailey-Wilson JE; Trent JM; Kallioniemi O-P
Article: BIOINFORMATICS. 2003;19(16):2031-2038
A novel strategy for microarray quality control using Bayesian networks.
Hautaniemi S; Edgren H; Vesanen P; Wolf M; Järvinen A-K; Yli-Harja O; Astola J; Kallioniemi O; Monni O
Article: CLINICAL CANCER RESEARCH. 2003;9(13):4914-4925
Elevated expression of inhibitor of apoptosis proteins in prostate cancer.
Krajewska M; Krajewski S; Banares S; Huang X; Turner B; Bubendorf L; Kallioniemi O-P; Shabaik A; Vitiello A; Peehl D; Gao G-J; Reed JC
Article: GENOME RESEARCH. 2003;13(10):2341-2347
RNAi microarray analysis in cultured mammalian cells.
Mousses S; Caplen NJ; Cornelison R; Weaver D; Basik M; Hautaniemi S; Elkahloun AG; Lotufo RA; Choudary A; Dougherty ER; Suh E; Kallioniemi O
Article: CLINICAL CANCER RESEARCH. 2003;9(11):4165-4171
Thymidylate synthase expression predicts the response to 5-fluorouracil-based adjuvant therapy in pancreatic cancer.
Hu YC; Komorowski RA; Graewin S; Hostetter G; Kallioniemi O-P; Pitt HA; Ahrendt SA
Article: NEOPLASIA: AN INTERNATIONAL JOURNAL FOR ONCOLOGY RESEARCH. 2003;5(5):397-404
Candidate genes for testicular cancer evaluated by in situ protein expression analyses on tissue microarrays.
Skotheim RI; Abeler VM; Nesland JM; Fosså SD; Holm R; Wagner U; Flørenes VA; Aass N; Kallioniemi OP; Lothe RA
Article: JOURNAL OF MEDICAL GENETICS. 2003;40(8):e98-98
BRCA1 and BRCA2 mutations have no major role in predisposition to prostate cancer in Finland.
Ikonen T; Matikainen MP; Syrjäkoski K; Mononen N; Koivisto PA; Rökman A; Seppälä EH; Kallioniemi O-P; Tammela TLJ; Schleutker J
Article: MACHINE LEARNING. 2003;52(1-2):45-66
Analysis and visualization of gene expression microarray data in human cancer using self-organizing maps
Hautaniemi S; Yli-Harja O; Astola J; Kauraniemi P; Kallioniemi A; Wolf M; Ruiz J; Mousses S; Kallioniemi OP
Article: JOURNAL OF THE NATIONAL CANCER INSTITUTE. 2003;95(11):812-818
New paraoxonase 1 polymorphism I102V and the risk of prostate cancer in Finnish men.
Marchesani M; Hakkarainen A; Tuomainen T-P; Kaikkonen J; Pukkala E; Uimari P; Seppälä E; Matikainen M; Kallioniemi O-P; Schleutker J; Lehtimäki T; Salonen JT
Article: AMERICAN JOURNAL OF HUMAN GENETICS. 2003;72(5):1117-1130
Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case Series unselected for family history: a combined analysis of 22 studies.
Antoniou A; Pharoah PDP; Narod S; Risch HA; Eyfjord JE; Hopper JL; Loman N; Olsson H; Johannsson O; Borg A; Pasini B; Radice P; Manoukian S; Eccles DM; Tang N; Olah E; Anton-Culver H; Warner E; Lubinski J; Gronwald J; Gorski B; Tulinius H; Thorlacius S; Eerola H; Nevanlinna H; Syrjäkoski K; Kallioniemi O-P; Thompson D; Evans C; Peto J; Lalloo F; Evans DG; Easton DF
Article: ONCOGENE. 2003;22(13):2021-2033
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.
Kominsky SL; Argani P; Korz D; Evron E; Raman V; Garrett E; Rein A; Sauter G; Kallioniemi O-P; Sukumar S
Article: BREAST CANCER RESEARCH AND TREATMENT. 2003;77(2):167-170
Androgen receptor gene alterations in Finnish male breast cancer.
Syrjäkoski K; Hyytinen E-R; Kuukasjärvi T; Auvinen A; Kallioniemi O-P; Kainu T; Koivisto PA
Article: NATURE GENETICS. 2003;33(1):19-20
High frequency of BRAF mutations in nevi.
Pollock PM; Harper UL; Hansen KS; Yudt LM; Stark M; Robbins CM; Moses TY; Hostetter G; Wagner U; Kakareka J; Salem G; Pohida T; Heenan P; Duray P; Kallioniemi O; Hayward NK; Trent JM; Meltzer PS
Article: GENES CHROMOSOMES AND CANCER. 2002;35(4):311-317
Cloning of BCAS3 (17q23) and BCAS4 (20q13) genes that undergo amplification, overexpression, and fusion in breast cancer.
Bärlund M; Monni O; Weaver JD; Kauraniemi P; Sauter G; Heiskanen M; Kallioniemi O-P; Kallioniemi A
Article: CANCER RESEARCH. 2002;62(21):6240-6245
Impact of DNA amplification on gene expression patterns in breast cancer.
Hyman E; Kauraniemi P; Hautaniemi S; Wolf M; Mousses S; Rozenblum E; Ringnér M; Sauter G; Monni O; Elkahloun A; Kallioniemi O-P; Kallioniemi A
Article: AMERICAN JOURNAL OF HUMAN GENETICS. 2002;71(2):432-438
A CHEK2 genetic variant contributing to a substantial fraction of familial breast cancer.
Vahteristo P; Bartkova J; Eerola H; Syrjäkoski K; Ojala S; Kilpivaara O; Tamminen A; Kononen J; Aittomäki K; Heikkilä P; Holli K; Blomqvist C; Bartek J; Kallioniemi O-P; Nevanlinna H
Article: HUMAN GENETICS. 2002;111(2):166-171
Androgen receptor CAG polymorphism and prostate cancer risk.
Mononen N; Ikonen T; Autio V; Rökman A; Matikainen MP; Tammela TLJ; Kallioniemi O-P; Koivisto PA; Schleutker J
Article: REAL-TIME IMAGING. 2002;8(3):203-212
Simulation toolbox for 3D-FISH spot-counting algorithms
Grigoryan AM; Hostetter G; Kallioniemi O; Dougherty ER
Article: AMERICAN JOURNAL OF HUMAN GENETICS. 2002;70(5):1299-1304
Germline alterations of the RNASEL gene, a candidate HPC1 gene at 1q25, in patients and families with prostate cancer.
Rökman A; Ikonen T; Seppälä EH; Nupponen N; Autio V; Mononen N; Bailey-Wilson J; Trent J; Carpten J; Matikainen MP; Koivisto PA; Tammela TLJ; Kallioniemi O-P; Schleutker J
Article: CANCER RESEARCH. 2002;62(8):2359-2364
New insights into testicular germ cell tumorigenesis from gene expression profiling.
Skotheim RI; Monni O; Mousses S; Fosså SD; Kallioniemi O-P; Lothe RA; Kallioniemi A
Article: CANCER RESEARCH. 2002;62(5):1256-1260
Clinical validation of candidate genes associated with prostate cancer progression in the CWR22 model system using tissue microarrays.
Mousses S; Bubendorf L; Wagner U; Hostetter G; Kononen J; Cornelison R; Goldberger N; Elkahloun AG; Willi N; Koivisto P; Ferhle W; Raffeld M; Sauter G; Kallioniemi O-P
Article: NEOPLASIA: AN INTERNATIONAL JOURNAL FOR ONCOLOGY RESEARCH. 2002;4(2):129-140
Expression of Bcl-2 family member Bid in normal and malignant tissues.
Krajewska M; Zapata JM; Meinhold-Heerlein I; Hedayat H; Monks A; Bettendorf H; Shabaik A; Bubendorf L; Kallioniemi O-P; Kim H; Reifenberger G; Reed JC; Krajewski S
Article: NATURE GENETICS. 2002;30(2):181-184
Germline mutations in the ribonuclease L gene in families showing linkage with HPC1.
Carpten J; Nupponen N; Isaacs S; Sood R; Robbins C; Xu J; Faruque M; Moses T; Ewing C; Gillanders E; Hu P; Bujnovszky P; Makalowska I; Baffoe-Bonnie A; Faith D; Smith J; Stephan D; Wiley K; Brownstein M; Gildea D; Kelly B; Jenkins R; Hostetter G; Matikainen M; Schleutker J; Klinger K; Connors T; Xiang Y; Wang Z; De Marzo A; Papadopoulos N; Kallioniemi O-P; Burk R; Meyers D; Grönberg H; Meltzer P; Silverman R; Bailey-Wilson J; Walsh P; Isaacs W; Trent J
Article: HUMAN GENETICS. 2002;110(2):111-121
A genomic map of a 6-Mb region at 13q21-q22 implicated in cancer development: identification and characterization of candidate genes.
Rozenblum E; Vahteristo P; Sandberg T; Bergthorsson JT; Syrjakoski K; Weaver D; Haraldsson K; Johannsdottir HK; Vehmanen P; Nigam S; Golberger N; Robbins C; Pak E; Dutra A; Gillander E; Stephan DA; Bailey-Wilson J; Juo S-HH; Kainu T; Arason A; Barkardottir RB; Nevanlinna H; Borg A; Kallioniemi O-P
Article: JOURNAL OF BIOMEDICAL OPTICS. 2002;7(1):109-122
Morphological spot counting from stacked images for automated analysis of gene copy numbers by fluorescence in situ hybridization.
Grigoryan AM; Dougherty ER; Kononen J; Bubendorf L; Hostetter G; Kallioniemi O
Article: AMERICAN JOURNAL OF PATHOLOGY. 2001;159(6):2249-2256
Tissue microarrays for rapid linking of molecular changes to clinical endpoints.
Torhorst J; Bucher C; Kononen J; Haas P; Zuber M; Köchli OR; Mross F; Dieterich H; Moch H; Mihatsch M; Kallioniemi OP; Sauter G
Article: CLINICAL CANCER RESEARCH. 2001;7(11):3465-3471
Association of E-cadherin germ-line alterations with prostate cancer.
Ikonen T; Matikainen M; Mononen N; Hyytinen ER; Helin HJ; Tommola S; Tammela TL; Pukkala E; Schleutker J; Kallioniemi OP; Koivisto PA
Article: ONCOGENE. 2001;20(47):6881-6890
Amplification and overexpression of PRUNE in human sarcomas and breast carcinomas-a possible mechanism for altering the nm23-H1 activity.
Forus A; D'Angelo A; Henriksen J; Merla G; Maelandsmo GM; Flørenes VA; Olivieri S; Bjerkehagen B; Meza-Zepeda LA; del Vecchio Blanco F; Müller C; Sanvito F; Kononen J; Nesland JM; Fodstad Ø; Reymond A; Kallioniemi OP; Arrigoni G; Ballabio A; Myklebost O; Zollo M
Article: ONCOGENE. 2001;20(46):6718-6723
Failure of hormone therapy in prostate cancer involves systematic restoration of androgen responsive genes and activation of rapamycin sensitive signaling.
Mousses S; Wagner U; Chen Y; Kim JW; Bubendorf L; Bittner M; Pretlow T; Elkahloun AG; Trepel JB; Kallioniemi OP
Article: INTERNATIONAL JOURNAL OF CANCER. 2001;94(1):1-5
Tissue microarrays (TMAs) for high-throughput molecular pathology research.
Nocito A; Kononen J; Kallioniemi OP; Sauter G
Article: SEMINARS IN CANCER BIOLOGY. 2001;11(5):395-401
From chromosomal alterations to target genes for therapy: integrating cytogenetic and functional genomic views of the breast cancer genome.
Monni O; Hyman E; Mousses S; Barlund M; Kallioniemi A; Kallioniemi OP
Article: EUROPEAN JOURNAL OF HUMAN GENETICS. 2001;9(10):773-779
Haplotype analysis in Icelandic and Finnish BRCA2 999del5 breast cancer families
Barkardottir RB; Sarantaus L; Arason A; Vehmanen P; Bendahl PO; Kainu T; Syrjäkoski K; Krahe R; Huusko P; Pyrhönen S; Holli K; Kallioniemi OP; Egilsson V; Kere J; Nevanlinna H
Article: CANCER RESEARCH. 2001;61(16):6038-6041
ELAC2/HPC2 involvement in hereditary and sporadic prostate cancer.
Rökman A; Ikonen T; Mononen N; Autio V; Matikainen MP; Koivisto PA; Tammela TL; Kallioniemi OP; Schleutker J
Article: BRITISH JOURNAL OF CANCER. 2001;84(10):1344-1347
A missense substitution A49T in the steroid 5-alpha-reductase gene (SRD5A2) is not associated with prostate cancer in Finland.
Mononen N; Ikonen T; Syrjäkoski K; Matikainen M; Schleutker J; Tammela TL; Koivisto PA; Kallioniemi OP
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2001;98(8):4575-4580
ANX7, a candidate tumor suppressor gene for prostate cancer.
Srivastava M; Bubendorf L; Srikantan V; Fossom L; Nolan L; Glasman M; Leighton X; Fehrle W; Pittaluga S; Raffeld M; Koivisto P; Willi N; Gasser TC; Kononen J; Sauter G; Kallioniemi OP; Srivastava S; Pollard HB
Article: HUMAN MOLECULAR GENETICS. 2001;10(7):657-662
Tissue microarray technology for high-throughput molecular profiling of cancer.
Kallioniemi OP; Wagner U; Kononen J; Sauter G
Article: CANCER CAUSES AND CONTROL. 2001;12(3):223-230
Relatives of prostate cancer patients have an increased risk of prostate and stomach cancers: a population-based, cancer registry study in Finland.
Matikaine MP; Pukkala E; Schleutker J; Tammela TL; Koivisto P; Sankila R; Kallioniemi OP
Article: ANNALS OF MEDICINE. 2001;33(2):142-147
Biochip technologies in cancer research.
Kallioniemi OP
Article: NEW ENGLAND JOURNAL OF MEDICINE. 2001;344(8):539-548
Gene-expression profiles in hereditary breast cancer.
Hedenfalk I; Duggan D; Chen Y; Radmacher M; Bittner M; Simon R; Meltzer P; Gusterson B; Esteller M; Kallioniemi OP; Wilfond B; Borg A; Trent J; Raffeld M; Yakhini Z; Ben-Dor A; Dougherty E; Kononen J; Bubendorf L; Fehrle W; Pittaluga S; Gruvberger S; Loman N; Johannsson O; Olsson H; Sauter G
Article: PROSTATE. 2001;46(3):233-239
Genetic changes in familial prostate cancer by comparative genomic hybridization.
Rökman A; Koivisto PA; Matikainen MP; Kuukasjärvi T; Poutiainen M; Helin HJ; Karhu R; Kallioniemi OP; Schleutker J
Article: BRITISH JOURNAL OF CANCER. 2001;84(1):116-119
Germline TP53 alterations in Finnish breast cancer families are rare and occur at conserved mutation-prone sites.
Rapakko K; Allinen M; Syrjäkoski K; Vahteristo P; Huusko P; Vähäkangas K; Eerola H; Kainu T; Kallioniemi OP; Nevanlinna H; Winqvist R
Article: DISEASE MARKERS. 2001;17(2):115-120
ANX7 as a bio-marker in prostate and breast cancer progression.
Srivastava M; Bubendorf L; Nolan L; Glasman M; Leighton X; Miller G; Fehrle W; Raffeld M; Eidelman O; Kallioniemi OP; Srivastava S; Pollard HB
Article: ADVANCES IN ANATOMIC PATHOLOGY. 2001;8(1):14-20
Tissue microarrays: what will they bring to molecular and anatomic pathology?
Moch H; Kononen T; Kallioniemi OP; Sauter G
Article: CELLULAR ONCOLOGY (DORDRECHT). 2001;22(4):229-234
CGH, cDNA and tissue microarray analyses implicate FGFR2 amplification in a small subset of breast tumors.
Heiskanen M; Kononen J; Bärlund M; Torhorst J; Sauter G; Kallioniemi A; Kallioniemi O
Article: CANCER GENETICS. 2000;123(2):128-132
Novel findings in gene expression detected in human osteosarcoma by cDNA microarray.
Wolf M; El-Rifai W; Tarkkanen M; Kononen J; Serra M; Eriksen EF; Elomaa I; Kallioniemi A; Kallioniemi OP; Knuutila S
Article: CLINICAL CANCER RESEARCH. 2000;6(12):4810-4815
A genetic epidemiological study of hereditary prostate cancer (HPC) in Finland: frequent HPCX linkage in families with late-onset disease.
Schleutker J; Matikainen M; Smith J; Koivisto P; Baffoe-Bonnie A; Kainu T; Gillanders E; Sankila R; Pukkala E; Carpten J; Stephan D; Tammela T; Brownstein M; Bailey-Wilson J; Trent J; Kallioniemi OP
Article: CANCER RESEARCH. 2000;60(23):6617-6622
Identification of differentially expressed genes in human gliomas by DNA microarray and tissue chip techniques.
Sallinen SL; Sallinen PK; Haapasalo HK; Helin HJ; Helén PT; Schraml P; Kallioniemi OP; Kononen J
Article: JOURNAL OF UROLOGY. 2000;164(6):1992-1995
Androgen receptor gene amplification at primary progression predicts response to combined androgen blockade as second line therapy for advanced prostate cancer.
Palmberg C; Koivisto P; Kakkola L; Tammela TL; Kallioniemi OP; Visakorpi T
Article: CANCER RESEARCH. 2000;60(22):6503-6509
Construction of evolutionary tree models for renal cell carcinoma from comparative genomic hybridization data.
Jiang F; Desper R; Papadimitriou CH; Schäffer AA; Kallioniemi OP; Richter J; Schraml P; Sauter G; Mihatsch MJ; Moch H
Article: CANCER RESEARCH. 2000;60(22):6479-6481
Two percent of Finnish prostate cancer patients have a germ-line mutation in the hormone-binding domain of the androgen receptor gene.
Mononen N; Syrjäkoski K; Matikainen M; Tammela TL; Schleutker J; Kallioniemi OP; Trapman J; Koivisto PA
Article: CANCER RESEARCH. 2000;60(21):6111-6115
Loss of NKX3.1 expression in human prostate cancers correlates with tumor progression.
Bowen C; Bubendorf L; Voeller HJ; Slack R; Willi N; Sauter G; Gasser TC; Koivisto P; Lack EE; Kononen J; Kallioniemi OP; Gelmann EP
Article: INTERNATIONAL JOURNAL OF CANCER. 2000;88(2):307-312
Nationwide cancer family ascertainment using Finnish Cancer Registry data on family names and places of birth for 35,761 prostate cancer patients.
Matikainen MP; Sankila R; Schleutker J; Kallioniemi OP; Pukkala E
Article: CANCER RESEARCH. 2000;60(19):5340-5344
Multiple genes at 17q23 undergo amplification and overexpression in breast cancer.
Bärlund M; Monni O; Kononen J; Cornelison R; Torhorst J; Sauter G; Kallioniemi OLLI-P; Kallioniemi A
Article: EUROPEAN JOURNAL OF HUMAN GENETICS. 2000;8(10):757-763
Multiple founder effects and geographical clustering of BRCA1 and BRCA2 families in Finland
Sarantaus L; Huusko P; Eerola H; Launonen V; Vehmanen P; Rapakko K; Gillanders E; Syrjäkoski K; Kainu T; Vahteristo P; Krahe R; Pääkkönen K; Hartikainen J; Blomqvist C; Löppönen T; Holli K; Ryynänen M; Bützow R; Borg Å; Arver BW; Holmberg E; Mannermaa A; Kere J; Kallioniemi OP; Winqvist R; Nevanlinna H
Article: JOURNAL OF THE NATIONAL CANCER INSTITUTE. 2000;92(18):1529-1531
Population-based study of BRCA1 and BRCA2 mutations in 1035 unselected Finnish breast cancer patients.
Syrjäkoski K; Vahteristo P; Eerola H; Tamminen A; Kivinummi K; Sarantaus L; Holli K; Blomqvist C; Kallioniemi OP; Kainu T; Nevanlinna H
Article: AMERICAN JOURNAL OF PATHOLOGY. 2000;157(3):787-794
High-throughput tissue microarray analysis of cyclin E gene amplification and overexpression in urinary bladder cancer.
Richter J; Wagner U; Kononen J; Fijan A; Bruderer J; Schmid U; Ackermann D; Maurer R; Alund G; Knönagel H; Rist M; Wilber K; Anabitarte M; Hering F; Hardmeier T; Schönenberger A; Flury R; Jäger P; Fehr JL; Schraml P; Moch H; Mihatsch MJ; Gasser T; Kallioniemi OP; Sauter G
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2000;97(17):9603-9608
Somatic deletions in hereditary breast cancers implicate 13q21 as a putative novel breast cancer susceptibility locus.
Kainu T; Juo SH; Desper R; Schaffer AA; Gillanders E; Rozenblum E; Freas-Lutz D; Weaver D; Stephan D; Bailey-Wilson J; Kallioniemi OP; Tirkkonen M; Syrjäkoski K; Kuukasjärvi T; Koivisto P; Karhu R; Holli K; Arason A; Johannesdottir G; Bergthorsson JT; Johannsdottir H; Egilsson V; Barkardottir RB; Johannsson O; Haraldsson K; Sandberg T; Holmberg E; Grönberg H; Olsson H; Borg A; Vehmanen P; Eerola H; Heikkila P; Pyrhönen S; Nevanlinna H
Article: CANCER RESEARCH. 2000;60(16):4519-4525
Comparative genomic hybridization analysis of 38 breast cancer cell lines: a basis for interpreting complementary DNA microarray data.
Forozan F; Mahlamäki EH; Monni O; Chen Y; Veldman R; Jiang Y; Gooden GC; Ethier SP; Kallioniemi A; Kallioniemi OP
Article: JOURNAL OF THE NATIONAL CANCER INSTITUTE. 2000;92(15):1252-1259
Detecting activation of ribosomal protein S6 kinase by complementary DNA and tissue microarray analysis.
Bärlund M; Forozan F; Kononen J; Bubendorf L; Chen Y; Bittner ML; Torhorst J; Haas P; Bucher C; Sauter G; Kallioniemi OP; Kallioniemi A
Article: JOURNAL OF COMPUTATIONAL BIOLOGY. 2000;7(6):789-803
Distance-based reconstruction of tree models for oncogenesis.
Desper R; Jiang F; Kallioniemi OP; Moch H; Papadimitriou CH; Schäffer AA
Article: BRITISH JOURNAL OF CANCER. 1999;81(8):1328-1334
Molecular cytogenetic analysis of 11 new breast cancer cell lines.
Forozan F; Veldman R; Ammerman CA; Parsa NZ; Kallioniemi A; Kallioniemi OP; Ethier SP
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 1999;274(48):34283-34293
A nuclear factor, ASC-2, as a cancer-amplified transcriptional coactivator essential for ligand-dependent transactivation by nuclear receptors in vivo.
Lee SK; Anzick SL; Choi JE; Bubendorf L; Guan XY; Jung YK; Kallioniemi OP; Kononen J; Trent JM; Azorsa D; Jhun BH; Cheong JH; Lee YC; Meltzer PS; Lee JW
Article: CLINICAL CANCER RESEARCH. 1999;5(11):3578-3582
Androgen receptor gene alterations and chromosomal gains and losses in prostate carcinomas appearing during finasteride treatment for benign prostatic hyperplasia.
Koivisto PA; Schleutker J; Helin H; Ehren-van Eekelen C; Kallioniemi OP; Trapman J
Article: JOURNAL OF THE NATIONAL CANCER INSTITUTE. 1999;91(20):1758-1764
Hormone therapy failure in human prostate cancer: analysis by complementary DNA and tissue microarrays.
Bubendorf L; Kolmer M; Kononen J; Koivisto P; Mousses S; Chen Y; Mahlamäki E; Schraml P; Moch H; Willi N; Elkahloun AG; Pretlow TG; Gasser TC; Mihatsch MJ; Sauter G; Kallioniemi OP
Article: CLINICAL CANCER RESEARCH. 1999;5(8):1966-1975
Tissue microarrays for gene amplification surveys in many different tumor types.
Schraml P; Kononen J; Bubendorf L; Moch H; Bissig H; Nocito A; Mihatsch MJ; Kallioniemi OP; Sauter G
Article: CLINICAL CANCER RESEARCH. 1999;5(6):1275-1279
Detection of subclinical cancers by prostate-specific antigen screening in asymptomatic men from high-risk prostate cancer families.
Matikainen MP; Schleutker J; Mörsky P; Kallioniemi OP; Tammela TL
Article: CANCER RESEARCH. 1999;59(11):2682-2689
Reduced Fhit expression in sporadic and BRCA2-linked breast carcinomas.
Ingvarsson S; Agnarsson BA; Sigbjornsdottir BI; Kononen J; Kallioniemi OP; Barkardottir RB; Kovatich AJ; Schwarting R; Hauck WW; Huebner K; McCue PA
Article: AMERICAN JOURNAL OF PATHOLOGY. 1999;154(4):981-986
High-throughput tissue microarray analysis to evaluate genes uncovered by cDNA microarray screening in renal cell carcinoma.
Moch H; Schraml P; Bubendorf L; Mirlacher M; Kononen J; Gasser T; Mihatsch MJ; Kallioniemi OP; Sauter G
Article: CANCER RESEARCH. 1999;59(4):803-806
Survey of gene amplifications during prostate cancer progression by high-throughout fluorescence in situ hybridization on tissue microarrays.
Bubendorf L; Kononen J; Koivisto P; Schraml P; Moch H; Gasser TC; Willi N; Mihatsch MJ; Sauter G; Kallioniemi OP
Article: JOURNAL OF CLINICAL ENDOCRINOLOGY AND METABOLISM (JCEM). 1999;84(2):730-735
Genotyping of adrenocortical tumors:: Very frequent deletions of the MEN1 locus in 11q13 and of a 1-centimorgan region in 2p16
Kjellman M; Roshani L; Teh BT; Kallioniemi OP; Höög A; Gray S; Farnebo LO; Holst M; Bäckdahl M; Larsson C
Article: VERHANDLUNGEN DER DEUTSCHEN GESELLSCHAFT F�R PATHOLOGIE. 1999;83:225-232
[Identification of prognostic parameters for renal cell carcinoma by cDNA arrays and cell chips].
Moch H; Schraml P; Bubendorf L; Mirlacher M; Kononen J; Gasser T; Mihatsch MJ; Kallioniemi OP; Sauter G
Article: JOURNAL OF COMPUTATIONAL BIOLOGY. 1999;6(1):37-51
Inferring tree models for oncogenesis from comparative genome hybridization data.
Desper R; Jiang F; Kallioniemi OP; Moch H; Papadimitriou CH; Schäffer AA
Article: ANTICANCER RESEARCH. 1999;19(1A):7-12
Comparison of comparative genomic hybridization, fluorescence in situ hybridization and flow cytometry in urinary bladder cancer
Mahdy E; Yoshihiro S; Zech L; Wester K; Pan Y; Busch C; Döhner H; Kallioniemi O; Bergerheim U; Malmström PU
Article: GENES CHROMOSOMES AND CANCER. 1999;24(1):56-61
Somatic genetic alterations in BRCA2-associated and sporadic male breast cancer.
Tirkkonen M; Kainu T; Loman N; Jóhannsson OT; Olsson H; Barkardóttir RB; Kallioniemi OP; Borg A
Article: NATURE GENETICS. 1998;20(2):175-179
Evidence for a prostate cancer susceptibility locus on the X chromosome.
Xu J; Meyers D; Freije D; Isaacs S; Wiley K; Nusskern D; Ewing C; Wilkens E; Bujnovszky P; Bova GS; Walsh P; Isaacs W; Schleutker J; Matikainen M; Tammela T; Visakorpi T; Kallioniemi OP; Berry R; Schaid D; French A; McDonnell S; Schroeder J; Blute M; Thibodeau S; Grönberg H; Emanuelsson M; Damber JE; Bergh A; Jonsson BA; Smith J; Bailey-Wilson J; Carpten J; Stephan D; Gillanders E; Amundson I; Kainu T; Freas-Lutz D; Baffoe-Bonnie A; Van Aucken A; Sood R; Collins F; Brownstein M; Trent J
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 1998;95(15):8703-8708
Positional cloning of ZNF217 and NABC1: genes amplified at 20q13.2 and overexpressed in breast carcinoma.
Collins C; Rommens JM; Kowbel D; Godfrey T; Tanner M; Hwang SI; Polikoff D; Nonet G; Cochran J; Myambo K; Jay KE; Froula J; Cloutier T; Kuo WL; Yaswen P; Dairkee S; Giovanola J; Hutchinson GB; Isola J; Kallioniemi OP; Palazzolo M; Martin C; Ericsson C; Pinkel D; Albertson D; Li WB; Gray JW
Article: NATURE MEDICINE. 1998;4(7):844-847
Tissue microarrays for high-throughput molecular profiling of tumor specimens.
Kononen J; Bubendorf L; Kallioniemi A; Bärlund M; Schraml P; Leighton S; Torhorst J; Mihatsch MJ; Sauter G; Kallioniemi OP
Article: GENES CHROMOSOMES AND CANCER. 1998;21(3):177-184
Molecular cytogenetics of primary breast cancer by CGH.
Tirkkonen M; Tanner M; Karhu R; Kallioniemi A; Isola J; Kallioniemi OP
Article: CYTOGENETIC AND GENOME RESEARCH. 1998;82(3-4):189-191
Molecular cytogenetic mapping of 24 CEPH YACs and 24 gene-specific large insert probes to chromosome 17.
Bärlund M; Nupponen NN; Karhu R; Tanner MM; Paavola P; Kallioniemi OP; Kallioniemi A
Article: HUMAN MOLECULAR GENETICS. 1997;6(13):2309-2315
Low proportion of BRCA1 and BRCA2 mutations in Finnish breast cancer families: evidence for additional susceptibility genes.
Vehmanen P; Friedman LS; Eerola H; McClure M; Ward B; Sarantaus L; Kainu T; Syrjäkoski K; Pyrhönen S; Kallioniemi OP; Muhonen T; Luce M; Frank TS; Nevanlinna H
Article: GENES CHROMOSOMES AND CANCER. 1997;20(4):383-391
Comparative genomic hybridization reveals frequent gains of 20q, 8q, 11q, 12p, and 17q, and losses of 18q, 9p, and 15q in pancreatic cancer.
Mahlamäki EH; Höglund M; Gorunova L; Karhu R; Dawiskiba S; Andrén-Sandberg A; Kallioniemi OP; Johansson B
Article: GENES CHROMOSOMES AND CANCER. 1997;20(4):372-376
Increased copy number at 17q22-q24 by CGH in breast cancer is due to high-level amplification of two separate regions.
Bärlund M; Tirkkonen M; Forozan F; Tanner MM; Kallioniemi O; Kallioniemi A
Article: SCIENCE. 1997;277(5328):965-968
AIB1, a steroid receptor coactivator amplified in breast and ovarian cancer.
Anzick SL; Kononen J; Walker RL; Azorsa DO; Tanner MM; Guan XY; Sauter G; Kallioniemi OP; Trent JM; Meltzer PS
Article: GENES CHROMOSOMES AND CANCER. 1997;19(4):286-290
Frequent loss of the 11q14-24 region in chronic lymphocytic leukemia: a study by comparative genomic hybridization. Tampere CLL Group.
Karhu R; Knuutila S; Kallioniemi OP; Siltonen S; Aine R; Vilpo L; Vilpo J
Article: CYTOMETRY. 1997;28(3):198-205
Quality control of CGH: impact of metaphase chromosomes and the dynamic range of hybridization.
Karhu R; Kähkönen M; Kuukasjärvi T; Pennanen S; Tirkkonen M; Kallioniemi O
Article: CANCER RESEARCH. 1997;57(8):1597-1604
Genetic heterogeneity and clonal evolution underlying development of asynchronous metastasis in human breast cancer.
Kuukasjärvi T; Karhu R; Tanner M; Kähkönen M; Schäffer A; Nupponen N; Pennanen S; Kallioniemi A; Kallioniemi OP; Isola J
Article: CANCER RESEARCH. 1997;57(7):1222-1227
Distinct somatic genetic changes associated with tumor progression in carriers of BRCA1 and BRCA2 germ-line mutations.
Tirkkonen M; Johannsson O; Agnarsson BA; Olsson H; Ingvarsson S; Karhu R; Tanner M; Isola J; Barkardottir RB; Borg A; Kallioniemi OP
Article: AMERICAN JOURNAL OF PATHOLOGY. 1997;150(4):1465-1471
Genetic changes in intraductal breast cancer detected by comparative genomic hybridization.
Kuukasjärvi T; Tanner M; Pennanen S; Karhu R; Kallioniemi OP; Isola J
Article: CANCER RESEARCH. 1997;57(2):314-319
Androgen receptor gene amplification: a possible molecular mechanism for androgen deprivation therapy failure in prostate cancer.
Koivisto P; Kononen J; Palmberg C; Tammela T; Hyytinen E; Isola J; Trapman J; Cleutjens K; Noordzij A; Visakorpi T; Kallioniemi OP
Article: EUROPEAN UROLOGY. 1997;31(2):216-219
Androgen receptor gene amplification in a recurrent prostate cancer after monotherapy with the nonsteroidal potent antiandrogen Casodex (bicalutamide) with a subsequent favorable response to maximal androgen blockade.
Palmberg C; Koivisto P; Hyytinen E; Isola J; Visakorpi T; Kallioniemi OP; Tammela T
Article: BRITISH JOURNAL OF CANCER. 1997;75(2):190-195
Genetic changes associated with the acquisition of androgen-independent growth, tumorigenicity and metastatic potential in a prostate cancer model.
Hyytinen ER; Thalmann GN; Zhau HE; Karhu R; Kallioniemi OP; Chung LW; Visakorpi T
Article: CYTOMETRY. 1996;25(4):394-398
Evaluation of camera requirements for comparative genomic hybridization.
Tirkkonen M; Karhu R; Kallioniemi O; Isola J
Article: SCIENCE. 1996;274(5291):1371-1374
Major susceptibility locus for prostate cancer on chromosome 1 suggested by a genome-wide search.
Smith JR; Freije D; Carpten JD; Grönberg H; Xu J; Isaacs SD; Brownstein MJ; Bova GS; Guo H; Bujnovszky P; Nusskern DR; Damber JE; Bergh A; Emanuelsson M; Kallioniemi OP; Walker-Daniels J; Bailey-Wilson JE; Beaty TH; Meyers DA; Walsh PC; Collins FS; Trent JM; Isaacs WB
Article: CANCER RESEARCH. 1996;56(20):4778-4781
Gain of 17q24-qter detected by comparative genomic hybridization in malignant tumors from patients with von Recklinghausen's neurofibromatosis.
Lothe RA; Karhu R; Mandahl N; Mertens F; Saeter G; Heim S; Borresen-Dale AL; Kallioniemi OP
Article: CANCER RESEARCH. 1996;56(18):4219-4223
Genetic aberrations in adrenocortical tumors detected using comparative genomic hybridization correlate with tumor size and malignancy
Kjellman M; Kallioniemi OP; Karhu R; Hoog A; Farnebo LO; Auer G; Larsson C; Backdahl M
Article: CANCER RESEARCH. 1996;56(15):3441-3445
Independent amplification and frequent co-amplification of three nonsyntenic regions on the long arm of chromosome 20 in human breast cancer.
Tanner MM; Tirkkonen M; Kallioniemi A; Isola J; Kuukasjärvi T; Collins C; Kowbel D; Guan XY; Trent J; Gray JW; Meltzer P; Kallioniemi OP
Article: CANCER GENETICS. 1996;89(1):7-13
Gains and losses of DNA sequences in malignant mesothelioma by comparative genomic hybridization.
Kivipensas P; Björkqvist AM; Karhu R; Pelin K; Linnainmaa K; Tammilehto L; Mattson K; Kallioniemi QP; Knuutila S
Article: INTERNATIONAL JOURNAL OF CANCER. 1996;66(1):6-10
Low biological aggressiveness of screen-detected lung cancers may indicate over-diagnosis.
Hakama M; Holli K; Visakorpi T; Pekola M; Kallioniemi OP
Article: CIRCULATION. 1996;93(6):1079-1082
Novel human vascular endothelial growth factor genes VEGF-B and VEGF-C localize to chromosomes 11q13 and 4q34, respectively.
Paavonen K; Horelli-Kuitunen N; Chilov D; Kukk E; Pennanen S; Kallioniemi OP; Pajusola K; Olofsson B; Eriksson U; Joukov V; Palotie A; Alitalo K
Article: NEW BIOTECHNOLOGY. 1996;12(5-6):179-184
Fiber-FISH: experiences and a refined protocol.
Heiskanen M; Kallioniemi O; Palotie A
Article: BRITISH JOURNAL OF CANCER. 1996;73(5):620-623
c-erbB-2 in astrocytomas: infrequent overexpression by immunohistochemistry and absence of gene amplification by fluorescence in situ hybridization.
Haapasalo H; Hyytinen E; Sallinen P; Helin H; Kallioniemi OP; Isola J
Article: METHODS. 1996;9(1):113-121
Gene Copy Number Analysis by Fluorescence in Situ Hybridization and Comparative Genomic Hybridization.
Kallioniemi A; Visakorpi T; Karhu R; Pinkel D; Kallioniemi OP
Article: SCANDINAVIAN JOURNAL OF CLINICAL AND LABORATORY INVESTIGATION, SUPPLEMENT. 1996;226:57-63
Androgen receptor gene amplification: a novel molecular mechanism for endocrine therapy resistance in human prostate cancer.
Koivisto P; Visakorpi T; Kallioniemi OP
Article: CLINICAL CANCER RESEARCH. 1995;1(12):1455-1461
Amplification of chromosomal region 20q13 in invasive breast cancer: prognostic implications.
Tanner MM; Tirkkonen M; Kallioniemi A; Holli K; Collins C; Kowbel D; Gray JW; Kallioniemi OP; Isola J
Article: AMERICAN JOURNAL OF PATHOLOGY. 1995;147(6):1608-1614
Analysis of genetic changes underlying local recurrence of prostate carcinoma during androgen deprivation therapy.
Koivisto P; Hyytinen E; Palmberg C; Tammela T; Visakorpi T; Isola J; Kallioniemi OP
Article: GENOMICS. 1995;30(1):31-36
Visual mapping by fiber-FISH.
Heiskanen M; Hellsten E; Kallioniemi OP; Mäkelä TP; Alitalo K; Peltonen L; Palotie A
Article: AMERICAN JOURNAL OF PATHOLOGY. 1995;147(4):905-911
Genetic aberrations detected by comparative genomic hybridization predict outcome in node-negative breast cancer.
Isola JJ; Kallioniemi OP; Chu LW; Fuqua SA; Hilsenbeck SG; Osborne CK; Waldman FM
Article: GENOME RESEARCH. 1995;5(1):13-20
Mechanically stretched chromosomes as targets for high-resolution FISH mapping.
Laan M; Kallioniemi OP; Hellsten E; Alitalo K; Peltonen L; Palotie A
Article: NATURE GENETICS. 1995;9(4):401-406
In vivo amplification of the androgen receptor gene and progression of human prostate cancer.
Visakorpi T; Hyytinen E; Koivisto P; Tanner M; Keinänen R; Palmberg C; Palotie A; Tammela T; Isola J; Kallioniemi OP
Article: CANCER RESEARCH. 1995;55(6):1334-1338
Gains and losses of DNA sequences in osteosarcomas by comparative genomic hybridization.
Tarkkanen M; Karhu R; Kallioniemi A; Elomaa I; Kivioja AH; Nevalainen J; Böhling T; Karaharju E; Hyytinen E; Knuutila S
Article: GENES CHROMOSOMES AND CANCER. 1995;12(3):213-219
Identification of gains and losses of DNA sequences in primary bladder cancer by comparative genomic hybridization.
Kallioniemi A; Kallioniemi OP; Citro G; Sauter G; DeVries S; Kerschmann R; Caroll P; Waldman F
Article: THE LANCET. 1995;345(8944):221-224
Aggressiveness of screen-detected breast cancers.
Hakama M; Holli K; Isola J; Kallioniemi OP; Kärkkäinen A; Visakorpi T; Pukkala E; Saarenmaa I; Geiger U; Ikkala J
Article: CANCER RESEARCH. 1995;55(2):342-347
Genetic changes in primary and recurrent prostate cancer by comparative genomic hybridization.
Visakorpi T; Kallioniemi AH; Syvänen AC; Hyytinen ER; Karhu R; Tammela T; Isola JJ; Kallioniemi OP
Article: CYTOGENETIC AND GENOME RESEARCH. 1995;68(1-2):61-63
The human gene for xanthine dehydrogenase (XDH) is localized on chromosome band 2q22.
Rytkönen EM; Halila R; Laan M; Saksela M; Kallioniemi OP; Palotie A; Raivio KO
Article: CYTOMETRY. 1995;19(1):4-9
Hardware and software requirements for quantitative analysis of comparative genomic hybridization.
du Manoir S; Kallioniemi OP; Lichter P; Piper J; Benedetti PA; Carothers AD; Fantes JA; García-Sagredo JM; Gerdes T; Giollant M
Article: CYTOMETRY. 1995;19(1):10-26
Computer image analysis of comparative genomic hybridization.
Piper J; Rutovitz D; Sudar D; Kallioniemi A; Kallioniemi OP; Waldman FM; Gray JW; Pinkel D
Article: CLINICAL CANCER RESEARCH. 1995;1(1):11-18
DNA-SEQUENCE AMPLIFICATION IN HUMAN PROSTATE-CANCER IDENTIFIED BY CHROMOSOME MICRODISSECTION - POTENTIAL PROGNOSTIC IMPLICATIONS
VANDENBERG C; GUAN XY; VONHOFF D; JENKINS R; BITTNER M; GRIFFIN C; KALLIONIEMI O; VISAKORPI T; MCGILL J; HERATH J; EPSTEIN J; SAROSDY M; MELTZER P; TRENT J
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Corrigendum: JOURNAL OF PROTEOME RESEARCH. 2022;21(7):1787
Correction to "Integration of Metabolomics and Expression of Glycerol-3-phosphate Acyltransferase (GPAM) in Breast Cancer─Link to Patient Survival, Hormone Receptor Status, and Metabolic Profiling".
Brockmöller SF; Bucher E; Müller BM; Budczies J; Hilvo M; Griffin JL; Orešič M; Kallioniemi O; Iljin K; Loibl S; Darb-Esfahani S; Sinn BV; Klauschen F; Prinzler J; Bangemann N; Ismaeel F; Fiehn O; Dietel M; Denkert C
Letter: LEUKEMIA. 2020;34(10):2780-2784
KIT pathway upregulation predicts dasatinib efficacy in acute myeloid leukemia
Malani D; Yadav B; Kumar A; Potdar S; Kontro M; Kankainen M; Javarappa KK; Porkka K; Wolf M; Aittokallio T; Wennerberg K; Heckman CA; Murumagi A; Kallioniemi O
Corrigendum: NATURE MEDICINE. 2020;26(8):1309
Publisher Correction: Building an international consortium for tracking coronavirus health status.
Segal E; Zhang F; Lin X; King G; Shalem O; Shilo S; Allen WE; Alquaddoomi F; Altae-Tran H; Anders S; Balicer R; Bauman T; Bonilla X; Booman G; Chan AT; Cohen O; Coletti S; Davidson N; Dor Y; Drew DA; Elemento O; Evans G; Ewels P; Gale J; Gavrieli A; Geiger B; Grad YH; Greene CS; Hajirasouliha I; Jerala R; Kahles A; Kallioniemi O; Keshet A; Kocarev L; Landua G; Meir T; Muller A; Nguyen LH; Oresic M; Ovchinnikova S; Peterson H; Prodanova J; Rajagopal J; Rätsch G; Rossman H; Rung J; Sboner A; Sigaras A; Spector T; Steinherz R; Stevens I; Vilo J; Wilmes P
Editorial comment: NATURE MEDICINE. 2020;26(8):1161-1165
Building an international consortium for tracking coronavirus health status
Segal E; Zhang F; Lin X; King G; Shalem O; Shilo S; Allen WE; Alquaddoomi F; Altae-Tran H; Anders S; Balicer R; Bauman T; Bonilla X; Booman G; Chan AT; Cohen O; Coletti S; Davidson N; Dor Y; Drew DA; Elemento O; Evans G; Ewels P; Gale J; Gavrieli A; Geiger B; Grad YH; Greene CS; Hajirasouliha I; Jerala R; Kahles A; Kallioniemi O; Keshet A; Kocarev L; Landua G; Meir T; Muller A; Nguyen LH; Oresic M; Ovchinnikova S; Peterson H; Prodanova J; Rajagopal J; Ratsch G; Rossman H; Rung J; Sboner A; Sigaras A; Spector T; Steinherz R; Stevens I; Vilo J; Wilmes P
Letter: LEUKEMIA. 2019;33(10):2548-2553
Elevated expression of S100A8 and S100A9 correlates with resistance to the BCL-2 inhibitor venetoclax in AML.
Karjalainen R; Liu M; Kumar A; He L; Malani D; Parsons A; Kontro M; Kallioniemi O; Porkka K; Heckman CA
Corrigendum: JOURNAL OF PATHOLOGY. 2019;247(1):147
Spatial aspects of oncogenic signalling determine the response to combination therapy in slice explants from Kras-driven lung tumours (vol 245, pg 101, 2018)
Narhi K; Nagaraj AS; Parri E; Turkki R; van Duijn PW; Hemmes A; Lahtela J; Uotinen V; Mayranpaa MI; Salmenkivi K; Rasanen J; Linder N; Trapman J; Rannikko A; Kallioniemi O; Af Hallstrom TM; Lundin J; Sommergruber W; Anders S; Verschuren EW
Letter: LEUKEMIA AND LYMPHOMA. 2018;59(12):3002-3005
Case studies investigating genetic heterogeneity between anatomically distinct bone marrow compartments in acute myeloid leukemia
Ojamies PN; Kontro M; Edgren H; Ellonen P; Heckman C; Porkka K; Wolf M; Kallioniemi O
Letter: NATURE. 2016;540(7631):E5-E6
Consistency in drug response profiling
Mpindi JP; Yadav B; Ostling P; Gautam P; Malani D; Murumagi A; Hirasawa A; Kangaspeska S; Wennerberg K; Kallioniemi O; Aittokallio T
Published conference paper: BIOINFORMATICS. 2016;32(17):i455-i463
Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization
Ammad-ud-din M; Khan SA; Malani D; Murumagi A; Kallioniemi O; Aittokallio T; Kaski S
Editorial comment: EMBO MOLECULAR MEDICINE. 2015;7(8):994-995
Circulating tumor DNA in early-stage breast cancer: personalized biomarkers for occult metastatic disease and risk of relapse?
af Hällström TM; Puhka M; Kallioniemi O
Published conference paper: BIOINFORMATICS. 2014;30(17):i497-i504
Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis.
Khan SA; Virtanen S; Kallioniemi OP; Wennerberg K; Poso A; Kaski S
Letter: LEUKEMIA. 2014;28(8):1738-1742
Novel activating STAT5B mutations as putative drivers of T-cell acute lymphoblastic leukemia.
Kontro M; Kuusanmäki H; Eldfors S; Burmeister T; Andersson EI; Bruserud O; Brümmendorf TH; Edgren H; Gjertsen BT; Itälä-Remes M; Lagström S; Lohi O; Lundán T; Martí JML; Majumder MM; Parsons A; Pemovska T; Rajala H; Vettenranta K; Kallioniemi O; Mustjoki S; Porkka K; Heckman CA
Editorial comment: CLINICAL CHEMISTRY. 2012;58(12):1717-1718
Introducing tissue microarrays to molecular pathology.
Kallioniemi OP; Kononen J; Sauter G
Corrigendum: BREAST CANCER RESEARCH AND TREATMENT. 2012;131(3):1085-1086
Enhanced serine production by bone metastatic breast cancer cells stimulates osteoclastogenesis (vol 125, pg 421, 2011)
Pollari S; Kakonen S-M; Edgren H; Wolf M; Kohonen P; Sara H; Guise T; Nees M; Kallioniemi O
Editorial comment: CANCER DISCOVERY. 2011;1(1):12-13
KRAS oncogene rearrangements and gene fusions: unexpected rare encounters in late-stage prostate cancers.
Edgren H; Kangaspeska S; Kallioniemi O
Editorial comment: BIOINFORMATICS. 2011;27(10):1345
On the organization of bioinformatics core services in biology-based research institutes.
Kallioniemi O; Wessels L; Valencia A
Review: EUROPEAN UROLOGY. 2011;59(5):671-681
MicroRNA in prostate, bladder, and kidney cancer: a systematic review.
Catto JWF; Alcaraz A; Bjartell AS; De Vere White R; Evans CP; Fussel S; Hamdy FC; Kallioniemi O; Mengual L; Schlomm T; Visakorpi T
Review: NATURE REVIEWS CLINICAL ONCOLOGY. 2011;8(3):142-150
Emerging molecular biomarkers--blood-based strategies to detect and monitor cancer.
Hanash SM; Baik CS; Kallioniemi O
Editorial comment: CLINICAL CHEMISTRY. 2010;56(11):1660-1664
Cancer genomes.
Diamandis EP; Hudson T; Kallioniemi O; Liu ET; López-Otín C
Review: METHODS IN MOLECULAR BIOLOGY. 2010;576:61-87
A decade of cancer gene profiling: from molecular portraits to molecular function.
Sara H; Kallioniemi O; Nees M
Editorial comment: MOLECULAR ONCOLOGY. 2009;3(1):9-17
Report on EU-USA Workshop: How Systems Biology Can Advance Cancer Research (27 October 2008)
Aebersold R; Auffray C; Baney E; Barillot E; Brazma A; Brett C; Brunak S; Butte A; Califano A; Celis J; Cufer T; Ferrell J; Galas D; Gallahan D; Gatenby R; Goldbeter A; Hace N; Henney A; Hood L; Iyengar R; Jackson V; Kallioniemi O; Klingmueller U; Kolar P; Kolch W; Kyriakopoulou C; Laplace F; Lehrach H; Marcus F; Matrisian L; Nolan G; Pelkmans L; Potti A; Sander C; Seljak M; Singer D; Sorger P; Stunnenberg H; Superti-Furga G; Uhlen M; Vidal M; Weinstein J; Wigle D; Williams M; Wolkenhauer O; Zhivotousky B; Zinovyev A; Zupan B
Published conference paper: BMC BIOINFORMATICS. 2009;10 Suppl 1(Suppl 1):S24
Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations.
Autio R; Kilpinen S; Saarela M; Kallioniemi O; Hautaniemi S; Astola J
Corrigendum: BRITISH JOURNAL OF CANCER. 2008;98(12):2015
The BOADICEA model of genetic susceptibility to breast and ovarian cancers: updates and extensions (vol 98, pg 1457, 2008)
Antoniou AC; Cunningham AP; Peto J; Evans DG; Lalloo F; Narod SA; Risch HA; Eyfjord JE; Hopper JL; Southey MC; Olsson H; Johannsson O; Borg A; Pasini B; Radice P; Manoukian S; Eccles DM; Tang N; Olah E; Anton-Culver H; Warner E; Lubinski J; Gronwald J; Gorski B; Tryggvadottir L; Syrjakoski K; Kallioniemi O-P; Eerola H; Nevanlinna H; Pharoah PDP; Easton DF
Other: BULLETIN DU CANCER. 2008;95(4):475-480
Omics' approaches in cancer: clinical applications
Stratton M; Birnbaum D; Borresen-Dale A-L; Van de Vijver M; Chinnaiyan A; Kallioniemi O; Zucman-Rossi J; Hoheisel J; Kallioniemi O
Corrigendum: NATURE METHODS. 2007;4(2):126
ProteomeBinders:: planning a European resource of affinity reagents for analysis of the human proteome (vol 4, pg 13, 2007)
Taussig MJ; Stoevesandt O; Borrebaeck CAK; Bradbury AR; Cahill D; Cambillau C; de Daruvar A; Duebel S; Eichler J; Frank R; Gibson TJ; Gloriam D; Gold L; Herberg FW; Hermjakob H; Hoheisel JD; Joos TO; Kallioniemi O; Koegl M; Konthur Z; Korn B; Kremmer E; Krobitsch S; Landegren U; van der Maarel S; McCafferty J; Muyldermans S; Nygren P-A; Palcy S; Plueckthun A; Polic B; Przybylski M; Saviranta P; Sawyer A; Sherman DJ; Skerra A; Templin M; Ueffing M; Uhlen M
Editorial comment: CANCER CELL. 2006;10(6):453-454
Integrated breast cancer genomics.
Edgren H; Kallioniemi O
Editorial comment: TRENDS IN BIOTECHNOLOGY. 2006;24(5):195-197
Human Protein Atlas charts a diverse terrain.
Saviranta P; Kallioniemi O
Review: BJU INTERNATIONAL. 2005;96 Suppl 2:10-15
Functional genomics and transcriptomics of prostate cancer: promises and limitations.
Kallioniemi O
Corrigendum: HUMAN GENETICS. 2005;118(2):307
A major locus for hereditary prostate cancer in Finland:: localization by linkage disequilibrium of a haplotype in the HPCX region (vol 117, pg 307, 2005)
Baffoe-Bonnie AB; Smith JR; Stephan DA; Schleutker J; Carpten JD; Kainu T; Gillanders EM; Matikainen M; Teslovich TM; Tammela T; Sood R; Balshem AM; Scarborough SD; Xu JF; Isaacs WB; Trent JM; Kallioniemi OP; Bailey-Wilson JE
Review: CELLULAR ONCOLOGY (DORDRECHT). 2005;27(3):169-173
NMD microarray analysis for rapid genome-wide screen of mutated genes in cancer.
Wolf M; Edgren H; Muggerud A; Kilpinen S; Huusko P; Sørlie T; Mousses S; Kallioniemi O
Other: EUROPEAN JOURNAL OF HUMAN GENETICS. 2004;12(8):603
Claes Lundsteen - in memoriam
Graham J; Blennow E; Boavida MG; Carter N; Cremer C; Cremer T; Delattre O; Gerdes T; Granum E; Hagemeijer A; Rivas JMH; Kallioniemi O; Kirchhoff M; Kolvraa S; Lichter P; Pearson P; Philip J; Piper J; van der Ploeg M; Raap AK; Rocchi M; Rosenberg C; Speicher M; Speleman F; Tommerup N; van Roy N; Veltman J; Young T
Editorial comment: NATURE. 2004;428(6981):379-382
Medicine: profile of a tumour.
Kallioniemi O
Letter: JOURNAL OF MEDICAL GENETICS. 2003;40(3):e19-19
No fumarate hydratase (FH) mutations in hereditary prostate cancer.
Lehtonen R; Kiuru M; Rökman A; Ikonen T; Cunningham JM; Schaid DJ; Matikainen M; Nupponen NN; Karhu A; Kallioniemi O-P; Thibodeau SN; Schleutker J; Aaltonen LA
Review: CURRENT OPINION IN CHEMICAL BIOLOGY. 2002;6(1):97-101
Clinical and functional target validation using tissue and cell microarrays.
Mousses S; Kallioniemi A; Kauraniemi P; Elkahloun A; Kallioniemi O-P
Review: DUODECIM; LAAKETIETEELLINEN AIKAKAUSKIRJA. 2002;118(11):1157-1166
[Gene chip technique and associated bioinformatics].
Monni O; Hautaniemi S; Kallioniemi O
Review: DUODECIM; LAAKETIETEELLINEN AIKAKAUSKIRJA. 2002;118(11):1149-1156
[From gene chips to biochips: challenges and possibilities of the new biotechnology].
Kallioniemi O
Letter: JOURNAL OF THE NATIONAL CANCER INSTITUTE. 2001;93(2):153-154
Re:: Population-based study of BRCA1 and BRCA2 mutations in 1035 unselected Finnish breast cancer patients -: Response
Vahteristo P; Syrjäkoski K; Eerola H; Kainu T; Holli K; Blomqvist C; Kallioniemi OP; Nevanlinna H
Review: DUODECIM; LAAKETIETEELLINEN AIKAKAUSKIRJA. 1999;115(21):2365-2374
[Susceptibility genes of familial breast cancer in Finland].
Nevanlinna H; Kallioniemi OP
Review: AMERICAN JOURNAL OF PATHOLOGY. 1998;152(1):1-9
Androgen receptor gene and hormonal therapy failure of prostate cancer.
Koivisto P; Kolmer M; Visakorpi T; Kallioniemi OP
Review: TRENDS IN GENETICS. 1997;13(10):405-409
Genome screening by comparative genomic hybridization.
Forozan F; Karhu R; Kononen J; Kallioniemi A; Kallioniemi OP
Editorial comment: DUODECIM; LAAKETIETEELLINEN AIKAKAUSKIRJA. 1997;113(6):461-462
[ Hereditary prostate cancer with gene location].
Matikainen M; Schleutker J; Visakorpi T; Kallioniemi OP
Editorial comment: NATURE GENETICS. 1997;15(1):5-6
Linking chromosomal clues.
Kallioniemi OP
Editorial comment: TRENDS IN GENETICS. 1996;12(6):237-238
Comparative genomic hybridization gaining in popularity
Kallioniemi OP
Review: ADVANCES IN CANCER RESEARCH. 1996;68:225-255
Genetic basis and clonal evolution of human prostate cancer.
Kallioniemi OP; Visakorpi T
Review: DUODECIM; LAAKETIETEELLINEN AIKAKAUSKIRJA. 1996;112(4):297-305
[From pedigree analysis to gene defects].
Kere J; Kallioniemi OP
Other: GENOMICS. 1995;26(1):134-137
A physical map of chromosome 20 established using fluorescence in situ hybridization and digital image analysis.
Stokke T; Collins C; Kuo WL; Kowbel D; Shadravan F; Tanner M; Kallioniemi A; Kallioniemi OP; Pinkel D; Deaven L
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