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A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions
Nymark P, Rieswijk L, Ehrhart F, Jeliazkova N, Tsiliki G, Sarimveis H, et al
Toxicological sciences : an official journal of the Society of Toxicology 2018;162(1):264-275

Macrophage sensing of single-walled carbon nanotubes via Toll-like receptors
Mukherjee Sp, Bondarenko O, Kohonen P, Andón Ft, Brzicová T, Gessner I, et al
Scientific reports 2018;8(1):1115-

toxFlow: A Web-Based Application for Read-Across Toxicity Prediction Using Omics and Physicochemical Data
Varsou Dd, Tsiliki G, Nymark P, Kohonen P, Grafström R, Sarimveis H
Journal of chemical information and modeling 2018;58(3):543-549

Toxic and Genomic Influences of Inhaled Nanomaterials as a Basis for Predicting Adverse Outcome
Nymark P, Kohonen P, Hongisto V, Grafström Rc
Annals of the American Thoracic Society 2018;15(Supplement_2):S91-S97

A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury
Kohonen P, Parkkinen Ja, Willighagen El, Ceder R, Wennerberg K, Kaski S, et al
Nature communications 2017;8():15932-

RDFIO: extending Semantic MediaWiki for interoperable biomedical data management
Lampa S, Willighagen E, Kohonen P, King A, Vrandečić D, Grafström R, et al
Journal of biomedical semantics 2017;8(1):35-

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, et al
Journal of molecular biochemistry 2016;5(1):12-22

Systematic Identification of MicroRNAs That Impact on Proliferation of Prostate Cancer Cells and Display Changed Expression in Tumor Tissue
Aakula A, Kohonen P, Leivonen Sk, Mäkelä R, Hintsanen P, Mpindi Jp, et al
European urology 2016;69(6):1120-8

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, et al
INTERNATIONAL JOURNAL OF CANCER 2015;136(11):2535-45

miR-183 in prostate cancer cells positively regulates synthesis and serum levels of prostate-specific antigen
Larne O, Östling P, Haflidadóttir Bs, Hagman Z, Aakula A, Kohonen P, et al
European urology 2015;68(4):581-8

Next-generation sequencing reveals low-dose effects of cationic dendrimers in primary human bronchial epithelial cells
Feliu N, Kohonen P, Ji J, Zhang Y, Karlsson Hl, Palmberg L, et al
ACS nano 2015;9(1):146-63

Proteomics Analysis Reveals Distinct Corona Composition on Magnetic Nanoparticles with Different Surface Coatings: Implications for Interactions with Primary Human Macrophages
Vogt C, Pernemalm M, Kohonen P, Laurent S, Hultenby K, Vahter M, et al
PloS one 2015;10(10):e0129008-

The eNanoMapper database for nanomaterial safety information
Jeliazkova N, Chomenidis C, Doganis P, Fadeel B, Grafström R, Hardy B, et al
Beilstein journal of nanotechnology 2015;6():1609-34

Toward the Replacement of Animal Experiments through the Bioinformatics-driven Analysis of 'Omics' Data from Human Cell Cultures
Grafström Rc, Nymark P, Hongisto V, Spjuth O, Ceder R, Willighagen E, et al
Alternatives to laboratory animals : ATLA 2015;43(5):325-32

Cancer biology, toxicology and alternative methods development go hand-in-hand
Kohonen P, Ceder R, Smit I, Hongisto V, Myatt G, Hardy B, et al
Basic & clinical pharmacology & toxicology 2014;115(1):50-8

CIP2A oncoprotein controls cell growth and autophagy through mTORC1 activation
Puustinen P, Rytter A, Mortensen M, Kohonen P, Moreira Jm, Jäättelä M
The Journal of cell biology 2014;204(5):713-27

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, et al
Oncogene 2014;33(27):3538-49

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, et al
CELL DEATH & DISEASE 2014;:e1043-

Functional profiling of precursor MicroRNAs identifies MicroRNAs essential for glioma proliferation
Haapa-paananen S, Chen P, Hellström K, Kohonen P, Hautaniemi S, Kallioniemi O, et al
PloS one 2013;8(4):e60930-

Novel pyrimidine-2,4-diamine derivative suppresses the cell viability and spindle assembly checkpoint activity by targeting Aurora kinases
Salmela Al, Pouwels J, Mäki-jouppila J, Kohonen P, Toivonen P, Kallio L, et al
Carcinogenesis 2013;34(2):436-45

The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing
Kohonen P, Benfenati E, Bower D, Ceder R, Crump M, Cross K, et al
MOLECULAR INFORMATICS 2013;32(1):47-63

Transcriptomics analyses of normal and transformed keratinocyte lines generated novel biomarkers for prognosticating outcome in head and neck cancer
Grafstrom Rc, Merne M, Kohonen P, Jerhammar F, Nees M, Roberg K, et al
CANCER RESEARCH 2013;73(8)

Enhanced serine production by bone metastatic breast cancer cells stimulates osteoclastogenesis (vol 125, pg 421, 2011)
Pollari S, Kakonen Sm, Edgren H, Wolf M, Kohonen P, Sara H, et al
BREAST CANCER RESEARCH AND TREATMENT 2012;131(3):1085-1086

ErbB2-Driven Breast Cancer Cell Invasion Depends on a Complex Signaling Network Activating Myeloid Zinc Finger-1-Dependent Cathepsin B Expression
Rafn B, Nielsen Cf, Andersen Sh, Szyniarowski P, Corcelle-termeau E, Valo E, et al
MOLECULAR CELL 2012;45(6):764-76

Genotoxic and epigenetic effects of silver nanoparticles
Karlsson H, Gliga Ar, Kohonen P, Wallberg A, Fadeel B
TOXICOLOGY LETTERS 2012;:S40-S40

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, et al
ONCOGENE 2012;31(10):1299-310

High-Throughput Transcriptomic and RNAi Analysis Identifies AIM1, ERGIC1, TMED3 and TPX2 as Potential Drug Targets in Prostate Cancer
Vainio P, Mpindi Jp, Kohonen P, Fey V, Mirtti T, Alanen Ka, et al
PLOS ONE 2012;7(6):e39801-

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 Jp, et al
PROSTATE 2012;72(7):789-802

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, et al
ONCOGENE 2012;31(16):2075-89

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 Jp, Rantala J, et al
ONCOGENE 2012;31(29):3444-56

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 Jp, Kohonen P, et al
AMERICAN JOURNAL OF PATHOLOGY 2011;178(2):525-36

Enhanced serine production by bone metastatic breast cancer cells stimulates osteoclastogenesis
Pollari S, Kakonen Sm, Edgren H, Wolf M, Kohonen P, Sara H, et al
BREAST CANCER RESEARCH AND TREATMENT 2011;125(2):421-30

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, et al
PLOS ONE 2011;6(2):e17259-

Identification of miR-193b Targets in Breast Cancer Cells and Systems Biological Analysis of Their Functional Impact
Leivonen Sk, Rokka A, Ostling P, Kohonen P, Corthals Gl, Kallioniemi O, et al
MOLECULAR & CELLULAR PROTEOMICS 2011;10(7):M110.005322-

Systematic Analysis of MicroRNAs Targeting the Androgen Receptor in Prostate Cancer Cells
Ostling P, Leivonen Sk, Aakula A, Kohonen P, Makela R, Hagman Z, et al
CANCER RESEARCH 2011;71(5):1956-67

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 Jp, Knuuttila M, et al
PLOS ONE 2010;5(5):e10431-

Concerted action of Helios and Ikaros controls the expression of the inositol 5-phosphatase SHIP
Alinikula J, Kohonen P, Nera Kp, Lassila O
EUROPEAN JOURNAL OF IMMUNOLOGY 2010;40(9):2599-607

Drugs with known pharmacological profiles, such as monensin, disulfiram and salinomycin, show cancer-selective inhibition of prostate cancer cell growth by increasing oxidative stress
Ketola K, Vainio P, Fey V, Kohonen P, Kallioniemi O, Iljin K
EJC SUPPLEMENTS 2010;8(5):61-62

Enhanced serine production by bone metastatic breast cancer cells stimulates osteoclastogenesis
Pollari S, Kakonen S, Edgren H, Wolf M, Kohonen P, Sara H, et al
BONE 2010;:S291-S291

HES6 AS A GLIOMA BIOMARKER WITH FUNCTIONAL SIGNIFICANCE FOR CANCER GROWTH
Haapa-paananen S, Kiviluoto S, Waltari M, Puputti M, Mpindi Jp, Kohonen P, et al
NEURO-ONCOLOGY 2010;:34-34

Inhibition of receptor tyrosine kinase signalling by small molecule agonist of T-cell protein tyrosine phosphatase
Mattila E, Marttila H, Sahlberg N, Kohonen P, Tahtinen S, Halonen P, et al
BMC CANCER 2010;:7-

Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme
Ovaska K, Laakso M, Haapa-paananen S, Louhimo R, Chen P, Aittomäki V, et al
Genome medicine 2010;2(9):65-

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, et al
CLINICAL CANCER RESEARCH 2009;15(19):6070-8

Protein lysate microarray analysis to identify microRNAs regulating estrogen receptor signaling in breast cancer cell lines
Leivonen Sk, Makela R, Ostling P, Kohonen P, Haapa-paananen S, Kleivi K, et al
ONCOGENE 2009;28(44):3926-36

MicroRNA expression profiling and functional screening in bone metastatic breast cancer cells
Pollari S, Hellstrom K, Haapa-paananen S, Leivonena Sk, Kohonen P, Sahberg N, et al
CANCER TREATMENT REVIEWS 2008;:S65-S65

Avian model for B-cell immunology - New genomes and phylotranscriptomics
Kohonen P, Nera Kp, Lassila O
SCANDINAVIAN JOURNAL OF IMMUNOLOGY 2007;66(2-3):113-21

Loss of Pax5 promotes plasma cell differentiation
Nera Kp, Kohonen P, Narvi E, Peippo A, Mustonen L, Terho P, et al
IMMUNITY 2006;24(3):283-93

Development of early PCLP1-expressing haematopoietic cells within the avian dorsal aorta
Suonpaa P, Kohonen P, Koskela K, Koskiniemi H, Salminen-mankonen H, Lassila O
SCANDINAVIAN JOURNAL OF IMMUNOLOGY 2005;62(3):218-23

Avian Helios and evolution of the Ikaros family
Kohonen P, Nera Kp, Lassila O
SCANDINAVIAN JOURNAL OF IMMUNOLOGY 2004;60(1-2):100-7

Chicken B-cell-activating factor: Regulator of B-cell survival in the bursa of Fabricius
Koskela K, Nieminen P, Kohonen P, Salminen H, Lassila O
SCANDINAVIAN JOURNAL OF IMMUNOLOGY 2004;59(5):449-57

Identification of a novel cytokine-like transcript differentially expressed in avian gamma delta T cells
Koskela K, Kohonen P, Salminen H, Uchida T, Buerstedde Jm, Lassila O
IMMUNOGENETICS 2004;55(12):845-54

Insight into lymphoid development by gene expression profiling of avian B cells
Koskela K, Kohonen P, Nieminen P, Buerstedde Jm, Lassila O
IMMUNOGENETICS 2003;55(6):412-22

The Ikaros family and the development of early intraembryonic hematopoietic stem cells
Liippo J, Nera Kp, Kohonen P, Lampisuo M, Koskela K, Nieminen P, et al
LYMPHOID ORGANOGENESIS 2000;:51-8

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