Pekka Kohonen

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Articles

Article: ADVANCED SCIENCE. 2024;11(9):e2306268
Meta-Analysis of Integrated Proteomic and Transcriptomic Data Discerns Structure-Activity Relationship of Carbon Materials with Different Morphologies
Dumit VI; Liu Y-C; Bahl A; Kohonen P; Grafstrom RC; Nymark P; Mueller-Graf C; Haase A; Pink M
Article: TOXICOLOGY LETTERS. 2023;383:33-42
The Precision Toxicology initiative.
PrecisionTox Consortium
Article: NATURE NANOTECHNOLOGY. 2021;16(6):644-654
Towards FAIR nanosafety data
Jeliazkova N; Apostolova MD; Andreoli C; Barone F; Barrick A; Battistelli C; Bossa C; Botea-Petcu A; Chatel A; De Angelis I; Dusinska M; El Yamani N; Gheorghe D; Giusti A; Gomez-Fernandez P; Grafstrom R; Gromelski M; Jacobsen NR; Jeliazkov V; Jensen KA; Kochev N; Kohonen P; Manier N; Mariussen E; Mech A; Navas JM; Paskaleva V; Precupas A; Puzyn T; Rasmussen K; Ritchie P; Llopis IR; Runden-Pran E; Sandu R; Shandilya N; Tanasescu S; Haase A; Nymark P
Article: NANOMATERIALS. 2020;10(12):E2493-2493
Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies?
Lynch I; Afantitis A; Exner T; Himly M; Lobaskin V; Doganis P; Maier D; Sanabria N; Papadiamantis AG; Rybinska-Fryca A; Gromelski M; Puzyn T; Willighagen E; Johnston BD; Gulumian M; Matzke M; Etxabe AG; Bossa N; Serra A; Liampa I; Harper S; Tamm K; Jensen ACO; Kohonen P; Slater L; Tsoumanis A; Greco D; Winkler DA; Sarimveis H; Melagraki G
Article: TOXICOLOGY IN VITRO. 2019;54:23-32
Integrated analysis of in vitro data and the adverse outcome pathway framework for prioritization and regulatory applications: An exploratory case study using publicly available data on piperonyl butoxide and liver models
Oki NO; Farcal L; Abdelaziz A; Florean O; Doktorova TY; Exner T; Kohonen P; Grafstrom R; Hardy B
Article: JOURNAL OF CHEMICAL INFORMATION AND MODELING. 2018;58(3):543-549
toxFlow: A Web-Based Application for Read-Across Toxicity Prediction Using Omics and Physicochemical Data
Varsou D-D; Tsiliki G; Nymark P; Kohonen P; Grafstrom R; Sarimveis H
Article: TOXICOLOGICAL SCIENCES. 2018;162(1):264-275
A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions
Nymark P; Rieswijk L; Ehrhart F; Jeliazkova N; Tsiliki G; Sarimveis H; Evelo CT; Hongisto V; Kohonen P; Willighagen E; Grafstrom RC
Article: SCIENTIFIC REPORTS. 2018;8(1):1115
Macrophage sensing of single-walled carbon nanotubes via Toll-like receptors
Mukherjee SP; Bondarenko O; Kohonen P; Andon FT; Brzicova T; Gessner I; Mathur S; Bottini M; Calligari P; Stella L; Kisin E; Shvedova A; Autio R; Salminen-Mankonen H; Lahesmaa R; Fadeel B
Article: SMALL METHODS. 2017;1(11)
Enriching Nanomaterials Omics Data: An Integration Technique to Generate Biological Descriptors
Tsiliki G; Nymark P; Kohonen P; Grafstrom R; Sarimveis H
Article: JOURNAL OF BIOMEDICAL SEMANTICS. 2017;8(1):35
RDFIO: extending Semantic MediaWiki for interoperable biomedical data management
Lampa S; Willighagen E; Kohonen P; King A; Vrandecic D; Grafstrom R; Spjuth O
Article: NATURE COMMUNICATIONS. 2017;8:15932
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; Grafstrom RC
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: 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
Journal article: HEALTH SYSTEMS AND POLICY RESEARCH. 2016;03(04)
Improving Taxation to Achieve the Millennium Development Goals in Africa: The Right to Health
Waris A; Kohonen P; Kohonen M
Article: ATLA ALTERNATIVES TO LABORATORY ANIMALS. 2015;43(5):325-332
Toward the Replacement of Animal Experiments through the Bioinformatics-driven Analysis of 'Omics' Data from Human Cell Cultures
Grafstrom RC; Nymark P; Hongisto V; Spjuth O; Ceder R; Willighagen E; Hardy B; Kaski S; Kohonen P
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: 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: ACS NANO. 2015;9(1):146-163
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; Nystrom A; Fadeel B
Article: PLOS ONE. 2015;10(10):e0129008
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; Lehtio J; Toprak MS; Fadeel B
Article: BEILSTEIN JOURNAL OF NANOTECHNOLOGY. 2015;6:1609-1634
The eNanoMapper database for nanomaterial safety information
Jeliazkova N; Chomenidis C; Doganis P; Fadeel B; Grafstrom R; Hardy B; Hastings J; Hegi M; Jeliazkov V; Kochev N; Kohonen P; Munteanu CR; Sarimveis H; Smeets B; Sopasakis P; Tsiliki G; Vorgrimmler D; Willighagen E
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: JOURNAL OF CELL BIOLOGY. 2014;204(5):713-727
CIP2A oncoprotein controls cell growth and autophagy through mTORC1 activation
Puustinen P; Rytter A; Mortensen M; Kohonen P; Moreira JM; Jaattela 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
Journal article: CANCER RESEARCH. 2013;73(8_Supplement):5273
Abstract 5273: Systematic functional screening, miRNA and target expression analyses reveal miR-19, -124, -583, -129 and -876 as key nodes in prostate cancer proliferation networks.
Östling P; Leivonen S-K; Kohonen P; Aakula A; Hintsanen P; Aittokallio T; Perälä M; Kallioniemi O
Journal article: CANCER RESEARCH. 2013;73(8_Supplement):4170
Abstract 4170: MicroRNA-135b influences androgen and estrogen receptor protein levels and regulates proliferation of hormone-receptor positive prostate and breast cancer cells.
Aakula A; Leivonen S-K; Kohonen P; Hintsanen P; Aittokallio T; Ceder Y; Børresen-Dale A-L; Perälä M; Östling P; Kallioniemi O
Journal article: CANCER RESEARCH. 2013;73(8_Supplement):3179
Abstract 3179: The head and neck cancer biomarker wiki: A tool for data mining and biomarker meta-analyses.
Ceder R; Kohonen P; Grafström RC
Article: CARCINOGENESIS. 2013;34(2):436-445
Novel pyrimidine-2,4-diamine derivative suppresses the cell viability and spindle assembly checkpoint activity by targeting Aurora kinases
Salmela A-L; Pouwels J; Maki-Jouppila J; Kohonen P; Toivonen P; Kallio L; Kallio M
Article: MOLECULAR INFORMATICS. 2013;32(1):47-63
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; Grafstrom RC; Healy L; Helma C; Jeliazkova N; Jeliazkov V; Maggioni S; Miller S; Myatt G; Rautenberg M; Stacey G; Willighagen E; Wiseman J; Hardy B
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(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: 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: 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: MOLECULAR CELL. 2012;45(6):764-776
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; Fehrenbacher N; Olsen CJ; Daugaard M; Egebjerg C; Bottzauw T; Kohonen P; Nylandsted J; Hautaniemi S; Moreira J; Jaattela M; Kallunki T
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: 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
Journal article: PLOS ONE. 2012;7(6)
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; Perala M; Kallioniemi O; Iljin K
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: 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
Journal article: PLOS ONE. 2011;6(4):10.1371/annotation/7d5718
Correction: 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; BjÃ¶rkman M; Gupta S; Kohonen P; Nees M; 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):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: 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: GENOME MEDICINE. 2010;2(9):65
Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme
Ovaska K; Laakso M; Haapa-Paananen S; Louhimo R; Chen P; Aittomaki V; Valo E; Nunez-Fontarnau J; Rantanen V; Karinen S; Nousiainen K; Lahesmaa-Korpinen A-M; Miettinen M; Saarinen L; Kohonen P; Wu J; Westermarck J; Hautaniemi S
Article: EUROPEAN JOURNAL OF IMMUNOLOGY. 2010;40(9):2599-2607
Concerted action of Helios and Ikaros controls the expression of the inositol 5-phosphatase SHIP
Alinikula J; Kohonen P; Nera K-P; Lassila O
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
Journal article: CANCER RESEARCH. 2010;70(8_Supplement):4708
Abstract 4708: Hes6 as a glioma biomarker with functional significance for cancer growth
Haapa-Paananen SM; Waltari M; Puputti M; Kiviluoto S; Mpindi J-P; Kohonen P; Tynninen O; Haapasalo H; Joensuu H; Perälä M; Kallioniemi O
Article: BMC CANCER. 2010;10:7
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; Perala M; Ivaska J
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(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: IMMUNITY. 2006;24(3):283-293
Loss of Pax5 promotes plasma cell differentiation
Nera KP; Kohonen P; Narvi E; Peippo A; Mustonen L; Terho P; Koskela K; Buerstedde JM; Lassila O
Article: SCANDINAVIAN JOURNAL OF IMMUNOLOGY. 2005;62(3):218-223
Development of early PCLP1-expressing haematopoietic cells within the avian dorsal aorta
Suonpää P; Kohonen P; Koskela K; Koskiniemi H; Salminen-Mankonen H; Lassila O
Article: SCANDINAVIAN JOURNAL OF IMMUNOLOGY. 2004;60(1-2):100-107
Avian Helios and evolution of the Ikaros family
Kohonen P; Nera KP; Lassila O
Article: SCANDINAVIAN JOURNAL OF IMMUNOLOGY. 2004;59(5):449-457
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
Article: IMMUNOGENETICS. 2004;55(12):845-854
Identification of a novel cytokine-like transcript differentially expressed in avian γδ T cells
Koskela K; Kohonen P; Salminen H; Uchida T; Buerstedde JM; Lassila O
Article: IMMUNOGENETICS. 2003;55(6):412-422
Insight into lymphoid development by gene expression profiling of avian B cells
Koskela K; Kohonen P; Nieminen P; Buerstedde JM; Lassila O
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All other publications

Review: NANOTOXICOLOGY. 2024;18(4):373-400
Bioinformatics and machine learning to support nanomaterial grouping
Bahl A; Halappanavar S; Wohlleben W; Nymark P; Kohonen P; Wallin H; Vogel U; Haase A
Editorial comment: NATURE NANOTECHNOLOGY. 2022;17(1):19-20
Reply to: Prospects and challenges for FAIR toxicogenomics data
Grafstrom R; Haase A; Kohonen P; Jeliazkova N; Nymark P
Conference publication: TOXICOLOGY LETTERS. 2021;350:S9-S10
In vitro-based high-throughput screening and toxicogenomics to support effective safety evaluation of engineered nanomaterials
Nymark P; Hongisto V; Kohonen P; Jeliazkova N; Karlsson HL; Grafstrom R
Conference publication: TOXICOLOGY LETTERS. 2021;350:S38
Novel means of enabling high-throughput toxicogenomics and adverse outcome pathways for prediction of lung toxicity
Nymark P; Martens M; Willighagen E; Hongisto V; Kohonen P; Grafstrom RC; Beronius A; Halappanavar S
Review: NANOMATERIALS. 2020;10(5):E903-903
Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data
Federico A; Serra A; Ha MK; Kohonen P; Choi J-S; Liampa I; Nymark P; Sanabria N; Cattelani L; Fratello M; Kinaret PAS; Jagiello K; Puzyn T; Melagraki G; Gulumian M; Afantitis A; Sarimveis H; Yoon T-H; Grafstrom R; Greco D
Review: NANOMATERIALS. 2020;10(4):E750-750
Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects
Kinaret PAS; Serra A; Federico A; Kohonen P; Nymark P; Liampa I; Ha MK; Choi J-S; Jagiello K; Sanabria N; Melagraki G; Cattelani L; Fratello M; Sarimveis H; Afantitis A; Yoon T-H; Gulumian M; Grafstrom R; Puzyn T; Greco D
Review: NANOMATERIALS. 2020;10(4):E708-708
Transcriptomics in Toxicogenomics, Part III: Data Modelling for Risk Assessment
Serra A; Fratello M; Cattelani L; Liampa I; Melagraki G; Kohonen P; Nymark P; Federico A; Kinaret PAS; Jagiello K; Ha MK; Choi J-S; Sanabria N; Gulumian M; Puzyn T; Yoon T-H; Sarimveis H; Grafstrom R; Afantitis A; Greco D
Review: SMALL. 2020;16(6):e1904749
Toward Rigorous Materials Production: New Approach Methodologies Have Extensive Potential to Improve Current Safety Assessment Practices
Nymark P; Bakker M; Dekkers S; Franken R; Fransman W; Garcia-Bilbao A; Greco D; Gulumian M; Hadrup N; Halappanavar S; Hongisto V; Hougaard KS; Jensen KA; Kohonen P; Koivisto AJ; Dal Maso M; Oosterwijk T; Poikkimaki M; Rodriguez-Llopis I; Stierum R; Sorli JB; Grafstrom R
Review: COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL. 2020;18:583-602
NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment
Afantitis A; Melagraki G; Isigonis P; Tsoumanis A; Varsou DD; Valsami-Jones E; Papadiamantis A; Ellis L-JA; Sarimveis H; Doganis P; Karatzas P; Tsiros P; Liampa I; Lobaskin V; Greco D; Serra A; Kinaret PAS; Saarimaki LA; Grafstrom R; Kohonen P; Nymark P; Willighagen E; Puzyn T; Rybinska-Fryca A; Lyubartsev A; Jensen KA; Brandenburg JG; Lofts S; Svendsen C; Harrison S; Maier D; Tamm K; Janes J; Sikk L; Dusinska M; Longhin E; Runden-Pran E; Mariussen E; El Yamani N; Unger W; Radnik J; Tropsha A; Cohen Y; Leszczynski J; Hendren CO; Wiesner M; Winkler D; Suzuki N; Yoon TH; Choi J-S; Sanabria N; Gulumian M; Lynch I
Conference publication: INTERNATIONAL JOURNAL OF TOXICOLOGY. 2019;38(1):55
Integrated Analysis of Transcriptomics Data With the AOP Framework for Adverse Outcome Identification and Risk Assessment of Chemicals: Piperonyl Butoxide Case Study
Oki NO; Farcal L; Abdelaziz A; Florean O; Hollinger F; Exner T; Kohonen P; Grafstrom R; Hardy B
Book chapter: ADVANCES IN COMPUTATIONAL TOXICOLOGY: CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS. 2019;p. 57-74
Matrix and Tensor Factorization Methods for Toxicogenomic Modeling and Prediction
Khan SA; Aittokallio T; Scherer A; Grafström R; Kohonen P
Conference publication: TOXICOLOGY LETTERS. 2019;314:S69
Predictive toxicogenomics space modeling serves effectively to sensitive biomarker-based read across from capturing toxic mode-of-action of lowest-observable effect levels
Kohonen PJ; Nymark P; Hongisto V; Grafstrom R
Conference publication: TOXICOLOGY LETTERS. 2019;314:S62-S63
Grouping of representative nanomaterials is efficiently executed by combining high-throughput-generated biological data with physicochemical data
Nymark P; Hongisto V; Kohonen PJ; Haase A; Jensen KA; Grafstrom RC
Conference publication: TOXICOLOGY LETTERS. 2019;314:S25
Systems toxicology to support development of adverse outcome pathways
Grafstrom RC; Hongisto V; Kohonen PJ; Nymark P
Published conference paper: ANNALS OF THE AMERICAN THORACIC SOCIETY. 2018;15(Suppl 2):S91-S97
Toxic and Genomic Influences of Inhaled Nanomaterials as a Basis for Predicting Adverse Outcome
Nymark P; Kohonen P; Hongisto V; Grafstrom RC
Book chapter: NANOTOXICOLOGY: ISSUES IN TOXICOLOGY. 2017;p. 276-303
Chapter 11 Computational Modelling of Biological Responses to Engineered Nanomaterials
Doganis P; Tsiliki G; Drakakis G; Chomenidis C; Nymark P; Kohonen P; Grafström R; Abdelaziz A; Farcal L; Exner T; Hardy B; Sarimveis H
Meeting abstract: TOXICOLOGY LETTERS. 2016;258:S118-S119
eNanoMapper - A database and ontology framework for design and safety assessment of nanomaterials
Kilic G; Fadeel B; Farcal L; Sarimveis H; Doganis P; Drakakis G; Tsiliki G; Chomenidis C; Helma C; Rautenberg M; Gebele D; Jeliazkova N; Kochev N; Owen G; Chang J; Willighagen EL; Ehrhart F; Rieswijk L; Hongisto V; Nymark P; Kohonen P; Grafstrom R; Hardy B
Conference publication: 2014;:1-9
The First eNanoMapper Prototype: A Substance Database to Support Safe-by-Design
Jeliazkova N; Doganis P; Fadeel B; Grafström R; Hastings J; Jeliazkov V; Kohonen P; Munteanu CR; Sarimveis H; Smeets B; Tsiliki G; Vorgrimmler D; Willighagen E
Review: BASIC AND CLINICAL PHARMACOLOGY AND TOXICOLOGY. 2014;115(1):50-58
Cancer Biology, Toxicology and Alternative Methods Development Go Hand-in-Hand
Kohonen P; Ceder R; Smit I; Hongisto V; Myatt G; Hardy B; Spjuth O; Grafstrom R
Conference publication: ACS NATIONAL MEETING BOOK OF ABSTRACTS. 2014;248
Systems biology approaches reveal low-dose effects of dendrimers
Feliu N; Kohonen P; Palmberg L; Nystrom AM; Fadeel B
Meeting abstract: CANCER RESEARCH. 2013;73(8):4032
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; Ceder R
Conference publication: CANCER RESEARCH. 2013;73(8):5657
Polyamidoamine dendrimers induce epigenetic changes in cultured normal and malignant human lung epithelial cells.
Kohonen PJ; Feliu NT; Palmberg L; Karlsson HL; Wallberg AE; Grafstrom RC; Fadeel B
Meeting abstract: EUROPEAN JOURNAL OF CANCER. 2012;48:S140
Precursor MicroRNA Functional Profiling Identifies MicroRNAs Essential for Glioblastoma Proliferation
Haapa-Paananen S; Chen P; Hautaniemi S; Kohonen P; Perala M; Kallioniemi O
Meeting abstract: TOXICOLOGY LETTERS. 2012;211:S40
Genotoxic and epigenetic effects of silver nanoparticles
Karlsson H; Gliga AR; Kohonen P; Wallberg A; Fadeel B
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
Meeting abstract: CANCER RESEARCH. 2011;71:3977
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
Meeting abstract: CANCER RESEARCH. 2011;71:3800
HES6 gene is a strong glioma biomarker and a key transcriptional regulator needed for cancer cell growth
Haapa-Paananen SM; Kiviluoto S; Waltari M; Puputti M; Mpindi J-P; Kohonen P; Tynninen O; Haapasalo H; Joensuu H; Perala M; Kallioniemi O
Meeting abstract: EJC SUPPLEMENTS. 2010;8(7):177
Systematic functional analysis of microRNAs by transfection of 1129 miRNAs into prostate cancer cells
Bjerkvig R; Leivonen SK; Ostling P; Aakula A; Kohonen P; Makela R; Hagman Z; Edgren H; Ceder Y; Perala M; Kallioniemi O
Meeting abstract: EJC SUPPLEMENTS. 2010;8(5):61-62
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
Meeting abstract: CANCER RESEARCH. 2010;70:2072
Systematic functional analysis of microRNAs by transfection of 1129 miRNAs into prostate cancer cells
Ostling P; Leivonen S-K; Aakula A; Kohonen P; Makela R; Perala M; Kallioniemi O
Meeting abstract: CANCER RESEARCH. 2010;70:1953
Functional identification of microRNA targets by integrated proteomics and microarray profiling: miR-193b in breast cancer
Leivonen S-K; Rokka A; Ostling P; Kohonen P; Corthals G; Perala M; Kallioniemi O
Meeting abstract: BONE. 2010;47:S291
Enhanced serine production by bone metastatic breast cancer cells stimulates osteoclastogenesis
Pollari S; Kakonen S; Edgren H; Wolf M; Kohonen P; Sara H; Guise T; Nees M; Kallioniemi O
Conference publication: NEURO-ONCOLOGY. 2010;12:34
HES6 AS A GLIOMA BIOMARKER WITH FUNCTIONAL SIGNIFICANCE FOR CANCER GROWTH
Haapa-Paananen S; Kiviluoto S; Waltari M; Puputti M; Mpindi JP; Kohonen P; Tynninen O; Haapasalo H; Joensuu H; Perala M; Kallioniemi O
Conference publication: CANCER RESEARCH. 2009;69
High-throughput functional screens and clinical profiling identify microRNAs regulating estrogen receptor (ER)-\#945; signaling in breast cancer
Leivonen S-K; Makela R; Ostling P; Kohonen P; Haapa-Paananen S; Sahlberg N; Helstrom K; Aakula A; Kleivi K; Enerly E; Kristensen V; Berresen-Dale A-L; Saviranta P; Perala M; Kallioniemi O
Conference publication: CANCER RESEARCH. 2008;68(9)
MicroRNAs in bone metastatic breast cancer cells - expression and effects on IL-11 production and cell survival
Pollari S; Hellstrom K; Haapa-Paananen S; Leivonen S-K; Kohonen P; Sahlberg N; Perala M; Kakonen S-M; Nees M; Kallioniemi O
Meeting abstract: CANCER TREATMENT REVIEWS. 2008;34:S65
MicroRNA expression profiling and functional screening in bone metastatic breast cancer cells
Pollari S; Hellstrom K; Haapa-Paananen S; Leivonena S-K; Kohonen P; Sahberg N; Perala M; Kakonen S-M; Nees M; Kattioniemi O
Review: SCANDINAVIAN JOURNAL OF IMMUNOLOGY. 2007;66(2-3):113-121
Avian model for B-cell immunology - New genomes and phylotranscriptomics
Kohonen P; Nera K-P; Lassila O
Published conference paper: CURRENT TOPICS IN MICROBIOLOGY AND IMMUNOLOGY. 2000;251:51-58
The Ikaros family and the development of early intraembryonic hematopoietic stem cells
Liippo J; Nera KP; Kohonen P; Lampisuo M; Koskela K; Nieminen P; Lassila O
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Cell culture-based toxicogenomics for toxicity prediction
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