Search Results - "Jennen, Danyel G.j."

Gene expression responses reflecting 5-FU-induced toxicity: Comparison between patient colon tissue and 3D human colon organoids: Comparison between patient colon tissue and 3D human colon organoids

Authors: Rodrigues, Daniela van Kampen, Roel van Bodegraven, Ad A. et al.

Source: Toxicology Letters

Subject Terms: 0301 basic medicine, 0303 health sciences, 03 medical and health sciences, 3. Good health

Access URL: https://pubmed.ncbi.nlm.nih.gov/36183961
https://cris.maastrichtuniversity.nl/en/publications/0e704454-fe5b-42c8-b719-60252b6f5d42
https://doi.org/10.1016/j.toxlet.2022.09.013

Report of the First ONTOX Stakeholder Network Meeting:Digging Under the Surface of ONTOX Together With the Stakeholders

Authors: Diemar, Michael G. Vinken, Mathieu Teunis, Marc et al.

Source: Diemar, M G, Vinken, M, Teunis, M, Krul, C A M, Busquet, F, Zajac, J D, Kandarova, H, Corvi, R, Rossi, M Z, Kharina, A, Bryndum, L S, Santillo, M, Bloch, D, Kucheryavenko, O, Panagiotakos, D, Rogiers, V, Beekhuijzen, M, Giusti, A, Najjar, A, Courage, C, Koenig, T, Kolle, S, Boonen, H, Dhalluin, S, Boberg, J, Müller, B P, Kukic, P, Ritskes-Hoitinga, M, Grasselli, E, Zietek, T, Stoddart, G, Heusinkveld, H J, Castell, J V, Benfenati, E, Yang, H, Perera, S, Paini, A, Kramer, N I, Hartung, T, Janssen, M, Fritsche, E, Jennen, D G J, Piumatti, M, Rathman, ....

Subject Terms: artificial intelligence, confidence, end-user acceptance, hackathon, NAMs, new approach methodologies, next generation risk assessment, non-animal, probabilistic risk assessment, stakeholder network, toxicology

Relation: info:eu-repo/semantics/altIdentifier/pissn/0261-1929

Availability: https://cris.maastrichtuniversity.nl/en/publications/b7f77fc2-2e77-469c-86c2-f65fd427ed2e
https://doi.org/10.1177/02611929231225730
https://www.scopus.com/pages/publications/85182697833

Report of the First ONTOX Stakeholder Network Meeting: Digging Under the Surface of ONTOX Together With the Stakeholders

Authors: Diemar, Michael G. Vinken, Mathieu Teunis, Marc et al.

Contributors: Diemar, Michael G. Vinken, Mathieu Teunis, Marc et al.

Subject Terms: artificial intelligence, confidence, end-user acceptance, hackathon, NAMs, new approach methodologies, next generation risk assessment, non-animal, probabilistic risk assessment, stakeholder network, toxicology, General Biochemistry,Genetics and Molecular Biology, Medical Laboratory Technology

File Description: application/pdf

Relation: https://dspace.library.uu.nl/handle/1874/437833

Availability: https://dspace.library.uu.nl/handle/1874/437833

Reply to Kaminski, N.E.; Cohen, S.M. Comment on 'Bischoff et al. The Effects of the Food Additive Titanium Dioxide (E171) on Tumor Formation and Gene Expression in the Colon of a Transgenic Mouse Model for Colorectal Cancer. Nanomaterials 2022, 12, 1256'

Authors: Bischoff, Nicolaj S. Proquin, Heloise Jetten, Marlon J. et al.

Source: Nanomaterials, Vol 13, Iss 9, p 1552 (2023)

Subject Terms: Technology, Science & Technology, 1007 Nanotechnology, Chemistry, Multidisciplinary, Physics, Materials Science, Materials Science, Multidisciplinary, 01 natural sciences, 0104 chemical sciences, Physics, Applied, Chemistry, n/a, 4016 Materials engineering, 0103 physical sciences, Physical Sciences, Science & Technology - Other Topics, 4018 Nanotechnology, Nanoscience & Nanotechnology, 0912 Materials Engineering, QD1-999

Access URL: https://doaj.org/article/b88bc0b67aea469da3f6bec087dad66d

Application of transfer learning to predict drug-induced human in vivo gene expression changes using rat in vitro and in vivo data

Authors: Donovan, Shauna D.O. Cavill, Rachel Wimmenauer, Florian et al.

Source: Donovan, S D O, Cavill, R, Wimmenauer, F, Lukas, A, Stumm, T, Smirnov, E, Lenz, M, Ertaylan, G, Jennen, D G J, van Riel, N A W, Driessens, K, Peeters, R L M & de Kok, T M C M 2023, 'Application of transfer learning to predict drug-induced human in vivo gene expression changes using rat in vitro and in vivo data', PLoS ONE, vol. 18, no. 11, e0292030. https://doi.org/10.1371/journal.pone.0292030

Subject Terms: Humans, Rats, Animals, Neural Networks, Computer, Liver, Learning, Machine Learning, Gene Expression

File Description: application/pdf

Relation: info:eu-repo/semantics/altIdentifier/pmid/38032940; info:eu-repo/semantics/altIdentifier/pissn/1932-6203

Availability: https://research.tue.nl/en/publications/b2686d53-ed32-4f14-bf26-b674773a8e62
https://doi.org/10.1371/journal.pone.0292030
https://pure.tue.nl/ws/files/315761263/journal.pone.0292030.pdf
https://www.scopus.com/pages/publications/85178503290

Drug-induced gene expression profile changes in relation to intestinal toxicity: State-of-the-art and new approaches

Authors: Rodrigues, Daniela Souza, Terezinha Jennen, Danyel G.J. et al.

Source: Cancer Treatment Reviews

Subject Terms: 0301 basic medicine, Intestinal Diseases, 0303 health sciences, 03 medical and health sciences, Anti-Inflammatory Agents, Non-Steroidal, Humans, Fluorouracil, Transcriptome, Protein Kinase Inhibitors, 3. Good health

Access URL: http://www.cancertreatmentreviews.com/article/S0305737219300829/pdf
https://pubmed.ncbi.nlm.nih.gov/31279169
https://pubmed.ncbi.nlm.nih.gov/31279169/
https://www.narcis.nl/publication/RecordID/oai%3Acris.maastrichtuniversity.nl%3Apublications%2F20d466db-3b0c-4782-bff0-5bc17c8ebea6
https://www.ncbi.nlm.nih.gov/pubmed/31279169
https://www.sciencedirect.com/science/article/abs/pii/S0305737219300829
https://www.sciencedirect.com/science/article/pii/S0305737219300829
https://europepmc.org/abstract/MED/31279169

The Effects of the Food Additive Titanium Dioxide (E171) on Tumor Formation and Gene Expression in the Colon of a Transgenic Mouse Model for Colorectal Cancer

Authors: Bischoff, Nicolaj S. Proquin, Heloise Jetten, Marlon J. et al.

Source: ISSN:2079-4991 ; Nanomaterials, vol. 12 (8), Art.No. ARTN 1256.

Subject Terms: Science & Technology, Physical Sciences, Technology, Chemistry, Multidisciplinary, Nanoscience & Nanotechnology, Materials Science, Physics, Applied, Science & Technology - Other Topics, titanium dioxide, E171, mice, transgenic, tumor formation, gene expression, toxicology, in vivo, INFLAMMATION, RHYTHMS, NODULAR LYMPHOID HYPERPLASIA, GASTROINTESTINAL-TRACT, NANOPARTICLES, 0912 Materials Engineering, 1007 Nanotechnology, 4016 Materials engineering, 4018 Nanotechnology

File Description: application/pdf

Relation: https://lirias.kuleuven.be/handle/20.500.12942/706171; https://doi.org/10.3390/nano12081256; https://pubmed.ncbi.nlm.nih.gov/35457963

Availability: https://lirias.kuleuven.be/handle/20.500.12942/706171
https://hdl.handle.net/20.500.12942/706171
https://lirias.kuleuven.be/retrieve/32e79ec9-3eca-4bcc-a76f-5c7a0cc84378
https://doi.org/10.3390/nano12081256
https://pubmed.ncbi.nlm.nih.gov/35457963

Integrating SNPs-based genetic risk factor with blood epigenomic response of differentially arsenic-exposed rural subjects reveals disease-associated signaling pathways

Authors: Rehman, Muhammad Yasir Abdur Briedé, Jacco Jan van Herwijnen, Marcel et al.

Source: Environmental Pollution ; volume 292, page 118279 ; ISSN 0269-7491

Availability: http://dx.doi.org/10.1016/j.envpol.2021.118279
https://api.elsevier.com/content/article/PII:S0269749121018613?httpAccept=text/xml
https://api.elsevier.com/content/article/PII:S0269749121018613?httpAccept=text/plain

Use of deep learning methods to translate drug-induced gene expression changes from rat to human primary hepatocytes

Authors: O'Donovan, Shauna D. Driessens, Kurt Lopatta, Daniel et al.

Source: PLoS ONE 15 (2020) 8 ; ISSN: 1932-6203

Subject Terms: Life Science

File Description: application/pdf

Relation: https://edepot.wur.nl/530242

Availability: https://research.wur.nl/en/publications/use-of-deep-learning-methods-to-translate-drug-induced-gene-expre
https://doi.org/10.1371/journal.pone.0236392
https://edepot.wur.nl/530242

Report of the First ONTOX Stakeholder Network Meeting: Digging Under the Surface of ONTOX Together With the Stakeholders

Authors: IRAS OH Toxicology Afd Pharmacology IRAS – One Health Toxicology et al.

URL: https://doi.org/10.1177/02611929231225730
http://hdl.handle.net/1874/437833
https://dspace.library.uu.nl/handle/1874/437833
http://www.scopus.com/inward/record.url?scp=85182697833&partnerID=8YFLogxK
0261-1929
Alternatives to Laboratory Animals
52
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117
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Inter-laboratory study of human in vitro toxicogenomics-based tests as alternative methods for evaluating chemical carcinogenicity: a bioinformatics perspective

Authors: Herwig, Ralf Gmuender, Hans Corvi, Raffaella et al.

Contributors: Herwig, Ralf Gmuender, Hans Corvi, Raffaella et al.

Source: Archives of Toxikology

Subject Terms: 0301 basic medicine, Laboratory Proficiency Testing, Time Factors, Bioinformatics, in vitro assays, pre-validation, Risk Assessment, Toxicogenetics, Workflow, Kidney Tubules, Proximal, 03 medical and health sciences, Inter-laboratory assessment, Cell Line, Tumor, Humans, Oligonucleotide Array Sequence Analysis, Observer Variation, 0303 health sciences, Carcinogenicity, Dose-Response Relationship, Drug, Gene Expression Profiling, Pre-validation, Computational Biology, Reproducibility of Results, Toxicogenomics, 3. Good health, Gene Expression Regulation, Liver, In vitro assays, Carcinogens, Transcriptome, Genome-Wide Association Study

File Description: application/pdf

Access URL: https://pure.mpg.de/pubman/item/item_2417101_4/component/file_2442493/Herwig.pdf
https://pubmed.ncbi.nlm.nih.gov/26525393
https://cris.maastrichtuniversity.nl/en/publications/91fa9853-b78f-4660-9a0e-b99f1967379b
https://doi.org/10.1007/s00204-015-1617-3
https://www.narcis.nl/publication/RecordID/oai%3Acris.maastrichtuniversity.nl%3Apublications%2F91fa9853-b78f-4660-9a0e-b99f1967379b
https://pubmed.ncbi.nlm.nih.gov/26525393/
https://core.ac.uk/display/45616341
https://link.springer.com/article/10.1007/s00204-015-1617-3
https://www.ncbi.nlm.nih.gov/pubmed/26525393
https://publications.jrc.ec.europa.eu/repository/handle/JRC96286
http://hdl.handle.net/11858/00-001M-0000-002D-4784-3
http://hdl.handle.net/11858/00-001M-0000-002D-4786-0
https://hdl.handle.net/20.500.14017/99beb1cf-5f3a-48f8-9497-409d2775d4db
https://biblio.vub.ac.be/vubir/interlaboratory-study-of-human-in-vitro-toxicogenomicsbased-tests-as-alternative-methods-for-evaluating-chemical-carcinogenicity-a-bioinformatics-perspective(99beb1cf-5f3a-48f8-9497-409d2775d4db).html
https://doi.org/10.1007/s00204-015-1617-3

Integrative omics data analyses of repeated dose toxicity of valproic acid in vitro reveal new mechanisms of steatosis induction

Authors: van Breda, Simone G.J. Claessen, Sandra M.H. van Herwijnen, Marcel et al.

Contributors: van Breda, Simone G.J. Claessen, Sandra M.H. van Herwijnen, Marcel et al.

Source: Toxicology ; volume 393, page 160-170 ; ISSN 0300-483X

Availability: http://dx.doi.org/10.1016/j.tox.2017.11.013
https://api.elsevier.com/content/article/PII:S0300483X17303438?httpAccept=text/xml
https://api.elsevier.com/content/article/PII:S0300483X17303438?httpAccept=text/plain

Molecular Signatures of N-nitroso Compounds in Caco-2 Cells: Implications for Colon Carcinogenesis

Authors: Hebels, Dennie G.A.J. Jennen, Danyel G.J. Kleinjans, Jos C.S. et al.

Source: Toxicological Sciences. 108:290-300

Subject Terms: Genetic Markers, 0301 basic medicine, Apoptosis, colon carcinogenesis, 03 medical and health sciences, gene expression profiling, Humans, nitrosamines, In Situ Hybridization, Oligonucleotide Array Sequence Analysis, 0303 health sciences, N-nitroso compounds, Cell Cycle, nitrosamides, Caco-2, Flow Cytometry, Immunohistochemistry, 3. Good health, Gene Expression Regulation, Neoplastic, Phenotype, Colonic Neoplasms, RNA, Comet Assay, Caco-2 Cells, Nitroso Compounds

Access URL: https://academic.oup.com/toxsci/article-pdf/108/2/290/16680441/kfp035.pdf
https://pubmed.ncbi.nlm.nih.gov/19221148
https://cris.maastrichtuniversity.nl/en/publications/01c5e6d0-a5ca-476b-a252-4f57c0c73e1d
https://doi.org/10.1093/toxsci/kfp035
http://europepmc.org/abstract/MED/19221148
https://cris.maastrichtuniversity.nl/ws/files/65822189/hebels_2009_molecular_signatures_of_N_nitroso.pdf
https://academic.oup.com/toxsci/article-pdf/108/2/290/16680441/kfp035.pdf
https://core.ac.uk/display/90632797
https://paperity.org/p/54361593/molecular-signatures-of-n-nitroso-compounds-in-caco-2-cells-implications-for-colon
https://academic.oup.com/toxsci/article/108/2/290/1669773

Identification of essential transcription factors for adequate DNA damage response after benzo(a)pyrene and aflatoxin B1 exposure by combining transcriptomics with functional genomics

Authors: Smit, Evelyn Souza, Terezinha Jennen, Danyel G.J. et al.

Source: Toxicology ; volume 390, page 74-82 ; ISSN 0300-483X

Availability: http://dx.doi.org/10.1016/j.tox.2017.09.002
https://api.elsevier.com/content/article/PII:S0300483X17302470?httpAccept=text/xml
https://api.elsevier.com/content/article/PII:S0300483X17302470?httpAccept=text/plain

Bischoff et al. The Effects of the Food Additive Titanium Dioxide (E171) on Tumor Formation and Gene Expression in the Colon of a Transgenic Mouse Model for Colorectal Cancer(vol 12 , 1256, 2022)

Authors: Bischoff, Nicolaj S. Proquin, Heloise Jetten, Marlon J. et al.

Source: ISSN:2079-4991 ; Nanomaterials, vol. 13 (21), Art.No. ARTN 2888.

Subject Terms: Science & Technology, Physical Sciences, Technology, Chemistry, Multidisciplinary, Nanoscience & Nanotechnology, Materials Science, Physics, Applied, Science & Technology - Other Topics, 0912 Materials Engineering, 1007 Nanotechnology, 4016 Materials engineering, 4018 Nanotechnology

File Description: application/pdf

Relation: https://lirias.kuleuven.be/handle/20.500.12942/731706; https://doi.org/10.3390/nano13212888; https://pubmed.ncbi.nlm.nih.gov/37947754

Availability: https://lirias.kuleuven.be/handle/20.500.12942/731706
https://hdl.handle.net/20.500.12942/731706
https://lirias.kuleuven.be/retrieve/cb1147a6-8d60-4896-aa76-e460d52ebb0a
https://doi.org/10.3390/nano13212888
https://pubmed.ncbi.nlm.nih.gov/37947754

Sex-Specific Associations between Particulate Matter Exposure and Gene Expression in Independent Discovery and Validation Cohorts of Middle-Aged Men and Women

Authors: Vrijens, Karen Winckelmans, Ellen Tsamou, Maria et al.

Contributors: Vrijens, Karen Winckelmans, Ellen Tsamou, Maria et al.

Subject Terms: Air Pollution/statistics & numerical data, Male, particulate matter, Respiratory Tract Diseases/epidemiology, Sex Factors, Environmental Exposure/statistics & numerical data, Cardiovascular Diseases/epidemiology, Gene Expression, Humans, Female, Middle Aged, Models, Theoretical

Access URL: https://biblio.vub.ac.be/vubir/sexspecific-associations-between-particulate-matter-exposure-and-gene-expression-in-independent-discovery-and-validation-cohorts-of-middleaged-men-and-women(42465d40-33b9-4605-a8de-fdb6c9c5b1da).html

Distinct genotype-dependent differences in transcriptome responses in humans exposed to environmental carcinogens

Authors: Espín-Pérez, Almudena de Kok, Theo M.C.M. Jennen, Danyel G.J. et al.

Source: Carcinogenesis ; volume 36, issue 10, page 1154-1161 ; ISSN 0143-3334 1460-2180

Availability: https://doi.org/10.1093/carcin/bgv111
http://academic.oup.com/carcin/article-pdf/36/10/1154/14134095/bgv111.pdf

diXa: a data infrastructure for chemical safety assessment

Authors: Hendrickx, Diana M. Caiment, Florian Clark, Dominic et al.

Source: Bioinformatics

Subject Terms: Proteomics, 0301 basic medicine, Technology, Biochemistry & Molecular Biology, Bioinformatics, TOXICOLOGY, Statistics & Probability, Chemical, Toxicogenetics, Biochemical Research Methods, Databases, 03 medical and health sciences, Animals, Humans, Metabolomics, Interdisciplinary Applications, 01 Mathematical Sciences, 2. Zero hunger, 0303 health sciences, Science & Technology, 9. Industry and infrastructure, Gene Expression Profiling, 06 Biological Sciences, Applications Notes, Rats, 3. Good health, Biotechnology & Applied Microbiology, Physical Sciences, Computer Science, Computer Science, Interdisciplinary Applications, Mathematical & Computational Biology, 08 Information and Computing Sciences, Life Sciences & Biomedicine, Mathematics, Databases, Chemical

File Description: application/pdf

Access URL: https://academic.oup.com/bioinformatics/article-pdf/31/9/1505/17085671/btu827.pdf
https://pubmed.ncbi.nlm.nih.gov/25505093
https://cris.maastrichtuniversity.nl/en/publications/e4829e92-1cb5-4efc-969e-259d8ace1ef5
https://doi.org/10.1093/bioinformatics/btu827
https://pure.mpg.de/pubman/faces/ViewItemOverviewPage.jsp?itemId=item_2139319
https://academic.oup.com/bioinformatics/article/31/9/1505/200092
https://dash.harvard.edu/handle/1/15034935
http://pubman.mpdl.mpg.de/pubman/item/escidoc:2139319
http://dblp.uni-trier.de/db/journals/bioinformatics/bioinformatics31.html#HendrickxACCEEG15
http://bioinformatics.oxfordjournals.org/content/31/9/1505.abstract
http://hdl.handle.net/10044/1/93305
http://hdl.handle.net/11858/00-001M-0000-0026-B069-5
http://hdl.handle.net/11858/00-001M-0000-0026-B067-9
http://doc.rero.ch/record/290968/files/btu827.pdf

Toxicogenomics and Toxicoinformatics: Supporting Systems Biology in the Big Data Era

Authors: Souza, Terezinha M. Kleinjans, Jos C.S. Jennen, Danyel G.J. et al.

Contributors: Souza, Terezinha M. Kleinjans, Jos C.S. Jennen, Danyel G.J. et al.

Source: Souza, T M, Kleinjans, J C S & Jennen, D G J 2020, Toxicogenomics and Toxicoinformatics: Supporting Systems Biology in the Big Data Era. in D Neagu & A-N Richarz (eds), Big Data in Predictive Toxicology. 41 edn, vol. 2020-January, Royal Society of Chemistry, Issues in Toxicology, vol. 2020-January, pp. 214-241. https://doi.org/10.1039/9781782623656-00214

Availability: https://cris.maastrichtuniversity.nl/en/publications/8fc634ab-48ed-4f0e-ad36-0c8686977ebb
https://doi.org/10.1039/9781782623656-00214

Can Transcriptomics Provide Insight into the Chemopreventive Mechanisms of Complex Mixtures of Phytochemicals in Humans?

Authors: van Breda, Simone G.J. Wilms, Lonneke C. Gaj, Stan et al.

Source: Antioxidants & Redox Signaling ; volume 20, issue 14, page 2107-2113 ; ISSN 1523-0864 1557-7716

Availability: https://doi.org/10.1089/ars.2013.5528
http://www.liebertpub.com/doi/pdf/10.1089/ars.2013.5528