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Research Output 2013 2019

  • 18 Article
  • 2 Conference Abstract/Poster in journal
  • 1 Comment/Letter to the editor
2019

DMSO induces drastic changes in human cellular processes and epigenetic landscape in vitro

Verheijen, M., Lienhard, M., Schrooders, Y., Clayton, O., Nudischer, R., Boerno, S., Timmermann, B., Selevsek, N., Schlapbach, R., Gmuender, H., Gotta, S., Geraedts, J., Herwig, R., Kleinjans, J. & Caiment, F., 15 Mar 2019, In : Scientific Reports. 9, p. 1-12 12 p., 4641.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Identification of key transcription factor networks mediating valproic acid-induced mitochondrial dysfunctioning in primary human hepatocytes

Caiment, F., Wolters, J., Smit, E., Schrooders, Y., Kleinjans, J. C. S. & van den Beucken, T., 15 Oct 2019, In : Toxicology Letters. 314, p. S162-S162 1 p.

Research output: Contribution to journalConference Abstract/Poster in journalAcademic

2018

A model-based assay design to reproduce in vivo patterns of acute drug-induced toxicity

Kuepfer, L., Clayton, O., Thiel, C., Cordes, H., Nudischer, R., Blank, L. M., Baier, V., Heymans, S., Caiment, F., Roth, A., Fluri, D. A., Kelm, J. M., Castell, J., Selevsek, N., Schlapbach, R., Keun, H., Hynes, J., Sarkans, U., Gmuender, H., Herwig, R. & 4 others, Niederer, S., Schuchhardt, J., Segall, M. & Kleinjans, J., 1 Jan 2018, In : Archives of Toxicology. 92, 1, p. 553-555 3 p.

Research output: Contribution to journalComment/Letter to the editorAcademicpeer-review

Open Access

Bringing in vitro analysis closer to in vivo: Studying doxorubicin toxicity and associated mechanisms in 3D human microtissues with PBPK-based dose modelling

Verheijen, M., Schrooders, Y., Gmuender, H., Nudischer, R., Clayton, O., Hynes, J., Niederer, S., Cordes, H., Kuepfer, L., Kleinjans, J. & Caiment, F., 15 Sep 2018, In : Toxicology Letters. 294, p. 184-192 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Integrated 'omics analysis reveals new drug-induced mitochondrial perturbations in human hepatocytes

Wolters, J. E. J., van Breda, S. G. J., Grossmann, J., Fortes, C., Caiment, F. & Kleinjans, J. C. S., 1 Jun 2018, In : Toxicology Letters. 289, p. 1-13 13 p.

Research output: Contribution to journalArticleAcademicpeer-review

RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database

Bushel, P. R., Caiment, F., Wu, H., O'Lone, R., Day, F., Calley, J., Smith, A. & Li, J., 19 Nov 2018, In : BMC Genomics. 19, p. 1-13 13 p., 825.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Short-term exposure to ambient motor vehicle emissions perturb the human circulating miRNA genome

Krauskopf, J., Caiment, F., van Veldhoven, K., Chadeau-Hyam, M., Sinharay, R., Chung, K. F., Cullinan, P., Collins, P., Barratt, B., Kelly, F. J., Vermeulen, R., de Kok, T. M. & Kleinjans, J. C. S., 10 Oct 2018, In : Toxicology Letters. 295, p. S85-S85 1 p.

Research output: Contribution to journalConference Abstract/Poster in journalAcademic

The human circulating miRNome reflects multiple organ disease risks in association with short-term exposure to traffic-related air pollution

Krauskopf, J., Caiment, F., van Veldhoven, K., Chadeau-Hyam, M., Sinharay, R., Chung, K. F., Cullinan, P., Collins, P., Barratt, B., Kelly, F. J., Vermeulen, R., Vineis, P., de Kok, T. M. & Kleinjans, J. C., 1 Apr 2018, In : Environment International. 113, p. 26-34 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Transcriptomic study of the toxic mechanism triggered by beauvericin in Jurkat cells

Escriva, L., Jennen, D., Caiment, F. & Manyes, L., 1 Mar 2018, In : Toxicology Letters. 284, p. 213-221 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

Translational regulation is a key determinant of the cellular response to benzo[a]pyrene

Smit, E., Caiment, F., Piepers, J., Kleinjans, J. C. S. & van den Beucken, T., 1 Oct 2018, In : Toxicology Letters. 295, p. 144-152 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

2017
Open Access

Serum microRNA signatures as "liquid biopsies" for interrogating hepatotoxic mechanisms and liver pathogenesis in human

Krauskopf, J., de Kok, T. M., Schomaker, S. J., Gosink, M., Burt, D. A., Chandler, P., Warner, R. L., Johnson, K. J., Caiment, F., Kleinjans, J. C. & Aubrecht, J., 17 May 2017, In : PLOS ONE. 12, 5, 17 p., 0177928.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2016
5 Citations (Scopus)

The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog

Smith, A., Calley, J., Mathur, S., Qian, H-R., Wu, H., Farmen, M., Caiment, F., Bushel, P. R., Li, J., Fisher, C., Kirby, P., Koenig, E., Hall, D. G. & Watson, D. E., 30 Aug 2016, In : BMC Genomics. 17, 694.

Research output: Contribution to journalArticleAcademicpeer-review

2015
23 Citations (Scopus)

Application of High-Throughput Sequencing to Circulating microRNAs Reveals Novel Biomarkers for Drug-Induced Liver Injury

Krauskopf, J., Caiment, F., Claessen, S. M., Johnson, K. J., Warner, R. L., Schomaker, S. J., Burt, D. A., Aubrecht, J. & Kleinjans, J., Feb 2015, In : Toxicological Sciences. 143, 2, p. 268-276

Research output: Contribution to journalArticleAcademicpeer-review

3 Citations (Scopus)

Development and regulatory application of microRNA biomarkers

Krauskopf, J., Verheijen, M., Kleinjans, J. C., de Kok, T. M. & Caiment, F., 2015, In : Biomarkers in Medicine. 9, 11, p. 1137-1151

Research output: Contribution to journalArticleAcademicpeer-review

7 Citations (Scopus)

diXa: a data infrastructure for chemical safety assessment

Hendrickx, D., Aerts, H., Caiment, F., Clark, D., Ebbels, T. M., Evelo, C. T., Gmuender, H., Hebels, D. G., Herwig, R., Hescheler, J., Jennen, D. G., Jetten, M. J., Kanterakis, S., Keun, H. C., Matser, V., Overington, J. P., Pilicheva, E., Sarkans, U., Segura-Lepe, M. P., Sotiriadou, I. & 4 others, Wittenberger, T., Wittwehr, C., Zanzi, A. & Kleinjans, J. C., 1 May 2015, In : Bioinformatics. 31, 9, p. 1505-1507 3 p.

Research output: Contribution to journalArticleAcademicpeer-review

11 Citations (Scopus)

High-throughput data integration of RNA-miRNA-circRNA reveals novel insights into mechanisms of benzo[a]pyrene-induced carcinogenicity

Caiment, F., Gaj, S., Claessen, S. & Kleinjans, J., 11 Mar 2015, In : Nucleic Acids Research. 43, 5, p. 2525-2534

Research output: Contribution to journalArticleAcademicpeer-review

2014
165 Citations (Scopus)

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

Su, Z., Labaj, P. P., Li, S., Thierry-Mieg, J., Thierry-Mieg, D., Shi, W., Wang, C., Schroth, G. P., Setterquist, R. A., Thompson, J. F., Jones, W. D., Xiao, W., Xu, W., Jensen, R. V., Kelly, R., Xu, J., Conesa, A., Furlanello, C., Gao, H., Hong, H. & 142 others, Jafari, N., Letovsky, S., Liao, Y., Lu, F., Oakeley, E. J., Peng, Z., Praul, C. A., Santoyo-Lopez, J., Scherer, A., Shi, T., Smyth, G. K., Staedtler, F., Sykacek, P., Tan, X-X., Thompson, E. A., Vandesompele, J., Wang, M. D., Wang, J., Wolfinger, R. D., Zavadil, J., Auerbach, S. S., Bao, W., Binder, H., Blomquist, T., Brilliant, M. H., Bushel, P. R., Cain, W., Catalano, J. G., Chang, C-W., Chen, T., Chen, G., Chen, R., Chierici, M., Chu, T-M., Clevert, D-A., Deng, Y., Derti, A., Devanarayan, V., Dong, Z., Dopazo, J., Du, T., Fang, H., Fang, Y., Fasold, M., Fernandez, A., Fischer, M., Furio-Tari, P., Fuscoe, J. C., Caiment, F., Gaj, S., Gandara, J., Gao, H., Ge, W., Gondo, Y., Gong, B., Gong, M., Gong, Z., Green, B., Guo, C., Guo, L., Guo, L-W., Hadfield, J., Hellemans, J., Hochreiter, S., Jia, M., Jian, M., Johnson, C. D., Kay, S., Kleinjans, J., Lababidi, S., Levy, S., Li, Q-Z., Li, L., Li, L., Li, P., Li, Y., Li, H., Li, J., Li, S., Lin, S. M., Lopez, F. J., Lu, X., Luo, H., Ma, X., Meehan, J., Megherbi, D. B., Mei, N., Mu, B., Ning, B., Pandey, A., Perez-Florido, J., Perkins, R. G., Peters, R., Phan, J. H., Pirooznia, M., Qian, F., Qing, T., Rainbow, L., Rocca-Serra, P., Sambourg, L., Sansone, S-A., Schwartz, S., Shah, R., Shen, J., Smith, T. M., Stegle, O., Stralis-Pavese, N., Stupka, E., Suzuki, Y., Szkotnicki, L. T., Tinning, M., Tu, B., van Deft, J., Vela-Boza, A., Venturini, E., Walker, S. J., Wan, L., Wang, W., Wang, J., Wang, J., Wieben, E. D., Willey, J. C., Wu, P-Y., Xuan, J., Yang, Y., Ye, Z., Yin, Y., Yu, Y., Yuan, Y-C., Zhang, J., Zhang, K. K., Zhang, W., Zhang, W., Zhang, Y., Zhao, C., Zheng, Y., Zhou, Y., Zumbo, P., Tong, W., Kreil, D. P., Mason, C. E. & Shi, L., Sep 2014, In : Nature Biotechnology. 32, 9, p. 903-914

Research output: Contribution to journalArticleAcademicpeer-review

16 Citations (Scopus)

Assessing compound carcinogenicity in vitro using connectivity mapping

Caiment, F., Tsamou, M., Jennen, D. & Kleinjans, J., Jan 2014, In : Carcinogenesis. 35, 1, p. 201-207

Research output: Contribution to journalArticleAcademicpeer-review

105 Citations (Scopus)

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

Wang, C., Gong, B., Bushel, P. R., Thierry-Mieg, J., Thierry-Mieg, D., Xu, J., Fang, H., Hong, H., Shen, J., Su, Z., Meehan, J., Li, X., Yang, L., Li, H., Labaj, P. P., Kreil, D. P., Megherbi, D., Gaj, S., Caiment, F., van Delft, J. & 26 others, Kleinjans, J., Scherer, A., Devanarayan, V., Wang, J., Yang, Y., Qian, H-R., Lancashire, L. J., Bessarabova, M., Nikolsky, Y., Furlanello, C., Chierici, M., Albanese, D., Jurman, G., Riccadonna, S., Filosi, M., Visintainer, R., Zhang, K. K., Li, J., Hsieh, J-H., Svoboda, D. L., Fuscoe, J. C., Deng, Y., Shi, L., Paules, R. S., Auerbach, S. S. & Tong, W., Sep 2014, In : Nature Biotechnology. 32, 9, p. 926-932

Research output: Contribution to journalArticleAcademicpeer-review

2013

Deep sequencing reveals abundant noncanonical retroviral microRNAs in B-cell leukemia/lymphoma

Rosewick, N., Momont, M., Durkin, K., Takeda, H., Caiment, F., Cleuter, Y., Vernin, C., Mortreux, F., Wattel, E., Burny, A., Georges, M. & Van den Broeke, A., 5 Feb 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 6, p. 2306-2311

Research output: Contribution to journalArticleAcademicpeer-review