Cluster scientific publications

S. B. Leite, T. Roosens , A. El Taghdouini , I. Mannaerts , A. J. Smout , M. Najimi , E. Sokal , F. Noor , C. Chesne , L. A. van Grunsven Novel human hepatic organoid model enables testing of drug-induced liver fibrosis in vitro 2016 Biomaterials Vol. 78 pp. 1-10 10.1016/j.biomaterials.2015.11.026

E. Berggren, P. Amcoff, R. Benigni, K. Blackburn, E. Carney, M. Cronin, H. Deluyker, F. Gautier, R. S. Judson, G. E. N. Kass, D. Keller, D. Knight, W. Lilienblum, C. Mahony, I. Rusyn, T. Schultz, M. Schwarz, G. Schüürmann, A. White, J. Burton, A. M. Lostia, S. Munn, A. Worth Chemical Safety Assessment Using Read-Across: Assessing the Use of Novel Testing Methods to Strengthen the Evidence Base for Decision Making Environ Health Perspect 2015 10.1289/ehp.1409342

J. Bolleyn Functionality testing of primary hepatocytes in culture by measuring urea synthesis 2015 Methods in Molecular Biology-Protocols in In Vitro Hepatocyte Research 1250 pp. 317-321 10.1007/978-1-4939-2074-7_24

M. D. Nelms Proposal of an in silico profiler for categorisation of repeat dose toxicity data of hair dyes Archives of Toxicology 2015 733-741 10.1007/s00204-014-1277-8

E. Ramboer Immortalized human hepatic cell lines for in vitro testing and research purposes 2015 Methods in Molecular Biology – Protocols in In Vitro Hepatocyte Research 1250 53-76 10.1007/978-1-4939-2074-7_4

M. Vinken Establishment and characterization of an in vitro model of Fas-mediated hepatocyte cell death 2015 Methods in Molecular Biology – Protocols in In Vitro Hepatocyte Research 1250 95-104 10.1007/978-1-4939-2074-7_6

J. De Kock Human skin-derived precursor cells: isolation, expansion and hepatic differentiation 2015 Methods in Molecular Biology – Protocols in In Vitro Hepatocyte Research 1250 113-122 10.1007/978-1-4939-2074-7_8

R. M. Rodrigues Measurement of cytochrome P450 enzyme induction and inhibition in HepaRG cells 2015 Methods in Molecular Biology – Protocols in In Vitro Hepatocyte Research 1250 279-286 10.1007/978-1-4939-2074-7_20

K. Buyl Measurement of albumin secretion as functionality test in primary hepatocyte cultures 2015 Methods in Molecular Biology – Protocols in In Vitro Hepatocyte Research 1250 303-308 10.1007/978-1-4939-2074-7_22

M. Maes Measurement of apoptotic and necrotic cell death in primary hepatocyte cultures 2015 Methods in Molecular Biology – Protocols in In Vitro Hepatocyte Research 1250 349-362 10.1007/978-1-4939-2074-7_27

O. Morales-Ibanez et al Kinase analysis in alcoholic hepatitis identifies p90RSK as a potential mediator of liver fibrogenesis. GUT 2015 10.1136/gutjnl-2014-307979

E. Wolfs et al. Radiolabeling strategies for radionuclide imaging of stem cells 2015 Stem Cell Rev 11(2) 254-74 10.1007/s12015-014-9575-3

Prill, Bavli et al. Real-time monitoring of oxygen uptake in hepatic bioreactor shows CYP450-independent mitochondrial toxicity of acetaminophen and amiodarone Archives of Toxicology 2015 10.1007/s00204-015-1537-2

M. Coll, et al. Integrative miRNA and Gene expression Profiling Analysis of Human Quiescent Hepatic Stellate Cells 2015 Scientific Reports 10.1038/srep11549

Y. Avior Microbial-derived lithocholic acid and vitamin K2 drive the metabolic maturation of pluripotent stem cells–derived and fetal hepatocytes 2015 Hepatology 62(1) 265-278 10.1002/hep.27803

E. Ezra Microprocessor­Based Integration of Microfluidic Platforms for the Realization of Multithreaded Optimization Algorithms 2015 Biomed Microdevices 17(4) 82 10.1007/s10544-015-9989-y

L. Delang et al. Understanding the molecular mechanism of host-based statin resistance in hepatitis C virus replicon containing cells 2015 Biochem Pharmacol 96(3) 190-201 10.1053/j.gastro.2014.01.039

El Taghdouini et al. Genome-wide analysis of DNA methylation and gene expression patterns in purified, uncultured human liver cells and activated hepatic stellate cells 2015 Oncotarget 6 (29) 26729-45 10.18632/oncotarget.4925

B. Turonova, L. Marsalek, T. Davidovic and P. Slusallek Progressive Stochastic Reconstruction Technique (PSRT) for Cryo Electron Tomography 2015 Journal of Structural Biology March 2015 pp. 195-206 10.1016/j.jsb.2015.01.011

A. Friebel, J. Neitsch, T. Johann, S. Hammad, J. Hengstler, D. Drasdo, S. Hoehme TiQuant: software for tissue analysis, quantification and surface reconstruction 2015 Bioinformatics Epub ahead of print 10.1093/bioinformatics/btv346

T. Dahmen, H. Kohr, N. de Jonge, and P. Slusallek Matched Backprojection Operator for Combined Scanning Transmission Electron Microscopy Tilt- and Focal Series 2015 Microscopy and Microanalysis Volume 21 / Issue 03 / June 2015 pp. 725-738 10.1017/S1431927615000525

R. Reif, J. Karlsson, G. Günther, L. Beattie, D. Wrangborg, S. Hammad, B. Begher-Tibbe, A. Vartak, S. Melega, P.M. Kaye, J. G. Hengstler, M. Jirstrand Bile canalicular dynamics in hepatocyte sandwich cultures 2015 Archives of Toxicology 2015 Aug 18. 10.1007/s00204-015-1575-9

S. Klein, S. Maggioni, J. Bucher, D. Mueller, J. Niklas, V. Shevchenko, K. Mauch, E. Heinzle and F. Noor In silico modeling for the prediction of dose and pathway related adverse effects in humans from in vitro repeated-dose studies 2015 Toxicological Sciences, 2015 Sep 29 10.1093/toxsci/kfv218

P. Trampert, S. Bogatchev, N. Marniok, T. Dahmen, P. Slusallek Marker detection in Electron Tomography: A comparative study 2015 Microscopy and Microanalysis Volume 21 / Issue 06 10.1017/S1431927615015433

A. Ghallab, G. Cellière, S.G. Henkel, D. Driesch, S. Hoehme, U. Hofmann, S. Zellmer, P. Godoy, A. Sachinidis, M. Blaszkewicz, R. Reif, R. Marchan, L. Kuepfer, D. Häussinger, D. Drasdo, R. Gebhardt, J.G. Hengstler Model guided identification and therapeutic implications of an ammonia sink mechanism 2015 Journal of Hepatology http://dx.doi.org/10.1016/j.jhep.2015.11.018

F. Noor A shift in paradigm towards human biology-based systems for cholestatic-liver diseases 2015 Journal of Physiology Vol. 593/Issue 23 pp. 5043-5055 10.1113/JP271124

R. Gorris et al. Pluripotent stem cell-derived radial glia-like cells as stable intermediate for efficient generation of human oligodendrocytes 2015 Glia 10.1002/glia.22882.

A. Elanzew et al. A reproducible and versatile system for the dynamic expansion of human pluripotent stem cells in suspensions 2015 Biotechnology Journal 10.1002/biot.201400757.

D. Peric D and I. Barragan Cytostatic Effect of Repeated Exposure to Simvastatin: A Mechanism for Chronic Myotoxicity Revealed by the Use of Mesodermal Progenitors Derived from Human Pluripotent Stem Cells 2015 Stem Cells 10.1002/stem.2107.

F. Nguemo, J. Semmler, J. Hescheler Label-Free Impedance Measurements for Profiling Drug-Induced Cardiotoxicity Springer 2015 Methods in Pharmacology and Toxicology 1557-2153 pp. 283-305 10.1007/978-1-4939-2617-6_16

R.M. Rodrigues In vitro assessment of drug-induced liver steatosis based on human dermal stem cell-derived hepatic cells Springer 2015 Archives of Toxicology

J. Bolleyn Functionality testing of primary hepatocytes in culture by measuring urea synthesis Humana Press 2015 Methods in Molecular Biology-Protocols in In Vitro Hepatocyte Research 1250 pp. 317-321 10.1007/978-1-4939-2074-7_24

M. Vinken Adverse outcome pathways and drug-induced liver injury testing ACS Publications 2015 Chemical Research in Toxicology

Godoy Gene networks and transcription factor motifs defining the differentiation of stem cells into hepatocyte-like cells Elsevier 2015 Journal of Hepatology 10.1016/j.jhep.2015.05.013

A. Limonciel and P. Jennings Transcriptomics hit the target: Monitoring of ligand-activated and stress response pathways for chemical testing Elsevier 2015 Toxicology in Vitro

B. Herpers, S. Wink, L. Fredriksson, G. Di Z, Hendriks, H. Vrieling, H. de Bont, B. van de Water Activation of the Nrf2 response by intrinsic hepatotoxic drugs correlates with suppression of NF-κB activation and sensitizes toward TNFα-induced cytotoxicity 2015 Arch Toxicol.

M. Gajewska, A. Paini, J.V. Sala Benito, J. Burton, A. Worth, C. Urani, H. Briesen, K.-W. Schramm In vitro-to-in vivo correlation of the skin penetration, liver clearance and hepatotoxicity of caffeine 2015 Food and Chemical Toxicology 75 pp. 9-49

A. Plosnik, J. Zupan, M. Vracko Evaluation of toxic endpoints for a set of cosmetic ingredients with CAESAR models 2015 Chemosphere 120 pp. 492-499

F.P. Steinmetz, C.L. Mellor, T. Meinl, M.T.D. Cronin Screening chemicals for receptor-mediated toxicological and pharmacological endpoints: Using public data to build screening tools within a KNIME workflow 2015 Mol. Inf. 34 pp. 171–178

E. Berggren, P. Amcoff, R. Benigni, K. Blackburn, E. Carney, M. Cronin, H. Deluyker, F. Gautier, R.S. Judson, GEN Kass, D. Keller, D. Knight, W. Lilienblum, C. Mahony, I. Rusyn, T. Schultz, M. Schwarz, G. Schüürman, A. White, J. Burton, A. Lostia, S. Munn, A. Worth A Chemical safety assessment using readacross: How can novel testing methods strengthen evidence base for decisionmaking? 2015 Environ. Health Perspect., in press

T.W. Schultz, P. Amcoff P, E. Berggren, F. Gautier, M. Klaric, D. Knight, C. Mahony, M. Schwarz, A. White, M.T.D. Cronin A strategy for structuring and reporting a read-across prediction of toxicity 2015 Reg. Toxicol. Pharmacol. 72: pp. 586–601

F. Fratev, I. Tsakovska, M. Al Sharif, E. Mihaylova, I. Pajeva Structural and dynamical insight into PPARγ antagonism: in silico study of the ligand-receptor interactions of non-covalent antagonists 2015 Int. J. Mol. Sci. 16(7): pp. 15405-15424

A. Bal-Price, K.M. Crofton, M. Sachana, T.J. Shafer, M. Behl, A. Forsby, A. Hargreaves, B. Landesmann, P.J. Lein, J. Louisse, F. Monnet-Tschudi, A. Paini, A. Rolaki, A. Schrattenholz, C. Suñol, C. van Thriel, M. Whelan, E. Fritsche Putative adverse outcome pathways relevant to neurotoxicity 2015 Crit. Rev. Toxicol., 45 pp. 83-91

G. Daston, D.J. Knight, M. Schwarz, T. Gocht, R.S. Thomas, C. Mahony, M. Whelan SEURAT: Safety Evaluation Ultimately Replacing Animal Testing – Recommendations for future research in the field of predictive toxicology 2015 Arch. Toxicol., 89 PP. 15-23

T. Gocht, E. Berggren, H.J. Ahr, I. Cotgreave, M.T.D. Cronin, G. Daston, B. Hardy, E. Heinzle, J. Hescheler, D.J. Knight, C. Mahony, M. Peschanski, M. Schwarz, R.S. Thomas, C. Verfaillie, A. White, M. Whelan, The SEURAT-1 approach towards animal free human safety assessment 2015 ALTEX, 32 pp. 9-24

M. Vinken, M. Maes, A. G.Oliveira, B. Cogliati, P. E.Marques, G. B.Menezes, M. Lúcia, Z. Dagli, T. Vanhaecke, V. Rogiers Primary hepatocytes and their cultures in liver apoptosis research Springer Verlag 2014 Vol. 88/Issue 2 pp.199-212 DOI: 10.1007/s00204-013-1123-4

S. Affo , O. Morales-Ibanez , D. Rodrigo-Torres , J. Altamirano , D. Blaya , D. H. Dapito , C. Millan , M. Coll , J. M. Caviglia, V. Arroyo , J. Caballeria , R. F. Schwabe , P. Gines , R. Bataller , P. Sancho-Bru CCL20 mediateslipopolysaccharide induced liver injuryand is a potential driver of inflammation and fibrosis in alcoholic hepatitis BMJ Publishing Group, United Kingdom 2014 Gut 10.1136/gutjnl-2013-306098

M. Vinken , M. Whelan , V. Rogiers Adverse outcome pathways: hype or hope? Springer Verlag, Germany 2014 Archives of Toxicology, Vol. 88/Issue 1 pp. 1-2

R. M. Rodrigues , J. De Kock , S. Branson , M. Vinken , K. Meganathan, U. Chaudhari , A. Sachinidis ,O. Govaere ,T. Roskams , V. De Boe , T.Vanhaecke , V. Rogiers Human Skin-Derived Stem Cells as a Novel Cell Source for In Vitro Hepatotoxicity Screening of Pharmaceuticals Mary Ann Liebert Inc. Publishers, United States 2014 Stem Cells and Development, Vol. 23/Issue 1 pp. 44-55 10.1089/scd.2013.0157

S. Prill, M. S. Jaeger, C. Duschl Long-term microfluidic glucose and lactate monitoring in hepatic cell culture 2014 Biomicrofluidics 8, 034102

M. Vinken, M. Maes, A.G. Oliveira, B. Cogliati, P. Elias, G.B. Menezes, M.L. Zaidan Dagli, T. Vanhaecke, V. Rogiers Primary hepatocytes and their cultures in liver apoptosis research 2014 Archives of Toxicology 88(2) 199-212

K. Buyl, J. De Kocka, M. Najarb, L. Lagneauxb, S. Bransona, V. Rogiers, T. Vanhaecke Characterization of hepatic markers in human Wharton’s Jelly-derived mesenchymal stem cells 2014 Archives of Toxicology 88(2) 199-212

CM. Verfaillie Biliary cells to the rescue of Prometheus 2014 Gastroenterology 146(3) 611-614 10.1053/j.gastro.2014.01.039

Y. Park et al. Hepatic differentiation of human embryonic stem cells on microcarriers 2014 J Biotechnol 174 39-48 10.1016/j.jbiotec.2014.01.025

E. Wolfs et al. Optimization of multimodal imaging of mesenchymal stem cells using the human sodium iodide symporter for PET and Cerenkov luminescence imaging 2014 PLoS One 9(4) e94833 10.1371/journal.pone.0094833

Y. Chen, C.M. Verfaillie MicroRNAs: the fine modulators of liver development and function 2014 Liver Int 34(7) pp. 39-48 10.1111/liv.12496

E. Ramboer Strategies for immortalization of primary hepatocytes 2014 Journal of Hepatology 61 (4) pp. 925-943 10.1016/j.jhep.2014.05.046

J.C. Madden Application of in silico and in vitro methods in the development of adverse outcome pathway constructs in wildlife Philosophical Transactions of The Royal Society B Biological Sciences 2014 369 (1656) 20130584 10.1098/rstb.2013.0584

L. Perea et al Assessment of Liver Fibrotic Insults In Vitro 2014 Protocols in In Vitro Hepatocyte Research 391-401 10.1007/978-1-4939-2074-7_30

D. Mueller, L. Krämer, E. Hoffmann, S. Klein S, F. Noor 3D organotypic HepaRG cultures as in vitro model for acute and repeated dose toxicity studies 2014 Toxicol In Vitro 28 pp. 104-12 10.1016/j.tiv.2013.06.024

C. Carapito, A. Burel, P. Guterl, A. Walter, F. Varrier, F. Bertile, A. van Dorsselaer MSDA, a proteomics software suite for in-depth Mass Spectrometry Data Analysis using grid computing 2014 PROTEOMICS 10.1002/pmic.201300415

T. Dahmen, J.-P. Baudoin, A. R. Lupini, C. Kübel, P. Slusallek, and N. de Jonge Combined Scanning Transmission Electron Microscopy Tilt- and Focal Series 2014 Microscopy and Microanalysis Vol. 20/Issue 02 pp. 548-560 10.1017/S1431927614000075

S. Hammad, S. Hoehme, A. Friebel, I. von Recklinghausen, A. Othman, B. Begher-Tibbe, et al. Protocols for staining of bile canalicular and sinusoidal networks of human, mouse and pig livers, three-dimensional reconstruction and quantification of tissue microarchitecture by image processing and analysis 2014 Arch Toxicol 88 pp. 1161–1183 10.1007/s00204-014-1243-5

G. Campos, W. Schmidt-Heck, A. Ghallab, …, J. Hengstler, P. Godoy The transcription factor CHOP, a central component of the transcriptional regulatory network induced upon CCl4 intoxication in mouse liver, is not a critical mediator of hepatotoxicity 2014 Archives of Toxicology 2014 Jun;88(6) pp. 1267-80 10.1007/s00204-014-1240-8

F. Schliess, S. Hoehme, S.G. Henkel, A. Ghallab, D. Driesch, J. Böttger, R. Guthke, M. Pfaff, J. Hengstler, R. Gebhardt, D. Häussinger, D. Drasdo, S. Zellmer Integrated metabolic spatial-temporal model for the prediction of ammonia detoxification during liver damage and regeneration 2014 Hepatology 60(6) 2040-51 10.1002/hep.27136

D. Becker, P. Lutsik, P. Ebert, C. Bock, T. Lengauer and J. Walter BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives 2014 Nucleic Acids Res 2014 July 1; 42 10.1093/nar/gku457

M. Unterberg, L. Leffers, F. Hübner, H.U. Humpf, K. Lepikhov, J. Walter, F. Ebert and T. Schwerdtle: Toxicity of arsenite and thio-DMAV after long-term (21 days) incubation of human urothelial cells: cytotoxicity, genotoxicity and epigenetics 2014 Toxicology Research 10.1039/C4TX00036F

D. Drasdo, S. Hoehme, J. Hengstler How predictive quantitative modelling of tissue organisation can inform liver disease pathogenesis 2014 Journal of Hepatology Volume 61, Issue 4 pp. 951–956 10.1016/j.jhep.2014.06.013

L.M. Voortman, M. Vulović, M. Maletta, A. Voigt, E.M. Franken, A. Simonetti, P.J. Peters, L.J. van Vliet, B. Rieger Quantifying resolution limiting factors in subtomogram averaged cryo-electron tomography using simulations 2014 Journal of Structural Biology Volume 187, Issue 2 pp. 103–111 10.1016/j.jsb.2014.06.007

N. Alépée, T. Bahinski, M. Daneshian, B. De Wever, E. Fritsche, A. Goldberg, J. Hansmann, T. Hartung, J. Haycock, H. Hogberg, L. Hoelting, J.M. Kelm, S. Kadereit, E. McVey, R. Landsiedel, M. Leist, M. Lübberstedt, F. Noor, C. Pellevoisin, D. Petersohn, U. Pfannenbecker, K. Reisinger, Ram State-of-the-art of 3D cultures (organs-on-a-chip) in safety testing and pathophysiology 2014 ALTEX (31)4 pp. 441-477 10.14573/altex1406111.

A. Ryll, J. Bucher, A. Bonin, S. Bongard, E. Gonçalves, J. Saez-Rodriguez, J. Niklas, S. Klamt A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models Biosystems ;124:26-38. 2014 Oct 124 2014 pp. 26-38 10.1016/j.biosystems.2014.07.002

T. Dahmen, J.-P. Baudoin, A. R. Lupini, C. Kübel, P. Slusallek, and N. de Jonge TFS: Combined Tilt- and Focal Series Scanning Transmission Electron Microscopy 2014 Microscopy and Microanalysis 20 (Suppl 3) pp. 786-787 10.1017/S1431927614005650

Y. Assenov, F. Müller, P. Lutsik, J. Walter, T. Lengauer & C. Bock Comprehensive analysis of DNA methylation data with RnBeads 2014 Nature Methods 11, 2014 pp. 1138–1140 10.1038/nmeth.3115

M.J. Bonder, S. Kasela, M. Kals, R. Tamm, K. Lokk, I. Barragan, W.A. Buurman, P. Deelen, J.W. Greve, M. Ivanov, S.S. Rensen, J.V. van Vliet-Ostaptchouk, M.G. Wolfs, J. Fu, M.H. Hofker, C. Wijmenga, A. Zhernakova, M. Ingelman-Sundberg, L. Franke, L. Milani Genetic and epigenetic regulation of gene expression in fetal and adult human livers 2014 BMC Genomics 2014, 15:860 10.1186/1471-2164-15-860

C. Priesnitz, S. Sperber, R. Garg, M. Orsini, F. Noor Fluorescence based cell counting in collagen monolayer cultures of primary hepatocytes 2014 Cytotechnol 10.1007/s10616-014-9821-1

L.A D’Alessandro, S. Hoehme, A. Henney, D. Drasdo, U. Klingmüller Unraveling liver complexity from molecular to organ level: Challenges and perspectives 2014 Prog Biophys Mol Biol 10.1016/j.pbiomolbio.2014.11.005

Holmgren et al Long-term chronic toxicity testing using human pluripotent stem cell-derived hepatocytes 2014 Drug Metabolism and Disposition 42(9) pp. 1401-06 10.1124/dmd.114.059154

Sjögren et al. Critical differences in toxicity mechanisms in induced pluripotent stem cell-derived hepatocytes, cell lines and primary hepatocytes 2014 Arch Toxicol. 88(7) pp. 14127-1437 10.1007/s00204-014-1265-z

R.M. Rodrigues Human stem cell-derived hepatocytes: breakthrough of an expedient tool for preclinical assessment of drug-induced liver injury? Springer 2014 Archives of Toxicology 88 (2) pp. 183-184

M.D. Nelms Proposal of an in silico profiler for categorisation of repeat dose toxicity data of hair dyes Springer 2014 Archives of Toxicology 89 (5) pp. 733-741

E. Ramboer Strategies for immortalization of primary hepatocytes Elsevier 2014 Journal of Hepatology 61 (4) pp. 925-943

C. Willett Building shared experience to advance practical application of pathway-based toxicology: liver toxicity mode-of-action ALTEX 2014 Alternatives to Animal Experimentation 31 (4) pp. 407-421

J. Bolley MicroRNAs as key regulators of xenobiotic biotransformation and drug response Springer 2014 Archives of Toxicology

J.C. Madden Application of in silico and in vitro methods in the development of adverse outcome pathway constructs in wildlife Royal Society Publishing 2014 Philosophical Transactions of The Royal Society B Biological Sciences 369 (1656)

M. Grinberg, R.M. Stöber, K. Edlund, E. Rempel, P. Godoy, R. Reif, A. Widera, K. Madjar, W. Schmidt-Heck, R. Marchan, A. Sachinidis, D. Spitkovsky, J. Hescheler, H. Carmo, M.D. Arbo, B. van de Water, S. Wink, M. Vinken, V. Rogiers, S. Escher, B. Hardy, D. Mitic, G. Myatt, T. Waldmann, A. Mardinoglu, G. Damm, D. Seehofer, A. Nüssler, T.S. Weiss, A. Oberemm, A. Lampen, M.M. Schaap, M. Luijten, H. van Steeg, W.E. Thasler, J.C. Kleinjans, R.H. Stierum, M. Leist, J. Rahnenführer, J. Hengstler Toxicogenomics directory of chemically exposed human hepatocytes Springer 2014 Archives of Toxicology 88 (12) pp. 2261-2287

R.M. Rodrigues Identification of potential biomarkers of hepatitis B-induced acute liver failure in human skin-derived precursors upon hepatogenic differentiation Elsevier 2014 Toxicology In Vitro 29 (6) pp. 1231-1239

K. Buyl Evaluation of a new standardized enzymatic isolation protocol for human umbilical cord-derived stem cells Elsevier 2014 Toxicology In Vitro 29 (6) pp. 1254-1262

P. Jennings, M. Schwarz, B. Landesmann, S. Maggioni, M. Goumenou, D. Bower, M.O. Leonard, J.S. Wiseman SEURAT-1 liver gold reference compounds: a mechanism-based review Springer 2014 Archives of Toxicology

A. Limonciel and P. Jennings A Review of the Evidence that Ochratoxin A Is an Nrf2 Inhibitor: Implications for Nephrotoxicity and Renal Carcinogenicity MDPI 2014 Toxins pp. 371-9

E. van Vliet, M. Daneshian, M. Beilmann, A. Davies, E. Fava, R. Fleck, Y. Julé, M. Kansy, S. Kustermann, P. Macko, W.R. Mundy, A. Roth, I. Shah, M. Uteng, B. van de Water, T. Hartung, M. Leist Current approaches and future role of high content imaging in safety sciences and drug discovery. ALTEX 2014

S. Wink, S. Hiemstra, S. Huppelschoten, E. Danen, M. Niemeijer, G. Hendriks, H. Vrieling, B. Herpers, B. van de Water Quantitative high content imaging of cellular adaptive stress response pathways in toxicity for chemical safety assessment 2014 Chem Res Toxicol. 17;27(3) pp. 338-55

L. Fredriksson, S. Wink, B. Herpers, G. Benedetti, M. Hadi, H. de Bont, G. Groothuis, M. Luijten, E. Danen, M. de Graauw, J. Meerman, B. van de Water Drug-induced endoplasmic reticulum and oxidative stress responses independently sensitize toward TNFα-mediated hepatotoxicity 2014 Toxicol Sci. 2014 Jul;140(1) pp. 144-59

M. Leist Design principles of concentration-dependent transcriptome deviations in drug-exposed differentiating stem cells American Chemical Society 2014 Chemical research in toxicology pp. 408-420

F.P. Steinmetz, S.J. Enoch, J.C. Madden, M.D. Nelms, N. Rodriguez-Sanchez, P.H. Rowe, Y. Wen, M.T. Cronin Methods for assigning confidence to toxicity data with multiple values – Identifying experimental outliers 2014 Sci Total Environ 482-483: pp. 358-365

M. Al Sharif, P. Alov, V. Vitcheva, I. Pajeva, I. Tsakovska Modes-of-action related to repeated dose toxicity: from PPARgamma ligand-dependent dysregulation to non-alcoholic fatty liver disease 2014 PPAR Research, Special issue „PPARs and Metabolic Syndrome”, Volume 2014 (2014), Article ID 432647

A.N. Richarz, T.W. Schultz, M.T.D. Cronin, S.J. Enoch Experimental verification of structural alerts for the protein binding of sulfur-containing compounds 2014 SAR and QSAR in Environmental Research 25(4) pp. 325-341

M. Gajewska, A. Worth, C. Urani, H. Briesen, K.-W. Schramm Application of physiologically based toxicokinetic modelling in oral-to-dermal extrapolation of threshold doses of cosmetic ingredients 2014 Toxicology Letters 227 pp. 189-202

I. Tsakovska, M. Al Sharif, P. Alov, A. Diukendjieva, E. Fioravanzo, M.T.D. Cronin, I. Pajeva Molecular modelling study of the PPARγ receptor in relation to the Mode of Action/Adverse Outcome Pathway framework for liver steatosis 2014 Int. J. Mol. Sci. 15(5) pp. 7651-7666

K.R. Przybylak, A.R. Alzahrani, M.T.D. Cronin How does the quality of phospholipidosis data influence the predictivity of structural alerts? 2014 J. Chem. Inf. Model 54 pp. 2224−2232

M. Gajewska, A. Worth, C. Urani, H. Briesen, K.-W. Schramm The acute effects of daily nicotine intake on heart rate – A toxicokinetic and toxicodynamic modelling study 2014 Regulatory Toxicology and Pharmacology 70(1) pp. 312-324

P. Jennings, M. Schwarz, B. Landesmann, S. Maggioni, M. Goumenou, D. Bower, M.O. Leonard, J.S. Wiseman SEURAT-1 liver gold reference compounds: a mechanism-based review 2014 Arch. Toxicol., 88 pp. 2099-2133

T.W. Schultz, P. Amcoff, E. Berggren, F. Gautier, M. Klaric, D.J. Knight, C. Mahony, M. Schwarz, A. White and M.T.D. Cronin A strategy for structuring and reporting a read-across prediction of toxicity 2014 Regul. Toxicol. Pharmacol. 72 pp. 586-601

K. Buyl, J. De Kock Characterization of hepatic markers in human Wharton’s Jelly-derived mesenchymal stem cells Elsevier 2013 Toxicology In Vitro DOI: 10.1016/j.tiv.2013.06.014

P. Godoy, N.J. Hewitt Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signalling and ADME Springer 2013 Archives of Toxicology p.1315-1530 http://link.springer.com/article/10.1007%2Fs00204-013-1078-5

M.T.D. Cronin The state of the art and future directions of category formation and read-across for toxicity prediction M.T.D. Cronin, J.C. Madden, S.J. Enoch, D.W. Roberts (eds) Chemical Toxicity Prediction: Category Formation and Read-Across. The Royal Society of Chemistry, Cambridge 2013 pp. 168-179

E. Ramboer Primary hepatocyte cultures as prominent in vitro tools to study hepatic drug transporters Informa Healthcare 2013 Drug Metabolism Reviews p.196-217 DOI: 10.3109/03602532.2012.756010

M. Vinken, M. Maes, T. Vanhaecke and V. Rogiers Drug-induced liver injury: mechanisms types and biomarkers Bentham Science Publishers 2013 Current Medicinal Chemistry p.3011-3021 DOI: 10.2174/0929867311320240006

M. Vinken Adverse outcome pathways: hype or hope? Springer 2013 Archives of Toxicology DOI: 10.1007/s00204-013-1093-6

M. Vinken The adverse outcome pathway concept: a pragmatic tool in toxicology Elsevier 2013 Toxicology p.158-165 DOI: 10.1016/j.tox.2013.08.011

Robim M. Rodrigues Human skin-derived stem cells as a novel cell source for in vitro hepatotoxicity screening of pharmaceuticals Mary Ann Liebert Inc. Publishers 2013 Stem Cells and Development DOI: 10.1089/scd.2013.0157

M. Vinken Development of an adverse outcome pathway from drug-mediated bile salt export pump inhibition to cholestatic liver injury Oxford Journals 2013 Toxicological Sciences DOI: 10.1093/toxsci/kft177

D. Canovas-Jorda, J. Louisse, F. Pistollato, D. Zagoura & S. Bremer Regenerative toxicology”: the role of stem cells in the development of chronic toxicities Informa Healthcare 2013 Expert Opinion On Drug Metabolism and Toxicology

M. Hewitt, S.J. Enoch, J.C. Madden, K.R. Przybylak, M.T.D Cronin Hepatotoxicity: A scheme for generating chemical categories for read-across, structural alerts and insights into mechanism(s) of action Critical Reviews in Toxicology 2013 43: pp. 537–558

M. D. Nelms, M.T.D. Cronin, S.J. Enoch, T.W. Schultz Experimental verification, and domain definition, of structural alerts for protein binding: epoxides, lactones, nitroso, nitros, aldehydes and ketones SAR and QSAR in Environmental Research 2013 24(9): pp. 695-709

S.J. Enoch, M.T.D. Cronin, T.W. Schultz The definition of the toxicologically relevant applicability domain for the SNAr reaction for substituted pyridines and pyrimidines SAR and QSAR in Environmental Research 2013 24(5): pp. 385-392

P. Piechota, M.T.D. Cronin, M. Hewitt, J.C. Madden Pragmatic approaches to using computational methods to predict xenobiotic metabolism J. Chem. Inf. Model. 2013 53 (6), pp. 1282–1293

A.R.R. Péry, C. Brochot, F. Zeman, E. Mombelli, S. Desmots, M. Pavan, E. Fioravanzo, J.-M. Zaldivar Prediction of dose – hepatotoxic response in humans based on toxicokinetic/toxicodynamic modeling with or without in vivo data: A case study with acetaminophen Toxicology Letters 220 2013 pp. 26–34

A. Palczewska, X. Fu, P.T. Trundle, L. Yang, D. Neagu Towards Model Governance in Predictive Toxicology International Journal of Information Management 2013 33(3): pp. 567-582

L. Yang, D. Neagu, M.T.D. Cronin, M. Hewitt, S.J. Enoch, J.C. Madden, K. Przybylak Towards a fuzzy expert system on toxicological data quality assessment 2013 Mol. Inf. 32(1): pp. 65-78

J. Niklas, J.G. Diaz Ochoa, J. Bucher, K. Mauch Quantitative evaluation and prediction of drug effects and toxicological risk using mechanistic multiscale models 2013 Mol. Inf. 32(1): pp. 14-23

J.G. Diaz Ochoa, J. Bucher, A.R.R. Péry, J.M. Zaldivar Comenges, J. Niklas, K. Mauch A multi-scale modeling framework for individualized, spatiotemporal prediction of drug effects and toxicological risk Front Pharmacol 2013 3: p. 204 doi: 10.3389/fphar.2012.00204

M.T.D. Cronin An introduction to chemical grouping, categories and read-across to predict toxicity M.T.D. Cronin, J.C. Madden, S.J. Enoch, D.W. Roberts (eds) Chemical Toxicity Prediction: Category Formation and Read-Across. The Royal Society of Chemistry, Cambridge, 2013 pp. 1-29

S.J. Enoch, D.W. Roberts Approaches for grouping chemicals into categories M.T.D. Cronin, J.C. Madden, S.J. Enoch, D.W. Roberts (eds) Chemical Toxicity Prediction: Category Formation and Read-Across. The Royal Society of Chemistry, Cambridge 2013 pp. 30-43

K.R. Przybylak, T.W. Schultz Informing chemical categories through the development of Adverse Outcome Pathways M.T.D. Cronin, J.C. Madden, S.J. Enoch, D.W. Roberts (eds) Chemical Toxicity Prediction: Category Formation and Read-Across. The Royal Society of Chemistry, Cambridge 2013 pp. 44-71

M.T.D. Cronin ,K.R. Przybylak, S.J. Enoch Category formation case studies M.T.D. Cronin, J.C. Madden, S.J. Enoch, D.W. Roberts (eds) Chemical Toxicity Prediction: Category Formation and Read-Across. The Royal Society of Chemistry, Cambridge 2013 pp. 127-154

J.C. Madden Tools for grouping chemicals and forming categories M.T.D. Cronin, J.C. Madden, S.J. Enoch, D.W. Roberts (eds) Chemical Toxicity Prediction: Category Formation and Read-Across. The Royal Society of Chemistry, Cambridge 2013 pp. 72-97

J.C. Madden Sources of chemical information, toxicity data and assessment of their quality M.T.D. Cronin, J.C. Madden, S.J. Enoch, D.W. Roberts (eds) Chemical Toxicity Prediction: Category Formation and Read-Across. The Royal Society of Chemistry, Cambridge 2013 pp. 98-126

M.T.D. Cronin Evaluation of categories and read-across for toxicity prediction allowing for regulatory acceptance M.T.D. Cronin, J.C. Madden, S.J. Enoch, D.W. Roberts (eds) Chemical Toxicity Prediction: Category Formation and Read-Across. The Royal Society of Chemistry, Cambridge 2013 pp. 155-167

J. Madden, M. Hewitt, S. Enoch, P. Piechota, A. Richarz, M.T.D. Cronin Modelling local and systemic toxicity: incorporation of in silico predictions in the development of adverse outcome pathways 2013 ALTEX Proceedings 2(2): 74

J. Madden, A. Richarz, D. Neagu, C. Yang, E. Fioravanzo, A. Pery, A. Worth, M. Berthold, M. Cronin The COSMOS project – developing integrated computational approaches to predict repeated dose toxicity 2013 ALTEX Proceedings 2(2): 75

F.M. Williams, M. Ambrosio, G. Barrett, M. Cronin, R.H. Guy, J. Plautz, C. Roper, H. Rothe, D. Rua, M. Verwei, C. Yang Threshold of toxicological concern (TTC) task force: a strategy to support application of TTC to dermally applied cosmetic ingredients 2013 Toxicology Letters 221 Supplement: S35

H.M. Hollnagel, M. Ambrosio, A.R. Boobis, M.T.D. Cronin, S.P. Felter, D. Keller, K.L. Muldoon Jacobs, R. Safford, V. Vitcheva, A.P. Worth, C. Yang TTC Task Force: Development of a cosmetics database to support application of TTC to cosmetic ingredients 2013 Toxicology Letters 221 Supplement: S35

M.T.D. Cronin, J.C. Madden, A.-N. Richarz, M.D. Nelms, F. Steinmetz Applying read-across for quantitative chronic toxicity prediction 2013 Toxicology Letters 221 Supplement: S52

M. Cronin, S. Enoch, J. Madden, A. Richarz, D. Roberts Category formation and read-across for toxicity prediction: A review of the current status and future directions 2013 Toxicology Letters 221 Supplement: S79-S80

C. Yang, M. Ambrosio, K. Arvidson, S. Barlow, S. Boobis, M. Checheva, M.T.D. Cronin, S. Felter, E. Fioravanzo, H. Hollnagel, D. Hristozov, K. Jacobs, D. Keller, A. Mostrag-Szylchtying, M. Nelms, J. Rathman, A. Richarz, I. Tsakovska, S. Vidry, V. Vitcheva, et al. Development of new COSMOS oRepeatDose and non-cancer Threshold of Toxicological Concern (TTC) databases to support alternative testing methods for cosmetics related chemicals 2013 Toxicology Letters 221 Supplement: S80

V. Vitcheva, A. Mostrag-Szychtying, M. Nelms, P. Alov, S. Enoch, I. Tsakovka, J. Rathman, M.T.D. Cronin Data mining toxicity effects through an ontology approach to investigate toxicity mode of action 2013 Toxicology Letters 221 Supplement: S80

A.-N. Richarz, D. Neagu, C. Yang, E. Fioravanzo, A. Péry, A. Worth, M. Berthold, M.T.D. Cronin Development of integrated in silico models for toxicity prediction focussing on cosmetic ingredients 2013 Toxicology Letters 221 Supplement: S81

A.-N. Richarz, S. Enoch, M. Hewitt, J. Madden, M. Nelms, K. Przybylak, C. Yang, M. Berthold, T. Meinl, P. Ohl, M.T.D. Cronin In silico workflows for toxicity prediction implemented into KNIME 2013 Toxicology Letters 221 Supplement: S81

A. Paini, J.V. Sala Benito, M. Mennecozzi, M. Gajewska, A. Worth, J.M. Zaldivar Comenges Modelling chemically-induced cell toxicity: An open source implementation of a virtual cell based assay model 2013 Toxicology Letters 221 Supplement: S82

A. Paini, J.V. Sala Benito, M. Gajewska, A. Worth, J.M. Zaldivar Comenges Human bioaccumulation potential simulated in R and implemented into KNIME interface 2013 Toxicology Letters 221 Supplement: S82

E. Fioravanzo, A. Bassan, M.T.D. Cronin, S. Kovarich, C. Manelfi, A.-N. Richarz, I. Tsakovska, A.P. Worth Molecular modelling of LXR binding to evaluate the potential for liver steatosis 2013 Toxicology Letters 221 Supplement: S83

J.G. Diaz Ochoa, J. Bucher, J. Niklas, K. Mauch Multi-scale modeling for individualized spatiotemporal prediction of drug effects 2013 Toxicology Letters 221 Supplement: S83-84

M. Al Sharif, P. Alov, M.T.D. Cronin, E. Fioravanzo, I. Tsakovska, V. Vitcheva, A. Worth, C. Yang, I. Pajeva Toward better understanding of liver steatosis MoA: Molecular modelling study of PPAR gamma receptor 2013 Toxicology Letters 221 Supplement: S85

M.T.D. Cronin, S.J. Enoch, M. Hewitt, J.C. Madden, M.D. Nelms, K.R. Przybylak, A.-N. Richarz Improved in silico methods to group liver toxicants related to Adverse Outcome Pathways 2013 The Toxicologist – A Supplement to Toxicological Sciences 132: 189

A.-N. Richarz, S.J. Enoch, M. Hewitt, J.C. Madden, K. Przybylak, C. Yang, M.R. Berthold, T. Meinl, P. Ohl, M.T.D. Cronin Flexible and transparent computational workflows for the prediction of target organ toxicity 2013 The Toxicologist – A Supplement to Toxicological Sciences 132: 183

J. Rathman, C. Yang, K. Arvidson, M.T.D. Cronin, S. Enoch, D. Hristozov, Y. Lan, J.C. Madden, D. Neagu, A.N. Richarz, M. Ridley, O. Sacher, C. Schwab, L. Yang Development of a COSMOS Database to support in silico modelling for cosmetics ingredients and related chemicals 2013 The Toxicologist – A Supplement to Toxicological Sciences 132: 185

J.G. Diaz Ochoa, J. Bucher, J. Niklas, K. Mauch Multiscale modeling for individualized spatiotemporal prediction of drug effects 2013 The Toxicologist – A Supplement to Toxicological Sciences 132: 118

A.-N. Richarz, M.R. Berthold, E. Fioravanzo, D. Neagu, C. Yang, J.-M. Zaldıvar-Comenges, M.T.D. Cronin Integrated in silico modeling for the prediction of chronic toxicity 2013 International Journal of Toxicology 32: 72-73

M.T.D. Cronin, S.J. Enoch, M.D. Nelms, J.C. Madden, A.-N. Richarz, C. Yang Linking chemical categories to adverse outcome pathways for chronic toxicity 2013 International Journal of Toxicology 32: 65

L. Yang, D. Neagu Toxicity risk assessment from heterogeneous uncertain data with possibility-probability distribution 2013 Proceedings of the 2013 IEEE International Conference on Fuzzy Systems (FUZZ), Hyderabad, India. 1-8

A.-N. Richarz, E. Fioravanzo, S. Kovarich, A.R.R. Péry, J.G. Diaz Ochoa, D. Neagu, C. Yang, M.R. Berthold, A.P. Worth, M.T.D. Cronin COSMOS: Integrated in Silico Models for the Prediction of Human Repeated Dose Toxicity of COSMetics to Optimise Safety. 2013 Gocht T, Schwarz M (eds) Towards the replacement of in vivo repeated dose systemic toxicity testing. Volume 3, pp. 146-178

S. Kovarich, A. Bassan, M.T..D. Cronin, E. Fioravanzo, C. Manelfi, A.P. Worth, C. Yang Molecular modelling to predict and understand chemical toxicity in the AOP framework – Case study: MoA from LXR activation to liver steatosis. 2013 Gocht T, Schwarz M (eds) Towards the replacement of in vivo repeated dose systemic toxicity testing. Volume 3, pp. 249-252

A. Paini, J.V. Sala Benito, M. Gajewska, A. Worth, J.M. Zaldivar Comenges Human bioaccumulation potential simulated in R and implemented in the KNIME interface 2013 Gocht T, Schwarz M (eds) Towards the replacement of in vivo repeated dose systemic toxicity testing. Volume 3, pp. 253-256

O. Morales-Ibanez , M. Domínguez , S. H. Ki , M. Marcos , J. F. Chaves , E. Nguyen-Khac , H. Houchi , S. Affò , P. Sancho-Bru , J. Altamirano , J. Michelena , J. C. García-Pagán, J. G. Abraldes , V. Arroyo , J. Caballería ,F.- J. Laso , B. Gao , R. Bataller Human and experimental evidence supporting a role for osteopontin in alcoholic hepatitis. John Wiley and Sons Ltd, United Kingdom 2013 Hepatology, Vol. 58/Issue 5 pp. 1742-1756 10.1002/hep.26521

M. Vinken , B. Landesmann, M. Goumenou , S. Vinken , I. Shah , H. Jaeschke , C. Willett , M. Whelan , V. Rogiers Development of an Adverse Outcome Pathway From Drug-Mediated Bile Salt Export Pump Inhibition to Cholestatic Liver Injury Oxford University Press, United Kingdom 2013 Toxicological Sciences, Vol. 136/Issue 1 pp. 97-106 10.1093/toxsci/kft177

M. Vinken The adverse outcome pathway concept: A pragmatic tool in toxicology Elsevier, Ireland Ltd 2013 Toxicology, Vol. 312 pp. 158-165 10.1016/j.tox.2013.08.011

M. Vinken , M. Maes , T. Vanhaecke , V. Rogiers Drug-Induced Liver Injury: Mechanisms, Types and Biomarkers Bentham Science Publishers B.V., Netherlands 2013 Current Medicinal Chemistry, Vol. 20/Issue 24 pp. 3011-3021 10.2174/0929867311320240006

E. Ramboer , T. Vanhaecke , V. Rogiers, M. Vinken Primary hepatocyte cultures as prominent in vitro tools to study hepatic drug transporters Informa Healthcare, United Kingdom 2013 Drug Metabolism Reviews, Vol. 45/Issue 2 pp. 196-217 10.3109/03602532.2012.756010

M. Ulvestad , P. Nordell , A. Asplund , M. Rehnström , S. Jacobsson , G. Holmgren , L. Davidson , G. Brolén , J. Edsbagge , P. Björquist , B. Küppers-Munther , T. B. Andersson Drug metabolizing enzyme and transporter protein profiles of hepatocytes derived from human embryonic and induced pluripotent stem cells Elsevier Inc. 2013 Biochemical Pharmacology, Vol. 86/Issue 5 pp. 691-702 10.1016/j.bcp.2013.06.029

H.-G. Jahnke , D. Steel , S. Fleischer , D. Seidel , R. Kurz , S. Vinz , K. Dahlenborg , P. Sartipy , A. A. Robitzki A Novel 3D Label-Free Monitoring System of hES-Derived Cardiomyocyte Clusters: A Step Forward to In Vitro Cardiotoxicity Testing Public Library of Science, United States 2013 PLoS One, Vol. 8/Issue 7 pp. 145-156 10.1371/journal.pone.0068971

L. Sivertsson , J. Synnergren , J. Jensen , P. Björquist, M. Ingelman-Sundberg Hepatic Differentiation and Maturation of Human Embryonic Stem Cells Cultured in a Perfused Three-Dimensional Bioreactor Mary Ann Liebert Inc. Publishers, United States 2013 Stem Cells and Development, Vol. 22/Issue 4 pp. 581-594 10.1089/scd.2012.0202

J. Niklas Quantitative Evaluation and Prediction of Drug Effects and Toxicological Risk Using Mechanistic Multiscale Models Wiley – VCH Verlag GmbH & CO. KGaA 2013 Molecular Informatics, 1/32 14 – 23 10.1002/minf.201200043

M. Ivanov In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes Oxford University Press, United Kingdom 2013 Nucleic Acids Research, 6/41 e72 – e72 10.1093/nar/gks1467

J. G. Diaz Ochoa A multi-scale modeling framework for individualized, spatiotemporal prediction of drug effects and toxicological risk Frontiers Research Foundation 2013 Frontiers in Pharmacology 10.3389/fphar.2012.00204

D. Mueller , E. Heinzle , F. Noor 3D Hepatic In Vitro Models as Tools for Toxicity Studies Bentham Science Publishers B.V., Netherlands 2013 Current Tissue Engineering, Vol. 2/Issue 1 78-89 10.2174/2211542011302010007

P. Gunness 3D Organotypic Cultures of Human HepaRG Cells: A Tool for In Vitro Toxicity Studies Oxford University Press 2013 Toxicological Sciences, 1/133 67 – 78 10.1093/toxsci/kft021

M. Schug Pharmacokinetics explain in vivo/in vitro discrepancies of carcinogen-induced gene expression alterations in rat liver and cultivated hepatocytes Springer Verlag, Germany 2013 Archives of Toxicology, 2/87 337 – 345 10.1007/s00204-012-0999-8

D. Mueller Stable isotope-assisted metabolomics to detect metabolic flux changes in mammalian cell cultures Elsevier Limited 2013 Current Opinion in Biotechnology, 1 / 24 54 – 59 10.1016/j.copbio.2012.10.015

J. Gries , D. Schumacher , J. Arand , P. Lutsik , M. R. Markelova , I. Fichtner , J. Walter , C. Sers , S. Tierling Bi-PROF: Bisulfite profiling of target regions using 454 GS FLX Titanium technology Landes Bioscience 2013 Epigenetics, Vol. 8/Issue 7 765-771 10.4161/epi.25242

D. Mueller , L. Krämer , E. Hoffmann , S. Klein , F. Noor 3D organotypic HepaRG cultures as in vitro model for acute and repeated dose toxicity studies Elsevier Limited 2013 Toxicology in Vitro, Vol. 28/Issue 1 104-112 10.1016/j.tiv.2013.06.024

P. Godoy et al. Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME Springer Verlag, Germany 2013 Archives of Toxicology, Vol. 87/Issue 8 1315-1530 10.1007/s00204-013-1078-5

S. Klein , D. Mueller , V. Schevchenko , F. Noor Long-term maintenance of HepaRG cells in serum-free conditions and application in a repeated dose study John Wiley and Sons Ltd, United Kingdom 2013 Journal of Applied Toxicology 10.1002/jat.2929

T. Odenthal Analysis of Initial Cell Spreading Using Mechanistic Contact Formulations for a Deformable Cell Model Public Library of Science, United States 2013 PLoS Computational Biology, 10 / 9 10.1371/journal.pcbi.1003267

J. Fraczek, J. Bolleyn, T. Vanhaecke, V. Rogiers, M. Vinken Primary hepatocyte cultures for pharmaco-toxicological studies: at the busy crossroad of various anti-dedifferentiation strategies 2013 Archives of Toxicology 87(4) pp. 577-610

M. Vinken, M. Maes, R. Cavill, D. Valkenborg, J. K. Ellis, E. Decrock, L. Leybaert, A. Staes, K. Gevaert, A.G. Oliveira, G.B. Menezes, B. Cogliati, M.L. Dagli, T.M. Ebbels, E. Witters, H.C. Keun, T. Vanhaecke, V. Rogiers Proteomic and metabolomic responses to connexin43 silencing in primary hepatocyte cultures 2013 Archives of Toxicology 87(5) 883-94

M. Vinken Primary hepatocytes and their cultures in liver apoptosis research Springer 2013 Archives of Toxicology 88 (2) pp. 199-212

T.Y. Doktorova Way forward in case of a false positive in vitro genotoxicity result for a cosmetic substance? Elsevier 2013 Toxicology In Vitro 28 (1) pp. 54-59

T. Gocht, M. Schwarz, E. Berggren, M. Whelan SEURAT-1: Development of a research strategy for the replacement of in vivo repeated dose systemic toxicity testing 2013 AltTox.org

M. Vinken, B. Landesmann, M. Goumenou, S. Vinken, I. Shah, H. Jaeschke, C. Willet, M. Whelan, V. Rogiers Development of an adverse outcome pathway from drug-mediated bile salt export pump inhibition to cholestatic liver injury 2013 Toxicol. Sci. 136 pp. 97-106

T. Heise In vitro – in vivo correlation of gene expression Bentham Science Publishers 2012 Current Medicinal Chemistry pp. 1721-30 PMID: 2241

M. Vinken Modifications in connexin expression in liver development and cancer Informa Healthcare 2012 Cell Communication and Adhesion p.55-62 DOI:10.3109/15419061.2012.712576

J. Fraczek Primary hepatocyte cultures for pharmaco-toxicological studies: at the busy crossroad of various anti-dedifferentiation strategies Springer 2012 Archives of Toxicology pp. 577-610 DOI: 10.1007/s0024-012-0983-3

M. Vinken Proteomic and metabolomic responses to connexin43 silencing in primary hepatocyte cultures Springer 2012 Archives of Toxicology pp. 883-894 DOI: 10.1007/s00204-012-0994-0

C. Seeliger Decrease of global Methylation improves significantly hepatic Differentiation of Ad-MSCs: Possible future Application for Urea Detoxification IngentaConnect 2012 Cell Transplantation pp. 151-167 PMID: 22507189

M. Leist, B.A. Lidbury, C. Yang, P.J. Hayden, J.M. Kelm, S. Ringeissen, A. Detroyer, J.R. Meunier, J.F. Rathman, G.R. Jackson Jr., G. Stolper, N. Hasiwa Novel Technologies and an Overall Strategy to Allow Hazard Assessment and Risk Prediction of Chemicals, Cosmetics, and Drugs with Animal-Free Methods Altex 2012 29: pp. 373–388

A. Tonnelier, S. Coecke, J.M. Zaldivar Screening of chemicals for human bioaccumulative potential with a physiologically based toxicokinetic model Archives of Toxicology 2012 86(3): pp. 393–403

J.M. Zaldívar Comenges, J. Wambaugh, R. Judson Modelling in vitro cell-based assays experiments: Cell population dynamics Jordán F, Jørgensen SE (Eds) Models of the ecological hierarchy. From molecules to the ecosphere. Developments in Environmental Modelling, Volume 25. Elsevier, Amsterdam, The Netherlands 2012 pp. 51-71 ISBN: 978-0-444-59396-2

K. Jacobs, K. Arvidson, M.T.D. Cronin, S. Enoch, S.P. Felter, E. Fioravanzo, J.C. Madden, M. Pavan, A. Richarz, R. Safford, A. Worth, C. Yang, ILSI EU Expert Group Development of a new non-cancer TTC database for cosmetics ingredients: a collaborative project between the EC, COLIPA and ILSI Europe. 2012 The Toxicologist – A Supplement to Toxicological Sciences 126: 52

J. Aungst, K. Muldoon-Jacobs, D. Rua, K. Arvidson, D. Hristozov, B. Mugabe, E.J. Matthews, A. McCarthy, C. Yang, M.A. Cheeseman Revisiting the TTC approach for cancer assessment: Part of a road map of computational methods at FDA CFSAN OFAS 2012 The Toxicologist – A Supplement to Toxicological Sciences 126: 61

C. Yang, A.P. Worth, K.B. Arvidson, A.M. Richard A Mode-of-Action-based QSAR approach to improve understanding of developmental toxicity 2012 The Toxicologist – A Supplement to Toxicological Sciences 126: 385

S. Anzali, M.R. Berthold, E. Fioravanzo, D. Neagu, A.R.R. Péry, A.P. Worth, C. Yang, M.T.D. Cronin, A.-N. Richarz Development of computational models for the risk assessment of cosmetic ingredients 2012 IFSCC Magazine 15 (4): 249-255

L. Yang, D. Neagu Towards the integration of heterogeneous uncertain data Proceedings of the 2012 IEEE 13th International Conference on Information Reuse and Integration IEEE IRI 2012, Zhang C, Joshi J, Bertino E, Thuraisingham B (eds), 8-10 August 2012, Las Vegas, NV, USA. 2012 295-302

M. Makhtar, L. Yang, D. Neagu, M.J. Ridley Optimisation of classifier ensemble for predictive toxicology applications 2012 Proceedings of the UKSim 14th International Conference on Computer Modelling and Simulation. 236-24

A. Worth, M.T.D. Cronin, S. Enoch, E. Fioravanzo, M. Fuart-Gatnik, M. Pavan, C. Yang Applicability of the Threshold of Toxicological Concern (TTC) approach to cosmetics – preliminary analysis 2012 JRC report EUR 25162EN. Publications Office of the European Union, Luxembourg

M.D. Nelms, S.J. Enoch, E. Fioravanzo, J.C. Madden, T. Meinl, A.-N. Richarz, C.H. Schwab, A.P. Worth, C. Yang, M.T.D. Cronin Strategies to form chemical categories from Adverse Outcome Pathways 2012 Gocht T, Schwarz M (eds) Towards the replacement of in vivo repeated dose systemic toxicity testing. Volume 2, pp. 263-267

M.T.D. Cronin, A.-N. Richarz Mode of Action Working Group: Use of Mode of Action related to repeated dose systemic toxicity – A framework for capturing Information. 2012 Gocht T, Schwarz M (eds) Towards the replacement of in vivo repeated dose systemic toxicity testing. Volume 2, pp. 284-289

Ulvestad et al Evaluation of OATP1B1 and CYP3A4 activities in primary human hepatocytes and HepaRG cells cultured in a dynamic three-dimensional bioreactor system 2012 Journal of Pharmacol and Experimental Therapeutics 10.1124/jpet.112.195750

Darnell et al. In vitro evaluation of major in vivo drug metabolic pathways using primary human hepatocytes and HepaRG cells in suspension and in a dynamic threedimensional bioreactor system. 2012 Journal of Pharmacology and Experimental Therapy 10.1124/jpet.112.195834

Haupt et al. Automated selection and harvesting of pluripotent stem cell colonies 2012 Biotechnology and Applied Biochemistry, 59 (2) pp. 77-87 10.1002/bab.1014

B. Hardy Food for thought … A toxicology ontology roadmap Spektrum Akademische Verlag 2012 ALTEX, 29(2)/12 129-137 10.14573/altex.2012.2.129

I. Ramis-Conde From genotypes to phenotypes: classification of the tumour profiles for different variants of the cadherin adhesion pathway Institute of Physics Publishing 2012 Physical Biology, 3/9 036008- 10.1088/1478-3975/9/3/036008

M. Vinken, M. Pauwels, G. Ates, M. Vivier M, T. Vanhaecke, V. Rogiers Screening of repeated dose toxicity data present in SCC(NF)P/SCCS safety evaluations of cosmetic ingredients 2012 Archives of Toxicology 86 (3) 405-412

P. Roelandt, S. Obeid, J. Paeshuyse, J. Vanhove, A. Van Lommel, Y. Nahmias, F. Nevens, J. Neyts and C.M. Verfaillie Human pluripotent stem cell-derived hepatocytes support complete replication of hepatitis C virus 2012 Hepatology 57 (2) 246 – 251

E. L. Guimarães, J. Best, L. Dollé, M. Najimi, E. Sokal and L. van Grunsven Mitochondrial uncouplers inhibit hepatic stellate cell activation 2012 BMC Gastroenterology 12:68

B. Landesmann, M. Goumenou, S. Munn and M. Whelan Description of Prototype Modes-of-Action Related to Repeated Dose Toxicity 2012 JRC Scientific and Policy Report, Nr. JRC75689 10.2788/71112

M. Vinken Screening of repeated dose toxicity data present in SCC(NF)P/SCCS safety evaluations of cosmetic ingredients Springer 2011 pp. 405-412 PMID: 22038139

M.T.D. Cronin, C.M. Ellison, S.J. Enoch, M. Hewitt, J.C. Madden, K. Przybylak, J.A.H. Schwöbel Electrophilic reaction chemistry to predict genotoxicity through mechanistically derived grouping and read-across: links to Adverse Outcome Pathways. 2011 Altex 28 (Special Issue) 108

A.N. Richarz, M.T.D. Cronin, D.C. Neagu, C. Yang, J.M. Zaldivar-Comenges, M. Berthold COSMOS – A new European project to develop computational models for the repeat dose toxicity of cosmetic ingredients. 2011 Altex 28 (Special Issue) 39-40

S. Colleoni et al. Development of a Neural Teratogenicity Test Based on Human Embryonic Stem Cells: Response to Retinoic Acid Exposure Oxford University Press 2011 Toxicological Sciences, Vol. 124(2) pp. 370 – 377

F. Pistollato et al. Standardization of Pluripotent Stem Cell Cultures for Toxicity Testing 2011 Expert Opin. Drug Metab. Toxicol., 8 (2) pp. 239-57

J. Synnergren et al Global transcriptional profiling reveals similarities and differences between human stem cell-derived cardiomyocyte clusters 2011 Physiol Genomics, 44 (4) pp. 245-58

Koch et al. Excitation-induced ataxin-3 aggregation in neurons from patients with Machado-Joseph disease 2011 Nature, 480 (7378) pp. 543-6 10.1038/nature10671

S.H. Rahman, M.L. Maeder, J.K. Joung and T. Cathomen Zinc-Finger Nucleases for Somatic Gene Therapy: The Next Frontier 2011 Human Gene Therapy 22 (8) 925 – 933