Publications
2016
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Sofia B. Leite, Tiffany Roosens , Adil El Taghdouini , Inge Mannaerts , Ayla J. Smout , Mustapha Najimi , Etienne Sokal , Fozia Noor , Christophe Chesne , Leo A. van Grunsven:
Novel human hepatic organoid model enables testing of drug-induced liver fibrosis in vitro
Biomaterials Vol. 78, 1-10, 10.1016/j.biomaterials.2015.11.026
2015
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Noor F:
A shift in paradigm towards human biology-based systems for cholestatic-liver diseases
Journal of Physiology Vol. 593/Issue 23, 5043-5055, 10.1113/JP271124
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Noor F:
A shift in paradigm towards human biology-based systems for cholestatic-liver diseases
Journal of Physiology Vol. 593/Issue 23, 5043-5055, 10.1113/JP271124
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Ghallab, A., Cellière, G., Henkel, S.G., Driesch, D., Hoehme, S., Hofmann, U., Zellmer, S., Godoy, P., Sachinidis, A., Blaszkewicz, M., Reif, R., Marchan, R., Kuepfer, L., Häussinger, D., Drasdo, D., Gebhardt, R., Hengstler, J.G.:
Model guided identification and therapeutic implications of an ammonia sink mechanism
Journal of Hepatology, Epub ahead of print, http://dx.doi.org/10.1016/j.jhep.2015.11.018
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Patrick Trampert, Sviatoslav Bogatchev, Nico Marniok, Tim Dahmen, Philipp Slusallek:
Marker detection in Electron Tomography: A comparative study
Microscopy and Microanalysis Volume 21 / Issue 06, doi: 10.1017/S1431927615015433
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Sebastian Klein, Silvia Maggioni, Joachim Bucher, Daniel Mueller, Jens Niklas, Valery Shevchenko, Klaus Mauch, Elmar Heinzle and Fozia Noor:
In silico modeling for the prediction of dose and pathway related adverse effects in humans from in vitro repeated-dose studies
Toxicological Sciences, 2015 Sep 29, Epub ahead of print, doi: 10.1093/toxsci/kfv218
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Raymond Reif, Johan Karlsson, Georgia Günther, Lynette Beattie, David Wrangborg, Seddik Hammad, Brigitte Begher-Tibbe, Amruta Vartak, Simone Melega, Paul M. Kaye, Jan G. Hengstler, Mats Jirstrand:
Bile canalicular dynamics in hepatocyte sandwich cultures
Archives of Toxicology 2015 Aug 18. [Epub ahead of print], 10.1007/s00204-015-1575-9
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T. Dahmen, H. Kohr, N. de Jonge, and P. Slusallek:
Matched Backprojection Operator for Combined Scanning Transmission Electron Microscopy Tilt- and Focal Series
Microscopy and Microanalysis Volume 21 / Issue 03 / June 2015 , 725-738, 10.1017/S1431927615000525
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Friebel A, Neitsch J, Johann T, Hammad S, Hengstler JG, Drasdo D, Hoehme S:
TiQuant: software for tissue analysis, quantification and surface reconstruction.
Bioinformatics Epub ahead of print, 10.1093/bioinformatics/btv346
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Turonova Beata, Marsalek Lukas, Davidovic Tomas and Slusallek Philipp:
Progressive Stochastic Reconstruction Technique (PSRT) for Cryo Electron Tomography
Journal of Structural Biology March 2015, 195-206, 10.1016/j.jsb.2015.01.011
2014
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D'Alessandro LA, Hoehme S, Henney A, Drasdo D, Klingmüller U :
Unraveling liver complexity from molecular to organ level: Challenges and perspectives
Prog Biophys Mol Biol, 10.1016/j.pbiomolbio.2014.11.005
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Priesnitz C, Sperber S, Garg R, Orsini M, Noor F :
Fluorescence based cell counting in collagen monolayer cultures of primary hepatocytes
Cytotechnol, doi: 10.1007/s10616-014-9821-1
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Bonder MJ, Kasela S, Kals M, Tamm R, Lokk K, Barragan I, Buurman WA, Deelen P, Greve JW, Ivanov M, Rensen SS, van Vliet-Ostaptchouk JV, Wolfs MG, Fu J, Hofker MH, Wijmenga C, Zhernakova A, Ingelman-Sundberg M, Franke L, Milani L:
Genetic and epigenetic regulation of gene expression in fetal and adult human livers
BMC Genomics 2014, 15:860, doi:10.1186/1471-2164-15-860
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Yassen Assenov, Fabian Müller, Pavlo Lutsik, Jörn Walter, Thomas Lengauer & Christoph Bock:
Comprehensive analysis of DNA methylation data with RnBeads
Nature Methods 11, 2014, 1138–1140 , 10.1038/nmeth.3115
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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
Microscopy and Microanalysis 20 (Suppl 3), 786-787, 10.1017/S1431927614005650
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Ryll A, Bucher J, Bonin A, Bongard S, Gonçalves E, Saez-Rodriguez J, Niklas J, Klamt S:
A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models
Biosystems ;124:26-38. 2014 Oct 124, 26-38, doi: 10.1016/j.biosystems.2014.07.002
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Alépée N, Bahinski T, Daneshian M, De Wever B, Fritsche E, Goldberg A, Hansmann J, Hartung T, Haycock J, Hogberg H, Hoelting L, Kelm JM, Kadereit S, McVey E, Landsiedel R, Leist M, Lübberstedt M, Noor F, Pellevoisin C, Petersohn D, Pfannenbecker U, Reisinger K, Ram:
State-of-the-art of 3D cultures (organs-on-a-chip) in safety testing and pathophysiology
ALTEX (31)4, 441-477, doi: 10.14573/altex1406111.
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Voortman LM, Vulović M, Maletta M, Voigt A, Franken EM, Simonetti A, Peters PJ, van Vliet LJ, Rieger B.:
Quantifying resolution limiting factors in subtomogram averaged cryo-electron tomography using simulations
Journal of Structural Biology Volume 187, Issue 2, 103–111, doi: 10.1016/j.jsb.2014.06.007
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Dirk Drasdo, Stefan Hoehme, Jan G. Hengstler:
How predictive quantitative modelling of tissue organisation can inform liver disease pathogenesis
Journal of Hepatology Volume 61, Issue 4, 951–956, doi: 10.1016/j.jhep.2014.06.013
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Marlies Unterberg, Larissa Leffers, Florian Hübner, Hans-Ulrich Humpf, Konstantin Lepikhov, Jörn Walter, Franziska Ebert and Tanja Schwerdtle:
Toxicity of arsenite and thio-DMAV after long-term (21 days) incubation of human urothelial cells: cytotoxicity, genotoxicity and epigenetics
Toxicology Research, doi: 10.1039/C4TX00036F
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Daniel Becker, Pavlo Lutsik, Peter Ebert, Christoph Bock, Thomas Lengauer and Jörn Walter:
BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives
Nucleic Acids Res 2014 July 1; 42, doi: 10.1093/nar/gku457
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Schliess F, Hoehme S, Henkel SG, Ghallab A, Driesch D, Böttger J, Guthke R, Pfaff M, Hengstler JG, Gebhardt R, Häussinger D, Drasdo D, Zellmer S:
Integrated metabolic spatial-temporal model for the prediction of ammonia detoxification during liver damage and regeneration
Hepatology 60(6), 2040-51, doi: 10.1002/hep.27136
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Campos G,, Schmidt-Heck W, Ghallab A, …, Hengstler JG., Godoy P:
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
Archives of Toxicology 2014 Jun;88(6):1267-80, doi: 10.1007/s00204-014-1240-8
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Hammad S, Hoehme S, Friebel A, von Recklinghausen I, Othman A, Begher-Tibbe B, 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.
Arch Toxicol 88, 1161–1183, doi: 10.1007/s00204-014-1243-5
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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
Microscopy and Microanalysis Vol. 20/Issue 02, 548-560, 10.1017/S1431927614000075
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Carapito C, Burel A, Guterl P, Walter A, Varrier F, Bertile F, van Dorsselaer A :
MSDA, a proteomics software suite for in-depth Mass Spectrometry Data Analysis using grid computing
PROTEOMICS , doi: 10.1002/pmic.201300415
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Mueller D, Krämer L, Hoffmann E, Klein S, Noor F.:
3D organotypic HepaRG cultures as in vitro model for acute and repeated dose toxicity studies
Toxicol In Vitro 28, 104-12, doi: 10.1016/j.tiv.2013.06.024
2013
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Tim Odenthal, B. Smeets, P. Van Liedekerke, E. Tijskens, H. Van Oosterwijck, H Ramon:
Analysis of Initial Cell Spreading Using Mechanistic Contact Formulations for a Deformable Cell Model
Plos computational biology, e1003267, 10.1371/journal.pcbi.1003267
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SEURAT Initiative:
SEURAT-1 Annual Book Volume 3
Towards the replacement of in vivo repeated dose systemic toxicity testing 3rd Annual Book of the SEURAT-1 Initiative, September 2013
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Godoy P, 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
Arch Toxicol. 2013 Aug;87(8):1315-530. , doi: 10.1007/s00204-013-1078-5.
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Ivanov M, , Kals M, Kacevska M, Barragan I, Kasuga K, Rane A, Metspalu A, Milani L, Ingelman-Sundberg M.:
Ontogeny, distribution and potential roles of 5-hydroxymethylcytosine in human liver function
Genome Biology 14(8):R83, 10.1186/gb-2013-14-8-r83
Additional link
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Daniel Mueller, Lisa Kraemer, Esther Hoffmann, Sebastian Klein, Fozia Noor:
3D organotypic HepaRG cultures as in vitro model for acute and repeated dose toxicity studies.
Toxicology in Vitro 28 (2014), 104-112, 10.1016/j.tiv.2013.06.024
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Jasmin Gries, Dirk Schumacher, Julia Arand, Pavlo Lutsik, Maria Rivera Markelova, Iduna Fichtner, Jörn Walter, Christine Sers, Sascha Tierling:
Bi-PROF: Bisulfite profiling of target regions using 454 GS FLX Titanium technology
8 7, 7, doi:10.4161/epi.25242
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Daniel Mueller, Elmar Heinzle:
Stable isotope-assisted metabolomics to detect metabolic flux changes in mammalian cell cultures
Current Opinion in Biotechnology 2013, 24, doi: 10.1016/j.copbio.2012.10.015
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Daniel Mueller, Elmar heinzle, Fozia Noor:
3D Hepatic In Vitro Models as Tools for Toxicity Studies
Current Tissue Engineering Vol. 2 Issue 1, 78-89, DOI: 10.2174/2211542011302010007
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Patrina Gunness, Daniel Mueller, Valery Shevchenko, Elmar Heinzle, Magnus Ingelman-Sundberg, Fozia Noor:
3D organotypic cultures of human HepaRG cells: a tool for in vitro toxicity studies
Toxicological Sciences, doi: 10.1093/toxsci/kft021
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Schug, Markus; Stoeber, Regina; Heise, Tanja;, Mielke, Hans; Gundert-remy, Ursula; Godoy, Patricio; Reif, Raymond; Blaszkewicz, Meinolf; Ellinger-ziegelbauer, Heidrun; Ahr, Hans-Juergen; Selinski, Silvia; Guenther, Georgia; Marchan, Rosemarie; Sachinidis, Agapios; Nuessler, Andreas; Oberemm, Axel; Hen:
Pharmacokinetics explain in vivo/in vitro discrepancies of carcinogen-induced gene expression alterations in rat liver and cultivated hepatocytes
Archives of Toxicology February 2013, Volume 87, Issue 2, , pp 337-345, doi:10.1007/s00204-012-0999-8
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Juan G. Diaz Ochoa, Joachim Bucher, Alexandre R. R. Péry, José M. Zaldivar Comenges, Jens Niklas and Klaus Mauch:
A multi-scale modeling framework for individualized, spatiotemporal prediction of drug effects and toxicological risk
Front. Pharmacol., doi: 10.3389/fphar.2012.00204
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Maxim Ivanov, Mart Kals, Marina Kacevska, Andres Metspalu, Magnus Ingelman-Sundberg and Lili Milani:
In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes
Nucleic Acids Research Vol. 41, No. 6 e72, doi:10.1093/nar/gks1467
Additional link
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Jens Niklas, Juan G Diaz Ochoa, Joachim Bucher, Klaus Mauch:
Quantitative Evaluation and Prediction of Drug Effects and Toxicological Risk Using Mechanistic Multiscale Models
Molecular Informatics 2013 , 32, 14–23, DOI: 10.1002/minf.201200043
2012
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SEURAT-1 Initiative:
SEURAT-1 Annual Book Volume 2
Towards the replacement of in vivo repeated dose systemic toxicity testing / 2nd Annual Book of the SEURAT-1 Initiative, July 2012
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Ignacio Ramis-Conde, Dirk Drasdo:
From genotypes to phenotypes: classification of the tumour profiles for different variants of the cadherin adhesion pathway
Phsyical Biology 9 (2012) 036008, 11p, doi:10.1088/1478-3975/9/3/036008
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Barry Hardy, Gordana Apic, Philip Carthew, Dominic Clark, David Cook, Ian Dix, Sylvia Escher, Janna Hastings, David J. Heard, Nina Jeliazkova, Philip Judson, Sherri Matis-Mitchell, Dragana Mitic, Glenn Myatt, Imran Shah, Ola Spjuth, Olga Tcheremenskaia, Luca Toldo, Da:
Toxicology Ontology Perspectives
ALTEX 29(2)/12, 139-156
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Barry Hardy, Gordana Apic, Philip Carthew, Dominic Clark, David Cook, Ian Dix,Sylvia Escher, Janna Hastings, David J. Heard, Nina Jeliazkova, Philip Judson, Sherri Matis-Mitchell, Dragana Mitic, Glenn Myatt, Imran Shah, Ola Spjuth, Olga Tcheremenskaia, Luca Toldo, Dav:
Food for thought … A toxicology ontology roadmap
ALTEX 29(2)/12, 129-137
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Dr. Gordana Apic:
Data management/text mining/data integration in the SEURAT cluster
Book of Abstracts Conference Data Mining in Bioinformatics June 26th-28th 2012, 1-2
2011
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SEURAT-1 Initiative:
SEURAT-1 Annual Book Volume 1
Towards the replacement of in vivo repeated dose systemic toxicity testing / 1st Annual Book of the SEURAT-1 Initiative, September 2011