Publications

2016*


2017

M Lienhard, S Grasse, J Rolff, S Frese, U Schirmer, M Becker, S Börno, B Timmermann, L Chavez, H Sültmann, G Leschber, I Fichtner, M R Schweiger and R Herwig QSEA––modelling of genome-wide DNA methylation from sequencing enrichment experiments Nucleic Acids Research, 2017, Vol. 45, No. 6 e44 [DOI]



2016

Ralf Herwig, Christopher Hardt, Matthias Lienhard & Atanas Kamburov. Analyzing and interpreting genome data at the network level with ConsensusPathDB. Nature Pprotocols. VOL.11 NO.10. 2016, 1889. [DOI]

Hendrickx D, Souza T, Jennen D, Kleinjans J. DTNI: a novel toxicogenomics data analysis tool for identifying the molecular mechanisms underlying the adverse effects of toxic compounds. Archives of Toxicology, 2016, doi:10.1007/s00204-016-1922-5. [DOI]

Hebels DG, Rasche A, Herwig R, van Westen GJ, Jennen DG, Kleinjans JC. A Systems Biology Approach for Identifying Hepatotoxicant Groups Based on Similarity in Mechanisms of Action and Chemical Structure. Methods Mol Biol. 2016;1425:339-59. [DOI]



2015

Jo McEntyre, Ugis Sarkans & Alvis Brazma. The BioStudies database. Molecular Systems Biology 11: 847 | 2015. [DOI] 10.15252/msb.20156658

Caiment F, Gaj S, Claessen S, Kleinjans J. High-throughput data integration of RNA–miRNA–circRNA reveals novel insights into mechanisms of benzo[a]pyrene-induced carcinogenicity. Nucleic Acids Research, 2015, Vol. 43, No. 5 2525–2534 doi: 10.1093/nar/gkv115.[DOI]

Diana M. Hendrickx, Hugo J.W.L. Aerts, Florian Caiment, Dominic Clark, Timothy M.D. Ebbels, Chris T. Evelo, Hans Gmuender, Dennie G.A.J. Hebels, Ralf Herwig, Jürgen Hescheler, Danyel G.J. Jennen, Marlon J.A. Jetten, Stathis Kanterakis, Hector C. Keun, Vera Matser, John P. Overington, Ekaterina Pilicheva, Ugis Sarkans, Marcelo P. Segura-Lepe, Isaia Sotiriadou, Timo Wittenberger, Clemens Wittwehr, Antonella Zanzi, and Jos C.S. Kleinjans. diXa: a data infrastructure for chemical safety assessment. Bioinformatics 2015 : btu827v2-btu827.[DOI]

Herwig R, Gmuender H, Corvi R, Bloch KM, Brandenburg A, Castell J, Ceelen L, Chesne C, Doktorova TY, Jennen D, Jennings P, Limonciel A, Lock EA, McMorrow T, Phrakonkham P, Radford R, Slattery C, Stierum R, Vilardell M, Wittenberger T, Yildirimman R, Ryan M, Rogiers V, Kleinjans J. Inter-laboratory study of human in vitro toxicogenomics-based tests as alternative methods for evaluating chemical carcinogenicity: a bioinformatics perspective. Arch Toxicol. 2016 Sep;90(9):2215-29. [DOI]



2014

Wang C, Gong B, Bushel PR, 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 PP, Kreil DP, Megherbi D, Gaj S, Caiment F, van Delft J, Kleinjans J, Scherer A, Devanarayan V, Wang J, Yang Y, Qian HR, Lancashire LJ, Bessarabova M, Nikolsky Y, Furlanello C, Chierici M, Albanese D, Jurman G, Riccadonna S, Filosi M, Visintainer R, Zhang KK, Li J, Hsieh JH, Svoboda DL, Fuscoe JC, Deng Y, Shi L, Paules RS, Auerbach SS, Tong W. The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nat Biotechnol. 2014 Aug . [Europe PMC]

SEQC/MAQC-III Consortium, SEQC/MAQC-III Consortium. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol. 2014 Aug . [Europe PMC]

Valcarcel, B., T.M. Ebbels, A.J. Kangas, P. Soininen, P. Elliot, M. Ala-Korpela, M.R. Jarvelin, and M. de Iorio, Genome metabolome integrated network analysis to uncover connections between genetic variants and complex traits: an application to obesity. J R Soc Interface, 2014. 11(94): p. 20130908. [DOI]

Valcarcel, B., T.M.D. Ebbels, and M. De Iorio, Variance and covariance heterogeneity analysis for detection of metabolites associated with cadmium exposure. Stat Appl Genet Mol Biol, 2014 [in press]



2013

Li, J., Maschke-Dutz, E., Heeger, F., Hache, H., Pandey, V., Kamburov, A., Kühn, A., Herwig, R., Lehrach, H., Wierling, C. (2013) PyBioS 2.4: A Web-based Tool for Design, Modeling, Simulation, and Analysis of Cellular Systems. Genome Biol. [Submitted]

Doktorova, T., Yildirimman, R., Ceelen, L., Vilardell, M., Vanhaecke, T., Vinken, M., Heymans, A., Gmuender, H., Bort, R., Corvi, R., Li, R., Mouchet, N., Chesne, C., vanDelft, J., Kleinjans, J., Castell, J., Herwig, R., Rogiers, V. (2013) Evaluation of the robustness of classification of carcinogenmodified transcriptomic responses in HepaRG cells and the interlaboratory reproducibility of the model. Carcinogenesis, [submitted]

Hebels, D, Jetten M, Aerts H, Theunissen D, Gaj S,  van Delft J, Kleinjans J , (2013) Evaluation of database-derived pathway development for enabling biomarker discovery for hepatotoxicity, Biomarkers in Medicine [Europe PMC]

Vilardell, M., Herwig, R. (2013) Predictive mechanisms in stem cells: an in vitro system based method for testing carcinogenicity. In: Sahu, S.C., and Casciano, D.A. (Eds.) Handbook of Nanomedicine, Nanotoxicology and Stem Cell Use in Toxicology, Wiley, Chichester, UK, [Accepted]

Blazquez, M., A. Carretero, J.K. Ellis, T.J. Athersuch, R. Cavill, T.M. Ebbels, H.C. Keun, J.V. Castell, A. Lahoz, and R. Bort, (2013) A Combination of Transcriptomics and Metabolomics Uncovers Enhanced Bile Acid Biosynthesis in HepG2 Cells Expressing CCAAT/Enhancer-Binding Protein beta (C/EBPbeta), Hepatocyte Nuclear Factor 4alpha (HNF4alpha), and Constitutive Androstane Receptor (CAR). Journal of Proteome Research 12: p. 1535-3893. [DOI]

Vinken, M., 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, and V. Rogiers, (2013) Proteomic and metabolomic responses to connexin43 silencing in primary hepatocyte cultures. Archives of Toxicology, 87(5): p. 883-94. [Europe PMC]

Doktorova, T., Yildirimman, R., Vinken, M., Vilardell, M., Vanhaecke, T., Gmuend er, H., Bort, R., Brolen, G., Mouchet, N., Chesne, C., van Delft, J., Kleinjans, J., Castell, J., Bjorquist, P., Herwig, R.*, Rogiers, V. (2013) Transcriptomic responses generated by hepatocarcinogens in a battery of liver-based in vitro models. Carcinogenesis, 34(6):1393-402. [Europe PMC]

Caiment, F., Tsamou, M., Jennen, D., Kleinjans, J., (2013) Assessing compound carcinogenicity in vitro using connectivity mapping. Carcinogenesis. Aug 12. [Europe PMC]

Kamburov, A., Stelzl, U., Lehrach, H., Herwig, R. (2013) The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Research 41(D1):D793-800 [Europe PMC]

Krug, AK., Kolde, R., Gaspar, JA., Rempel, E., Balmer, NV., Meganathan, K., Vojnits, K., Baquié, M., Waldmann, T., Ensenat-Waser, R., Jagtap, S., Evans, RM., Julien, S., Peterson, H., Zagoura, D., Kadereir, S., Gerhard, D., Sotiriadou, I., Heke, M., Matarajan, K., Henry, M., Winkler, J., Marchan, R., Stoppini, L., Bosgra, S., Westerhout, J., Verwei, M., Vilo, J., Kortenkamp, A., Hescheler, J., Hothorn, L., Bremer, S., van Thriel, C., Krause, K.H., Hengstler, J.G., Rahnenführer, J., Leist, M., Sachinidis, A., (2013) Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach. Archives of Toxicology 87(1):123-143 [Europe PMC]



2012

Kamburov, A., Grossmann, A., Herwig, R., Stelzl, U. (2012) Cluster-based assessment of protein-protein interaction confidence. BMC Bioinformatics. 13:262. [Europe PMC]

Kamburov, A., Stelzl, U., Herwig, R. (2012) IntScore - a web tool for confidence scoring of biological interactions. Nucleic Acids Research. 40(Web Server issue):W140-146. [Europe PMC]

van Delft, J., Gaj, S., Lienhard, M., Albrecht, M., Kirpiy, A., Brauers, K., Claessen, S., Lizarraga, D., Lehrach, H., Herwig, R., Kleinjans, J. (2012) RNA-seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene. Toxicol Sci. 130(2):427-439  [Europe PMC]

Wierling, C., Kühn, A., Hache, H., Daskalaki, A., Maschke-Dutz, E., Mareva, S., Li, J., Herwig, R., Lehrach H. (2012) Prediction in the face of uncertainty: A Monte Carlo-based approach for systems biology of cancer treatment. Mutation Res. 746(2):163-170 [Europe PMC]