List of publications

Journal Article (19)

1. 1.
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   Barel, G.; Herwig, R.: Network and Pathway Analysis of Toxicogenomics Data. Frontiers in Genetics (2018)
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   Verheijen, M. C. T.; Schrooders, Y.; Nudischer, R.; Börno, S. T.; Schlapbach, R.; Gotta, S.; Kleinjans, J. C. S.; Lienhard, M.; Clayton, O.; Timmermann, B. et al.; Selevsek, N.; Gmuender, H.; Herwig, R.; Caiment, F.: DMSO-induced drastic changes in cellular processes and epigenetic landscape in vitro. TOXICOLOGY LETTERS (2018)
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   Grasse, S.; Lienhard, M.; Frese, S.; Kerick, M.; Steinbach, A.; Grimm, C.; Hussong, M.; Rolff, J.; Becker, M.; Dreher, F. et al.; Schirmer, U.; Boerno, S. T.; Ramisch, A.; Leschber, G.; Timmermann, B.; Grohé, C.; Lüders, H.; Vingron, M.; Fichtner, I.; Klein, S.; Odenthal, M.; Büttner, R.; Lehrach, H.; Sültmann, H.; Herwig, R.; Schweiger, R. M.: Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance. Genome Medicine (2018)
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   Hu, H.; Kahrizi, K.; Musante, L.; Fattahi, Z.; Herwig, R.; Hosseini, M.; Oppitz, C.; Abedini, S. S.; Suckow, V.; Farzaneh, L. et al.; Beheshtian, M.; Lipkowitz, B.; Akhtarkhavari, T.; Mehvari, S.; Otto, S.; Mohseni, M.; Arzhangi, S.; Jamali, P.; Mojahedi, F.; Taghdiri, M.; Papari, E.; Soltani Banavandi, M. J.; Akbari, S.; Tonekaboni, S. H.; Dehghani, H.; Ebrahimpou, M. R.; Bader, I.; Davarnia, B.; Cohen, M.; Khodaei, H.; Albrecht, B.; Azimi, S.; Zirn, B.; Bastami, M.; Wieczorek, D.; Bahrami, G.; Keleman, K.; Vahid, L. N.; Timmermann, B.; Pourfatemi, F.; Jankhah, A.; Chen, W.; Nikuei, P.; Kalscheuer, V. M.; Oladnabi, M.; Wienker, T. F.; Ropers, H.-H.; Najmabadi, H.: Genetics of intellectual disability in consanguineous families. Molecular Psychiatry (2018)
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   Kuepfer, L.; Clayton, O.; Thiel, C.; Cordes, H.; Nudischer, R.; Blank, L. M.; Baier, V.; Heymans, S.; Caiment, F.; Roth, A. et al.; Fluri, D. A.; Kelm, J. M.; Castell, J.; Selevsek, N.; Schlapbach, R.; Keun, H.; Hynes, J.; Sarkans, U.; Gmuender, H.; Herwig, R.; Niederer, S.; Schuchhardt, J.; Segall, M.; Kleinjans, J.: A model-based assay design to reproduce in vivo patterns of acute drug-induced toxicity. Archives of Toxicology 92 (1), pp. 553 - 555 (2018)
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   Hoehe, M. R.; Herwig, R.; Mao, Q.; Peters, B. A.; Drmanac, R.; Church, G. M.; Huebsch, T.: Significant abundance of cis configurations of mutations in diploid human genomes. bioRxiv (2017)
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   Lienhard, M.; Grasse, S.; Rolff, J.; Frese, S.; Schirmer, U.; Becker, M.; Börno, S. T.; Timmermann, B.; Chavez, L.; Sültmann, H. et al.; Leschber, G.; Fichtner, I.; Schweiger, M. R.; Herwig, R.: QSEA – modelling of genome-wide DNA methylation from sequencing enrichment experiments. Nucleic Acids Research (London) (2017)
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   Schütte, M.; Risch, T.; Abdavi Azar, N.; Boehnke, K.; Schumacher, D.; Keil, M.; Yildiriman, R.; Jandrasits, C.; Borodina, T.; Amstislavskiy, V. et al.; Worth, C. L.; Schweiger, C.; Liebs, S.; Lange, M.; Warnatz, H. J.; Butcher, L. M.; Barrett, J. E.; Sultan, M.; Wierling, C.; Golob-Schwarzl, N.; Lax, S.; Uranitsch, S.; Becker, M.; Welte, Y.; Regan, J. L.; Silvestrov, M.; Kehler, I.; Fusi, A.; Kessler, T.; Herwig, R.; Landegren, U.; Wienke, D.; Nilsson, M.; Velasco, J. A.; Garin-Chesa, P.; Reinhard, C.; Beck, S.; Schafer, R.; Regenbrecht, C. R.; Henderson, D.; Lange, B.; Haybaeck, J.; Keilholz, U.; Hoffmann, J.; Lehrach, H.; Yaspo, M. L.: Molecular dissection of colorectal cancer in pre-clinical models identifies biomarkers predicting sensitivity to EGFR inhibitors. Nature Communications 8, 8:14262 (2017)
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   Herwig, R.; Hardt, C.; Lienhard, M.; Kamburov, A.: Analyzing and interpreting genome data at the network level with ConsensusPathDB. Nature Protocols 11 (10), pp. 1889 - 1907 (2016)
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    Herwig, R.; Gmuender, H.; Corvi, R.; Bloch, K. M.; Brandenburg, A.; Castell, J.; Ceelen, L.; Chesne, C.; Doktorova, T. Y.; Jennen, D. et al.; Jennings, P.; Limonciel, A.; Lock, E. A.; 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. Archives of Toxikology 90 (9), pp. 2215 - 2229 (2016)
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    Aretz, I.; Hardt, C.; Wittig, I.; Meierhofer, D.: An impaired respiratory electron chain triggers down-regulation of the energy metabolism and de-ubiquitination of solute carrier amino acid transporters. Molecular and Cellular Proteomics 15 (5), pp. 1526 - 1538 (2016)
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    Broecker, F.; Hardt, C.; Herwig, R.; Timmermann, B.; Kerick, M.; Wunderlich, A.; Schweiger, M. R.; Borsig, L.; Heikenwalder, M.; Lehrach, H. et al.; Moelling, K.: Transcriptional signature induced by a metastasis-promoting c-Src mutant in a human breast cell line. The FEBS Journal 283 (9), pp. 1669 - 1688 (2016)
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    Hardt, C.; Beber, M. E.; Rasche, A.; Kamburov, A.; Hebels, D. G.; Kleinjans, J. C.; Herwig, R.: ToxDB: pathway-level interpretation of drug-treatment data. Database (Oxford) (2016)
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    The 1000 Genome Project Consortium; Lehrach, H.; Amstislavskiy, V.; Lienhard, M.; Mertes, F.; Sultan, M.; Timmermann, B.; Yaspo, M.-L.; Herwig, R.: A global reference for human genetic variation. Nature 526 (7571), pp. 68 - 74 (2015)
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    Kang, J.; Lienhard, M.; Pastor, W. A.; Chawla, A.; Novotny, M.; Tsagaratou, A.; Lasken, R. S.; Thompson, E. C.; Surani, M. A.; Koralov, S. B. et al.; Kalantry, S.; Chavez, L.; Rao, A.: Simultaneous deletion of the methylcytosine oxidases Tet1 and Tet3 increases transcriptome variability in early embryogenesis. Proceedings of the National Academy of Sciences of the United States of America 112 (31), pp. E4236 - E4245 (2015)
16. 16.
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    Etchegaray, J. P.; Chavez, L.; Huang, Y.; Ross, K. N.; Choi, J.; Martinez-Pastor, B.; Walsh, R. M.; Sommer, C. A.; Lienhard, M.; Gladden, A. et al.; Kugel, S.; Silberman, D. M.; Ramaswamy, S.; Mostoslavsky, G.; Hochedlinger, K.; Goren, A.; Rao, A.; Mostoslavsky, R.: The histone deacetylase SIRT6 controls embryonic stem cell fate via TET-mediated production of 5-hydroxymethylcytosine. Nature Cell Biology 17 (5), pp. 545 - 557 (2015)
17. 17.
    MPG.PuRe

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    Hendrickx, D. M.; Aerts, H. J. W. L.; Caiment, F.; Clark, D.; Ebbels, T. M. D.; Evelo, C. T.; Gmuender, H.; Hebels, D. G. A. J.; Herwig, R.; Hescheler, J. et al.; Jennen, D. G. J.; Jetten, M. J. A.; Kanterakis, S.; Keun, H. C.; Matser, V.; Overington, J. P.; Pilicheva, E.; Sarkans, U.; Segura-Lepe, M. P.; Sotiriadou, I.; Wittenberger, T.; Wittwehr, C.; Zanzi, A.; Kleinjans, J. C. S.: diXa: a data infrastructure for chemical safety assessment. Bioinformatics 31 (9), pp. 1505 - 1507 (2015)
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    Zimmermann, K.; Jentsch, M.; Rasche, A.; Hummel, M.; Leser, U.: Algorithms for differential splicing detection using exon arrays: a comparative assessment. BMC Genomics (2015)
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    Herwig, R.: Computational modelling of drug response with applications to neuroscience. Dialogues in Clinical Neuroscience 16 (4), pp. 465 - 477 (2014)

Book Chapter (2)

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   Hebels, D. G.; Rasche, A.; Herwig, R.; van Westen, G. J.; Jennen, D. G.; Kleinjans, J. C.: A Systems Biology Approach for Identifying Hepatotoxicant Groups Based on Similarity in Mechanisms of Action and Chemical Structure. In: In Silico Methods for Predicting Drug Toxicity (Ed. Benfenati , E.) (2016)