List of publications

Journal Article (22)

1. 1.
   MPG.PuRe

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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 coding variants in diploid human genomes. Nucleic Acids Research (London) 47 (6), pp. 2981 - 2995 (2019)
2. 2.
   MPG.PuRe

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   Verheijen, M.; Lienhard, M.; Schrooders, Y.; Clayton, O.; Nudischer, R.; Boerno, S. T.; Timmermann, B.; Selevsek, N.; Schlapbach, R.; Gmuender, H. et al.; Gotta, S.; Geraedts, J.; Herwig, R.; Kleinjans, J.; Caiment, F.: DMSO induces drastic changes in human cellular processes and epigenetic landscape in vitro. Scientific Reports 9 (9) (2019)
3. 3.
   MPG.PuRe

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   Grimm, C.; Fischer, A.; Farrelly, A. M.; Kalachand, R.; Castiglione, R.; Wasserburger, E.; Hussong, M.; Schultheis, A. M.; Altmüller, J.; Thiele, H. et al.; Reinhardt, H. C.; Hauschulz, K.; Hennessy, B. T.; Herwig, R.; Lienhard, M.; Buettner, R.; Schweiger, M. R.: Combined Targeted Re-Sequencing of Cytosine DNA Methylation and Mutations of DNA Repair Genes with Potential Use for PARP1 Inhibitor Sensitivity Testing. The Journal of Molecular Diagnostics 21 (2), pp. 198 - 213 (2019)
4. 4.
   MPG.PuRe

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   Schallschmidt, T.; Lebek, S.; Altenhofen, D.; Damen, M.; Schulte, Y.; Knebel, B.; Herwig, R.; Rasche, A.; Stermann, T.; Kamitz, A. et al.; Hallahan, N.; Jähnert, M.; Vogel, H.; Schürmann, A.; Chadt, A.; Al-Hasani, H.: Identification of two novel candidate genes for insulin secretion by comparative genomics of multiple backcross populations. Genetics 210 (4), pp. 1527 - 1542 (2018)
5. 5.
   MPG.PuRe

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   Barel, G.; Herwig, R.: Network and Pathway Analysis of Toxicogenomics Data. Frontiers in Genetics 9 (2018)
6. 6.
   MPG.PuRe

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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 (2018)
7. 7.
   MPG.PuRe

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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 10 (1) (2018)
8. 8.
   MPG.PuRe

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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 24 (7) (2018)
9. 9.
   MPG.PuRe

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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)
10. 10.
    MPG.PuRe

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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) 45 (6) (2017)
11. 11.
    MPG.PuRe

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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)
12. 12.
    MPG.PuRe

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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)
13. 13.
    MPG.PuRe

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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)
14. 14.
    MPG.PuRe

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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)
15. 15.
    MPG.PuRe

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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)
16. 16.
    MPG.PuRe

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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 (2016)
17. 17.
    MPG.PuRe

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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)
18. 18.
    MPG.PuRe

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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)
19. 19.
    MPG.PuRe

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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)
20. 20.
    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)