Publications of Ralf Herwig

Bauer, C.; Herwig, R.; Lienhard, M.; Prasse, P.; Scheffer, T.; Schuchhardt, J.: Large-scale literature mining to assess the relation between anti-cancer drugs and cancer types. Journal of Translational Medicine 19, Article 274 (2021)

Cichońska, A.; Ravikumar, B.; Allaway, R. J.; Wan, F.; Park, S.; Isayev, O.; Li, S.; Mason, M.; Lamb, A.; Tanoli, Z. et al.; Jeon, M.; Kim, S.; Popova, M.; Capuzzi, S.; Zeng, J.; Dang, K.; Koytiger, G.; Kang, J.; Wells, C. I.; Willson, T. M.; Lienhard, M.; Prasse, P.; Bachmann, I.; Ganzlin, J.; Barel, G.; Herwig, R.; Oprea, T. I.; Schlessinger, A.; Drewry, D. H.; Stolovitzky, G.; Wennerberg, K.; Guinney, J.; Aittokallio, T.: Crowdsourced mapping of unexplored target space of kinase inhibitors. Nature Communications 12 (1), Article 3307 (2021)

Rehman, S. U.; Schallschmidt, T.; Rasche, A.; Knebel, B.; Stermann, T.; Altenhofen, D.; Herwig, R.; Schürmann, A.; Chadt, A.; Al‑Hasani, H.: Alternative exon splicing and differential expression in pancreatic islets reveals candidate genes and pathways implicated in early diabetes development. Mammalian Genome 32 (3), pp. 153 - 172 (2021)

Farrall, A.; Lienhard, M.; Grimm, C.; Kuhl, H.; Sluka, S. H. M.; Caparros Rodriguez, M.; Forejt, J.; Timmermann, B.; Herwig, R.; Herrmann, B. G. et al.; Morkel, M.: PWD/Ph-encoded genetic variants modulate the cellular Wnt/β-Catenin response to suppress ApcMin-triggered intestinal tumor formation. Cancer research: an official organ of the American Association for Cancer Research 81 (1), pp. 38 - 49 (2021)

Klymenko , O.; Brecklinghaus, T.; Dille, M.; Springer, C.; de Wendt, C.; Altenhofen, D.; Binsch, C.; Knebel , B.; Scheller, J.; Hardt, C. et al.; Herwig, R.; Chadt, A.; Pfluger, P. T.; Al-Hasani, H.; Kabra, D. G.: Histone deacetylase 5 regulates Interleukin 6 secretion and insulin action in skeletal muscle. Molecular Metabolism 42, 101062 (2020)

Selevsek, N.; Caiment, F.; Nudischer, R.; Gmuender, H.; Agarkova, I.; Atkinson, F. L.; Bachmann, I.; Baier, V.; Barel, G.; Bauer, C. et al.; Boerno, S.; Bosc, N.; Clayton, O.; Cordes, H.; Deeb, S.; Gotta, S.; Guye, P.; Hersey, A.; Hunter, F. M. I.; Kunz, L.; Lewalle, A.; Lienhard, M.; Merken, J.; Minguet, J.; Oliveira, B.; Pluess, C.; Sarkans, U.; Schrooders, Y.; Schuchhardt, J.; Smit, I.; Thiel, C.; Timmermann, B.; Verheijen, M.; Wittenberger, T.; Wolski, W.; Zerck, A.; Heymans, S.; Kuepfer, L.; Roth, A.; Schlapbach, R.; Niederer, S.; Herwig, R.; Kleinjans, J.: Network integration and modelling of dynamic drug responses at multi-omics levels. Communications Biology 3 (1), 573 (2020)

Barel, G.; Herwig, R.: NetCore: a network propagation approach using node coreness. Nucleic Acids Research 48 (17), e98 (2020)

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), pp. 1027 - 1039 (2019)

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 47 (6), pp. 2981 - 2995 (2019)

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), 4641 (2019)

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)

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)

Barel, G.; Herwig, R.: Network and Pathway Analysis of Toxicogenomics Data. Frontiers in Genetics 9, 9:484 (2018)

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, 295:S215 (2018)

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), 10:55 (2018)

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)

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), e44 (2017)

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)

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)

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)