Publications of Matthias Lienhard

Journal Article (25)

1.
Journal Article
Pacholewska, A.; Grimm, C.; Herling, C. D.; Lienhard, M.; Königs, A.; Timmermann, B.; Altmüller, J.; Mücke, O.; Reinhardt, H. C.; Plass, C. et al.; Herwig, R.; Hallek, M.; Schweiger, M. R.: Altered DNA Methylation Profiles in SF3B1 Mutated CLL Patients. International Journal of Molecular Sciences 22 (17), 9337 (2021)
2.
Journal Article
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, 19:274 (2021)
3.
Journal Article
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, 3307 (2021)
4.
Journal Article
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)
5.
Journal Article
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, 573 (2020)
6.
Journal Article
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)
7.
Journal Article
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)
8.
Journal Article
Grimm, C.; Fischer, A.; Farrelly, A. M.; Kalachand, R.; Castiglione, R.; Wasserburger, E.; Hussong, M.; Schultheis, A. M.; Altmuller, J.; Thiele, H. et al.; Reinhardt, H. C.; Hauschulz, K.; Hennessy, B. T.; Herwig, R.; Lienhard, M.; Buettner, R.; Schweiger, M. R.: Combined Targeted Resequencing of Cytosine DNA Methylation and Mutations of DNA Repair Genes with Potential Use for Poly(ADP-Ribose) Polymerase 1 Inhibitor Sensitivity Testing. The Journal of Molecular Diagnostics 21 (2), pp. 198 - 213 (2019)
9.
Journal Article
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)
10.
Journal Article
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)
11.
Journal Article
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)
12.
Journal Article
Poznik, G. D.; Xue, Y.; Mendez, F. L.; Willems, T. F.; Massaia, A.; Wilson Sayres, M. A.; The 1000 Genomes Projekt, C.; Lehrach, H.; Sudbrak, R.; Albrecht, M. W. et al.; Amstislavskiy, V.; Borodina, T. A.; Lienhard, M.; Mertes, F.; Sultan, M.; Timmermann, B.; Yaspo, M.-L.: Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nature Genetics 48 (6), pp. 593 - 599 (2016)
13.
Journal Article
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)
14.
Journal Article
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)
15.
Journal Article
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)
16.
Journal Article
Rasche, A.; Lienhard, M.; Yaspo, M.-L.; Lehrach, H.; Herwig, R.: ARH-seq: identification of differential splicing in RNA-seq data. Nucleic Acids Research (London) 42 (14), e110 (2014)
17.
Journal Article
Seumois, G.; Chavez, L.; Gerasimova, A.; Lienhard, M.; Omran, N.; Kalinke, L.; Vedanayagam, M.; Ganesan, A. P. V.; Chawla, A.; Djukanović, R. et al.; Ansel, K. M.; Peters, B.; Rao, A.; Vijayanand, P.: Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility. Nature Immunology 15 (8), pp. 777 - 788 (2014)
18.
Journal Article
Delaneau, O.; Marchini, J.; 1000 Genomes Project, C.; Lehrach, H.; Sudbrak, R.; Amstislavskiy, V. S.; Lienhard, M.; Mertes, F.; Sultan, M.; Timmermann, B. et al.; Yaspo, M. L.; Herwig, R.: Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nature Communications 5, 5:3934 (2014)
19.
Journal Article
Lienhard, M.; Grimm, C.; Morkel, M.; Herwig, R.; Chavez, L.: MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. Bioinformatics 30 (2), pp. 284 - 286 (2014)
20.
Journal Article
Lienhard, M.; Grimm, C.; Morkel, M.; Herwig, R.; Chavez, L.: MEDIPS: genome wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. Bioinformatics 30 (2), pp. 284 - 286 (2014)
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