Publications of Matthias Lienhard

Lienhard, M.; van den Beucken , T.; Timmermann, B.; Hochradel, M.; Boerno, S.; Caiment , F.; Vingron, M.; Herwig, R.: IsoTools: a flexible workflow for long-read transcriptome sequencing analysis. Bioinformatics, btad364 (2023)

Binsch, C.; Barbosa, D. M.; Hansen-Dille, G.; Hubert, M.; Hodge, S. M.; Kolasa, M.; Jeruschke, K.; Weiß, J.; Springer, C.; Gorressen, S. et al.; Fischer, J. W.; Lienhard, M.; Herwig, R.; Börno, S.; Timmermann, B.; Cremer, A. L.; Backes, H.; Chadt, A.; Al-Hasani, H.: Deletion of Tbc1d4/As160 abrogates cardiac glucose uptake and increases myocardial damage after ischemia/reperfusion. Cardiovascular Diabetology 22, 17 (2023)

Verheijen, M.; Sarkans, U.; Wolski, W.; Jennen, D.; Caiment , F.; Kleinjans, J.; HeCaToS , C.; Barel, G.; Boerno, S.; Herwig, R. et al.; Lienhard, M.; Timmermann, B. e. a.: Multi-omics HeCaToS dataset of repeated dose toxicity for cardiotoxic & hepatotoxic compounds. Scientific Data 9, 699 (2022)

Verheijen, M.; Sarkans, U.; Wolski, W.; Jennen, D.; Caiment, F.; Kleinjans, J.; HeCaToS Consortium; Herwig, R.; Lienhard, M.: Multi-omics HeCaToS dataset of repeated dose toxicity for cardiotoxic & hepatotoxic compounds. Scientific Data 9, 699 (2022)

Prasse, P.; Iversen, P.; Lienhard, M.; Thedinga, K.; Herwig, R.; Scheffer, T.: Pre-Training on In Vitro and Fine-Tuning on Patient-Derived Data Improves Deep Neural Networks for Anti-Cancer Drug-Sensitivity Prediction. Cancers / Molecular Diversity Preservation International (MDPI) 14 (16), 3950 (2022)

Thomalla, D.; Beckmann, L.; Grimm , C.; Oliverio, M.; Meder, L.; Herling, C. D.; Nieper, P.; Feldmann, T.; Merkel, O.; Lorsy, E. et al.; da Palma Guerreiro , A.; von Jan, J.; Kisis, I.; Wasserburger, E.; Claasen, J.; Faitschuk-Meyer, E.; Altmüller, J.; Nürnberg, P.; Yang, T.-P.; Lienhard, M.; Herwig, R.; Kreuzer, K.-A.; Pallasch, C. P.; Buettner, R.; Schäfer, S. C.; Hartley, J.; Abken, H.; Peifer, M.; Kashkar, H.; Knittel, G.; Eichhorst , B.; Ullrich, R. T.; Herling, M.; Reinhardt, H. C.; Hallek, M.; Schweiger, M. R.; Frenzel, L. P.: Deregulation and epigenetic modification of BCL2-family genes cause resistance to venetoclax in hematologic malignancies. Blood (2022)

Nguyen, N.; Lienhard, M.; Herwig, R.; Kleinjans, J.; Jennen, D.: Epirubicin Alters DNA Methylation Profiles Related to Cardiotoxicity. Frontiers in Bioscience-Landmark 27 (6), 173 (2022)

Prasse , P.; Iversen , P.; Lienhard, M.; Thedinga, K.; Bauer, C.; Herwig, R.; Scheffer, T.: Matching anticancer compounds and tumor cell lines by neural networks with ranking loss. NAR: genomics and bioinformatics 4 (1), lqab128 (2022)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)