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, baw052 (2016)

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)

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)

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)

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)

Zimmermann, K.; Jentsch, M.; Rasche, A.; Hummel, M.; Leser, U.: Algorithms for differential splicing detection using exon arrays: a comparative assessment. BMC Genomics 2015, 16:136 (2015)

Herwig, R.: Computational modelling of drug response with applications to neuroscience. Dialogues in Clinical Neuroscience 16 (4), pp. 465 - 477 (2014)

Hoehe, M. R.; Herwig, R.: Analysis of 1276 Haplotype-Resolved Genomes Allows Characterization of Cis- and Trans-Abundant Genes. In: Haplotyping. Methods in Molecular Biology (Springer Protocols), Vol. 2590, pp. 237 - 272 (Eds. Peters, B. A.; Drmanac, R.). Humana Press (Springer Science+Business Media, Springer-Verlag GmbH), New York, NY (2022)

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)

Lienhard, M.; Chavez, L.: Quantitative Comparison of Large-Scale DNA Enrichment Sequencing Data. In: Statistical Genomics (Eds. Mathé, E.; Davis, S.) (2016)

Lienhard, M.: Computational Analysis of Genome-wide Methylation Enrichment Experiments. Dissertation, xii, 125 pp., Freie Universität, Berlin (2017)

Lienhard, M.; van den Beucken, T.; Timmermann, B.; Hochradel, M.; Boerno, S.; Caiment, F.; Vingron, M.; Herwig, R.: Long-read transcriptome sequencing analysis with IsoTools. (2021)