Publications

Bi, Y.; Lankenau, T. L.; Lienhard, M.; Herwig, R.: IsoTools 2.0: Software for Comprehensive Analysis of Long-read Transcriptome Sequencing Data. Journal of Molecular Biology, Article 169049 (2025)

Turewicz, M.; Skagen, C.; Hartwig, S.; Majda, S.; Thedinga, K.; Herwig, R.; Binsch , C.; Altenhofen, D.; Ouwens, D. M.; Förster, P. M. et al.; Wachtmeister, T.; Köhrer, K.; Stermann, T.; Chadt, A.; Lehr, S.; Marschall , T.; Thoresen, G. H.; Al-Hasani, H.: Temporal phosphoproteomics reveals circuitry of phased propagation in insulin signaling. Nature Communications 16 (1), Article 1570 (2025)

Pacholewska, A.; Lienhard, M.; Brueggemann, M.; Haenel, H.; Bilalli, L.; Koenigs, A.; Hess, F.; Becker, K.; Koehrer, K.; Kaiser, J. F. et al.; Gohlke, H.; Gattermann, N.; Hallek, M.; Herling, C. D.; Koenig, J.; Grimm, C.; Herwig, R.; Zarnack, K.; Schweiger, M. R.: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations. Genome Research 34 (11), pp. 1832 - 1848 (2024)

Thedinga, K.: Machine Learning for Cancer Survival Prediction. Dissertation (2024)

Pardo-Palacios, F. J.; Wang, D.; Reese, F.; Diekhans, M.; Carbonell-Sala, S.; Williams, B.; Loveland, J. E.; De Maria, M.; Adams, M. S.; Balderrama-Gutierrez, G. et al.; Behera, A. K.; Gonzalez, J. M.; Hunt, T.; Lagarde, J.; Liang, C. E.; Li, H.; Jerryd Meade, M.; Moraga Amador, D. A.; Prjibelski, A. D.; Birol, I.; Bostan, H.; Brooks, A. M.; Hasan Celik, M.; Chen, Y.; Du, M. R. M.; Felton, C.; Goke, J.; Hafezqorani, S.; Herwig, R.; Kawaji, H.; Lee, J.; Liang Li, J.; Lienhard, M.; Mikheenko, A.; Mulligan, D.; Ming Nip, K.; Pertea, M.; Ritchie, M. E.; Sim, A. D.; Tang, A. D.; Kei Wan, Y.; Wang, C.; Wong, B. Y.; Yang, C.; Barnes, I.; Berry, A.; Capella, S.; Dhillon, N.; Fernandez-Gonzalez, J. M.; Ferrandez-Peral, L.; Garcia-Reyero, N.; Goetz, S.; Hernandez-Ferrer, C.; Kondratova, L.; Liu, T.; Martinez-Martin, A.; Menor, C.; Mestre-Tomas, J.; Mudge, J. M.; Panayotova, N. G.; Paniagua, A.; Repchevsky, D.; Rouchka, E.; Saint-John, B.; Sapena, E.; Sheynkman, L.; Laird Smith, M.; Suner, M. M.; Takahashi, H.; Youngworth, I. A.; Carninci, P.; Denslow, N. D.; Guigo, R.; Hunter, M. E.; Tilgner, H. U.; Wold, B. J.; Vollmers, C.; Frankish, A.; Fai Au, K.; Sheynkman, G. M.; Mortazavi, A.; Conesa, A.; Brooks, A. N.: Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature Methods 21 (7), pp. 1349 - 1363 (2024)

Springer, C.; Binsch, C.; Weide, D.; Toska, L.; Cremer, A. L.; Backes, H.; Scheel, A. K.; Espelage, L.; Kotzka, J.; Sill, S. et al.; Kurowski, A.; Daebin, K.; Karpinski, S.; Schnurr, T. M.; Hansen, T.; Hartwig, S.; Lehr, S.; Cames, S.; Brüning, J.; Lienhard, M.; Herwig, R.; Börno, S.; Timmermann, B.; Al-Hasani, H.; Chadt, A.: Depletion of TBC1D4 improves the metabolic exercise response by overcoming genetically induced peripheral insulin resistance. Diabetes 73 (7), pp. 1058 - 1071 (2024)

Campana , P. A.; Prasse , P.; Lienhard, M.; Thedinga, K.; Herwig, R.; Scheffer , T.: Cancer drug sensitivity estimation using modular deep Graph Neural Networks. NAR: Genomics and Bioinformatics 6 (2), Article lqae043 (2024)

Wei , X.; Rigopoulos, A.; Lienhard, M.; Pöhle-Kronawitter, S.; Kotsaris , G.; Franke, J.; Berndt, N.; Mejedo, J. O.; Wu, H.; Börno, S. et al.; Timmermann, B.; Murgai, A.; Glauben, R.; Stricker, S.: Neurofibromin 1 controls metabolic balance and Notch-dependent quiescence of murine juvenile myogenic progenitors. Nature Communications 15 (1), 1393 (2024)

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 39 (6), btad364 (2023)

Bouabid, C.; Rabhi, S.; Thedinga, K.; Barel, G.; Tnani, H.; Rabhi , I.; Benkahla, A.; Herwig, R.; Guizani-Tabbane, L.: Host M-CSF induced gene expression drives changes in susceptible and resistant mice-derived BMdMs upon Leishmania major infection. Frontiers in immunology 14, 1111072 (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 (1), 17 (2023)

Altenhofen, D.; Khuong, J. M.-A.; Kuhn, T.; Lebek, S.; Görigk, S.; Kaiser, K.; Binsch, C.; Griess, K.; Knebel, B.; Belgardt, B.-F. et al.; Cames, S.; Eickelschulte, S.; Stermann, T.; Rasche, A.; Herwig, R.; Weiss, J.; Vogel, H.; Schürmann, A.; Chadt, A.; Al-Hasani, H.: E96V Mutation in the Kdelr3 Gene Is Associated with Type 2 Diabetes Susceptibility in Obese NZO Mice. International Journal of Molecular Sciences 24 (1), 845 (2023)

Kuhn, T.; Kaiser, K.; Lebek, S.; Altenhofen, D.; Knebel, B.; Herwig, R.; Rasche, A.; Pelligra, A.; Görigk, S.; Khuong, J. M.-A. et al.; Vogel, H.; Schürmann, A.; Blüher, M.; Chadt, A.; Al-Hasani, H.: Comparative genomic analyses of multiple backcross mouse populations suggest SGCG as a novel potential obesity-modifier gene. Human Molecular Genetics 31 (23), pp. 4019 - 4033 (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 140 (20), pp. 2113 - 2126 (2022)

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 (1), 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)

Thedinga, K.; Herwig, R.: Gradient tree boosting and network propagation for the identification of pan-cancer survival networks. STAR Protocols 3 (2), 101353 (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)

Kamburov, A.; Herwig, R.: ConsensusPathDB 2022: molecular interactions update as a resource for network biology. Nucleic Acids Research 50 (D1), pp. D587 - D595 (2022)

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)

Thedinga, K.; Herwig, R.: A gradient tree boosting and network propagation derived pan-cancer survival network of the tumor microenvironment. iScience 25 (1), 103617 (2021)

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, 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)

Barel, G.: Network Propagation with Node Core for Genotype-Phenotype Associations and Module Identification. Dissertation, xii, 161 pp. (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.: Computational Analysis of Genome-wide Methylation Enrichment Experiments. Dissertation, xii, 125 pp. (2017)

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)

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)

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)

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)

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)

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)