Max Planck Institute for Molecular Genetics

Publications

The following publications were published exclusively under the affiliation of the Max Planck Society. For publications by the principal investigator outside of the Max Planck Society, see the links on the lower left.

Publications by the Herwig Lab

Published

2025

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)

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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)

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2024

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)

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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)

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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)

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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)

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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)

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2023

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)

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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)

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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)

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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)

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2022

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)

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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)

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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)

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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)

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Thedinga, K.; Herwig, R.: Gradient tree boosting and network propagation for the identification of pan-cancer survival networks. STAR Protocols 3 (2), 101353 (2022)

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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)

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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)

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

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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)

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2021

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)

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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)

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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)

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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)

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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)

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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)

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2020

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)

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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)

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

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2019

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)

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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)

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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)

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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)

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2018

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)

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

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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)

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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)

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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)

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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)

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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)

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2016

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)

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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)

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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)

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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)

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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)

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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)

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

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2015

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)

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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)

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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)

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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)

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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)

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2014

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

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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)

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2015

Sudmant, P. H.; Rausch, T.; Gardner, E. J.; Handsaker, R. E.; Abyzov, A.; Huddleston, J.; The 1000 Genomes Project Consortium; Timmermann, B.; Herwig, R.; Lehrach, H.: An integrated map of structural variation in 2,504 human genomes. Nature 526 (7571), pp. 75 - 81 (2015)

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2014

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

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Reiner, G.; Dreher, F.; Drungowski, M.; Hoeltig, D.; Bertsch, N.; Selke, M.; Willems, H.; Gerlach, G. F.; Probst, I.; Tuemmler, B. et al.; Waldmann, K.-H.; Herwig, R.: Pathway deregulation and expression QTLs in response to Actinobacillus pleuropneumoniae infection in swine. Mammalian Genome 25 (11-12), pp. 600 - 617 (2014)

MPG.PuRe

publisher-version

Hülsmann, H. J.; Rolff, J.; Bender, C.; Jarahian, M.; Korf, U.; Herwig, R.; Fröhlich, H.; Thomas, M.; Merk, J.; Fichtner, I. et al.; Sültmann, H.; Kuner, R.: Activation of AMP-activated protein kinase sensitizes lung cancer cells and H1299 xenografts to erlotinib. Lung Cancer 86 (2), pp. 151 - 157 (2014)

MPG.PuRe

publisher-version

Willems, T.; Gymrek, M.; Highnam, G.; The 1000 Genomes Project, C.; Herwig, R.; Lehrach, H.; Sudbrak, R.; Timmermann, B.; Mittelman, D.; Erlich, Y.: The landscape of human STR variation. Genome Research 24 (11), pp. 1894 - 1904 (2014)

MPG.PuRe

publisher-version

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)

MPG.PuRe

publisher-version

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)

MPG.PuRe

publisher-version

Colonna, V.; Ayub, Q.; Chen, Y.; Pagani, L.; Luisi, P.; Pybus, M.; Garrison, E.; Xue, Y.; Tyler-Smith, C.; 1000 Genomes Project, C. et al.; Sudbrak, R.; Albrecht, M.; Amstislavskiy, V.; Borodina, T. A.; Dahl, A.; Davydov, A.; Herwig, R.; Marquardt, P.; Mertes, F.; Nietfeld, W.; Parkhomchuk, D.; Soldatov, A. V.; Timmermann, B.; Tolzmann, M.; Lehrach, H.; Yaspo, M. L.: Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biology: Biology for the Post-Genomic Era 15 (6), R88 (2014)

MPG.PuRe

publisher-version

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)

MPG.PuRe

Doktorova, T. Y.; Yildirimman, R.; Ceelen, L.; Vilardell, M.; Vanhaecke, T.; Vinken, M.; Ates, G.; Heymans, A.; Gmuender, H.; Bort, R. et al.; Corvi, R.; Phrakonkham, P.; Li, R.; Mouchet, N.; Chesne, C.; van Delft, J.; Kleinjans, J.; Castell, J.; Herwig, R.; Rogiers, V.: Testing chemical carcinogenicity by using a transcriptomics HepaRG-based model. Experimental and Clinical Sciences Journal (EXCLI Journal) 13, pp. 623 - 637 (2014)

MPG.PuRe

publisher-version

Vilardell, M.; Herwig, R.: Predictive mechanisms in stem cells: an in vitro system based method for testing carcinogenicity. In: Handbook of Nanotoxicology, Nanomedicine and Stem Cell Use in Toxicology, pp. 337 - 346 (Eds. Sahu, . C.; Casciano, D. A.). John Wiley & Sons, Ltd, Hoboken, NJ (2014)

MPG.PuRe

Reiner, G.; Bertsch, N.; Hoeltig, D.; Selke, M.; Willems, H.; Gerlach, G. F.; Tuemmler, B.; Probst, I.; Herwig, R.; Drungowski, M. et al.; Waldmann, K. H.: Identification of QTL affecting resistance/susceptibility to acute Actinobacillus pleuropneumoniae infection in swine. Mammalian Genome 25 (3-4), pp. 180 - 191 (2014)

MPG.PuRe

publisher-version

Hebels, D. G. A.; Jetten, M. J. A.; Aerts, H. J. W.; Herwig, R.; Theunissen, D. H. J.; Gaj, S.; van Delft, J. H.; Kleinjans, J. C. S.: Evaluation of database-derived pathway development for enabling biomarker discovery for hepatotoxicity. Biomarkers in Medicine 8 (2), pp. 185 - 200 (2014)

MPG.PuRe

publisher-version

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)

MPG.PuRe

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)

MPG.PuRe

publisher-version

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)

MPG.PuRe

publisher-version

2013

Rabhi, I.; Rabhi, S.; Ben-Othman, R.; Aniba, M. R.; Sysco Consortium; Herwig, R.; Trentin, B.; Piquemal, D.; Regnault, B.; Guizani-Tabbane, L.: Comparative analysis of resistant and susceptible macrophage gene expression response to Leishmania major parasite. BMC Genomics 14, 14:723 (2013)

MPG.PuRe

publisher-version

Khurana, E.; Fu, Y.; Colonna, V.; Mu, X. J.; Kang, H. M.; Lappalainen, T.; Sboner, A.; Lochovsky, L.; Chen, J.; Harmanci, A. et al.; Das, J.; Abyzov, A.; Balasubramanian, S.; Beal, K.; Chakravarty, D.; Challis, D.; Chen, Y.; Clarke, D.; Clarke, L.; Cunningham, F.; Evani, U. S.; Flicek, P.; Fragoza, R.; Garrison, E.; Gibbs, R.; Gumus, Z. H.; Herrero, J.; Kitabayashi, N.; Kong, Y.; Lage, K.; Liluashvili, V.; Lipkin, S. M.; MacArthur, D. G.; Marth, G.; Muzny, D.; Pers, T. H.; Ritchie, G. R.; Rosenfeld, J. A.; Sisu, C.; Wei, X.; Wilson, M.; Xue, Y.; Yu, F.; 1000 Genomes Project, C.; Lehrach, H.; Sudbrak, R.; Albrecht, M. W.; Amstislavskiy, V.; Borodina, T. A.; Lienhard, M.; Mertes, F.; Sultan, M.; Timmermann, B.; Yaspo, M. L.; Dermitzakis, E. T.; Yu, H.; Rubin, M. A.; Tyler-Smith, C.; Gerstein, M.: Integrative annotation of variants from 1092 humans: application to cancer genomics. Science 342 (6154), p. 1235587 - 1235587 (2013)

MPG.PuRe

publisher-version

Lemaire, J.; Mkannez, G.; Guerfali, F. Z.; Gustin, C.; Attia, H.; Sghaier, R. M.; Sysco-Consortium; Herwig, R.; Dellagi, K.; Laouini, D. et al.; Renard, P.: MicroRNA expression profile in human macrophages in response to Leishmania major infection. PLoS Neglected Tropical Diseases 7 (10), e2478 (2013)

MPG.PuRe

publisher-version

Jankowski, V.; Schulz, A.; Kretschmer, A.; Mischak, H.; Boehringer, F.; van der Giet, M.; Janke, D.; Schuchardt, M.; Herwig, R.; Zidek, W. et al.; Jankowski, J.: The enzymatic activity of the VEGFR2-receptor for the biosynthesis of dinucleoside polyphosphates. Journal of Molecular Medicine 91 (9), pp. 1095 - 1107 (2013)

MPG.PuRe

publisher-version

Vilardell, M.; Civit, S.; Herwig, R.: An integrative computational analysis provides evidence for FBN1-associated network de-regulation in trisomy 21. Biology Open 2 (8), pp. 771 - 778 (2013)

MPG.PuRe

publisher-version

Grimm, C.; Chavez, L.; Vilardell, M.; Farrall, A.; Tierling, S.; Böhm, J. W.; Grote, P.; Lienhard, M.; Dietrich, J.; Timmermann, B. et al.; Walter, J.; Schweiger, M. R.; Lehrach, H.; Herwig, R.; Herrmann, B. G.; Morkel, M.: DNA–Methylome Analysis of Mouse Intestinal Adenoma Identifies a Tumour-Specific Signature That Is Partly Conserved in Human Colon Cancer. PLoS Genetics 9 (2), p. e1003250 - e1003250 (2013)

MPG.PuRe

publisher-version

Suter, B.; Fontaine, J. F.; Yildirimman, R.; Rasko, T.; Schaefer, M. H.; Rasche, A.; Porras, P.; Vazquez-Alvarez, B. M.; Russ, J.; Rau, K. et al.; Foulle, R.; Zenkner, M.; Saar, K.; Herwig, R.; Andrade-Navarro, M. A.; Wanker, E. E.: Development and application of a DNA microarray-based yeast two-hybrid system. Nucleic Acids Research (London) 41 (3), pp. 1496 - 1507 (2013)

MPG.PuRe

publisher-version

Doktorova, T. Y.; Yildirimman, R.; Vinken, M.; Vilardell, M.; Vanhaecke, T.; Gmuender, H.; Bort, R.; Brolen, G.; Holmgren, G.; Li, R. et al.; Chesne, C.; van Delft, J.; Kleinjans, J.; Castell, J.; Bjorquist, P.; Herwig, R.; Rogiers, V.: Transcriptomic responses generated by hepatocarcinogens in a battery of liver-based in vitro models. Carcinogenesis 34 (6), pp. 1393 - 402 (2013)

MPG.PuRe

Fogeron, M.-L.; Müller, H.; Schade, S.; Dreher, F.; Lehmann, V.; Kühnel, A.; Scholz, A. K.; Kashofer, K.; Zerck, A.; Fauler, B. et al.; Lurz, R.; Herwig, R.; Zatloukal, K.; Lehrach, H.; Gobom, J.; Nordhoff, E.; Lange, B.: LGALS3BP regulates centriole biogenesis and centrosome hypertrophy in cancer cells. Nature Communications 4, p. 4:1531 - 4:1531 (2013)

MPG.PuRe

Jankowski, V.; Schulz, A.; Kretschmer, A.; Mischak, H.; Boehringer, F.; van der Giet, M.; Janke, D.; Schuchardt, M.; Herwig, R.; Zidek, W. et al.; Jankowski, J.: The enzymatic activity of the VEGFR2 receptor for the biosynthesis of dinucleoside polyphosphates. Journal of Molecular Medicine-JMM 91 (9), pp. 1095 - 107 (2013)

MPG.PuRe

Kamburov, A.; Stelzl, U.; Lehrach, H.; Herwig, R.: The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Research (London) 41 (Database issue), pp. D793 - 800 (2013)

MPG.PuRe

publisher-version

Vilardell, M.; Civit, S.; Herwig, R.: An integrative computational analysis provides evidence for FBN1-associated network deregulation in trisomy 21. Biol Open 2 (8), pp. 771 - 8 (2013)

MPG.PuRe

publisher-version

Woodsmith, J.; Kamburov, A.; Stelzl, U.: Dual Coordination of Post Translational Modifications in Human Protein Networks. PLoS Computational Biology 9 (3), p. e1002933 - e1002933 (2013)

MPG.PuRe

publisher-version

2012

31st Animal Protection Research Prize of the Federal Ministry of Food, Agriculture and Consumer Protection for “A systems biology approach for predicting carcinogenesis of chemicals in the liver. (accepted)

MPG.PuRe

Xue, Y.; Chen, Y.; Ayub, Q.; Huang, N.; Ball, E. V.; Mort, M.; Phillips, A. D.; Shaw, K.; Stenson, P. D.; Cooper, D. N. et al.; Tyler-Smith, C.; The 1000 Genomes Project Consortium; Timmermann, B.; Lehrach, H.; Herwig, R.: Deleterious- and Disease-Allele Prevalence in Healthy Individuals: Insights from Current Predictions, Mutation Databases, and Population-Scale Resequencing. The American Journal of Human Genetics 91 (6), pp. 1022 - 1031 (2012)

MPG.PuRe

publisher-version

van Delft, J.; Gaj, S.; Lienhard, M.; Albrecht, M.; Kirpiy, A.; Brauers, K.; Claessen, S.; Lizarraga, D.; Lehrach, H.; Herwig, R. et al.; Kleinjans, J.: RNA-Seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene. Toxicological Sciences 130 (2), pp. 427 - 439 (2012)

MPG.PuRe

publisher-version

Abecasis, G. R.; Auton, A.; Brooks, L. D.; DePristo, M. A.; Durbin, R. M.; Handsaker, R. E.; Kang, H. M.; Marth, G. T.; McVean, G. A.; The 1000 Genomes Project Consortium et al.; Sudbrak, R.; Albrecht, M.; Amstislavskiy, V.; Borodina, T. A.; Davydov, A.; Herwig, R.; Lienhard, M.; Mertes, F.; Sultan, M.; Timmermann, B.; Yaspo, M. L.; Lehrach, H.: An integrated map of genetic variation from 1,092 human genomes. Nature 491 (7422), pp. 56 - 65 (2012)

MPG.PuRe

publisher-version

Kamburov, A.; Grossmann, A.; Herwig, R.; Stelzl, U.: Cluster-based assessment of protein-protein interaction confidence. BMC Bioinformatics, p. 13:262 - 13:262 (2012)

MPG.PuRe

publisher-version

Wierling, C.; Kühn, A.; Hache, H.; Daskalaki, A.; Maschke-Dutz, E.; Peycheva, S.; Li, J.; Herwig, R.; Lehrach, H.: Prediction in the face of uncertainty: a Monte Carlo-based approach for systems biology of cancer treatment. Mutation Research-Genetic Toxixology and Environmental Mutagenesis 746 (2), pp. 163 - 170 (2012)

MPG.PuRe

publisher-version

Kamburov, A.; Stelzl, U.; Herwig, R.: IntScore: a web tool for confidence scoring of biological interactions. Nucleic Acids Research (London) 40 (Web Server issue), pp. W140 - W146 (2012)

MPG.PuRe

publisher-version

Dreher, F.; Kreitler, T.; Hardt, C.; Kamburov, A.; Yildirimman, R.; Schellander, K.; Lehrach, H.; Lange, B. M. H.; Herwig, R.: DIPSBC--data integration platform for systems biology collaborations. BMC Bioinformatics 13, 13:85 (2012)

MPG.PuRe

publisher-version

The 1000 Genomes Project Consortium; Sudbrak, R.; Albrecht, M.; Amstislavskiy, V.; Borodina, T. A.; Dahl, A.; Davydov, A.; Herwig, R.; Marquardt, P.; Mertes, F. et al.; Nietfeld, W.; Parkhomchuk, D.; Soldatov, A.; Timmermann, B.; Tolzmann, M.; Lehrach, H.: The 1000 Genomes Project: data management and community access. Nature methods 9 (5), pp. 459 - 462 (2012)

MPG.PuRe

publisher-version

Ereman, J.: A computational network based approach for the prediction of biological features based on high throughput experiments. Magister (2012)

MPG.PuRe

Hegele, A.; Kamburov, A.; Großmann, A.; Sourlis, C.; Wowro, S. J.; Weimann, M.; Will, C. L.; Pena, V.; Lührmann, R.; Stelzel, U.: Dynamic protein-protein interaction wiring of the human spliceosome. Molecular Cell 45 (4), pp. 567 - 580 (2012)

MPG.PuRe

publisher-version

Kamburov, A.: More complete and more accurate interactomes for elucidating the mechanisms of complex diseases. Dissertation (2012)

MPG.PuRe

MacArthur, D. G.; Balasubramanian, S.; Frankish, A.; 1000 Genomes Project, C.; Sudbrak, R.; Albrecht , M. W.; Amstislavskiy, V.; Borodina, T. A.; Dahl, A.; Davydov, A. et al.; Herwig, R.; Marquardt, P.; Mertes, F.; Nietfeld, W.; Parkhomchuk, D.; Soldatov, A.; Timmermann, B.; Tolzmann, M.; Lehrach, H.: A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes. Science 335 (6070), pp. 823 - 828 (2012)

MPG.PuRe

publisher-version

Clark, M. S.; Denekamp, N. Y.; Thorne, M. A.; Reinhardt, R.; Drungowski, M.; Albrecht, M.; Klages, S.; Beck, A.; Kube, M.; Lubzens, E.: Long-term survival of hydrated resting eggs from Brachionus plicatilis. PLoS One 7 (1), p. e29365 - e29365 (2012)

MPG.PuRe

publisher-version

Dreher, F.; Kamburov, A.; Herwig, R.: Construction of a pig physical interactome using sequence homology and a comprehensive reference human interactome. Evolutionary Bioinformatics 8, pp. 119 - 126 (2012)

MPG.PuRe

publisher-version

Rabhi, I.; Rabhi, S.; Ben-Othman, R.; Rasche, A.; Daskalaki, A.; Trentin, B.; Piquemal, D.; Regnault, B.; Descoteaux, A.; Guizani-Tabbane, L.: Transcriptomic signature of Leishmania infected mice macrophages: a metabolic point of view. PLoS Neglected Tropical Diseases 6 (8), e1763 (2012)

MPG.PuRe

publisher-version

2011

Meinel, T.; Schweiger, M. R.; Ludewig, A. H.; Chenna, R.; Krobitsch, S.; Herwig, R.: Ortho2ExpressMatrix--a web server that interprets cross-species gene expression data by gene family information. BMC Genomics 12, 12:483 (2011)

MPG.PuRe

publisher-version

Lienhard, M.: Analysis of RNA-seq experiments. Master, Freie Universität, Berlin (2011)

MPG.PuRe

Galicka, H.: Integriertes Konzept zur Bestimmung von Homologie zwischen verschiedenen Spezies. Master, Freie Universität, Berlin (2011)

MPG.PuRe

Braunholz, D.; Hullings, M.; Gil-Rodriguez, M. C.; Fincher, C. T.; Mallozzi, M. B.; Loy, E.; Albrecht, M.; Kaur, M.; Limon, J.; Rampuria, A. et al.; Clark, D.; Kline, A.; Dalski, A.; Eckhold, J.; Tzschach, A.; Hennekam, R.; Gillessen-Kaesbach, G.; Wierzba, J.; Krantz, I. D.; Deardorff, M. A.; Kaiser, F. J.: Isolated NIBPL missense mutations that cause Cornelia de Lange syndrome alter MAU2 interaction. Eur J Hum Genet (2011)

MPG.PuRe

Cavill, R.; Kamburov, A.; Ellis, J. K.; Athersuch, T. J.; Blagrove, M. S.; Herwig, R.; Ebbels, T. M.; Keun, H. C.: Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells. PLoS Computational Biology 7 (3), p. e1001113 (2011)

MPG.PuRe

Donnarumma, F.; Schober, M.; Greilberger, J.; Matzi, V.; Lindenmann, J.; Maier, A.; Herwig, R.; Wintersteiger, R.: Method development and validation for the analysis of a new anti-cancer infusion solution via HPLC. Journal of Separation Science 34 (2), pp. 135 - 41 (2011)

MPG.PuRe

Kamburov, A.; Cavill, R.; Ebbels, T. M.; Herwig, R.; Keun, H. C.: Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA. Bioinformatics 27 (20), pp. 2917 - 8 (2011)

MPG.PuRe

Kamburov, A.; Pentchev, K.; Galicka, H.; Wierling, C.; Lehrach, H.; Herwig, R.: ConsensusPathDB: toward a more complete picture of cell biology. Nucleic Acids Research (London) 39 (Database issue), pp. D712 - D717 (2011)

MPG.PuRe

publisher-version

Muller, H.; Schmidt, D.; Dreher, F.; Herwig, R.; Ploubidou, A.; Lange, B. M.: Gene ontology analysis of the centrosome proteomes of Drosophila and human. Communicative & Integrative Biology 4 (3), pp. 308 - 11 (2011)

MPG.PuRe

Rasche, A.; Yildirimman, R.; Herwig, R.: Integrative Analysis of microarray data - a path for systems toxicology. In: Handbook of Systems Toxicology (Ed. Casciano Saura C., D. A. S.). Wiley-VCH, Weinheim (2011)

MPG.PuRe

Thormann, A.; Rasche, A.: Functional Context Network of T2DM, Medical Complications of Type 2 Diabetes. Intech Publishing (2011)

MPG.PuRe

Vilardell, M.; Rasche, A.; Thormann, A.; Maschke-Dutz, E.; Perez-Jurado, L. A.; Lehrach, H.; Herwig, R.: Meta-analysis of heterogeneous Down Syndrome data reveals consistent genome-wide dosage effects related to neurological processes. BMC Genomics 12, p. 229 (2011)

MPG.PuRe

Yildirimman, R.; Brolen, G.; Vilardell, M.; Eriksson, G.; Synnergren, J.; Gmuender, H.; Kamburov, A.; Ingelman-Sundberg, M.; Castell, J.; Lahoz, A. et al.; Kleinjans, J.; van Delft, J.; Bjorquist, P.; Herwig, R.: Human embryonic stem cell derived hepatocyte-like cells as a tool for in vitro hazard assessment of chemical carcinogenicity. Toxicological Sciences: an Official Journal of the Society of Toxicology 124 (2), pp. 278 - 90 (2011)

MPG.PuRe

2010

Pentchev, K.; Ono, K.; Herwig, R.; Ideker, T.; Kamburov, A.: Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. (2010)

MPG.PuRe

Müller, H.; Schmidt, D.; Steinbrink, S.; Mirgorodskaya, E.; Lehmann, V.; Habermann, K.; Dreher, F.; Gustavsson, N.; Kessler, T.; Lehrach, H. et al.; Herwig, R.; Gobom, J.; Ploubidou, A.; Boutros, M.; Lange, B. M.: Proteomic and functional analysis of the mitotic Drosophila centrosome. The EMBO Journal 29 (19), pp. 3344 - 3357 (2010)

MPG.PuRe

Neubert, K.: Detection of copy number variants in sequencing data. Master, FREIE UNIVERSITAET BERLIN, Berlin (2010)

MPG.PuRe

Richard, H.; Schulz, M. H.; Sultan, M.; Nurnberger, A.; Schrinner, S.; Balzereit, D.; Dagand, E.; Rasche, A.; Lehrach, H.; Vingron, M. et al.; Haas, S. A.; Yaspo, M. L.: Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Research 38 (10), p. e112 - e112 (2010)

MPG.PuRe

Meinel, T.; Mueller, M. S.; Ahmed, J.; Yildiriman, R.; Dunkel, M.; Herwig, R.; R. Preissner, R.: SOAP/WSDL-Based Web Services for Biomedicine: Demonstrating the Technique with the CancerResource. XII Mediterranean Conference on Medical and Biological Engineering and Computing 2010, Chalkidiki, Greece, May 27, 2010 - May 30, 2010. Proceedings of the Medicon 2010 (Part 5), pp. 835 - 838 (2010)

MPG.PuRe

Ravasi, T.; Suzuki, H.; Cannistraci, C. V.; Katayama, S.; Bajic, V. B.; Tan, K.; Akalin, A.; Schmeier, S.; Kanamori-Katayama, M.; Bertin, N. et al.; Carninci, P.; Daub, C. O.; Forrest, A. R.; Gough, J.; Grimmond, S.; Han, J. H.; Hashimoto, T.; Hide, W.; Hofmann, O.; Kamburov, A.; Kaur, M.; Kawaji, H.; Kubosaki, A.; Lassmann, T.; van Nimwegen, E.; MacPherson, C. R.; Ogawa, C.; Radovanovic, A.; Schwartz, A.; Teasdale, R. D.; Tegner, J.; Lenhard, B.; Teichmann, S. A.; Arakawa, T.; Ninomiya, N.; Murakami, K.; Tagami, M.; Fukuda, S.; Imamura, K.; Kai, C.; Ishihara, R.; Kitazume, Y.; Kawai, J.; Hume, D. A.; Ideker, T.; Hayashizaki, Y.: An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140 (5), pp. 744 - 752 (2010)

MPG.PuRe

Dreja, T.; Jovanovic, Z.; Rasche, A.; Kluge, R.; Herwig, R.; Tung, Y. C.; Joost, H. G.; Yeo, G. S.; Al-Hasani, H.: Diet-induced gene expression of isolated pancreatic islets from a polygenic mouse model of the metabolic syndrome. Diabetologia 53 (2), pp. 309 - 320 (2010)

MPG.PuRe

Rasche, A.: nformation Theoretical Prediction of Alternative Splicing with Application to Type-2 Diabetes Mellitus. Dissertation, Freie Universität Berlin, Berlin (2010)

MPG.PuRe

Daskalaki, A.; Rasche, A.: Meta-Analysis approach for the identification of molecular networks related to infections of the oral cavity. In: Informatics in oral medicine: advanced techniques in clinical and diagnostic technologies, pp. 237 - 250 (Ed. Daskalaki, A.). IGI Global, Hershey, PA 17033, USA (2010)

MPG.PuRe

2009

Chavez, L.; Bais, A. S.; Vingron, M.; Lehrach, H.; Adjaye, J.; Herwig, R.: In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach. BMC Genomics 10, p. 314 - 314 (2009)

MPG.PuRe

Klipp, E.; Liebermeister, W.; Wierling, C.; Kowald, A.; Lehrach, H.; Herwig, R.: Systems Biology: A Textbook. Wiley-VCH, Weinheim (2009), XXI, 569 pp: Ill., graphs. pp.

MPG.PuRe

Hache, H.; Lehrach, H.; Herwig, R.: Reverse Engineering of Gene Regulatory Networks: A Comparative Study. EURASIP Journal on Bioinformatics and Systems Biology 2009, ID 617281 (2009)

MPG.PuRe

Hache, H.; Wierling, C.; Lehrach, H.; Herwig, R.: GeNGe: systematic generation of gene regulatory networks. Bioinformatics. Bioinformatics 25 (9), pp. 1205 - 1207 (2009)

MPG.PuRe

2008

Kamburov, A.; Wierling, C.; Lehrach, H.; Herwig, R.: ConsensusPathDB—a database for integrating human functional interaction networks. Nucleic Acids Research 37 (Database issue), pp. D623 - D628 (2008)

MPG.PuRe

Erehman, J.: Theoretische Untersuchungen von Proteinstrukturen alternativ gespleißter Proteine. Bachelor, Freie Universität Berlin, Berlin (2008)

MPG.PuRe

Rasche, A.; Al-Hasani, H.; Herwig, R.: Meta-analysis approach identifies candidate genes and associated molecular networks for Type-2 Diabetes Mellitus. BMC Genomics 9, p. 9:310 - 9:310 (2008)

MPG.PuRe

Hardt, C.: Evolutionary Rate Dynamics of Protein Families. Bachelor, Freie Universität Berlin, Berlin (2008)

MPG.PuRe

2007

Kamburov, A.; Goldovsky, L.; Freilich, S.; Kapazoglou, A.; Kunin, V.; Enright, A. J.; Tsaftaris, A.; Ouzounis, C. A.: Denoising inferred functional association networks obtained by gene fusion analysis. BMC Genomics 8, p. 460 - 460 (2007)

MPG.PuRe

Adjaye, J.; Herwig, R.; Brink, T. C.; Herrmann, D.; Greber, B.; Sudheer, S.; Groth, D.; Carnwath, J. W.; Lehrach, H.; Niermann, H.: Conserved molecular portraits of bovine and human blastocysts as a consequence of the transition from maternal to embryonic control of gene expression. Physiological Genomics 31 (2), pp. 315 - 327 (2007)

MPG.PuRe

Wierling, C.; Herwig, R.; Lehrach, H.: Resources, standards and tools for systems biology. Briefings in Functional Genomics and Proteomics 6 (3), pp. 240 - 251 (2007)

MPG.PuRe

Poustka, A. J.; Kühn, A.; Groth, D.; Weise, V.; Yaguchi, S.; Burke, R. D.; Herwig, R.; Lehrach, H.; Panopoulou, G.: A global view of gene expression in lithium and zinc treated sea urchin embryos: new components of gene regulatory networks. Genome Biology 8 (5), p. R85 - R85 (2007)

MPG.PuRe

Sultan, M.; Piccini, I.; Balzereit, D.; Herwig, R.; Saran, N. G.; Lehrach, H.; Reeves, R. H.; Yaspo, M.-L.: Gene expression variation in Down's syndrome mice allows prioritization of candidate genes. Genome Biology 8 (5), p. R91 - R91 (2007)

MPG.PuRe

Bennett, J. D.; Joubin, K.; Cheng, S.; Aanstad, P.; Herwig, R.; Clark, M.; Lehrach, H.; Schier, A. F.: Nodal signaling activates differentiation genes during zebrafish gastrulation. Developmental Biology 304 (2), pp. 525 - 540 (2007)

MPG.PuRe

Albrecht, M.: Quality control and normalization of BeadArray data. Diploma, University of Applied Sciences, Berlin (2007)

MPG.PuRe

Reconstruction and validation of gene regulatory networks with neural networks. The 2nd Foundations of Systems Biology in Engineering Conference, FOSBE 2007, Stuttgart, September 09, 2007 - September 12, 2007. Universität Stuttgart, Stuttgart (2007), ? pp.

MPG.PuRe

Kamburov, A.: ConsensusPathDB - a database for matching pathway annotation for human. Master, Freie Universität, Berlin (2007)

MPG.PuRe

Liu, J.-P.; Drungowski, M.; Nyarsik, L.; Schwartz, R.; Lehrach, H.; Herwig, R.; Janitz, M.: Oligonucleotide fingerprinting of arrayed genomic DNA sequences using LNA-modified hybridization probes. Combinatorial Chemistry & High Throughput Screening 10 (4), pp. 269 - 276 (2007)

MPG.PuRe

Thormann, A.: Topologische Analyse von Protein-Protein-Interaktionsnetzwerken. Bachelor, Freie Universität, Berlin (2007)

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2006

Jann, O. C.; Aerts, J.; Jones, M.; Hastings, N.; Law, A.; McKay, S.; Marques, E.; Prasad, A.; Yu, J.; Moore, S. S. et al.; Floriot, S.; Mahé, M.-F.; Eggen, A.; Silveri, L.; Negrini, R.; Milanesi, E.; Ajmone-Marsan, P.; Valentini, A.; Marchitelli, C.; Savarese, M. C.; Janitz, M.; Herwig, R.; Hennig, S.; Gorni, C.; Connor, E. E.; Sonstegard, T. S.; Smith, T.; Drögemüller, C.; Williams, J. L.: A second generation radiation hybrid map to aid the assembly of the bovine genome sequence. BMC Genomics 7, p. 283 - 283 (2006)

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Assmus, H. E.; Herwig, R.; Cho, K.-H.; Wolkemhauer, O.: Dynamics of biological systems: role of systems biology in medical research. Expert Review of Molecular Diagnostics 6 (6), pp. 891 - 902 (2006)

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Babaie, Y.; Herwig, R.; Greber, B.; Brink, T. C.; Wruck, W.; Groth, D.; Lehrach, H.; Burdon, T.; Adjaye, J.: Analysis of Oct4-dependent transcriptional networks regulating self-renewal and pluripotency in human embryonic stem cells. Stem Cells Stem Cells Express, p. Epub - Epub (2006)

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Makrantonaki, E.; Adjaye, J.; Herwig, R.; Brink, T. C.; Groth, D.; Hultschig, C.; Lehrach, H.; Zouboulis, C. C.: Age-specific hormonal decline is accompanied by transcriptional changes in human sebocytes in vitro. Aging Cell 5 (4), pp. 331 - 344 (2006)

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Herwig, R.; Lehrach, H.: Expression profiling of drug response-from genes to pathways. Dialogues in Clinical Neuroscience 8 (3), pp. 283 - 293 (2006)

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Wierling, C.; Herwig, R.: Systems biology and drug discovery - a new path in genome research. Screening: Trends in Drug Discovery 7 (3), pp. 39 - 41 (2006)

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Wierling, C.; Herwig, R.: Vom Gen zum System. GIT Labor-Fachzeitschrift 50 (5), pp. 484 - 486 (2006)

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2005

Wolski, W. E.; Lalowski, M.; Martus, P.; Herwig, R.; Giavalisco, P.; Gobom, J.; Sickmann, A.; Lehrach, H.; Reinert, K.: Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process. BMC Bioinformatics 6, p. 285 - 285 (2005)

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Adjaye, J.; Huntriss, J.; Herwig, R.; BenKahla, A.; Brink, T. C.; Wierling, C.; Hultschig, C.; Groth, D.; Yaspo, M.-L.; Picton, H. M. et al.; Gosden, R. G.; Lehrach, H.: Primary differentiation in the human blastocyst: comparative molecular portraits of inner cell mass and trophectoderm cells. Stem Cells 23 (10), pp. 1514 - 1525 (2005)

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Papakonstantinou, E.; Aletras, A. J.; Glass, E.; Tsogas, P.; Dionyssopoulos, A.; Adjaye, J.; Fimmel, S.; Gouvousis, P.; Herwig, R.; Lehrach, H. et al.; Zouboulis, C. C.; Karakiulakis, G.: Matrix Metalloproteinases of Epithelial Origin in Facial Sebum of Patients with Acne and their Regulation by Isotretinoin. Journal of Investigative Dermatology (New York, NY) 125 (4), pp. 673 - 684 (2005)

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Klipp, E.; Herwig, R.; Kowald, A.; Wierling, C.; Lehrach, H.: Systems biology in practice: concepts, implementation and application. Wiley-VCH, Weinheim (2005), 466 pp pp.

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Yildirimman, R.: The GenomeMatrix: data mining from biological databases and data sources for building integrated functional genomics information. Diploma, Technische Universität Berlin, Fakultät III für Prozesswissenschaften, Institut für Biotechnologie, Berlin (2005)

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