More Herwig publications

  • DG Hebels et al. (2014)
    Evaluation of database-derived pathway development for enabling biomarker discovery for hepatotoxicity.
    Biomark Med.,
    8 (2): 185-200
  • G Reiner et al. (2014)
    Identification of QTL affecting resistance/susceptibility to acute Actinobacillus pleuropneumoniae infection in swine.
    Mamm Genome,
    25 (3-4): 180-91
  • M Lienhard, C Grimm, M Morkel, R Herwig, L Chavez (2014)
    MEDIPS: Genome wide differential coverage analysis of sequencing data derived from DNA enrichment experiments.
    Bioinformatics, 30 (2): 284-6
  • V Jankowski et al. (2013)
    The enzymatic activity of the VEGFR2 receptor for the biosynthesis of dinucleoside polyphosphates.
    J Mol Med (Berl), 91 (9): 1095-107.
  • ML Fogeron et al. (2013)
    LGALS3BP regulates centriole biogenesis and centrosome hypertrophy in cancer cells.
    Nat Commun., 4: 1531
  • C Grimm et al. (2013)
    DNA-methylome analysis of mouse intestinal adenoma identifies a tumour-specific signature that is partly conserved in human colon cancer.
    PLoS Genet., 9 (2): e1003250
  • TY Doktorova et al. (2013)
    Transcriptomic responses generated by hepatocarcinogens in a battery of liver-based in vitro models.
    Carcinogenesis, 34 (6): 1393-402
  • B Suter et al. (2012)
    Development and application of a DNA microarray-based yeast two-hybrid system.
    Nucleic Acids Res., 41 (3): 1496-507
  • A Kamburov, U Stelzl, H Lehrach, R Herwig (2012)
    The ConsensusPathDB interaction database: 2013 update.
    Nucleic Acids Res., 41 (D1): D793-800
  • A Kamburov, A Grossmann, R Herwig, U Stelzl (2012)
    Cluster-based assessment of protein-protein interaction confidence.
    BMC Bioinformatics, 13 (1): 262
  • F Dreher et al. (2012)
    DIPSBC - data integration platform for systems biology collaborations.
    BMC Bioinformatics, 13 (1): 85
  • J van Delft, S Gaj, M Lienhard et al. (2012)
    RNA-seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene.
    Toxicol Sci., 130 (2): 427-39
  • A Kamburov, U Stelzl, R Herwig (2012)
    IntScore: a web tool for confidence scoring of biological intractions.
    Nucleic Acids Res., 40 (Web Server issue): W140-6
  • F Dreher et al (2012)
    DIPSBC - Data Integration Platform for Systems Biology Collaborations.
    BMC Bioinformatics, 13 (1): 85
  • F Dreher, A Kamburov, R Herwig (2012)
    Construction of a pig physical interactome using a sequence homology and a comprehensive reference human interactome.
    Evol Bioinform Online., 8: 119-26
  • C Wierling et al.
    Prediction in the face of uncertainty: a Monte Carlo-based approach for systems biology of cancer treatment.
    Mutat Res., 746 (2): 163-70
  • T Meinel, MR Schweiger, AH Ludewig, R Chenna, S Krobitsch, R Herwig (2011)
    Ortho2ExpressMatrix - a web server that interprets cross-species gene expression data by gene family information.
    BMC Genomics, 12 (1): 483
  • H Müller, D Schmidt, F Dreher, R Herig, A Ploubidou, BM Lange (2011)
    Gene ontology analysis of the centrosome proteomes of Drosophila and human.
    Commun Integr Biol., 4 (3): 308-11
  • M Kerick et al. (2011)
    Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues,
    input amount and tumor heterogeneity.
    BMC Med Genomics., 4 (1): 68
  • A Kamburov, R Cavill, TM Ebbels, R Herwig, HC Keun (2011)
    Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA.
    Bioinformatics, 27 (20): 2917-8
  • R Yildirimman et al. (2011)
    Human embryonic stem cell derived hepatocyte-like cells as a tool for in vitro hazard assessment of chemical carcinogenicity.
    Toxicol Sci., 124 (2): 278-90
  • M Vilardell, A Rasche, A Thormann, E Maschke-Dutz, LA Pérez-Jurado, H Lehrach, R Herwig (2011)
    Meta-analysis of heterogeneous Down Syndrome data reveals consistent genome-wide dosage effects related to neurological processes.
    BMC Genomics, 12: 229
  • R Cavill, A Kamburov, JK Ellis, TJ Athersuch, MS Blagrove, R Herwig, TM Ebbels, HC Keun (2011)
    Consensus-phenotype integration of transcriptomics and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells.
    PLoS Comput Biol., 7 (3): e1001113
  • The 1000 Genomes Project Consortium (2010)
    A map of human genome variation from population-scale sequencing.
    Nature, 467(7319):1061-73
  • A Kamburov, K Pentchev, H Galicka, C Wierling, H Lehrach, R Herwig (2010)
    ConsensusPathDB: toward a more complete picture of cell biology.
    Nucleic Acids Res. 39 (Database issue): D712-7
  • K Pentchev, K Ono, R Herwig, T Ideker, A Kamburov (2010)
    Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape.
    Bioinformatics, 26(21):2796-7
  • H Müller et al. (2010)
    Proteomic and functional analysis of the mitotic Drosophila centrosome.
    EMBO J., 29(19):3344-57
  • L Chavez, J Jozefczuk, C Grimm, J Dietrich, B Timmermann, H Lehrach, R Herwig, J Adjaye (2010)
    Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage.
    Genome Res. 20(10):1441-50
  • J Jozefczuk, H Stachelscheid, L Chavez, R Herwig, H Lehrach, K Zeilinger, JC Gerlach, J Adjaye (2010)
    Molecular characterization of cultured adult human liver progenitor cells.
    Tissue Eng Part C Methods
  • A Rasche, R Herwig (2010)
    ARH: predicting splice variants from genome-wide data with modified entropy
    Bioinformatics, 26(1): 84-90
  • L Chavez, AS Bais, M Vingron, H Lehrach, J Adjaye, R Herwig (2009)
    In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach.
    BMC Genomics, 10:314
  • H Hache, C Wierling, H Lehrach, R Herwig (2009)
    GeNGe: systematic generation of gene regulatory networks.
    Bioinformatics, 25(9):1205-7
  • H Hache, H Lehrach, R Herwig (2009)
    Reverse engineering of gene regulatory networks: a comparative study.
    EURASIP J Bioinform Syst Biol.: 617281
  • A Kamburov, C Wierling, H Lehrach and R Herwig (2009)
    ConsensusPathDB - a database for integrating human functional interaction networks.
    Nucleic Acids Res., 37 (Database issue): D623-8
  • A Rasche, H Al-Hasani, R Herwig (2008)
    Meta-analysis approach identifies candidate genes and associated molecular networks for type-2 diabetes mellitus.
    BMC Genomics, 9:310
  • A Rasche, R Herwig (2007)
    Identification of marker genes for type 2 diabetes.
    Genes Nutr., 2(1): 137
  • Hache, H., Wierling, C., Lehrach, H., Herwig, R. (2007)
    Reconstruction and Validation of Gene Regulatory Networks with Neural Networks.
    Proceedings of the 2nd Foundations of Systems Biology in Engineering Conference (FOSBE), Stuttgart, 319-324.
  • Wierling, C. and Herwig, R. (2006)
    Systems biology and drug discovery - A new path in genome research.
    Screening - Trends in drug discovery, 7(3):39-41.
  • Herwig, R., and Lehrach, H. (2006)
    Expression profiling of drug response - from genes to pathways.
    Dialogues in Clinical Neuroscience, 8(3):283-293.
  • Dickmeis, T., Plessy, C., Rastegar, S., Aanstad, P., Herwig, R., Chalmel, F., Fischer, N. and Strähle, U. (2004).
    Expression profiling and comparative genomics identify a conserved regulatory region controlling midline expression in the zebrafish embryo.
    Genome Res. 14, 228-238
  • Panopoulou, G., Hennig, S., Groth, D., Krause, A., Poustka, A., Herwig, R., Vingron, M. and Lehrach, H. (2003). New Evidence for Genome-Wide Duplications at the Origin of Vertebrates Using an Amphioxus Gene Set and Completed Animal Genomes. Genome Res. 13, 1056-1066.
  • Gitton, Y., Dahmane, N., Baik, S. and Altaba, R. (Group 1), Neidhardt, L., Scholze, M. and Herrmann, B. (Group 2), Kahlem, P., Ben-Kahla, A., Schrinner, S., Yildirimman, R., Herwig, R., Lehrach, H. and Yaspo, M.-L. (Group 3) (Groups contributed equally) (2002).
    A gene expression map of human chromosome 21 orthologues in the mouse. Nature 420, 586-590
  • Wierling, C.K., Steinfath, M., Elge, T., Schulze-Kremer, S., Aanstad, P., Clark, M., Lehrach, H. and Herwig, R. (2002).
    Simulation of DNA array hybridization experiments and evaluation of critical parameters during subsequent image and data analysis. BMC Bioinformatics 3, 29
  • Herwig, R., Aanstad, P., Clark, M. and Lehrach, H. (2001).
    Statistical evaluation of differential expression on cDNA nylon arrays with replicated experiments.
    Nucleic Acids Res. 29, e117.
  • Clark, M., Hennig, S., Herwig, R., Clifton, S., Marra, M., Lehrach, H., Johnson, S. and the WU-GSC EST Group. (2001). An Oligonucleotide Fingerprint Normalized and Expressed Sequence Tag Zebrafish cDNA Library. Genome Res. 11, 1594-1602
  • Herwig, R., Schmitt, A.O., Steinfath, M., O'Brien, J., Seidel, H., Meier-Ewert, S., Lehrach, H. and Radelof, U. (2000).
    Information theoretical probe selection for hybridisation experiments.
    Bioinformatics 16, 890-898
  • Hennig, S., Herwig, R., Clark, M., Aanstad, P., Musa, A., O'Brien, J., Bull, C., Radelof, U., Panopoulou, G., Poustka, A. and Lehrach, H. (2000).
    A data-analysis pipeline for large-scale gene expression analysis.
    In Proceedings of the 4th Annual International Conference on Research in Computational Molecular Biology RECOMB 2000 (eds R. Shamir et al.), 165-173. ACM Press, New York.
  • Herwig, R., Poustka, A., Müller, C., Bull, C., Lehrach, H. and O'Brien, J. (1999).
    Large-scale clustering of cDNA fingerprinting data.
    Genome Res. 9, 1093-1105
  • Meier-Ewert, S., Lange, J., Gerst, H., Herwig, R., Schmitt, A.O., Freund, J., Elge, T., Mott, R., Herrmann, B., and Lehrach, H. (1998).
    Comparative gene expression profiling by oligo­nucleotide fingerprinting.
    Nucleic Acids Res. 26, 2216-2223
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