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List of works by Ralf Herwig

"4D Biology for health and disease" workshop report

scientific article published on 15 October 2010

A Systems Biology Approach for Identifying Hepatotoxicant Groups Based on Similarity in Mechanisms of Action and Chemical Structure

scientific article published on January 2016

A gene expression map of human chromosome 21 orthologues in the mouse

scientific article

A global view of gene expression in lithium and zinc treated sea urchin embryos: new components of gene regulatory networks

scientific article published in January 2007

A model-based assay design to reproduce in vivo patterns of acute drug-induced toxicity

scientific article published on 29 August 2017

A second generation radiation hybrid map to aid the assembly of the bovine genome sequence

scientific article published on 6 November 2006

ARH-seq: identification of differential splicing in RNA-seq data

scientific article

ARH: predicting splice variants from genome-wide data with modified entropy

scientific article

Activation of AMP-activated protein kinase sensitizes lung cancer cells and H1299 xenografts to erlotinib

scientific article published on 10 September 2014

Age-specific hormonal decline is accompanied by transcriptional changes in human sebocytes in vitro

scientific article published on 29 June 2006

Aging of human sebocytes in vitro induced by exposure to a defined hormone environment

scientific article published in January 2006

An integrative computational analysis provides evidence for FBN1-associated network deregulation in trisomy 21

scientific article published on 20 June 2013

An oligonucleotide fingerprint normalized and expressed sequence tag characterized zebrafish cDNA library

scientific article

Analysis of Oct4-dependent transcriptional networks regulating self-renewal and pluripotency in human embryonic stem cells

scientific article published on 26 October 2006

Analyzing and interpreting genome data at the network level with ConsensusPathDB

scientific article (publication date: 8 September 2016)

Cluster-based assessment of protein-protein interaction confidence

scientific article

Comparative gene expression profiling by oligonucleotide fingerprinting ⬇️

scientific article published on May 1, 1998

Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage

scientific article

Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells

scientific article

ConsensusPathDB--a database for integrating human functional interaction networks

scientific article published on 21 October 2008

ConsensusPathDB: toward a more complete picture of cell biology

scientific article

Conserved molecular portraits of bovine and human blastocysts as a consequence of the transition from maternal to embryonic control of gene expression

scientific article published on 26 June 2007

Construction of a 'unigene' cDNA clone set by oligonucleotide fingerprinting allows access to 25 000 potential sugar beet genes

scientific article

Construction of a pig physical interactome using sequence homology and a comprehensive reference human interactome

scientific article

Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays

scientific article

DEFOG: a practical scheme for deciphering families of genes

scientific article

DIPSBC--data integration platform for systems biology collaborations

scientific article

DNA-methylome analysis of mouse intestinal adenoma identifies a tumour-specific signature that is partly conserved in human colon cancer

scientific article

Diet-induced gene expression of isolated pancreatic islets from a polygenic mouse model of the metabolic syndrome.

scientific article

Dynamics of biological systems: role of systems biology in medical research

scientific article published on November 2006

Establishment of T cell-specific and natural killer cell-specific unigene sets: towards high-throughput genomics of leukaemia.

scientific article

Evaluation of database-derived pathway development for enabling biomarker discovery for hepatotoxicity

scientific article

Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape

scientific article

Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites

scientific article published in October 2003

Expression profiling and comparative genomics identify a conserved regulatory region controlling midline expression in the zebrafish embryo

scientific article published on 12 January 2004

GeNGe: systematic generation of gene regulatory networks

scientific article published on 27 February 2009

Gene expression variation in Down's syndrome mice allows prioritization of candidate genes

scientific article published in January 2007

Generation, annotation, evolutionary analysis, and database integration of 20,000 unique sea urchin EST clusters

scientific article

Human embryonic stem cell derived hepatocyte-like cells as a tool for in vitro hazard assessment of chemical carcinogenicity

scientific article published on 27 August 2011

Identification of QTL affecting resistance/susceptibility to acute Actinobacillus pleuropneumoniae infection in swine

scientific article published on 21 January 2014

Identification of marker genes for type 2 diabetes

scientific article published on October 2007

Identification of nodal signaling targets by array analysis of induced complex probes

scientific article published on 01 December 2001

In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach

scientific article published on 15 July 2009

IntScore: a web tool for confidence scoring of biological interactions

scientific article published on 30 May 2012

Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA.

scientific article

Inter-laboratory study of human in vitro toxicogenomics-based tests as alternative methods for evaluating chemical carcinogenicity: a bioinformatics perspective

scientific article published on 2 November 2015

LGALS3BP regulates centriole biogenesis and centrosome hypertrophy in cancer cells

scientific article published on January 2013

Large-scale clustering of cDNA-fingerprinting data

scientific article

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments

scientific article

Matrix metalloproteinases of epithelial origin in facial sebum of patients with acne and their regulation by isotretinoin

scientific article published in October 2005

Meta-analysis approach identifies candidate genes and associated molecular networks for type-2 diabetes mellitus

scientific article

Meta-analysis of heterogeneous Down Syndrome data reveals consistent genome-wide dosage effects related to neurological processes ⬇️

scientific article

Molecular characterization of cultured adult human liver progenitor cells

scientific article published on October 2010

Molecular dissection of colorectal cancer in pre-clinical models identifies biomarkers predicting sensitivity to EGFR inhibitors.

scientific article published on 10 February 2017

Multiplexed hybridizations of positively charge-tagged peptide nucleic acids detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

scientific article

Network integration and modelling of dynamic drug responses at multi-omics levels

scientific article published on 15 October 2020

New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes

scientific article

Nodal signaling activates differentiation genes during zebrafish gastrulation

scientific article published on 12 January 2007

Oligonucleotide fingerprinting of arrayed genomic DNA sequences using LNA-modified hybridization probes

scientific article

Ortho2ExpressMatrix--a web server that interprets cross-species gene expression data by gene family information

scientific article

PWD/Ph-encoded genetic variants modulate the cellular Wnt/β-Catenin response to suppress ApcMin-triggered intestinal tumor formation

scientific article published on 05 November 2020

Pathway deregulation and expression QTLs in response to Actinobacillus pleuropneumoniae infection in swine

scientific article published on 14 August 2014

Prediction in the face of uncertainty: a Monte Carlo-based approach for systems biology of cancer treatment

scientific article published on 23 January 2012

Primary differentiation in the human blastocyst: comparative molecular portraits of inner cell mass and trophectoderm cells

scientific article

Proteomic and functional analysis of the mitotic Drosophila centrosome

scientific article published on 3 September 2010

QSEA-modelling of genome-wide DNA methylation from sequencing enrichment experiments

scientific article

RNA-Seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene

scientific article

Resources, standards and tools for systems biology

scientific article published on September 2007

Reverse engineering of gene regulatory networks: a comparative study

scientific article published on 11 June 2009

Simulation of DNA array hybridization experiments and evaluation of critical parameters during subsequent image and data analysis

scientific article

Suppression of the transcription factor MSX1 gene delays bovine preimplantation embryo development in vitro

scientific article published on 22 February 2010

Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity

scientific article

The ConsensusPathDB interaction database: 2013 update

scientific article

The enzymatic activity of the VEGFR2 receptor for the biosynthesis of dinucleoside polyphosphates

scientific article published on May 2013

ToxDB: pathway-level interpretation of drug-treatment data

scientific article

Transcript level alterations reflect gene dosage effects across multiple tissues in a mouse model of down syndrome

scientific article published on July 2004

Transcriptional signature induced by a metastasis-promoting c-Src mutant in a human breast cell line

scientific article

Transcriptomic responses generated by hepatocarcinogens in a battery of liver-based in vitro models

scientific article published on 7 February 2013

Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process

scientific article

diXa: a data infrastructure for chemical safety assessment

scientific article

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