Chavez, Lukas, Bais, Abha S, Vingron, Martin, Lehrach, Hans, Adjaye, James, Herwig, Ralf
Abstract Background The transcription factor OCT4 is highly expressed in pluripotent embryonic stem cells which are derived from the inner cell mass of mammalian blastocysts. Pluripotency and self...
Reverse Engineering of Gene Regulatory Networks: A Comparative Study (2009)
Hendrik Hache, Hans Lehrach, Ralf Herwig
Reverse engineering of gene regulatory networks has been an intensively studied topic in bioinformatics since it constitutes an intermediate step from explorative to causative gene expression...
ConsensusPathDB--a database for integrating human functional interaction networks (2009)
Kamburov, Atanas, Wierling, Christoph, Lehrach, Hans, Herwig, Ralf
ConsensusPathDB is a database system for the integration of human functional interactions. Current knowledge of these interactions is dispersed in more than 200 databases, each having a specific...
GeNGe: systematic generation of gene regulatory networks (2009)
Hache, Hendrik, Wierling, Christoph, Lehrach, Hans, Herwig, Ralf
Summary: The analysis of gene regulatory networks (GRNs) is a central goal of bioinformatics highly accelerated by the advent of new experimental techniques, such as RNA interference. A battery of...
Reverse Engineering of Gene Regulatory Networks: A Comparative Study (2009)
Hendrik Hache, Hans Lehrach, Ralf Herwig
Reverse engineering of gene regulatory networks has been an intensively studied topic in bioinformatics since it constitutes an intermediate step from explorative to causative gene expression...
Rasche, Axel, Al-Hasani, Hadi, Herwig, Ralf
Abstract Background Multiple functional genomics data for complex human diseases have been published and made available by researchers worldwide. The main goal of these studies is the detailed...
ConsensusPathDB—a database for integrating human functional interaction networks (2008)
Kamburov, Atanas, Wierling, Christoph, Lehrach, Hans, Herwig, Ralf
ConsensusPathDB is a database system for the integration of human functional interactions. Current knowledge of these interactions is dispersed in more than 200 databases, each having a specific...
Rasche, Axel, Al-Hasani, Hadi, Herwig, Ralf
Background Multiple functional genomics data for complex human diseases have been published and made available by researchers worldwide. The main goal of these studies is the detailed analysis of a...
No abstract available.
A low power 12 bit flux shuttle shift register with Nb technology. (2007)
Lochschmied, Rainer, Herwig, Ralf, Neuhaus, Manfred, Jutzi, Wilhelm
YBCO step edge junctions for magnetically tunable resonators. (2007)
Vogt, Andreas, Matz, Hartmut, Dolata, Ralf, Herwig, Ralf, Neuhaus, Manfred, Marienhoff, Peter, ...
Gene expression variation in Down's syndrome mice allows prioritization of candidate genes (2007)
Sultan, Marc, Piccini, Ilaria, Balzereit, Daniela, Herwig, Ralf, Saran, Nidhi G, Lehrach, Hans, ...
Abstract Background Down's syndrome (DS), or trisomy 21, is a complex developmental disorder that exhibits many clinical signs that vary in occurrence and severity among patients. The molecular...
Poustka, Albert J, Kühn, Alexander, Groth, Detlef, Weise, Vesna, Yaguchi, Shunsuke, Burke, Robert D, ...
Abstract Background The genome of the sea urchin Strongylocentrotus purpuratus has recently been sequenced because it is a major model system for the study of gene regulatory networks. Embryonic...
Adjaye, James, Herwig, Ralf, Brink, Thore C., Herrmann, Doris, Greber, Boris, Sudheer, Smita, ...
The present study investigated mRNA expression profiles of bovine oocytes and blastocysts by using a cross-species hybridization approach employing an array consisting of 15,529 human cDNAs as probe,...
Nodal signaling activates differentiation genes during zebrafish gastrulation (2007)
Bennett, James D., Joubin, Katherine, Cheng, Simon, Aanstad, Pia, Herwig, Ralf, Clark, Matthew, ...
Nodal signals induce mesodermal and endodermal progenitors during vertebrate development. To determine the role of Nodal signaling at a genomic level, we isolated Nodal-regulated genes by expression...
Reconstruction and validation of gene regulatory networks with neural networks (2007)
Hache, Hendrik, Wierling, Christoph, Lehrach, Hans, Herwig, Ralf
Liu, Jian-Ping, Drungowski, Mario, Nyarsik, Lajos, Schwartz, Regine, Lehrach, Hans, Herwig, Ralf, ...
Recently, we established a robust method for the detection of hybridization events using a DNA microarray deposited on a nanoporous membrane. Here, in a follow-up study, we demonstrate the...
Poustka, Albert J., Kühn, Alexander, Groth, Detlef, Weise, Vesna, Yaguchi, Shunsuke, Burke, Robert D., ...
Background The genome of the sea urchin Strongylocentrotus purpuratus has recently been sequenced because it is a major model system for the study of gene regulatory networks. Embryonic expression...
Gene expression variation in Down's syndrome mice allows prioritization of candidate genes (2007)
Sultan, Marc, Piccini, Ilaria, Balzereit, Daniela, Herwig, Ralf, Saran, Nidhi G., Lehrach, Hans, ...
Background Down's syndrome (DS), or trisomy 21, is a complex developmental disorder that exhibits many clinical signs that vary in occurrence and severity among patients. The molecular mechanisms...
Resources, standards and tools for systems biology (2007)
Wierling, Christoph, Herwig, Ralf, Lehrach, Hans
Modelling and simulation techniques are valuable tools for the understanding of complex biological systems. The design of a computer model necessarily has many diverse inputs, such as information on...
Resources, standards and tools for systems biology (2007)
Wierling, Christoph, Herwig, Ralf, Lehrach, Hans
Modelling and simulation techniques are valuable tools for the understanding of complex biological systems. The design of a computer model necessarily has many diverse inputs, such as information on...
A second generation radiation hybrid map to aid the assembly of the bovine genome sequence (2006)
Jann, Oliver C, Aerts, Jan, Jones, Michelle, Hastings, Nicola, Law, Andy, McKay, Stephanie, ...
Background: Several approaches can be used to determine the order of loci on chromosomes and hence develop maps of the genome. However, all mapping approaches are prone to errors either arising from...
Babaie, Yasmin, Herwig, Ralf, Greber, Boris, Brink, Thore C., Wruck, Wasco, Groth, Detlef, ...
The POU domain transcription factor OCT4 is a key regulator of pluripotency in the early mammalian embryo and is highly expressed in the inner cell mass of the blastocyst. Consistent with its...
Dynamics of biological systems: role of systems biology in medical research (2006)
Assmus, Heike E., Herwig, Ralf, Cho, Kwang-Hyun, Wolkemhauer, Olaf
Cellular systems are networks of interacting components that change with time in response to external and internal events. Studying the dynamic behavior of these networks is the basis for an...
Expression profiling of drug response-from genes to pathways (2006)
Understanding individual response to a drug—what determines its efficacy and tolerability—is the major bottleneck in current drug development and clinical trials. Intracellular response and...
A second generation radiation hybrid map to aid the assembly of the bovine genome sequence (2006)
Jann, Oliver C., Aerts, Jan, Jones, Michelle, Hastings, Nicola, Law, Andy, McKay, Stephanie, ...
Background Several approaches can be used to determine the order of loci on chromosomes and hence develop maps of the genome. However, all mapping approaches are prone to errors either arising from...
Makrantonaki, Evgenia, Adjaye, James, Herwig, Ralf, Brink, Thore C., Groth, Detlef, Hultschig, Claus, ...
The importance of hormones in endogenous aging has been displayed by recent studies performed on animal models and humans. To decipher the molecular mechanisms involved in aging we maintained human...
Adjaye, James, Huntriss, John, Herwig, Ralf, BenKahla, Alia, Brink, Thore C., Wierling, Christoph, ...
The primary differentiation event during mammalian development occurs at the blastocyst stage and leads to the delineation of the inner cell mass (ICM) and the trophectoderm (TE). We provide the...
Papakonstantinou, Eleni, Aletras, Alexios J., Glass, Evelyn, Tsogas, Panagiotis, Dionyssopoulos, Alexander, Adjaye, James, ...
Acne vulgaris is a skin disorder of the sebaceous follicles, involving hyperkeratinization and perifollicular inflammation. Matrix metalloproteinases (MMP) have a predominant role in inflammatory...
Systems biology in practice : concepts, implementation and application (2005)
Klipp, Edda, Herwig, Ralf, Kowald, Axel, Wierling, Christoph, Lehrach, Hans
Wolski, Witold E., Lalowski, Maciej, Martus, Peter, Herwig, Ralf, Giavalisco, Patrick, Gobom, Johan, ...
Background: Biological Mass Spectrometry is used to analyse peptides and proteins. A mass spectrum generates a list of measured mass to charge ratios and intensities of ionised peptides, which is...
James Adjaye, John Huntriss, Ralf Herwig, Alia Benkahla, Thore Brink, Claus Hultschig, ...
The online version of this article, along with updated information and services, is located on the World Wide Web at:
Dickmeis, Thomas, Plessy, Charles, Rastegar, Sepand, Aanstad, Pia, Herwig, Ralf, Chalmel, Frédéric, ...
Differential gene transcription is a fundamental regulatory mechanism of biological systems during development, body homeostasis, and disease. Comparative genomics is believed to be a rapid means for...
Adjaye, James, Herwig, Ralf, Herrmann, Doris, Wruck, Wasco, BenKahla, Alia, Brink, Thore C., ...
Background Cross-species gene-expression comparison is a powerful tool for the discovery of evolutionarily conserved mechanisms and pathways of expression control. The usefulness of cDNA microarrays...
Bauer, Oliver, Guerasimova, Anna, Sauer, Sascha, Thamm, Sabine, Steinfath, Matthias, Herwig, Ralf, ...
Peptide nucleic acid (PNA) is a novel class of DNA analogues in which the entire sugar-phosphate backbone is replaced by a pseudopeptide counterpart. Owing to its neutral character and the consequent...
Kahlem, Pascal, Sultan, Marc, Herwig, Ralf, Steinfath, Matthias, Balzereit, Daniela, Eppens, Barbara, ...
Human trisomy 21, which results in Down syndrome (DS), is one of the most complicated congenital genetic anomalies compatible with life, yet little is known about the molecular basis of DS. It is...
Kahlem, Pascal, Sultan, Marc, Herwig, Ralf, Steinfath, Matthias, Balzereit, Daniela, Eppens, Barbara, ...
Human trisomy 21, which results in Down syndrome (DS), is one of the most complicated congenital genetic anomalies compatible with life, yet little is known about the molecular basis of DS. It is...
Dickmeis, Thomas, Plessy, Charles, Rastegar, Sepand, Aanstad, Pia, Herwig, Ralf, Chalmel, Frédéric, ...
Differential gene transcription is a fundamental regulatory mechanism of biological systems during development, body homeostasis, and disease. Comparative genomics is believed to be a rapid means for...
Dickmeis, Thomas, Plessy, Charles, Rastegar, Sepand, Aanstad, Pia, Herwig, Ralf, Chalmel, Frédéric, ...
Differential gene transcription is a fundamental regulatory mechanism of biological systems during development, body homeostasis, and disease. Comparative genomics is believed to be a rapid means for...
Poustka, Albert J., Groth, Detlef, Hennig, Steffen, Thamm, Sabine, Cameron, Andrew, Beck, Alfred, ...
Together with the hemichordates, sea urchins represent basal groups of nonchordate invertebrate deuterostomes that occupy a key position in bilaterian evolution. Because sea urchin embryos are also...
Panopoulou, Georgia, Hennig, Steffen, Groth, Detlef, Krause, Antje, Poustka, Albert J., Herwig, Ralf, ...
The 2R hypothesis predicting two genome duplications at the origin of vertebrates is highly controversial. Studies published so far include limited sequence data from organisms close to the...
Dieterich, Christoph, Herwig, Ralf, Vingron, Martin
Many cellular signaling pathways induce gene expression by activating specific transcription factor complexes. Conventional approaches to the prediction of transcription factor binding sites lead to...
Panopoulou, Georgia, Hennig, Steffen, Groth, Detlef, Krause, Antje, Poustka, Albert J., Herwig, Ralf, ...
The 2R hypothesis predicting two genome duplications at the origin of vertebrates is highly controversial. Studies published so far include limited sequence data from organisms close to the...
Poustka, Albert J., Groth, Detlef, Hennig, Steffen, Thamm, Sabine, Cameron, Andrew, Beck, Alfred, ...
Together with the hemichordates, sea urchins represent basal groups of nonchordate invertebrate deuterostomes that occupy a key position in bilaterian evolution. Because sea urchin embryos are also...
A gene expression map of human chromosome 21 orthologues in the mouse (2002)
Gitton, Yorick, Dahmane, Nadia, Baik, Sonya, I Altaba, Ariel Ruiz, Neidhardt, Lorenz, Scholze, Manuela, ...
The DNA sequence of human chromosome 21 (HSA21) has opened the route for a systematic molecular characterization of all of its genes. Trisomy 21 is associated with Down's syndrome, the most common...
Wierling, Christoph K., Steinfath, Matthias, Elge, Thorsten, Schulze-Kremer, Steffen, Aanstad, Pia, Clark, Matthew, ...
Background: Gene expression analyses based on complex hybridization measurements have increased rapidly in recent years and have given rise to a huge amount of bioinformatic tools such as image...
Herwig, Ralf, Schulz, Britta, Weisshaar, Bernd, Hennig, Steffen, Steinfath, Matthias, Drungowski, Mario, ...
Access to the complete gene inventory of an organism is crucial to understanding physiological processes like development, differentiation, pathogenesis, or adaptation to the environment. Transcripts...
DEFOG: A Practical Scheme for Deciphering Families of Genes (2002)
Fuchs, Tania, Malecova, Barbora, Linhart, Chaim, Sharan, Roded, Khen, Miriam, Herwig, Ralf, ...
We developed a novel efficient scheme, DEFOG (for "deciphering families of genes"), for determining sequences of numerous genes from a family of interest. The scheme provides a powerful means to...
Datenanalyse von Biochips: Von der Sequenz zum System (2002)
Herwig, Ralf, Schuchhardt, Johannes, Eickhoff, Holger, Herzel, Hanspeter, Lehrach, Hans
Die Zunahme unserer Kenntnisse über die molekularen Mechanismen u.a. von Wachstums-, Entwicklungs- und Differenzierungsprozessen hat die Grundlagen der molekularen Medizin innerhalb weniger Jahre...
Oligonucleotide fingerprinting including differental cDNA library screning (2002)
Bauer, Oliver, Janitz, Michal, Guerasimova, Anna, Herwig, Ralf, Lehrach, Hans, Radelof, Uwe
This book combines the experience of 225 experts on 900 pages. Scientists worldwide are currently overwhelmed by the ever-increasing number and diversity of genome projects. This handbook is your...
Clustering gene expression profiles (2002)
This book combines the experience of 225 experts on 900 pages. Scientists worldwide are currently overwhelmed by the ever-increasing number and diversity of genome projects. This handbook is your...
Clark, Matthew D., Hennig, Steffen, Herwig, Ralf, Clifton, Sandy W., Marra, Marco A., Lehrach, Hans, ...
Clark, Matthew D., Hennig, Steffen, Herwig, Ralf, Clifton, Sandy W., Marra, Marco A., Lehrach, Hans, ...
Clark, Matthew D., Hennig, Steffen, Herwig, Ralf, Clifton, Sandy W., Marra, Marco A., Lehrach, Hans, ...
Information theoretical probe selection for hybridisation experiments (2000)
Herwig, Ralf, Schmitt, Armin O., Steinfath, Matthias, OBrien, John, Seidel, Henrik, Meier-Ewert, Sebastian, ...
Motivation: The choice of probes is an important feature of hybridisation experiments. In this paper we present an algorithm that optimises probes with respect to a training set of sequences based on...
Large-Scale Clustering of cDNA-Fingerprinting Data (1999)
Herwig, Ralf, Poustka, Albert J., Müller, Christine, Bull, Christof, Lehrach, Hans, O'Brien, John
A low power 12 bit flux shuttle shift register with Nb technology. (1996)
Lochschmied, Rainer, Herwig, Ralf, Neuhaus, Manfred, Jutzi, Wilhelm
YBCO step edge junctions for magnetically tunable resonators. (1993)
Vogt, Andreas, Matz, Hartmut, Dolata, Ralf, Herwig, Ralf, Neuhaus, Manfred, Marienhoff, Peter, ...
Thesis (doctoral)--Universität Fridericiana zu Karlsruhe, 1984.
A second generation radiation hybrid map to aid the assembly of the bovine genome sequence
Jann, Oliver C, Aerts, Jan, Jones, Michelle, Hastings, Nicola, Law, Andy, McKay, Stephanie, ...
Statistical evaluation of differential expression on cDNA nylon arrays with replicated experiments
Herwig, Ralf, Aanstad, Pia, Clark, Matthew, Lehrach, Hans
In this paper we focus on the detection of differentially expressed genes according to changes in hybridization signals using statistical tests. These tests were applied to 14 208 zebrafish cDNA...
Wierling, Christoph K, Steinfath, Matthias, Elge, Thorsten, Schulze-Kremer, Steffen, Aanstad, Pia, Clark, Matthew, ...
Large-Scale Clustering of cDNA-Fingerprinting Data
Herwig, Ralf, Poustka, Albert J., Müller, Christine, Bull, Christof, Lehrach, Hans, O'Brien, John
Clustering is one of the main mathematical challenges in large-scale gene expression analysis. We describe a clustering procedure based on a sequential k-means algorithm with additional refinements...
Clark, Matthew D., Hennig, Steffen, Herwig, Ralf, Clifton, Sandy W., Marra, Marco A., Lehrach, Hans, ...
The zebrafish is a powerful system for understanding the vertebrate genome, allowing the combination of genetic, molecular, and embryological analysis. Expressed sequence tags (ESTs) provide a rapid...
Dickmeis, Thomas, Plessy, Charles, Rastegar, Sepand, Aanstad, Pia, Herwig, Ralf, Chalmel, Frédéric, ...
Differential gene transcription is a fundamental regulatory mechanism of biological systems during development, body homeostasis, and disease. Comparative genomics is believed to be a rapid means for...
Panopoulou, Georgia, Hennig, Steffen, Groth, Detlef, Krause, Antje, Poustka, Albert J., Herwig, Ralf, ...
The 2R hypothesis predicting two genome duplications at the origin of vertebrates is highly controversial. Studies published so far include limited sequence data from organisms close to the...
Poustka, Albert J., Groth, Detlef, Hennig, Steffen, Thamm, Sabine, Cameron, Andrew, Beck, Alfred, ...
Together with the hemichordates, sea urchins represent basal groups of nonchordate invertebrate deuterostomes that occupy a key position in bilaterian evolution. Because sea urchin embryos are also...
Kahlem, Pascal, Sultan, Marc, Herwig, Ralf, Steinfath, Matthias, Balzereit, Daniela, Eppens, Barbara, ...
Human trisomy 21, which results in Down syndrome (DS), is one of the most complicated congenital genetic anomalies compatible with life, yet little is known about the molecular basis of DS. It is...
Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays
Adjaye, James, Herwig, Ralf, Herrmann, Doris, Wruck, Wasco, BenKahla, Alia, Brink, Thore C, ...
Wolski, Witold E, Lalowski, Maciej, Martus, Peter, Herwig, Ralf, Giavalisco, Patrick, Gobom, Johan, ...
A second generation radiation hybrid map to aid the assembly of the bovine genome sequence
Jann, Oliver C, Aerts, Jan, Jones, Michelle, Hastings, Nicola, Law, Andy, McKay, Stephanie, ...
Poustka, Albert J, Kühn, Alexander, Groth, Detlef, Weise, Vesna, Yaguchi, Shunsuke, Burke, Robert D, ...
Novel territory-specific markers from the sea urchin Strongylocentrotus purpuratus have been identified using screens for genes that are differentially expressed in lithium-treated embryos, which...
Gene expression variation in Down's syndrome mice allows prioritization of candidate genes
Sultan, Marc, Piccini, Ilaria, Balzereit, Daniela, Herwig, Ralf, Saran, Nidhi G, Lehrach, Hans, ...
RNA from eight Ts65Dn mice (a model of Down syndrome) and eight euploid mice were analysed by real-time PCR to examine inter-individual gene expression levels as a function of trisomy.
ConsensusPathDB—a database for integrating human functional interaction networks
Kamburov, Atanas, Wierling, Christoph, Lehrach, Hans, Herwig, Ralf
ConsensusPathDB is a database system for the integration of human functional interactions. Current knowledge of these interactions is dispersed in more than 200 databases, each having a specific...
GeNGe: systematic generation of gene regulatory networks
Hache, Hendrik, Wierling, Christoph, Lehrach, Hans, Herwig, Ralf
Summary: The analysis of gene regulatory networks (GRNs) is a central goal of bioinformatics highly accelerated by the advent of new experimental techniques, such as RNA interference. A battery of...
Reverse Engineering of Gene Regulatory Networks: A Comparative Study
Hache, Hendrik, Lehrach, Hans, Herwig, Ralf
Reverse engineering of gene regulatory networks has been an intensively studied topic in bioinformatics since it constitutes an intermediate step from explorative to causative gene expression...