Regenbrecht, Christian RA, Jung, Marc, Lehrach, Hans, Adjaye, James
Abstract Background Genistein is an isoflavonoid present in soybeans that exhibits anti-carcinogenic properties. The issue of genistein as a potential anti-cancer drug has been addressed in some...
Ralser, Markus, Nebel, Almut, Kleindorp, Rabea, Krobitsch, Sylvia, Lehrach, Hans, Schreiber, Stefan, ...
Abstract Background Triosephosphate isomerase (TPI) is a central and conserved glycolytic enzyme. In humans, TPI is encoded by a single gene on 12p13, and associated with a rare genetic disorder, TPI...
Fiebitz, Andrea, Nyarsik, Lajos, Haendler, Bernard, Hu, Yu-Hui, Wagner, Florian, Thamm, Sabine, ...
Abstract Background Most of the biological processes rely on the formation of protein complexes. Investigation of protein-protein interactions (PPI) is therefore essential for understanding of...
Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress (2007)
Ralser, Markus, Wamelink, Mirjam M, Kowald, Axel, Gerisch, Birgit, Heeren, Gino, Struys, Eduard A, ...
Abstract Background Eukaryotic cells have evolved various response mechanisms to counteract the deleterious consequences of oxidative stress. Among these processes, metabolic alterations seem to play...
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...
Greber, Boris, Lehrach, Hans, Adjaye, James
Abstract Background Despite their distinct origins, human embryonic stem (hES) and embryonic carcinoma (hEC) cells share a number of similarities such as surface antigen expression, growth...
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...
Matrix-Assisted Laser Desorption/Ionization Mass Spectrometric Analysis of DNA on Microarrays (2007)
Kepper, Pamela, Reinhardt, Richard, Dahl, Andreas, Lehrach, Hans, Sauer, Sascha
Background: Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is a powerful tool in biomolecule analysis with a wide range of application possibilities, including genotyping of...
Matrix-Assisted Laser Desorption/Ionization Mass Spectrometric Analysis of DNA on Microarrays (2007)
Kepper, Pamela, Reinhardt, Richard, Dahl, Andreas, Lehrach, Hans, Sauer, Sascha
Background: Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is a powerful tool in biomolecule analysis with a wide range of application possibilities, including genotyping of...
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...
Quantitative PCR based expression analysis on a nanoliter scale using polymer nano-well chips (2007)
Dahl, Andreas, Sultan, Marc, Jung, Alexander, Schwartz, Regine, Lange, Matthias, Steinwand, Michael, ...
The analysis of gene expression is an essential element of functional genomics. Expression analysis is mainly based on DNA microarrays due to highly parallel readout and high throughput. Quantitative...
Gerisch, Birgit, Rottiers, Veerle, Li, Dongling, Motola, Daniel L., Cummins, Carolyn L., Lehrach, Hans, ...
Broad aspects of Caenorhabditis elegans life history, including larval developmental timing, arrest at the dauer diapause, and longevity, are regulated by the nuclear receptor DAF-12. Endogenous...
Greber, Boris, Lehrach, Hans, Adjaye, James
Background Despite their distinct origins, human embryonic stem (hES) and embryonic carcinoma (hEC) cells share a number of similarities such as surface antigen expression, growth characteristics,...
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...
Nonhoff, Ute, Ralser, Markus, Welzel, Franziska, Piccini, Ilaria, Balzereit, Daniela, Yaspo, Marie-Laure, ...
Tight control of translation is fundamental for eukaryotic cells, and deregulation of proteins implicated contributes to numerous human diseases. The neurodegenerative disorder spinocerebellar ataxia...
Nordhoff, Eckhard, Lehrach, Hans, Gobom, Johan
We have used a non-contact piezo-electric liquid dispensing workstation to transfer 200 pL aliquots of both a sample solution containing 12 peptides, each at a concentration of 5 or 50 fmol/μL, and...
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...
Genomic organization of transcriptomes in mammals: coregulation and cofunctionality (2007)
Purmann, Antje, Toedling, Joern, Schueler, Markus, Carninci, Piero, Lehrach, Hans, Hayashizaki, Yoshihide, ...
In studies of their transcriptional activity, genomes have shown a high order of organization. We assessed the question of how genomically neighboring genes are transcriptionally coupled across...
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...
TLR2 has a detrimental role in mouse transient focal cerebral ischemia (2007)
Ziegler, Gina, Harhausen, Denise, Schepers, Claudia, Hoffmann, Olaf, Röhr, Christina, Prinz, Vincent, ...
A significant up-regulation of Toll-like-receptor (TLR) mRNAs between 3 and 48 h reperfusion time after induction of transient focal cerebral ischemia for 1 h was revealed by applying global gene...
Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress (2007)
Ralser, Markus, Wamelink, Mirjam M., Kowald, Axel, Gerisch, Birgit, Heeren, Gino, Struys, Eduard A., ...
Background Eukaryotic cells have evolved various response mechanisms to counteract the deleterious consequences of oxidative stress. Among these processes, metabolic alterations seem to play an...
Analytical model of peptide mass cluster centres with applications (2006)
Wolski, Witold E, Farrow, Malcolm, Emde, Anne-Katrin, Lehrach, Hans, Lalowski, Maciej, Reinert, Knut
Abstract Background The elemental composition of peptides results in formation of distinct, equidistantly spaced clusters across the mass range. The property of peptide mass clustering is used to...
Hu, Yu-Hui, Warnatz, Hans-Jörg, Vanhecke, Dominique, Wagner, Florian, Fiebitz, Andrea, Thamm, Sabine, ...
Abstract Background Trisomy of human chromosome 21 (Chr21) results in Down's syndrome, a complex developmental and neurodegenerative disease. Molecular analysis of Down's syndrome, however, poses a...
The bovine IGF2 gene is differentially methylated in oocyte and sperm DNA (2006)
Gebert, Claudia, Wrenzycki, Christine, Herrmann, Doris, Gröger, Daniela, Reinhardt, Richard, Hajkova, Petra, ...
The insulin-like growth factor 2 gene (IGF2) encodes an essential growth factor and is imprinted in various mammalian species. Differentially methylated regions (DMRs) are often located within CpG...
The bovine IGF2 gene is differentially methylated in oocyte and sperm DNA (2006)
Gebert, Claudia, Wrenzycki, Christine, Herrmann, Doris, Gröger, Daniela, Reinhardt, Richard, Hajkova, Petra, ...
The insulin-like growth factor 2 gene (IGF2) encodes an essential growth factor and is imprinted in various mammalian species. Differentially methylated regions (DMRs) are often located within CpG...
The DNA sequence, annotation and analysis of human chromosome 3 (2006)
Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, ...
The DNA sequence, annotation and analysis of human chromosome 3 (2006)
Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, ...
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...
Greber, Boris, Lehrach, Hans, Adjaye, James
Fibroblast growth factor 2 (FGF2) is known to promote self-renewal of human embryonic stem cells (hESCs). In addition, it has been shown that transforming growth factor ß (TGFß) signaling is...
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...
Horn, Sabine, Lueking, Angelika, Murphy, Derek, Staudt, Alexander, Gutjahr, Claudia, Schulte, Kirsten, ...
Dilated cardiomyopathy (DCM) is a myocardial disease characterized by progressive depression of myocardial contractile function and ventricular dilatation. Thirty percent of DCM patients belong to...
Hu, Yu-Hui, Warnatz, Hans-Jörg, Vanhecke, Dominique, Wagner, Florian, Fiebitz, Andrea, Thamm, Sabine, ...
Background Trisomy of human chromosome 21 (Chr21) results in Down's syndrome, a complex developmental and neurodegenerative disease. Molecular analysis of Down's syndrome, however, poses a particular...
Recent advances of protein microarrays (2006)
Hultschig, Claus, Kreutzberger, Jürgen, Seitz, Harald, Konthur, Zoltán, Büssow, Konrad, Lehrach, Hans
Technological innovations and novel applications have greatly advanced the field of protein microarrays. Over the past two years, different types of protein microarrays have been used for serum...
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...
Aging of human sebocytes in vitro induced by exposure to a defined hormone environment (2006)
Makrantonaki, E., Adjaye, J., Herwig, R., Brink, T. C., Groth, D., Hultschig, C., ...
The DNA sequence, annotation and analysis of human chromosome 3 (2006)
Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, ...
Otterhag, Lotta, Gustavsson, Niklas, Alsterfjord, Magnus, Pical, Christophe, Lehrach, Hans, Gobom, Johan, ...
The Arabidopsis thaliana protein kinase AtPDK1 was identified as a homologue of the mammalian 3-phosphoinositide-dependent protein kinase-1 (PDK1), which is involved in a number of physiological...
Ralser, Markus, Heeren, Gino, Breitenbach, Michael, Lehrach, Hans, Krobitsch, Sylvia
Triosephosphate isomerase (TPI) deficiency is an autosomal recessive disorder caused by various mutations in the gene encoding the key glycolytic enzyme TPI. A drastic decrease in TPI activity and an...
An efficient and economic enhancer mix for PCR (2006)
Ralser, Markus, Querfurth, Robert, Warnatz, Hans-Jörg, Lehrach, Hans, Yaspo, Marie-Laure, Krobitsch, Sylvia
Polymerase chain reaction (PCR) has become a fundamental technique in molecular biology. Nonetheless, further improvements of the existing protocols are required to broaden the applicability of PCR...
Single-nucleotide polymorphisms: analysis by mass spectrometry (2006)
Sauer, Sascha, Reinhardt, Richard, Lehrach, Hans, Gut, Ivo G.
Matrix-assisted laser desorption-ionization (MALDI) mass spectrometry has evolved as a powerful method for analyzing nucleic acids. Here we provide protocols for genotyping single-nucleotide...
Analysis of NOD2-mediated Proteome Response to Muramyl Dipeptide in HEK293 Cells (2006)
Weichart, Dieter, Gobom, Johan, Klopfleisch, Sina, Häsler, Robert, Gustavsson, Niklas, Billmann, Susanne, ...
NOD2, a cytosolic receptor for the bacterial proteoglycan fragment muramyl dipeptide (MDP), plays an important role in the recognition of intracellular pathogens. Variants in the bacterial sensor...
Analytical model of peptide mass cluster centres with applications (2006)
Wolski, Witold E., Farrow, Malcolm, Emde, Anne-Katrin, Lehrach, Hans, Lalowski, Maciej, Reinert, Knut
Background The elemental composition of peptides results in formation of distinct, equidistantly spaced clusters across the mass range. The property of peptide mass clustering is used to calibrate...
Wolski, Witold E, Lalowski, Maciej, Martus, Peter, Herwig, Ralf, Giavalisco, Patrick, Gobom, Johan, ...
Abstract 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,...
Dissection of the Inflammatory Bowel Disease Transcriptome Using Genome-Wide cDNA Microarrays (2005)
Christine M. Costello, Nancy Mah, Robert Häsler, Philip Rosenstiel, Georg H. Waetzig, Andreas Hahn, ...
cDNA analysis of colonic samples from patients with Crohn disease and ulcerative colitis suggests substantial differences in pathophysiology between the two diseases.
Dissection of the Inflammatory Bowel Disease Transcriptome Using Genome-Wide cDNA Microarrays (2005)
Christine M. Costello, Nancy Mah, Robert Häsler, Philip Rosenstiel, Georg H. Waetzig, Andreas Hahn, ...
Background The differential pathophysiologic mechanisms that trigger and maintain the two forms of inflammatory bowel disease (IBD), Crohn disease (CD), and ulcerative colitis (UC) are only partially...
Büssow, Konrad, Scheich, Christoph, Sievert, Volker, Harttig, Ulrich, Schultz, Jörg, Simon, Bernd, ...
Abstract Background The availability of suitable recombinant protein is still a major bottleneck in protein structure analysis. The Protein Structure Factory, part of the international structural...
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...
Subnanoliter enzymatic assays on microarrays (2005)
Angenendt, Philipp, Lehrach, Hans, Kreutzberger, Jürgen, Glökler, Jörn
Many areas of research today are based on enzymatic assays most of which are still performed as enzyme-linked immunosorbent assays in microtiter plates. The demand for highly parallel screening of...
Bürkle, Lukas, Meyer, Svenja, Dortay, Hakan, Lehrach, Hans, Heyl, Alexander
In the postgenomic era many experiments rely on the availability of transcript sequence for cloning. As these clones usually originate from cDNA libraries, the quality of these libraries is crucial....
Büssow, Konrad, Scheich, Christoph, Sievert, Volker, Harttig, Ulrich, Schultz, Jörg, Simon, Bernd, ...
Background The availability of suitable recombinant protein is still a major bottleneck in protein structure analysis. The Protein Structure Factory, part of the international structural genomics...
Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays (2005)
Costello, Christine M., Mah, Nancy, Häsler, Robert, Rosenstiel, Philip, Waetzig, Georg H., Hahn, Andreas, ...
Background The differential pathophysiologic mechanisms that trigger and maintain the two forms of inflammatory bowel disease (IBD), Crohn disease (CD), and ulcerative colitis (UC) are only partially...
Feilner, Tanja, Hultschig, Claus, Lee, Justin, Meyer, Svenja, Immink, Richard G. H., Koenig, Andrea, ...
Mitogen-activated protein kinase (MAPK) cascades are universal and highly conserved signal transduction modules in eucaryotes, including plants. These protein phosphorylation cascades link...
Gade, Dörte, Theiss, Dorothea, Lange, Daniela, Mirgorodskaya, Ekaterina, Lombardot, Thierry, Glöckner, Frank Oliver, ...
The marine bacterium Rhodopirellula baltica, a member of the phylum Planctomycetes, has distinct morphological properties and contributes to remineralization of biomass in the natural environment. On...
High heterogeneity within the ribosomal proteins of the Arabidopsis thaliana 80S ribosome (2005)
Giavalisco, Patrick, Wilson, Daniel, Kreitler, Thomas, Lehrach, Hans, Klose, Joachim, Gobom, Johan, ...
Proteomic studies have addressed the composition of plant chloroplast ribosomes and 70S ribosomes from the unicellular organism Chlamydomonas reinhardtii But comprehensive characterization of...
Giavalisco, Patrick, Nordhoff, Eckhard, Kreitler, Thomas, Klöppel, Klaus-Dieter, Lehrach, Hans, Klose, Joachim, ...
In the present study we show results of a large-scale proteome analysis of the recently sequenced plant Arabidopsis thaliana. On the basis of a previously published sequential protein extraction...