Queiroz, Rafael, Benz, Corinna, Fellenberg, Kurt, Hoheisel, Jörg D, Clayton, Christine
Abstract Background Trypanosome gene expression is regulated almost exclusively at the post-transcriptional level, with mRNA degradation playing a decisive role. When trypanosomes are transferred...
Oncoproteomic profiling with antibody microarrays (2009)
Alhamdani, Mohamed SS, Schröder, Christoph, Hoheisel, Jörg D
Abstract The incidence of cancer and its associated mortality are increasing globally, indicating an urgent need to develop even more effective and sensitive sets of biomarkers that could help in...
Riazalhosseini, Yasser, Hoheisel, Jörg D
Abstract It is possible to miss potential DNA methylation markers of tumorigenesis because of the initial filtering of profiling results on the basis of inappropriate controls.
Pullat, Janne, Fleischer, Robert, Becker, Nikolaus, Beier, Markus, Metspalu, Andres, Hoheisel, Jörg D
Abstract Background Genetic variants in immune regulator genes have been associated with numerous diseases, including allergies and cancer. Increasing evidence suggests a substantially elevated...
Taussig, Michael J., Stoevesandt, Oda, Bradbury, Andrew R., Cahill, Dolores, Cambillau, Christian, ...
ProteomeBinders is a new European consortium aiming to establish a comprehensive resource of well-characterized affinity reagents, including but not limited to antibodies, for analysis of the human...
Systematic interpretation of microarray data using experiment annotations (2006)
Fellenberg, Kurt, Busold, Christian H, Witt, Olaf, Bauer, Andrea, Beckmann, Boris, Hauser, Nicole C, ...
Abstract Background Up to now, microarray data are mostly assessed in context with only one or few parameters characterizing the experimental conditions under study. More explicit experiment...
Angenendt, Philipp, Kreutzberger, Jürgen, Glökler, Jörn, Hoheisel, Jörg D.
Due to the success of DNA microarrays and the growing numbers of available protein expression clones, protein microarrays have become more and more popular for the high throughput screening of...
Hauser, Nicole C., Martinez, Rafael, Jacob, Anette, Rupp, Steffen, Hoheisel, Jörg D., Matysiak, Stefan
L-DNA is the perfect mirror-image form of the naturally occurring d-conformation of DNA. Therefore, L-DNA duplexes have the same physical characteristics in terms of solubility, duplex stability and...
Hauser, Nicole C., Martinez, Rafael, Jacob, Anette, Rupp, Steffen, Hoheisel, Jörg D., Matysiak, Stefan
L-DNA is the perfect mirror-image form of the naturally occurring d-conformation of DNA. Therefore, L-DNA duplexes have the same physical characteristics in terms of solubility, duplex stability and...
Hauser, Nicole C., Martinez, Rafael, Jacob, Anette, Rupp, Steffen, Hoheisel, Jörg D., Matysiak, Stefan
L-DNA is the perfect mirror-image form of the naturally occurring d-conformation of DNA. Therefore, L-DNA duplexes have the same physical characteristics in terms of solubility, duplex stability and...
Hauser, Nicole C., Martinez, Rafael, Jacob, Anette, Rupp, Steffen, Hoheisel, Jörg D., Matysiak, Stefan
L-DNA is the perfect mirror-image form of the naturally occurring d-conformation of DNA. Therefore, L-DNA duplexes have the same physical characteristics in terms of solubility, duplex stability and...
Hauser, Nicole C., Martinez, Rafael, Jacob, Anette, Rupp, Steffen, Hoheisel, Jörg D., Matysiak, Stefan
L-DNA is the perfect mirror-image form of the naturally occurring d-conformation of DNA. Therefore, L-DNA duplexes have the same physical characteristics in terms of solubility, duplex stability and...
Hauser, Nicole C., Martinez, Rafael, Jacob, Anette, Rupp, Steffen, Hoheisel, Jörg D., Matysiak, Stefan
L-DNA is the perfect mirror-image form of the naturally occurring d-conformation of DNA. Therefore, L-DNA duplexes have the same physical characteristics in terms of solubility, duplex stability and...
Hauser, Nicole C., Martinez, Rafael, Jacob, Anette, Rupp, Steffen, Hoheisel, Jörg D., Matysiak, Stefan
L-DNA is the perfect mirror-image form of the naturally occurring d-conformation of DNA. Therefore, L-DNA duplexes have the same physical characteristics in terms of solubility, duplex stability and...
Christian H. Busold, Stefan Winter, Nicole Hauser, Andrea Bauer, Jörg D. Hoheisel, Kurt Fellenberg
Motivation: The functional interpretation of microarray datasets still rep-resents a time consuming and challenging task. Up to now functional cate-gories being relevant for one or more experimental...
Busold, Christian H., Winter, Stefan, Hauser, Nicole, Bauer, Andrea, Dippon, Jürgen, Hoheisel, Jörg D., ...
Motivation: The functional interpretation of microarray datasets still represents a time-consuming and challenging task. Up to now functional categories that are relevant for one or more experimental...
Mund, Cora, Beier, Verena, Bewerunge, Peter, Dahms, Michael, Lyko, Frank, Hoheisel, Jörg D.
Aberrant DNA methylation at CpG dinucleotides can result in epigenetic silencing of tumour suppressor genes and represents one of the earliest events in tumourigenesis. To date, however,...
Busold, Christian H., Winter, Stefan, Hauser, Nicole, Bauer, Andrea, Dippon, Jürgen, Hoheisel, Jörg D., ...
Motivation: The functional interpretation of microarray datasets still represents a time consuming and challenging task. Up to now functional categories being relevant for one or more experimental...
Use of Complex DNA and Antibody Microarrays as Tools in Functional Analyses (2003)
Andrea Bauer, Boris Beckmann, Christian Busold, Ole Brandt, Wlad Kusnezow, Janne Pullat, ...
While the deciphering of basic sequence information on a genomic scale is yielding complete genomic sequences in ever-shorter intervals, experimental procedures for elucidating the cellular effects...
PNA microarrays for hybridisation of unlabelled DNA samples (2003)
Brandt, Ole, Feldner, Julia, Stephan, Achim, Schröder, Markus, Schnölzer, Martina, Arlinghaus, Heinrich F., ...
Several strategies have been developed for the production of peptide nucleic acid (PNA) microarrays by parallel probe synthesis and selective coupling of full‐length molecules. Such microarrays...
What's in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence (2003)
Mannhaupt, Gertrud, Montrone, Corinna, Haase, Dirk, Mewes, H. Werner, Aign, Verena, Hoheisel, Jörg D., ...
The German Neurospora Genome Project has assembled sequences from ordered cosmid and BAC clones of linkage groups II and V of the genome of Neurospora crassa in 13 and 12 contigs, respectively....
Scheideler,Marcel, Schlaich,Nikolaus L., Fellenberg,Kurt, Beissbarth,Tim, Hauser,Nicole C., Vingron,Martin, ...
Plants respond to pathogen attack by deploying several defense reactions. Some rely on the activation of preformed components, whereas others depend on changes in transcriptional activity. Using cDNA...
Fellenberg,Kurt, Hauser,Nicole C., Brors,Benedikt, Hoheisel,Jörg D., Vingron,Martin
Motivation: Microarray technology provides access to expression levels of thousands of genes at once, producing large amounts of data. These datasets are valuable only if they are annotated by...
Fellenberg, Kurt, Hauser, Nicole C., Brors, Benedikt, Hoheisel, Jörg D., Vingron, Martin
Motivation: Microarray technology provides access to expression levels of thousands of genes at once, producing large amounts of data. These datasets are valuable only if they are annotated by...
Scheideler, Marcel, Schlaich, Nikolaus L., Fellenberg, Kurt, Beissbarth, Tim, Hauser, Nicole C., Vingron, Martin, ...
Plants respond to pathogen attack by deploying several defense reactions. Some rely on the activation of preformed components, whereas others depend on changes in transcriptional activity. Using cDNA...
Manufacturing DNA microarrays from unpurified PCR products (2002)
Diehl, Frank, Beckmann, Boris, Kellner, Nadine, Hauser, Nicole C., Diehl, Susanne, Hoheisel, Jörg D.
For the production of DNA microarrays from PCR products, purification of the the DNA fragments prior to spotting is a major expense in cost and time. Also, a considerable amount of material is lost...
Whole Genome Analysis of a Wine Yeast Strain (2001)
Nicole C. Hauser, Kurt Fellenberg, Rosario Gil, Sonja Bastuck, Jörg D. Hoheisel
Saccharomyces cerevisiae strains frequently exhibit rather specific phenotypic features needed for adaptation to a special environment. Wine yeast strains are able to ferment musts, for example,...
Directed Gap Closure in Large-Scale Sequencing Projects (2001)
Frohme, Marcus, Camargo, Anamaria A., Czink, Claudia, Matsukuma, Adriana Y., Simpson, Andrew J.G., Hoheisel, Jörg D., ...
Manufacturing DNA microarrays of high spot homogeneity and reduced background signal (2001)
Diehl, Frank, Grahlmann, Susanne, Beier, Markus, Hoheisel, Jörg D.
Analyses on DNA microarrays depend considerably on spot quality and a low background signal of the glass support. By using betaine as an additive to a spotting solution made of saline sodium citrate,...
Beier, Markus, Hoheisel, Jörg D.
For DNA chip analyses, oligonucleotide quality has immense consequences for accuracy, sensitivity and dynamic range. The quality of chips produced by photolithographic in situ synthesis depends...
Mapping analysis of the Xylella fastidiosa genome (2000)
Frohme, Marcus, Camargo, Anamaria A., Heber, Steffen, Czink, Claudia, Simpson, Andrew J. D., Hoheisel, Jörg D., ...
A cosmid library was made of the 2.7 Mb genome of the Gram-negative plant pathogenic bacterium Xylella fastidiosa and analysed by hybridisation mapping. Clones taken from the library as well as...
Scholler, Patrik, Karger, Achim E., Meier-Ewert, Sebastian, Lehrach, Hans, Delius, Hajo, Hoheisel, Jörg D.
To test the effectiveness of ordering shotgun DNA- templates prior to sequence analysis, the 450 kb left arm of yeast chromosome XII was randomly subcloned into a phagemid vector. Clones were ordered...
Control of partial digestion combining the enzymes dam methylase and MboI (1989)
Hoheisel, Jörg D., Nizetic, Dean, Lehrach, Hans
A method is described which allows the preparation of reproducible partial digests without previous establishment of the incubation conditions. It is based on a combined application of dam methylase...
Manufacturing DNA microarrays of high spot homogeneity and reduced background signal
Diehl, Frank, Grahlmann, Susanne, Beier, Markus, Hoheisel, Jörg D.
Analyses on DNA microarrays depend considerably on spot quality and a low background signal of the glass support. By using betaine as an additive to a spotting solution made of saline sodium citrate,...
Correspondence analysis applied to microarray data
Fellenberg, Kurt, Hauser, Nicole C., Brors, Benedikt, Neutzner, Albert, Hoheisel, Jörg D., Vingron, Martin
Correspondence analysis is an explorative computational method for the study of associations between variables. Much like principal component analysis, it displays a low-dimensional projection of the...
Global Analysis of the General Stress Response of Bacillus subtilis
Petersohn, Anja, Brigulla, Matthias, Haas, Stefan, Hoheisel, Jörg D., Völker, Uwe, Hecker, Michael
Gene arrays containing all currently known open reading frames of Bacillus subtilis were used to examine the general stress response of Bacillus. By proteomics, transcriptional analysis, transposon...
Beier, Markus, Hoheisel, Jörg D.
For DNA chip analyses, oligonucleotide quality has immense consequences for accuracy, sensitivity and dynamic range. The quality of chips produced by photolithographic in situ synthesis depends...
Mapping analysis of the Xylella fastidiosa genome
Frohme, Marcus, Camargo, Anamaria A., Heber, Steffen, Czink, Claudia, Simpson, Andrew J. D., Hoheisel, Jörg D., ...
A cosmid library was made of the 2.7 Mb genome of the Gram-negative plant pathogenic bacterium Xylella fastidiosa and analysed by hybridisation mapping. Clones taken from the library as well as...
Manufacturing DNA microarrays from unpurified PCR products
Diehl, Frank, Beckmann, Boris, Kellner, Nadine, Hauser, Nicole C., Diehl, Susanne, Hoheisel, Jörg D.
For the production of DNA microarrays from PCR products, purification of the the DNA fragments prior to spotting is a major expense in cost and time. Also, a considerable amount of material is lost...
What’s in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence
Mannhaupt, Gertrud, Montrone, Corinna, Haase, Dirk, Mewes, H. Werner, Aign, Verena, Hoheisel, Jörg D., ...
The German Neurospora Genome Project has assembled sequences from ordered cosmid and BAC clones of linkage groups II and V of the genome of Neurospora crassa in 13 and 12 contigs, respectively....
PNA microarrays for hybridisation of unlabelled DNA samples
Brandt, Ole, Feldner, Julia, Stephan, Achim, Schröder, Markus, Schnölzer, Martina, Arlinghaus, Heinrich F., ...
Several strategies have been developed for the production of peptide nucleic acid (PNA) microarrays by parallel probe synthesis and selective coupling of full-length molecules. Such microarrays were...
Andersson, Björn, Åslund, Lena, Tammi, Martti, Tran, Anh-Nhi, Hoheisel, Jörg D., Pettersson, Ulf
We have initiated large-scale sequencing of the third smallest chromosome of the CL Brener strain of Trypanosoma cruzi and we report here the complete sequence of a contig consisting of three...
Directed Gap Closure in Large-Scale Sequencing Projects
Frohme, Marcus, Camargo, Anamaria A., Czink, Claudia, Matsukuma, Adriana Y., Simpson, Andrew J.G., Hoheisel, Jörg D., ...
A problem in many sequencing projects is the final closure of gaps left in the clone libraries, which serve as templates for sequencing, because of uncloned or unclonable genomic areas. By use of the...
Mund, Cora, Beier, Verena, Bewerunge, Peter, Dahms, Michael, Lyko, Frank, Hoheisel, Jörg D.
Aberrant DNA methylation at CpG dinucleotides can result in epigenetic silencing of tumour suppressor genes and represents one of the earliest events in tumourigenesis. To date, however,...
Marmé, Nicole, Friedrich, Achim, Müller, Matthias, Nolte, Oliver, Wolfrum, Jürgen, Hoheisel, Jörg D., ...
We demonstrate the specific identification of single nucleotide polymorphism (SNP) responsible for rifampicin resistance of Mycobacterium tuberculosis applying fluorescently labeled DNA-hairpin...
Functional Genomics of Stress Response in Pseudomonas putida KT2440
Reva, Oleg N., Weinel, Christian, Weinel, Miryam, Böhm, Kerstin, Stjepandic, Diana, Hoheisel, Jörg D., ...
The metabolically versatile soil bacterium Pseudomonas putida has to cope with numerous abiotic stresses in its habitats. The stress responses of P. putida KT2440 to 4°C, pH 4.5, 0.8 M urea, and 45...
Hauser, Nicole C., Martinez, Rafael, Jacob, Anette, Rupp, Steffen, Hoheisel, Jörg D., Matysiak, Stefan
L-DNA is the perfect mirror-image form of the naturally occurring d-conformation of DNA. Therefore, L-DNA duplexes have the same physical characteristics in terms of solubility, duplex stability and...
Manufacturing DNA microarrays of high spot homogeneity and reduced background signal
Diehl, Frank, Grahlmann, Susanne, Beier, Markus, Hoheisel, Jörg D.
Analyses on DNA microarrays depend considerably on spot quality and a low background signal of the glass support. By using betaine as an additive to a spotting solution made of saline sodium citrate,...
Correspondence analysis applied to microarray data
Fellenberg, Kurt, Hauser, Nicole C., Brors, Benedikt, Neutzner, Albert, Hoheisel, Jörg D., Vingron, Martin
Correspondence analysis is an explorative computational method for the study of associations between variables. Much like principal component analysis, it displays a low-dimensional projection of the...
Global Analysis of the General Stress Response of Bacillus subtilis
Petersohn, Anja, Brigulla, Matthias, Haas, Stefan, Hoheisel, Jörg D., Völker, Uwe, Hecker, Michael
Gene arrays containing all currently known open reading frames of Bacillus subtilis were used to examine the general stress response of Bacillus. By proteomics, transcriptional analysis, transposon...
Beier, Markus, Hoheisel, Jörg D.
For DNA chip analyses, oligonucleotide quality has immense consequences for accuracy, sensitivity and dynamic range. The quality of chips produced by photolithographic in situ synthesis depends...
Mapping analysis of the Xylella fastidiosa genome
Frohme, Marcus, Camargo, Anamaria A., Heber, Steffen, Czink, Claudia, Simpson, Andrew J. D., Hoheisel, Jörg D., ...
A cosmid library was made of the 2.7 Mb genome of the Gram-negative plant pathogenic bacterium Xylella fastidiosa and analysed by hybridisation mapping. Clones taken from the library as well as...
Manufacturing DNA microarrays from unpurified PCR products
Diehl, Frank, Beckmann, Boris, Kellner, Nadine, Hauser, Nicole C., Diehl, Susanne, Hoheisel, Jörg D.
For the production of DNA microarrays from PCR products, purification of the the DNA fragments prior to spotting is a major expense in cost and time. Also, a considerable amount of material is lost...
What’s in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence
Mannhaupt, Gertrud, Montrone, Corinna, Haase, Dirk, Mewes, H. Werner, Aign, Verena, Hoheisel, Jörg D., ...
The German Neurospora Genome Project has assembled sequences from ordered cosmid and BAC clones of linkage groups II and V of the genome of Neurospora crassa in 13 and 12 contigs, respectively....
PNA microarrays for hybridisation of unlabelled DNA samples
Brandt, Ole, Feldner, Julia, Stephan, Achim, Schröder, Markus, Schnölzer, Martina, Arlinghaus, Heinrich F., ...
Several strategies have been developed for the production of peptide nucleic acid (PNA) microarrays by parallel probe synthesis and selective coupling of full-length molecules. Such microarrays were...
Andersson, Björn, Åslund, Lena, Tammi, Martti, Tran, Anh-Nhi, Hoheisel, Jörg D., Pettersson, Ulf
We have initiated large-scale sequencing of the third smallest chromosome of the CL Brener strain of Trypanosoma cruzi and we report here the complete sequence of a contig consisting of three...
Directed Gap Closure in Large-Scale Sequencing Projects
Frohme, Marcus, Camargo, Anamaria A., Czink, Claudia, Matsukuma, Adriana Y., Simpson, Andrew J.G., Hoheisel, Jörg D., ...
A problem in many sequencing projects is the final closure of gaps left in the clone libraries, which serve as templates for sequencing, because of uncloned or unclonable genomic areas. By use of the...
Mund, Cora, Beier, Verena, Bewerunge, Peter, Dahms, Michael, Lyko, Frank, Hoheisel, Jörg D.
Aberrant DNA methylation at CpG dinucleotides can result in epigenetic silencing of tumour suppressor genes and represents one of the earliest events in tumourigenesis. To date, however,...
Functional Genomics of Stress Response in Pseudomonas putida KT2440
Reva, Oleg N., Weinel, Christian, Weinel, Miryam, Böhm, Kerstin, Stjepandic, Diana, Hoheisel, Jörg D., ...
The metabolically versatile soil bacterium Pseudomonas putida has to cope with numerous abiotic stresses in its habitats. The stress responses of P. putida KT2440 to 4°C, pH 4.5, 0.8 M urea, and 45...
Marmé, Nicole, Friedrich, Achim, Müller, Matthias, Nolte, Oliver, Wolfrum, Jürgen, Hoheisel, Jörg D., ...
We demonstrate the specific identification of single nucleotide polymorphism (SNP) responsible for rifampicin resistance of Mycobacterium tuberculosis applying fluorescently labeled DNA-hairpin...
Hauser, Nicole C., Martinez, Rafael, Jacob, Anette, Rupp, Steffen, Hoheisel, Jörg D., Matysiak, Stefan
L-DNA is the perfect mirror-image form of the naturally occurring d-conformation of DNA. Therefore, L-DNA duplexes have the same physical characteristics in terms of solubility, duplex stability and...
Systematic interpretation of microarray data using experiment annotations
Fellenberg, Kurt, Busold, Christian H, Witt, Olaf, Bauer, Andrea, Beckmann, Boris, Hauser, Nicole C, ...
Jesnowski, R, Zubakov, Dmitri, Faissner, Ralf, Ringel, Jörg, Hoheisel, Jörg D, Lösel, Ralf, ...
Pancreatic carcinoma has an extremely bad prognosis due to lack of early diagnostic markers and lack of effective therapeutic strategies. Recently, we have established an in vitro model...
Pullat, Janne, Fleischer, Robert, Becker, Nikolaus, Beier, Markus, Metspalu, Andres, Hoheisel, Jörg D
Genotypic resistance testing in HIV by arrayed primer extension
Schanné, Michaela, Bodem, Jochen, Gerhold-Ay, Aslihan, Jacob, Anette, Fellenberg, Kurt, Kräusslich, Hans-Georg, ...
The analysis of mutations that are associated with the occurrence of drug resistance is important for monitoring the antiretroviral therapy of patients infected with human immunodeficiency virus...
Whole Genome Analysis of a Wine Yeast Strain
Hauser, Nicole C., Fellenberg, Kurt, Gil, Rosario, Bastuck, Sonja, Hoheisel, Jörg D., Pérez-Ortín, José E.
Saccharomyces cerevisiae strains frequently exhibit rather specific phenotypic features needed for adaptation to a special environment. Wine yeast strains are able to ferment musts, for example,...
Use of Complex DNA and Antibody Microarrays as Tools in Functional Analyses
Bauer, Andrea, Beckmann, Boris, Busold, Christian, Brandt, Ole, Kusnezow, Wlad, Pullat, Janne, ...
While the deciphering of basic sequence information on a genomic scale is yielding complete genomic sequences in ever-shorter intervals, experimental procedures for elucidating the cellular effects...
Riazalhosseini, Yasser, Hoheisel, Jörg D
It is possible to miss potential DNA methylation markers of tumorigenesis because profiling results are initially filtered on the basis of inappropriate controls.
Oncoproteomic profiling with antibody microarrays
Alhamdani, Mohamed SS, Schröder, Christoph, Hoheisel, Jörg D
The incidence of cancer and its associated mortality are increasing globally, indicating an urgent need to develop even more effective and sensitive sets of biomarkers that could help in early...