Annotation-Driven Class Discovery User’s Guide to the Bioconductor package adSplit (2009)
Max Planck, Claudio Lottaz, Joern Toedling, Rainer Spang
Nr. 2005/02 This is the vignette of the Bioconductor compliant packege adSplit. We describe our implementation of annotation- driven clustering for microarray gene expression profiling studies.
BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm322 (2008)
Gene Expression, Claudio Lottaz, Joern Toedling, Rainer Spang
Annotation-based distance measures for patient subgroup discovery in clinical microarray studies
BIOINFORMATICS APPLICATIONS NOTE Gene expression MACAT—microarray chromosome analysis tool (2008)
Joern Toedling, Sebastian Schmeier, Matthias Heinig, Benjamin Georgi, Stefan Roepcke
Summary: By linking differential gene expression to the chromosomal localization of genes, one can investigate microarray data for characteristic patterns of expression phenomena involving sizeable...
Claudio Lottaz, Joern Toedling, Rainer Spang
Motivation: Clustering algorithms are widely used in the analysis of microarray data. In clinical studies, they are often applied to find groups of co-regulated genes. Clustering, however, can also...
Combinatorial effects of four histone modifications in transcription and differentiation (2008)
Fischer, Jenny J., Toedling, Joern, Krueger, Tammo, Schueler, Markus, Huber, Wolfgang, Sperling, Silke
Nucleosomes are involved in DNA compaction and transcriptional regulation. Yet it is unclear whether histone modification marks are primary or secondary to transcription and whether they interact to...
Ringo – an R/Bioconductor package for analyzing ChIP-chip readouts (2007)
Toedling, Joern, Skylar, Oleg, Krueger, Tammo, Fischer, Jenny J, Sperling, Silke, Huber, Wolfgang
No abstract available.
Lottaz, Claudio, Toedling, Joern, Spang, Rainer
Motivation: Clustering algorithms are widely used in the analysis of microarray data. In clinical studies, they are often applied to find groups of co-regulated genes. Clustering, however, can also...
Ringo – an R/Bioconductor package for analyzing ChIP-chip readouts (2007)
Toedling, Joern, Sklyar, Oleg, Huber, Wolfgang
Abstract Background Chromatin immunoprecipitation combined with DNA microarrays ( ChIP-chip ) is a high-throughput assay for DNA-protein-binding or post-translational chromatin/histone modifications....
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...
Ringo – an R/Bioconductor package for analyzing ChIP-chip readouts (2007)
Toedling, Joern, Skylar, Oleg, Krueger, Tammo, Fischer, Jenny J., Sperling, Silke, Huber, Wolfgang
Toedling, Joern, Rhein, Peter, Ratei, Richard, Karawajew, Leonid, Spang, Rainer
Abstract Background Identification of minor cell populations, e.g. leukemic blasts within blood samples, has become increasingly important in therapeutic disease monitoring. Modern flow cytometers...
BIOINFORMATICS ORIGINAL PAPER (2006)
Gene Expression, Wolfgang Huber, Joern Toedling, Lars M. Steinmetz
Transcript mapping with high-density oligonucleotide tiling arrays Vol. 22 no. 16 2006, pages 1963–1970 doi:10.1093/bioinformatics/btl289
BMC Bioinformatics BioMed Central (2006)
Joern Toedling, Peter Rhein, Richard Ratei, Leonid Karawajew, Rainer Spang
2Research article Automated in-silico detection of cell populations in flow cytometry readouts and its application to leukemia disease monitoring
Transcript mapping with high-density oligonucleotide tiling arrays (2006)
Huber, Wolfgang, Toedling, Joern, Steinmetz, Lars M.
Motivation: High-density DNA tiling microarrays are a powerful tool for the characterization of complete transcriptomes. The two major analytical challenges are the segmentation of the hybridization...
MACAT--microarray chromosome analysis tool (2005)
Toedling, Joern, Schmeier, Sebastian, Heinig, Matthias, Georgi, Benjamin, Roepcke, Stefan
By linking differential gene expression to the chromosomal localization of genes, one can investigate microarray data for characteristic patterns of expression phenomena involving sizeable parts of...
MACAT—microarray chromosome analysis tool (2005)
Toedling, Joern, Schmeier, Sebastian, Heinig, Matthias, Georgi, Benjamin, Roepcke, Stefan
By linking differential gene expression to the chromosomal localization of genes, one can investigate microarray data for characteristic patterns of expression phenomena involving sizeable parts of...
MACAT--microarray chromosome analysis tool (2005)
Toedling, Joern, Schmeier, Sebastian, Heinig, Matthias, Georgi, Benjamin, Roepcke, Stefan
Summary: By linking differential gene expression to the chromosomal localization of genes, one can investigate microarray data for characteristic patterns of expression phenomena involving sizeable...
MACAT - MicroArray chromosome analysis tool (2004)
Toedling, Joern, Schmeier, Sebastian, Heinig, Matthias, Georgi, Benjamin, Roepcke, Stefan
Summary: By linking differential gene expression to the chromosomal localization of genes, one can investigate microarray data for characteristic patterns of expression phenomena involving sizeable...
MACAT - MicroArray chromosome analysis tool (2004)
Toedling, Joern, Schmeier, Sebastian, Heinig, Matthias, Georgi, Benjamin, Roepcke, Stefan
Summary: By linking differential gene expression to the chromosomal localization of genes, one can investigate microarray data for characteristic patterns of expression phenomena involving sizeable...
A high-resolution map of transcription in the yeast genome
David, Lior, Huber, Wolfgang, Granovskaia, Marina, Toedling, Joern, Palm, Curtis J., Bofkin, Lee, ...
There is abundant transcription from eukaryotic genomes unaccounted for by protein coding genes. A high-resolution genome-wide survey of transcription in a well annotated genome will help relate...
A high-resolution map of transcription in the yeast genome
David, Lior, Huber, Wolfgang, Granovskaia, Marina, Toedling, Joern, Palm, Curtis J., Bofkin, Lee, ...
There is abundant transcription from eukaryotic genomes unaccounted for by protein coding genes. A high-resolution genome-wide survey of transcription in a well annotated genome will help relate...