Array-based genotyping in S.cerevisiae using semi-supervised clustering (2009)
Bourgon, Richard, Mancera, Eugenio, Brozzi, Alessandro, Steinmetz, Lars M., Huber, Wolfgang
Motivation: Microarrays provide an accurate and cost-effective method for genotyping large numbers of individuals at high resolution. The resulting data permit the identification of loci at which...
arrayQualityMetrics--a bioconductor package for quality assessment of microarray data (2009)
Kauffmann, Audrey, Gentleman, Robert, Huber, Wolfgang
Summary:: The assessment of data quality is a major concern in microarray analysis. arrayQualityMetrics is a Bioconductor package that provides a report with diagnostic plots for one or two colour...
Importing ArrayExpress datasets into R/Bioconductor (2009)
Kauffmann, Audrey, Rayner, Tim F., Parkinson, Helen, Kapushesky, Misha, Lukk, Margus, Brazma, Alvis, ...
Summary:ArrayExpress is one of the largest public repositories of microarray datasets. R/Bioconductor provides a comprehensive suite of microarray analysis and integrative bioinformatics software....
Umgelter, Andreas, Wagner, Katrin, Reindl, Wolfgang, Nurtsch, Nils, Huber, Wolfgang, Schmid, Roland M
Abstract Background Patients with advanced cirrhosis of the liver typically display circulatory disturbance. Haemodynamic management may be critical for avoiding and treating functional renal failure...
Estimating node degree in bait-prey graphs (2008)
Denise Scholtens, Tony Chiang, Wolfgang Huber
Motivation: Proteins work together to drive biological processes in cellular machines. Summarizing global and local properties of the set of protein interactions, the interactome, is necessary for...
Stephan Steigele, Wolfgang Huber, Claudia Fried, Peter F. Stadler, Kay Nieselt
Background: Non-coding RNAs (ncRNAs) are in emerging focus for both computational analysis and experimental research resulting in a growing number of novel, non-protein coding transcripts with often...
Analysis (A. Poustka) DKFZ Heidelberg Acknowledgements (2008)
Wolfgang Huber, Anja Von Heydebreck, Günther Sawitzki, Holger Sültmann, Klaus Steiner, Markus Vogt, ...
First analysis steps o quality control and optimization o calibration and error modeling o data transformations
News The Newsletter of the R Project Volume 6/5, December 2006 Editorial (2008)
Wolfgang Huber, Paul Murrell, Paul Murrell
Welcome to the fifth and final issue of R News for 2006, our third special issue of the year, with a focus on the use of R in Bioinformatics. Many thanks to guest editor Wolfgang Huber for doing a...
News The Newsletter of the R Project Volume 6/5, December 2006 Editorial (2008)
Wolfgang Huber, Paul Murrell, Paul Murrell
Welcome to the fifth and final issue of R News for 2006, our third special issue of the year, with a focus on the use of R in Bioinformatics. Many thanks to guest editor Wolfgang Huber for doing a...
Umgelter, Andreas, Reindl, Wolfgang, Wagner, Katrin S, Franzen, Michael, Stock, Konrad, Schmid, Roland M, ...
Abstract Introduction Circulatory dysfunction in cirrhotic patients may cause a specific kind of functional renal failure termed hepato-renal syndrome (HRS). It contributes to the high incidence of...
Mayr, Juliane, Haselhorst, Thomas Erwin, Langereis, Martijn A., Dyason, Jeffrey Clifford, Huber, Wolfgang, Frey, Barbara, ...
Yes
Mayr, Juliane, Haselhorst, Thomas Erwin, Langereis, Martijn A., Dyason, Jeffrey Clifford, Huber, Wolfgang, Frey, Barbara, ...
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...
Mayr, Juliane, Haselhorst, Thomas Erwin, Langereis, Martijn A., Dyason, Jeffrey Clifford, Huber, Wolfgang, Frey, Barbara, ...
Estimating node degree in bait-prey graphs (2008)
Scholtens, Denise, Chiang, Tony, Huber, Wolfgang, Gentleman, Robert
Motivation: Proteins work together to drive biological processes in cellular machines. Summarizing global and local properties of the set of protein interactions, the interactome, is necessary for...
Model-based variance-stabilizing transformation for Illumina microarray data (2008)
Lin, Simon M., Du, Pan, Huber, Wolfgang, Kibbe, Warren A.
Variance stabilization is a step in the preprocessing of microarray data that can greatly benefit the performance of subsequent statistical modeling and inference. Due to the often limited number of...
Chiang, Tony, Li, Nianhua, Orchard, Sandra, Kerrien, Samuel, Hermjakob, Henning, Gentleman, Robert, ...
Motivation: The IntAct repository is one of the largest and most widely used databases for the curation and storage of molecular interaction data. These datasets need to be analyzed by computational...
Casneuf, Tineke, Van De Peer, Yves, Huber, Wolfgang
Abstract Background Microarray co-expression signatures are an important tool for studying gene function and relations between genes. In addition to genuine biological co-expression, correlated...
A Fast Monte Carlo Algorithm for Non-Equilibrium Systems (2007)
Heinz-Peter Breuer, Wolfgang Huber, Francesco Petruccione
A fast method for the Monte Carlo solution of the balance equations which arise in non--equilibrium thermodynamics is suggested. It is applicable to chemical kinetics, reaction--diffusion processes,...
Heinz--Peter Breuer, Wolfgang Huber and Francesco Petruccione (2007)
Wolfgang Huber, Francesco Petruccione
Extensive numerical simulation of a reaction--diffusion--system reveal an unusual system size dependence of the fluctuation magnitude. If \Omega denotes the system size parameter, e. g. particle...
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.
Making the most of high-throughput protein-interaction data (2007)
Gentleman, Robert, Huber, Wolfgang
Abstract We review the estimation of coverage and error rate in high-throughput protein-protein interaction datasets and argue that reports of the low quality of such data are to a substantial extent...
Graphs in molecular biology (2007)
Huber, Wolfgang, Carey, Vincent J, Long, Li, Falcon, Seth, Gentleman, Robert
Abstract Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and...
Coverage and error models of protein-protein interaction data by directed graph analysis (2007)
Chiang, Tony, Scholtens, Denise, Sarkar, Deepayan, Gentleman, Robert, Huber, Wolfgang
Abstract Using a directed graph model for bait to prey systems and a multinomial error model, we assessed the error statistics in all published large-scale datasets for Saccharomyces cerevisiae and...
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....
Steigele, Stephan, Huber, Wolfgang, Stocsits, Claudia, Stadler, Peter F, Nieselt, Kay
Abstract Background Non-coding RNAs (ncRNAs) are an emerging focus for both computational analysis and experimental research, resulting in a growing number of novel, non-protein coding transcripts...
Girardot, Charles, Sklyar, Oleg, Grosz, Sophie, Huber, Wolfgang, Furlong, Eileen E. M.
Motivation: CoCo, ChIP-on-Chip online, is an open-source web application that supports the annotation and curation of regulatory regions and associated target genes discovered in ChIP-on-chip...
Is supra-ventricular arrhythmia a reason for the bad performance of the FlowTrac device? (2007)
Umgelter, Andreas, Reindl, Wolfgang, Schmid, Roland M, Huber, Wolfgang
No abstract available.
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
Girardot, Charles, Sklyar, Oleg, Grosz, Sophie, Huber, Wolfgang, Furlong, Eileen E. M.
Motivation: CoCo, ChIP-On-Chip Online, is an open-source web application that supports the annotation and curation of regulatory regions and associated target genes discovered in ChIP-on-chip...
Hahne, Florian, Arlt, Dorit, Sauermann, Mamatha, Majety, Meher, Poustka, Annemarie, Wiemann, Stefan, ...
Abstract Highthroughput cell-based assays with flow cytometric readout provide a powerful technique for identifying components of biologic pathways and their interactors. Interpretation of these...
Analysis of cell-based RNAi screens (2006)
Boutros, Michael, Brás, Lígia P, Huber, Wolfgang
Abstract RNA interference (RNAi) screening is a powerful technology for functional characterization of biological pathways. Interpretation of RNAi screens requires computational and statistical...
Visualizing Genomic Data (2006)
Gentleman, Robert, Hahne, Florian, Huber, Wolfgang
The advent of experimental techniques capable of probing biomolecules and cells at high levels of resolution has led to a rapid change in the methods used for the analysis of experimental molecular...
Visualizing Genomic Data (2006)
Gentleman, Robert, Hahne, Florian, Huber, Wolfgang
The advent of experimental techniques capable of probing biomolecules and cells at high levels of resolution has led to a rapid change in the methods used for the analysis of experimental molecular...
Visualizing Genomic Data (2006)
Gentleman, Robert, Hahne, Florian, Huber, Wolfgang
The advent of experimental techniques capable of probing biomolecules and cells at high levels of resolution has led to a rapid change in the methods used for the analysis of experimental molecular...
Visualizing Genomic Data (2006)
Gentleman, Robert, Hahne, Florian, Huber, Wolfgang
The advent of experimental techniques capable of probing biomolecules and cells at high levels of resolution has led to a rapid change in the methods used for the analysis of experimental molecular...
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
The LIFEdb database in 2006 (2006)
Er Mehrle, Heiko Rosenfelder, Coral Del Val, Dorit Arlt, Florian Hahne, Stephanie Bechtel, ...
LIFEdb
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...
The LIFEdb database in 2006 (2006)
Mehrle, Alexander, Rosenfelder, Heiko, Schupp, Ingo, Del Val, Coral, Arlt, Dorit, Hahne, Florian, ...
LIFEdb (http://www.LIFEdb.de) integrates data from large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. New features of LIFEdb...
An introduction to low-level analysis methods of DNA microarray data (2005)
Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin
This article gives an overview over the methods used in the low--level analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of...
An introduction to low-level analysis methods of DNA microarray data (2005)
Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin
This article gives an overview over the methods used in the low--level analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of...
An introduction to low-level analysis methods of DNA microarray data (2005)
Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin
This article gives an overview over the methods used in the low--level analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of...
An introduction to low-level analysis methods of DNA microarray data (2005)
Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin
This article gives an overview over the methods used in the low--level analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of...
On the Synthesis of Microarray Experiments (2005)
Gentleman, Robert, Ruschhaupt, Markus, Huber, Wolfgang
With many different investigators studying the same disease and with a strong commitment to publish supporting data in the scientific community, there are often many different datasets available for...
On the Synthesis of Microarray Experiments (2005)
Gentleman, Robert, Ruschhaupt, Markus, Huber, Wolfgang
With many different investigators studying the same disease and with a strong commitment to publish supporting data in the scientific community, there are often many different datasets available for...
On the Synthesis of Microarray Experiments (2005)
Gentleman, Robert, Ruschhaupt, Markus, Huber, Wolfgang
With many different investigators studying the same disease and with a strong commitment to publish supporting data in the scientific community, there are often many different datasets available for...
On the Synthesis of Microarray Experiments (2005)
Gentleman, Robert, Ruschhaupt, Markus, Huber, Wolfgang
With many different investigators studying the same disease and with a strong commitment to publish supporting data in the scientific community, there are often many different datasets available for...
Sueltmann, Holger, Von Heydebreck, Anja, Huber, Wolfgang, Kuner, Ruprecht, Buness, Andreas, Vogt, Markus, ...
Current diagnosis of renal cancer consists of histopathologic examination of tissue sections and classification into tumor stages and grades of malignancy. Until recently, molecular differences...
BIOINFORMATICS APPLICATIONS NOTE (2005)
Gene Expression, Steffen Durinck, Yves Moreau, Arek Kasprzyk, Sean Davis, Bart De Moor, ...
Vol. 21 no. 16 2005, pages 3439–3440 doi:10.1093/bioinformatics/bti525 BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
arrayMagic: twocolour cDNA microarray quality control and preprocessing (2005)
Andreas Buness, Wolfgang Huber, Klaus Steiner, Holger Sültmann, Annemarie Poustka
Summary: arrayMagic is a software package for quality control and preprocessing of two-colour cDNA microarray data. The automated analysis pipeline comprises data import, normalization, replica...
Edges: relationships between them A useful abstraction to talk about relationships and interactions (think of integer numbers, apples and fingers) Edges may have weights, directions, types...
David Arnosti, East Lansing, Luca Peliti Napoli, Alvis Brazma, Hinxton Nikolaus, Rajewsky New York, ...
The aim of this program is to bring together researchers and students from different backgrounds (including molecular biology, bioinformatics, biological physics) to discuss Networks and Regulation,...
Durinck, Steffen, Moreau, Yves, Kasprzyk, Arek, Davis, Sean, De Moor, Bart, Brazma, Alvis, ...
Summary: biomaRt is a new Bioconductor package that integrates BioMart data resources with data analysis software in Bioconductor. It can annotate a wide range of gene or gene product identifiers...
A Compendium to Ensure Computational Reproducibility in High-Dimensional Classification Tasks (2004)
Ruschhaupt, Markus, Huber, Wolfgang, Poustka, Annemarie, Mansmann, Ulrich
We demonstrate a concept and implementation of a compendium for the classification of high-dimensional data from microarray gene expression profiles. A compendium is an interactive document that...
A Compendium to Ensure Computational Reproducibility in High-Dimensional Classification Tasks (2004)
Ruschhaupt, Markus, Huber, Wolfgang, Poustka, Annemarie, Mansmann, Ulrich
We demonstrate a concept and implementation of a compendium for the classification of high-dimensional data from microarray gene expression profiles. A compendium is an interactive document that...
A Compendium to Ensure Computational Reproducibility in High-Dimensional Classification Tasks (2004)
Ruschhaupt, Markus, Huber, Wolfgang, Poustka, Annemarie, Mansmann, Ulrich
We demonstrate a concept and implementation of a compendium for the classification of high-dimensional data from microarray gene expression profiles. A compendium is an interactive document that...
A Compendium to Ensure Computational Reproducibility in High-Dimensional Classification Tasks (2004)
Ruschhaupt, Markus, Huber, Wolfgang, Poustka, Annemarie, Mansmann, Ulrich
We demonstrate a concept and implementation of a compendium for the classification of high-dimensional data from microarray gene expression profiles. A compendium is an interactive document that...
Bioconductor: open software development for computational biology and bioinformatics (2004)
Gentleman, Robert C, Carey, Vincent J, Bates, Douglas M, Bolstad, Ben, Dettling, Marcel, Dudoit, Sandrine, ...
Abstract The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering...
Differential Expression with the Bioconductor Project (2004)
Von Heydebreck,Anja, Huber,Wolfgang, Gentleman,Robert
A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. We...
Differential Expression with the Bioconductor Project (2004)
Von Heydebreck, Anja, Huber, Wolfgang, Gentleman, Robert
A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. We...
Differential Expression with the Bioconductor Project (2004)
Von Heydebreck, Anja, Huber, Wolfgang, Gentleman, Robert
A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. We...
Differential Expression with the Bioconductor Project (2004)
Von Heydebreck, Anja, Huber, Wolfgang, Gentleman, Robert
A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. We...
Differential Expression with the Bioconductor Project (2004)
Von Heydebreck, Anja, Huber, Wolfgang, Gentleman, Robert
A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. We...
Schneider, Jörg, Buneß, Andreas, Huber, Wolfgang, Volz, Joachim, Kioschis, Petra, Hafner, Mathias, ...
Abstract Background The requirement of a large amount of high-quality RNA is a major limiting factor for microarray experiments using biopsies. An average microarray experiment requires 10–100 μg...
Error models for microarray intensities (2004)
Huber,Wolfgang, Von Heydebreck,Anja, Vingron,Martin
We derive the additive-multiplicative error model for microarray intensities, and describe two applications. For the detection of differentially expressed genes, we obtain a statistic whose variance...
Error models for microarray intensities (2004)
Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin
We derive the additive-multiplicative error model for microarray intensities, and describe two applications. For the detection of differentially expressed genes, we obtain a statistic whose variance...
Error models for microarray intensities (2004)
Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin
We derive the additive-multiplicative error model for microarray intensities, and describe two applications. For the detection of differentially expressed genes, we obtain a statistic whose variance...
Error models for microarray intensities (2004)
Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin
We derive the additive-multiplicative error model for microarray intensities, and describe two applications. For the detection of differentially expressed genes, we obtain a statistic whose variance...
Error models for microarray intensities (2004)
Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin
We derive the additive-multiplicative error model for microarray intensities, and describe two applications. For the detection of differentially expressed genes, we obtain a statistic whose variance...
Bioconductor: Open software development for computational biology and bioinformatics (2004)
Gentleman, Robert C., Carey, Vincent J., Bates, Douglas J., Bolstad, Benjamin M., Dettling, Marcel, Dudoit, Sandrine, ...
The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. We detail some of the design decisions, software...
Bioconductor: Open software development for computational biology and bioinformatics (2004)
Gentleman, Robert C., Carey, Vincent J., Bates, Douglas J., Bolstad, Benjamin M., Dettling, Marcel, Dudoit, Sandrine, ...
The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. We detail some of the design decisions, software...
Bioconductor: Open software development for computational biology and bioinformatics (2004)
Gentleman, Robert C., Carey, Vincent J., Bates, Douglas J., Bolstad, Benjamin M., Dettling, Marcel, Dudoit, Sandrine, ...
The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. We detail some of the design decisions, software...
Bioconductor: Open software development for computational biology and bioinformatics (2004)
Gentleman, Robert C., Carey, Vincent J., Bates, Douglas J., Bolstad, Benjamin M., Dettling, Marcel, Dudoit, Sandrine, ...
The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. We detail some of the design decisions, software...
Differential Expression with the Bioconductor Project (2004)
Von Heydebreck, Anja, Huber, Wolfgang, Gentleman, Robert
A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. We...
Error models for microarray intensities (2004)
Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin
We derive the additive-multiplicative error model for microarray intensities, and describe two applications. For the detection of differentially expressed genes, we obtain a statistic whose variance...
Verfassung ohne Gottesbezug? (2004)
Goerlich, Helmut, Huber, Wolfgang, Lehmann, Karl
Originaltext vom Verlag; nicht vom SfBS bearbeitet.
matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements (2004)
Huber, Wolfgang, Gentleman, Robert
Summary: The nucleotide sequences of the probes on a microarray can be used for a variety of purposes in the analysis of microarray experiments. We describe software and a paradigm for the creation...
matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements (2004)
Huber, Wolfgang, Gentleman, Robert
Summary: The nucleotide sequences of the probes on a microarray can be used for a variety of purposes in the analysis of microarray experiments. We describe software and a paradigm for the creation...
arrayMagic: two-colour cDNA microarray quality control and preprocessing (2004)
Buneß, Andreas, Huber, Wolfgang, Steiner, Klaus, Sültmann, Holger, Poustka, Annemarie
Summary: arrayMagic is a software package for quality control and preprocessing of two-colour cDNA microarray data. The automated analysis pipeline comprises data import, normalisation, replica...
From ORFeome to Biology: A Functional Genomics Pipeline (2004)
Wiemann, Stefan, Arlt, Dorit, Huber, Wolfgang, Wellenreuther, Ruth, Schleeger, Simone, Mehrle, Alexander, ...
As several model genomes have been sequenced, the elucidation of protein function is the next challenge toward the understanding of biological processes in health and disease. We have generated a...
matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements (2004)
Huber, Wolfgang, Gentleman, Robert
Summary: The nucleotide sequences of the probes on a microarray can be used for a variety of purposes in the analysis of microarray experiments. We describe software and a paradigm for the creation...
arrayMagic: two-colour cDNA microarray quality control and preprocessing (2004)
Buneß, Andreas, Huber, Wolfgang, Steiner, Klaus, Sültmann, Holger, Poustka, Annemarie
Summary: arrayMagic is a software package for quality control and preprocessing of two-colour cDNA microarray data. The automated analysis pipeline comprises data import, normalisation, replica...
Gunawan,Bastian, Von Heydebreck,Anja, Fritsch,Thekla, Huber,Wolfgang, Ringert,Rolf-Hermann, Jakse,Gerhard, ...
We evaluated clinical characteristics, patient outcome (mean follow-up, 47 months), and cytogenetic abnormalities in the largest as yet reported cytogenetic series of 47 primary and 11 secondary...
Analysis of microarray gene expression data (2003)
Huber,Wolfgang, Heydebreck,Anja Von, Vingron,Martin
This article reviews the methods utilized in processing and analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of mRNA...
Parameter estimation for the calibration and variance stabilization of microarray data (2003)
Huber,Wolfgang, Von Heydebreck,Anja, Sültmann,Holger, Poustka,Annemarie, Vingron,Martin
We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances...
Parameter estimation for the calibration and variance stabilization of microarray data (2003)
Huber, Wolfgang, Von Heydebreck, Anja, Sueltmann, Holger, Poustka, Annemarie, Vingron, Martin
We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances...
Parameter estimation for the calibration and variance stabilization of microarray data (2003)
Huber, Wolfgang, Von Heydebreck, Anja, Sueltmann, Holger, Poustka, Annemarie, Vingron, Martin
We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances...
Parameter estimation for the calibration and variance stabilization of microarray data (2003)
Huber, Wolfgang, Von Heydebreck, Anja, Sueltmann, Holger, Poustka, Annemarie, Vingron, Martin
We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances...
Parameter estimation for the calibration and variance stabilization of microarray data (2003)
Huber, Wolfgang, Von Heydebreck, Anja, Sueltmann, Holger, Poustka, Annemarie, Vingron, Martin
We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances...
Gunawan, Bastian, Von Heydebreck, Anja, Fritsch, Thekla, Huber, Wolfgang, Ringert, Rolf-Hermann, Jakse, Gerhard, ...
We evaluated clinical characteristics, patient outcome (mean follow-up, 47 months), and cytogenetic abnormalities in the largest as yet reported cytogenetic series of 47 primary and 11 secondary...
Parameter estimation for the calibration and variance stabilization of microarray data (2003)
Huber, Wolfgang, Von Heydebreck, Anja, Sültmann, Holger, Poustka, Annemarie, Vingron, Martin
We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances...
Analysis of microarray gene expression data (2003)
Huber, Wolfgang, Heydebreck, Anja Von, Vingron, Martin
This article reviews the methods utilized in processing and analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of mRNA...
Analysis of Microarray Gene Expression Data (2003)
Wolfgang Huber, Anja Von Heydebreck, Martin Vingron
This article reviews the methods utilized in processing and analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of mRNA...
Huber,Wolfgang, Von Heydebreck,Anja, Sültmann,Holger, Poustka,Annemarie, Vingron,Martin
We introduce a statistical model for microarray gene expression data that comprises data calibration, the quantification of differential expression, and the quantification of measurement error. In...
Huber, Wolfgang, Von Heydebreck, Anja, Sültmann, Holger, Poustka, Annemarie, Vingron, Martin
We introduce a statistical model for microarray gene expression data that comprises data calibration, the quantification of differential expression, and the quantification of measurement error. In...
Kassie, Fekadu, Rabot, Sylvie, Uhl, Maria, Huber, Wolfgang, Qin, Hong Min, Helma, Christoph, ...
The chemoprotective effect of garden cress (GC, Lepidium sativum) and its constituents, glucotropaeolin (GT) and benzylisothiocyanate (BITC), a breakdown product of GT, towards...
Huber, Wolfgang, Von Heydebreck, Anja, Sültmann, Holger, Poustka, Annemarie, Vingron, Martin
We introduce a statistical model for microarray gene expression data that comprises data calibration, the quantification of differential expression, and the quantification of measurement error. In...
Von Heydebreck, Anja, Huber, Wolfgang, Poustka, Annemarie, Vingron, Martin
We present a new class discovery method for microarray gene expression data. Based on a collection of gene expression profiles from different tissue samples, the method searches for binary class...
Miscellaneous electricity use in U.S. homes (1999)
Sanchez, Marla C., Koomey, Jonathan G., Moezzi, Mithra M., Meier, Alan, Huber, Wolfgang
Historically, residential energy and carbon saving efforts have targeted conventional end uses such as water heating, lighting and refrigeration. The emergence of new household appliances has...
Reducing Leaking Electricity to 1 Watt (1998)
Meier, A.K., Huber, Wolfgang, Rosen, Karen
In this study we examine some specific opportunities to reduce standby losses in electronic appliances. A review of power consumption levels for the major components responsible for standby functions...
Dynamik stark getriebener offener Quantensysteme / (1998)
Freiburg (Breisgau), Universiẗat, Diss., 1998 (Nicht für den Austausch).
Results from the investigations on leaking electricity in the USA (1997)
Standby electricity use or leaking electricity is the energy consumed by appliances when they are switched off or not performing their principal function. The combination of field measurements and...
Zugl.: Regensburg, Universiẗat, Diss., 1996.
München, Techn. Universiẗat, Diss., 1994.
Fluctuation Effects on Wave Propagation in a Reaction-Diffusion Process (1993)
Heinz-Peter Breuer, Wolfgang Huber, Francesco Petruccione
The reaction--diffusion process corresponding to the Fisher--Kolmogorov equation is studied by means of a discrete multivariate master equation. For travelling wave fronts the stability criterion...
Grasl-Kraupp, Bettina, Huber, Wolfgang, Just, Wilhelm, Gibson, Gordon, Schulte-Hermann, Rolf
The peroxisome proliferator (PP) nafenopin (NAF) enhanced tumor development in rat liver through promotion of a subtype of putative preneoplastic cell foci, characterized by weak cytoplasmic...
Grasl-Kraupp, Bettina, Waldhör, Thomas, Huber, Wolfgang, Schulte-Hermann, Rolf
It is known that phenobarbital (PB) and the peroxisome proliferator (PP) nafenopin (NAF) promote tumor formation by stimulating selective growth of different subtypes of liver foci. While PB enhanced...
Grasl-Kraupp, Bettina, Huber, Wolfgang, Timmermann-Trosiener, Irene, Schulte-Hermann, Rolf
Putative preneoplastic foci of spontaneous origin could be detected in the livers of 2 year old, untreated male Wistar rats. The unaltered and preneoplastic hepatocytes showed an identical expression...
Organ-specific distribution of genotoxic effects in mice exposed to cooked food mutagens (1992)
Knasmüller, Siegfried, Kienzl, Harald, Huber, Wolfgang, Hermann, Rolf Schulte
The induction of organ-specific genotoxic effects of five cooked food mutagens in Swiss albino mice was investigated in microbial animal-mediated assays. The indicator of the induction of DNA damage...
Ursachen und Verletzungsmuster bei Skiunfällen. (1989)
Freiburg (Breisgau), Univ., Diss., 1990 (Nicht f.d. Austausch).
Heidelberg, Univ., Diss., 1984 (Nicht f.d. Austausch).
Thesis (doctoral)--Universität Wien, 1982.
Thesis (doctoral)--Technische Universität München, 1976.
Kirche und Öffentlichkeit. (1972)
Heidelberg, Univ., Theol. Fak., Habil.-Schr. 1972. (Nicht f. d. Austausch.).
El conocimiento del hombre por el psicoanálisis (1967)
Huber, Wolfgang, Piron, H., Vergote, Antoine
Traducción de: La Psichanalise, Science de l'Homme
Huber, Wolfgang, Piron, H., Vergote, Antoine
Traducción de: La Psichanalise, Science de l'Homme
Der Einfluss von Serotonin, Tryptamin und Lysergsäure auf menschliche Serumcholinesterase. (1962)
Heidelberg, Med. F., Diss. v. 19. Dez. 1962 (Nicht f. d. Aust.).
Thesis (doctoral)--Johann Wolfgang Goethe-Universität zu Frankfurt am Main, 1957.
Thesis (doctoral)--Ludwig-Maximilians Universität München, 1957.
(Über die Reaktion zwischen Schwefeltrioxyd und Ammoniak). (1955)
Heidelberg, Naturwiss.-math. F., Diss. v. 29. Juni 1955 (Nicht f. d. Aust.).
Thesis (doctoral)--Johannes Gutenberg-Universität in Mainz, 1953.
Münster, R.- u. staatswiss. Diss., 1938.
Göttingen, Math.-naturwiss. Diss., 1937.
Untersuchungen über die Genese der Asymmetrien am Kopf von Loxia curvirostra. (1932)
Aus: Morphol. Jahrbuch. Bd. 71, H. 4. 1933
Schneider, Jörg, Buneß, Andreas, Huber, Wolfgang, Volz, Joachim, Kioschis, Petra, Hafner, Mathias, ...
From ORFeome to Biology: A Functional Genomics Pipeline
Wiemann, Stefan, Arlt, Dorit, Huber, Wolfgang, Wellenreuther, Ruth, Schleeger, Simone, Mehrle, Alexander, ...
As several model genomes have been sequenced, the elucidation of protein function is the next challenge toward the understanding of biological processes in health and disease. We have generated a...
Bioconductor: open software development for computational biology and bioinformatics
Gentleman, Robert C, Carey, Vincent J, Bates, Douglas M, Bolstad, Ben, Dettling, Marcel, Dudoit, Sandrine, ...
A detailed description of the aims and methods of the Bioconductor project, an initiative for the collaborative creation of extensible software for computational biology and bioinformatics.
Mehrle, Alexander, Rosenfelder, Heiko, Schupp, Ingo, Del Val, Coral, Arlt, Dorit, Hahne, Florian, ...
LIFEdb () integrates data from large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. New features of LIFEdb include (i) an...
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...
Schneider, Jörg, Buneß, Andreas, Huber, Wolfgang, Volz, Joachim, Kioschis, Petra, Hafner, Mathias, ...
From ORFeome to Biology: A Functional Genomics Pipeline
Wiemann, Stefan, Arlt, Dorit, Huber, Wolfgang, Wellenreuther, Ruth, Schleeger, Simone, Mehrle, Alexander, ...
As several model genomes have been sequenced, the elucidation of protein function is the next challenge toward the understanding of biological processes in health and disease. We have generated a...
Bioconductor: open software development for computational biology and bioinformatics
Gentleman, Robert C, Carey, Vincent J, Bates, Douglas M, Bolstad, Ben, Dettling, Marcel, Dudoit, Sandrine, ...
A detailed description of the aims and methods of the Bioconductor project, an initiative for the collaborative creation of extensible software for computational biology and bioinformatics.
Mehrle, Alexander, Rosenfelder, Heiko, Schupp, Ingo, Del Val, Coral, Arlt, Dorit, Hahne, Florian, ...
LIFEdb () integrates data from large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. New features of LIFEdb include (i) an...
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...
Analysis of cell-based RNAi screens
Boutros, Michael, Brás, Lígia P, Huber, Wolfgang
cellHTS is a new method for the analysis and documentation of RNAi screens.
Hahne, Florian, Arlt, Dorit, Sauermann, Mamatha, Majety, Meher, Poustka, Annemarie, Wiemann, Stefan, ...
A software tool for the analysis of high-throughput cell-based assays is presented.
Huber, Wolfgang, Carey, Vincent J, Long, Li, Falcon, Seth, Gentleman, Robert
Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and their areas...
Is supra-ventricular arrhythmia a reason for the bad performance of the FlowTrac device?
Umgelter, Andreas, Reindl, Wolfgang, Schmid, Roland M, Huber, Wolfgang
Ringo – an R/Bioconductor package for analyzing ChIP-chip readouts
Toedling, Joern, Skylar, Oleg, Krueger, Tammo, Fischer, Jenny J, Sperling, Silke, Huber, Wolfgang
Making the most of high-throughput protein-interaction data
Gentleman, Robert, Huber, Wolfgang
Better methods of statistical analysis could make large-scale protein-interaction data more useful.
Model-based variance-stabilizing transformation for Illumina microarray data
Lin, Simon M., Du, Pan, Huber, Wolfgang, Kibbe, Warren A.
Variance stabilization is a step in the preprocessing of microarray data that can greatly benefit the performance of subsequent statistical modeling and inference. Due to the often limited number of...
Miscellaneous electricity in US homes: Historical decomposition and future trends
Sanchez, Marla C, Koomey, Jonathan G, Moezzi, Mithra M, Meier, Alan, Huber, Wolfgang
A Compendium to Ensure Computational Reproducibility in High-Dimensional Classification Tasks
Markus Ruschhaupt, Wolfgang Huber, Annemarie Poustka, Ulrich Mansmann
We demonstrate a concept and implementation of a compendium for the classification of high-dimensional data from microarray gene expression profiles. A compendium is an interactive document that...
Parameter estimation for the calibration and variance stabilization of microarray data
Wolfgang Huber, Anja Von Heydebreck, Holger Sueltmann, Annemarie Poustka, Martin Vingron
We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances...
Umgelter, Andreas, Reindl, Wolfgang, Wagner, Katrin S, Franzen, Michael, Stock, Konrad, Schmid, Roland M, ...
Coverage and error models of protein-protein interaction data by directed graph analysis
Chiang, Tony, Scholtens, Denise, Sarkar, Deepayan, Gentleman, Robert, Huber, Wolfgang
Directed graph and multinomial error models were used to assess and characterize the error statistics in all published large-scale datasets for Saccharomyces cerevisiae
Umgelter, Andreas, Wagner, Katrin, Reindl, Wolfgang, Nurtsch, Nils, Huber, Wolfgang, Schmid, Roland M
arrayQualityMetrics—a bioconductor package for quality assessment of microarray data
Kauffmann, Audrey, Gentleman, Robert, Huber, Wolfgang
Summary:: The assessment of data quality is a major concern in microarray analysis. arrayQualityMetrics is a Bioconductor package that provides a report with diagnostic plots for one or two colour...
Array-based genotyping in S.cerevisiae using semi-supervised clustering
Bourgon, Richard, Mancera, Eugenio, Brozzi, Alessandro, Steinmetz, Lars M., Huber, Wolfgang
Motivation: Microarrays provide an accurate and cost-effective method for genotyping large numbers of individuals at high resolution. The resulting data permit the identification of loci at which...
Genome-wide allele- and strand-specific expression profiling
Gagneur, Julien, Sinha, Himanshu, Perocchi, Fabiana, Bourgon, Richard, Huber, Wolfgang, Steinmetz, Lars M
Recent reports have shown that most of the genome is transcribed and that transcription frequently occurs concurrently on both DNA strands. In diploid genomes, the expression level of each allele...
In vitro activity of moxifloxacin and piperacillin/sulbactam against pathogens of acute cholangitis
Weber, Andreas, Huber, Wolfgang, Kamereck, Klaus, Winkle, Philipp, Voland, Petra, Weidenbach, Hans, ...
AIM: To analyze the in vitro activity of moxifloxacin and piperacillin/sulbactam against pathogens isolated from patients with acute cholangitis.
Importing ArrayExpress datasets into R/Bioconductor
Kauffmann, Audrey, Rayner, Tim F., Parkinson, Helen, Kapushesky, Misha, Lukk, Margus, Brazma, Alvis, ...
Summary:ArrayExpress is one of the largest public repositories of microarray datasets. R/Bioconductor provides a comprehensive suite of microarray analysis and integrative bioinformatics software....