Wolfgang Huber

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....

Haemodynamic effects of plasma-expansion with hyperoncotic albumin in cirrhotic patients with renal failure: a prospective interventional study (2008)

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...

Comparative Analysis of Structured RNAs in S. cerevisiae Indicates a Multitude of Different Functions (2008)

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...

Effects of plasma expansion with albumin and paracentesis on haemodynamics and kidney function in critically ill cirrhotic patients with tense ascites and hepatorenal syndrome: a prospective uncontrolled trial (2008)

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...

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...

Der christliche Glaube (2008)

Huber, Wolfgang

Originaltext vom Verlag; nicht vom SfBS bearbeitet.

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...

Rintact: enabling computational analysis of molecular interaction data from the IntAct repository (2008)

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...

In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation (2007)

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...

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....

Comparative analysis of structured RNAs in S. cerevisiaeindicates a multitude of different functions (2007)

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...

CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data (2007)

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...

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...

CoCo: A web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data. (2007)

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...

Statistical methods and software for the analysis of highthroughput reverse genetic assays using flow cytometry readouts (2006)

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

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...

Gene Expression in Kidney Cancer Is Associated with Cytogenetic Abnormalities, Metastasis Formation, and Patient Survival (2005)

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...

Representation (2005)

Wolfgang Huber

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...

Invited (2005)

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,...

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis (2005)

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...

Systematic analysis of T7 RNA polymerase based in vitrolinear RNA amplification for use in microarray experiments (2004)

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...

Cytogenetic and morphologic typing of 58 papillary renal cell carcinomas: Evidence for a cytogenetic evolution of type 2 from type 1 tumors (2003)

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...

Cytogenetic and morphologic typing of 58 papillary renal cell carcinomas: Evidence for a cytogenetic evolution of type 2 from type 1 tumors (2003)

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...

Variance stabilization applied to microarray data calibration and to the quantification of differential expression (2002)

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...

Variance stabilization applied to microarray data calibration and to the quantification of differential expression (2002)

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...

Chemoprotective effects of garden cress (Lepidium sativum) and its constituents towards 2-amino-3-methyl-imidazo[4,5-f]quinoline (IQ)-induced genotoxic effects and colonic preneoplastic lesions (2002)

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...

Variance stabilization applied to microarray data calibration and to the quantification of differential expression (2002)

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...

Identifying splits with clear separation: a new class discovery method for gene expression data (2001)

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)

Huber, Wolfgang.

Freiburg (Breisgau), Universiẗat, Diss., 1998 (Nicht für den Austausch).

Results from the investigations on leaking electricity in the USA (1997)

Meier, Alan, Huber, Wolfgang

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...

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...

Enhancement of peroxisomal enzymes, cytochrome P-452 and DNA synthesis in putative preneoplastic foci of rat liver treated with the peroxisome proliferator nafenopin (1993)

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...

Glutathione S-transferase isoenzyme patterns in different subtypes of enzyme-altered rat liver foci treated with the peroxisome proliferator nafenopin or with phenobarbital (1993)

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...

SHORT COMMUNICATION: Peroxisomal enzyme induction uncoupled from enhanced DNA synthesis in putative preneoplastic liver foci of rats treated with a single dose of the peroxisome proliferator nafenopin (1993)

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)

Huber, Wolfgang.

Freiburg (Breisgau), Univ., Diss., 1990 (Nicht f.d. Austausch).

Kirche und Öffentlichkeit. (1972)

Huber, Wolfgang.

Heidelberg, Univ., Theol. Fak., Habil.-Schr. 1972. (Nicht f. d. Austausch.).

Untersuchungen über die brauchbarkeit der photometrischen Blutalkoholbestimmung nach WidMark Gruener / (1957)

Huber, Wolfgang.

Thesis (doctoral)--Johann Wolfgang Goethe-Universität zu Frankfurt am Main, 1957.

(Über die Reaktion zwischen Schwefeltrioxyd und Ammoniak). (1955)

Huber, Wolfgang.

Heidelberg, Naturwiss.-math. F., Diss. v. 29. Juni 1955 (Nicht f. d. Aust.).

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.

The LIFEdb database in 2006

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...

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.

The LIFEdb database in 2006

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.

Graphs in molecular biology

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...

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...

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...

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

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....