Wolfgang Huber

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc Making the most of high-throughput protein-interaction data
    Robert Gentleman
    Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Genome Biol 8:112. 2007
  2. pmc Analysis of cell-based RNAi screens
    Michael Boutros
    Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Genome Biol 7:R66. 2006
  3. pmc Statistical methods and software for the analysis of highthroughput reverse genetic assays using flow cytometry readouts
    Florian Hahne
    Division of Molecular Genome Analysis, German Cancer Research Center, INF 580, 69120 Heidelberg, Germany
    Genome Biol 7:R77. 2006
  4. pmc Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3
    Ramona Schmid
    Boehringer Ingelheim Pharma GmbH and Co, KG, Birkendorfer Str, 65, 88397 Biberach Riss, Germany
    BMC Genomics 11:349. 2010
  5. pmc Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions
    Stephan Steigele
    Wilhelm Schickard Institut fur Informatik, ZBIT Center for Bioinformatics Tübingen, University of Tubingen, Tubingen, Germany
    BMC Biol 5:25. 2007
  6. pmc Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts
    Joern Toedling
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Bioinformatics 8:221. 2007
  7. pmc In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation
    Tineke Casneuf
    Department of Plant Systems Biology, VIB, B 9052 Ghent, Belgium
    BMC Bioinformatics 8:461. 2007
  8. pmc Graphs in molecular biology
    Wolfgang Huber
    European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge CB10 1SD, UK
    BMC Bioinformatics 8:S8. 2007
  9. ncbi request reprint Transcript mapping with high-density oligonucleotide tiling arrays
    Wolfgang Huber
    European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK
    Bioinformatics 22:1963-70. 2006
  10. pmc SpeCond: a method to detect condition-specific gene expression
    Florence M G Cavalli
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
    Genome Biol 12:R101. 2011

Detail Information

Publications40

  1. pmc Making the most of high-throughput protein-interaction data
    Robert Gentleman
    Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Genome Biol 8:112. 2007
    ..Probabilistic statistical models and methods can be used to estimate properties of interest and to make the best use of the available data...
  2. pmc Analysis of cell-based RNAi screens
    Michael Boutros
    Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Genome Biol 7:R66. 2006
    ..dkfz.de/signaling/cellHTS). The method is useful for the analysis and documentation of individual RNAi screens. Moreover, it is a prerequisite for the integration of multiple experiments...
  3. pmc Statistical methods and software for the analysis of highthroughput reverse genetic assays using flow cytometry readouts
    Florian Hahne
    Division of Molecular Genome Analysis, German Cancer Research Center, INF 580, 69120 Heidelberg, Germany
    Genome Biol 7:R77. 2006
    ..The software is freely available in the Bioconductor package prada. The method permits analysis of large screens to detect the effects of molecular interventions in cellular systems...
  4. pmc Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3
    Ramona Schmid
    Boehringer Ingelheim Pharma GmbH and Co, KG, Birkendorfer Str, 65, 88397 Biberach Riss, Germany
    BMC Genomics 11:349. 2010
    ..Major aim is to derive optimal results from the underlying experiment. Comparisons of different normalization methods have already been conducted, none of which, to our knowledge, comparing more than a handful of methods...
  5. pmc Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions
    Stephan Steigele
    Wilhelm Schickard Institut fur Informatik, ZBIT Center for Bioinformatics Tübingen, University of Tubingen, Tubingen, Germany
    BMC Biol 5:25. 2007
    ..To supplement these searches, we performed a computational analysis of seven yeast species and searched for new ncRNAs and RNA motifs...
  6. pmc Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts
    Joern Toedling
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Bioinformatics 8:221. 2007
    ..Identified enriched regions need to be bioinformatically annotated and compared to related datasets by statistical methods...
  7. pmc In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation
    Tineke Casneuf
    Department of Plant Systems Biology, VIB, B 9052 Ghent, Belgium
    BMC Bioinformatics 8:461. 2007
    ..An approach that is able to distinguish these factors permits the detection of more biologically relevant co-expression signatures...
  8. pmc Graphs in molecular biology
    Wolfgang Huber
    European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge CB10 1SD, UK
    BMC Bioinformatics 8:S8. 2007
    ..We discuss software that is available through the Bioconductor project and present a simple example application to the integration of a protein-protein interaction and a co-expression network...
  9. ncbi request reprint Transcript mapping with high-density oligonucleotide tiling arrays
    Wolfgang Huber
    European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK
    Bioinformatics 22:1963-70. 2006
    ....
  10. pmc SpeCond: a method to detect condition-specific gene expression
    Florence M G Cavalli
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
    Genome Biol 12:R101. 2011
    ..An implementation of SpeCond is freely available as a Bioconductor package at http://www.bioconductor.org/packages/release/bioc/html/SpeCond.html...
  11. pmc arrayQualityMetrics--a bioconductor package for quality assessment of microarray data
    Audrey Kauffmann
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 25:415-6. 2009
    ..bioconductor.org. A users guide and examples are provided with the package. Some examples of HTML reports generated by arrayQualityMetrics can be found at http://www.microarray-quality.org..
  12. pmc Coverage and error models of protein-protein interaction data by directed graph analysis
    Tony Chiang
    EMBL, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Genome Biol 8:R186. 2007
    ..These traits provide a prerequisite for the estimation of the protein interactome and its modules...
  13. ncbi request reprint Rintact: enabling computational analysis of molecular interaction data from the IntAct repository
    Tony Chiang
    EBI EMBL, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 24:1100-1. 2008
    ..These datasets need to be analyzed by computational methods. Software packages in the statistical environment R provide powerful tools for conducting such analyses...
  14. pmc Array-based genotyping in S.cerevisiae using semi-supervised clustering
    Richard Bourgon
    EMBL, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Bioinformatics 25:1056-62. 2009
    ..There is a need for improved statistical methods for array-based genotyping...
  15. pmc Independent filtering increases detection power for high-throughput experiments
    Richard Bourgon
    European Bioinformatics Institute, Cambridge CB10 1SD, UK
    Proc Natl Acad Sci U S A 107:9546-51. 2010
    ..Independent filtering-using filter/test pairs that are independent under the null hypothesis but correlated under the alternative-is a general approach that can substantially increase the efficiency of experiments...
  16. pmc Importing ArrayExpress datasets into R/Bioconductor
    Audrey Kauffmann
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 25:2092-4. 2009
    ..However, easy ways for importing datasets from ArrayExpress into R/Bioconductor have been lacking. Here, we present such a tool that is suitable for both interactive and automated use...
  17. doi request reprint Microarray data quality control improves the detection of differentially expressed genes
    Audrey Kauffmann
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
    Genomics 95:138-42. 2010
    ..Using array weights is similarly effective, but its applicability is more limited. The quality metrics presented here are implemented in the Bioconductor package arrayQualityMetrics...
  18. pmc EBImage--an R package for image processing with applications to cellular phenotypes
    Gregoire Pau
    EMBL European Bioinformatics Institute, Cambridge, UK
    Bioinformatics 26:979-81. 2010
    ..AVAILABILITY: EBImage is free and open source, released under the LGPL license and available from the Bioconductor project (http://www.bioconductor.org/packages/release/bioc/html/EBImage.html)...
  19. pmc Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi
    Elin Axelsson
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Bioinformatics 12:342. 2011
    ..It also provides insights into the role of epistasis on the way from genotype to phenotype. The interpretation of co-RNAi data requires computational and statistical analysis in order to detect interactions reliably and sensitively...
  20. ncbi request reprint Combinatorial effects of four histone modifications in transcription and differentiation
    Jenny J Fischer
    Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    Genomics 91:41-51. 2008
    ..Histones may primarily function as signaling marks for specific effectors rather than being a sufficient driving force for or a consequence of transcription...
  21. ncbi request reprint matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements
    Wolfgang Huber
    Department of Molecular Genome Analysis, German Cancer Research Center, INF 580, Heidelberg, 69120, Germany
    Bioinformatics 20:1651-2. 2004
    ..AVAILABILITY: The R package matchprobes is available under LGPL at http://www.bioconductor.org SUPPLEMENTARY INFORMATION: The package contains documentation in the form of a vignette and manual pages...
  22. ncbi request reprint Estimating node degree in bait-prey graphs
    Denise Scholtens
    Department of Preventive Medicine, Northwestern University Medical School, 680 N Lake Shore Drive Suite 1102, Chicago, IL 60611 4402, USA
    Bioinformatics 24:218-24. 2008
    ..We consider a relatively simple per-protein feature of the interactome: the number of interaction partners for a protein, which in graph terminology is the degree of the protein...
  23. pmc Model-based variance-stabilizing transformation for Illumina microarray data
    Simon M Lin
    Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA
    Nucleic Acids Res 36:e11. 2008
    ..The algorithms and Supplementary Data are included in the lumi package of Bioconductor, available at: www.bioconductor.org...
  24. pmc High-resolution mapping of meiotic crossovers and non-crossovers in yeast
    Eugenio Mancera
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 454:479-85. 2008
    ..In addition, because non-crossover hotspots create holes of reduced linkage within haplotype blocks, our results stress the need to incorporate non-crossovers into genetic linkage analysis...
  25. ncbi request reprint Variance stabilization applied to microarray data calibration and to the quantification of differential expression
    Wolfgang Huber
    Department of Molecular Genome Analysis, German Cancer Research Center, INF 280, Heidelberg, 69120, Germany
    Bioinformatics 18:S96-104. 2002
    ..We demonstrate our approach on data sets from different experimental platforms, including two-colour cDNA arrays and a series of Affymetrix oligonucleotide arrays...
  26. pmc From ORFeome to biology: a functional genomics pipeline
    Stefan Wiemann
    Molecular Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany
    Genome Res 14:2136-44. 2004
    ..All information is presented in a Web database (http://www.dkfz.de/LIFEdb). It is exploited for the identification of disease-relevant genes and proteins for diagnosis and therapy...
  27. ncbi request reprint arrayMagic: two-colour cDNA microarray quality control and preprocessing
    Andreas Buness
    Department of Molecular Genome Analysis, German Cancer Research Center INF 580, Heidelberg, 69120, Germany
    Bioinformatics 21:554-6. 2005
    ..bioconductor.org CONTACT: a.buness@dkfz.de SUPPLEMENTARY INFORMATION: The package contains documentation in the form of manual pages and a vignette with a guided tour of a typical workflow...
  28. ncbi request reprint Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality
    Antje Purmann
    Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    Genomics 89:580-7. 2007
    ..Our data point to so far uncharacterized cis-acting units and reject cofunctionality as a driving force...
  29. ncbi request reprint CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data
    Charles Girardot
    European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    Bioinformatics 23:771-3. 2007
    ..Regulatory relationships between the transcription factor-bound regions and putative target genes can be stored and expanded throughout different sessions...
  30. pmc A high-resolution map of transcription in the yeast genome
    Lior David
    Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304, USA
    Proc Natl Acad Sci U S A 103:5320-5. 2006
    ..These findings may suggest a regulatory role of antisense transcription in S. cerevisiae. Moreover, the data show that even this well studied genome has transcriptional complexity far beyond current annotation...
  31. ncbi request reprint BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
    Steffen Durinck
    Department of Electronical Engineering, ESAT SCD, K U Leuven, Kasteelpark Arenberg 10, 3001 Leuven Heverlee, Belgium
    Bioinformatics 21:3439-40. 2005
    ..g. Ensembl). The biomaRt package provides a tight integration of large, public or locally installed BioMart databases with data analysis in Bioconductor creating a powerful environment for biological data mining...
  32. pmc The LIFEdb database in 2006
    Alexander Mehrle
    Division Molecular Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, D 69120 Heidelberg, Germany
    Nucleic Acids Res 34:D415-8. 2006
    ..LIFEdb enables researchers to systematically select and characterize genes and proteins of interest, and presents data and information via its user-friendly web-based interface...
  33. ncbi request reprint Effectiveness of theophylline prophylaxis of renal impairment after coronary angiography in patients with chronic renal insufficiency
    Wolfgang Huber
    II Medizinische Klinik, Institut fur Klinische Chemie, Klinikum rechts der Isar, Technische Universitat Munchen, Munich, Germany
    Am J Cardiol 91:1157-62. 2003
    ..It should be used especially in patients receiving large amounts of contrast medium, and in patients with a Cigarroa quotient of >5 and/or elevated troponin T levels...
  34. ncbi request reprint Top-down standards will not serve systems biology
    John Quackenbush
    Nature 440:24. 2006
  35. ncbi request reprint Gene expression in kidney cancer is associated with cytogenetic abnormalities, metastasis formation, and patient survival
    Holger Sultmann
    Division of Molecular Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, D 69120 Heidelberg, Germany
    Clin Cancer Res 11:646-55. 2005
    ..The data highlight the benefit of microarrays to detect novel tumor classes and to identify genes that are associated with patient variables and tumor properties...
  36. pmc Systematic analysis of T7 RNA polymerase based in vitro linear RNA amplification for use in microarray experiments
    Jörg Schneider
    Department of Molecular Genome Analysis, German Cancer Research Centre, Heidelberg 69120, Germany
    BMC Genomics 5:29. 2004
    ..Several different approaches for RNA amplification in vitro have been described and applied for microarray studies. In most of these, systematic analyses of the potential bias introduced by the enzymatic modifications are lacking...
  37. pmc Is supra-ventricular arrhythmia a reason for the bad performance of the FlowTrac device?
    Andreas Umgelter
    Crit Care 11:406; author reply 406. 2007
  38. ncbi request reprint Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination
    Gordana Apic
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    J Struct Funct Genomics 4:67-78. 2003
    ..Of particular interest are those combinations that occur in the largest number of multi-domain proteins, and several of these frequent novel combinations contain DNA-binding domains...
  39. pmc Bioconductor: open software development for computational biology and bioinformatics
    Robert C Gentleman
    Department of Biostatistical Science, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
    Genome Biol 5:R80. 2004
    ..We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples...
  40. ncbi request reprint Functional profiling: from microarrays via cell-based assays to novel tumor relevant modulators of the cell cycle
    Dorit Arlt
    Division of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany
    Cancer Res 65:7733-42. 2005
    ..We have established a novel functional profiling strategy that links genomics to cell biology and showed its potential for discerning cancer relevant modulators of the cell cycle in the candidate lists from microarray studies...