Wolfgang Huber

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. ncbi request reprint Parameter estimation for the calibration and variance stabilization of microarray data
    Wolfgang Huber
    German Cancer Research Center, Heidelberg, Germany
    Stat Appl Genet Mol Biol 2:Article3. 2003
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. pmc Graphs in molecular biology
    Wolfgang Huber
    European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge CB10 1SD, UK
    BMC Bioinformatics 8:S8. 2007
  8. 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
  9. 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
  10. 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

Detail Information

Publications76

  1. ncbi request reprint Parameter estimation for the calibration and variance stabilization of microarray data
    Wolfgang Huber
    German Cancer Research Center, Heidelberg, Germany
    Stat Appl Genet Mol Biol 2:Article3. 2003
    ..Software is publicly available as an R package through the Bioconductor project (http://www.bioconductor.org)...
  2. 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...
  3. 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...
  4. 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...
  5. 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...
  6. 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...
  7. 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...
  8. 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
    ....
  9. 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...
  10. 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...
  11. 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...
  12. 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...
  13. pmc Bidirectional promoters generate pervasive transcription in yeast
    Zhenyu Xu
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 457:1033-7. 2009
    ....
  14. 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...
  15. pmc Genome-wide allele- and strand-specific expression profiling
    Julien Gagneur
    Gene Expression Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 5:274. 2009
    ..Our results provide the first high-resolution analysis of differential expression on all four strands of an eukaryotic genome...
  16. pmc Antisense expression increases gene expression variability and locus interdependency
    Zhenyu Xu
    Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 7:468. 2011
    ..These results indicate a general regulatory effect of antisense expression on sense genes and emphasize the importance of antisense-initiating regions downstream of genes in models of gene regulation...
  17. 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
    ..The diagnosis of quality remains, in principle, a context-dependent judgement, but our tool provides powerful, automated, objective and comprehensive instruments on which to base a decision...
  18. 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...
  19. ncbi request reprint High-throughput flow cytometry-based assay to identify apoptosis-inducing proteins
    Mamatha Sauermann
    Division of Molecular Genome Analysis, German Cancer Research Centre, Heidelberg, Germany
    J Biomol Screen 12:510-20. 2007
    ..The candidate proteins were all verified in an independent microscopy-based nuclear fragmentation assay, finally resulting in the identification of 6 apoptosis inducers...
  20. 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...
  21. 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...
  22. pmc High-resolution transcription atlas of the mitotic cell cycle in budding yeast
    Marina V Granovskaia
    EMBL European Molecular Biology Laboratory, Department of Genome Biology, Meyerhofstr, Heidelberg, Germany
    Genome Biol 11:R24. 2010
    ..To explore the complex transcriptome architecture underlying the budding yeast cell cycle, we used 8 bp tiling arrays to generate a 5 minute-resolution, strand-specific expression atlas of the whole genome...
  23. 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
    ..The script-based processing combines reproducibility and flexibility at high-throughput and provides quality-assured and preprocessed microarray data to high-level follow-up analysis...
  24. 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...
  25. pmc Genome-wide survey of post-meiotic segregation during yeast recombination
    Eugenio Mancera
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Genome Biol 12:R36. 2011
    ..This gives rise to somatic mosaicism in multicellular organisms and leads to unexpected allelic combinations among progeny. Despite its implications for inheritance, post-meiotic segregation has been studied at only a few loci...
  26. 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...
  27. doi request reprint Mapping of signaling networks through synthetic genetic interaction analysis by RNAi
    Thomas Horn
    German Cancer Research Center Deutsches Krebsforschungszentrum, Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg, Germany
    Nat Methods 8:341-6. 2011
    ..Large-scale genetic interaction mapping by RNAi is a versatile, scalable approach for revealing gene function and the connectivity of cellular networks...
  28. 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...
  29. ncbi request reprint Systematic comparison of surface coatings for protein microarrays
    Birgit Guilleaume
    Department of Molecular Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany
    Proteomics 5:4705-12. 2005
    ..In summary, we demonstrate that only suitable combinations of surface and fluorescent dyes allow the generation of highly reproducible data...
  30. pmc Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments
    Robert Petryszak
    European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL EBI, Hinxton, CB10 1SD, UK
    Nucleic Acids Res 42:D926-32. 2014
    ....
  31. 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...
  32. pmc Differential expression analysis for sequence count data
    Simon Anders
    European Molecular Biology Laboratory, Mayerhofstraße 1, 69117 Heidelberg, Germany
    Genome Biol 11:R106. 2010
    ..We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package...
  33. pmc Drift and conservation of differential exon usage across tissues in primate species
    Alejandro Reyes
    Genome Biology Unit and Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Proc Natl Acad Sci U S A 110:15377-82. 2013
    ..Our findings support the theory that isoform regulation is an important target of evolution in primates, and our method provides a powerful tool for discovering potentially functional tissue-dependent isoforms. ..
  34. pmc A map of directional genetic interactions in a metazoan cell
    Bernd Fischer
    Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    elife 4:. 2015
    ..Our study presents a powerful approach for reconstructing directional regulatory networks and provides a resource for the interpretation of functional consequences of genetic alterations...
  35. doi request reprint Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping
    Christina Laufer
    Division of Signalling and Functional Genomics, German Cancer Research Center DKFZ, Heidelberg, Germany
    Nat Methods 10:427-31. 2013
    ..Our study also revealed the prospects and challenges of studying genetic interactions in human cells using multiparametric phenotyping...
  36. pmc Detecting differential usage of exons from RNA-seq data
    Simon Anders
    European Molecular Biology Laboratory, 69111 Heidelberg, Germany
    Genome Res 22:2008-17. 2012
    ..The method facilitates the study of regulation and function of alternative exon usage on a genome-wide scale. An implementation of DEXSeq is available as an R/Bioconductor package...
  37. pmc A genetic interaction map of cell cycle regulators
    Maximilian Billmann
    Division of Signaling and Functional Genomics, German Cancer Research Center, and Department of Cell and Molecular Biology, Heidelberg University, 69120 Heidelberg, Germany
    Mol Biol Cell 27:1397-407. 2016
    ..Our results show that the combination of genome-scale RNAi screening and genetic interaction analysis using process-directed phenotypes provides a powerful two-step approach to assigning components to specific pathways and complexes. ..
  38. 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...
  39. 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
    ..While the implementation is specific to the Bioconductor project, the ideas and general strategies are more general and could be easily adopted by other projects...
  40. doi request reprint Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
    Simon Anders
    Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Nat Protoc 8:1765-86. 2013
    ..Hands-on time for typical small experiments (e.g., 4-10 samples) can be <1 h, with computation time <1 d using a standard desktop PC. ..
  41. 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...
  42. doi request reprint A large-scale RNAi screen identifies Deaf1 as a regulator of innate immune responses in Drosophila
    David Kuttenkeuler
    German Cancer Research Center DKFZ and University of Heidelberg, Division of Signaling and Functional Genomics, University of Heidelberg, Heidelberg, Germany
    J Innate Immun 2:181-94. 2010
    ..coli, infection. We determine that Deaf1 acts downstream of the NF-kappaB factors Dorsal and Dif. These results indicate that Deaf1 is an important contributor to innate immune responses in vivo...
  43. 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...
  44. pmc Single-cell polyadenylation site mapping reveals 3' isoform choice variability
    Lars Velten
    European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
    Mol Syst Biol 11:812. 2015
    ..Variability in 3' isoform choice has potential implications on functional cell-to-cell heterogeneity as well as utility in resolving cell populations. ..
  45. pmc Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants
    Robert Petryszak
    European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL EBI, Hinxton, UK
    Nucleic Acids Res 44:D746-52. 2016
    ....
  46. 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
    ..This allows the automation of such tasks using the R programming language and use of existing tools in the R environment for signal processing, statistical modeling, machine learning and data visualization...
  47. 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...
  48. pmc Orchestrating high-throughput genomic analysis with Bioconductor
    Wolfgang Huber
    European Molecular Biology Laboratory, Heidelberg, Germany
    Nat Methods 12:115-21. 2015
    ..Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors. ..
  49. pmc The genomic and transcriptomic landscape of a HeLa cell line
    Jonathan J M Landry
    European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
    G3 (Bethesda) 3:1213-24. 2013
    ..This study underscores the importance of accounting for the strikingly aberrant characteristics of HeLa cells when designing and interpreting experiments, and has implications for the use of HeLa as a model of human biology. ..
  50. doi request reprint Measuring genetic interactions in human cells by RNAi and imaging
    Christina Laufer
    1 German Cancer Research Center DKFZ, Division of Signaling and Functional Genomics, Heidelberg, Germany 2 Department of Cell and Molecular Biology, Heidelberg University, Heidelberg, Germany
    Nat Protoc 9:2341-53. 2014
    ..The whole workflow, depending on the size of the experiment, takes 3 or more weeks to complete. ..
  51. pmc Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions
    Ishaan Gupta
    European Molecular Biology Laboratory EMBL, Genome Biology Unit, Heidelberg, Germany
    Mol Syst Biol 10:719. 2014
    ....
  52. pmc Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages
    Yusuke Ohnishi
    Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nat Cell Biol 16:27-37. 2014
    ..These data lead us to propose a model where stochastic cell-to-cell expression heterogeneity followed by signal reinforcement underlies ICM lineage segregation by antagonistically separating equivalent cells. ..
  53. pmc A chemical-genetic interaction map of small molecules using high-throughput imaging in cancer cells
    Marco Breinig
    Division of Signaling and Functional Genomics, German Cancer Research Center DKFZ, Heidelberg, Germany Department of Cell and Molecular Biology, Heidelberg University, Heidelberg, Germany
    Mol Syst Biol 11:846. 2015
    ..Taken together, this study demonstrates how combining multiparametric phenotyping in different genetic backgrounds can be used to predict additional mechanisms of action and to reposition clinically used drugs. ..
  54. pmc HTSeq--a Python framework to work with high-throughput sequencing data
    Simon Anders
    Genome Biology Unit, European Molecular Biology Laboratory, 69111 Heidelberg, Germany
    Bioinformatics 31:166-9. 2015
    ..A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed...
  55. pmc Highly coordinated proteome dynamics during reprogramming of somatic cells to pluripotency
    Jenny Hansson
    European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
    Cell Rep 2:1579-92. 2012
    ..Along with the identification of proteins expressed in a stage-specific manner, this study provides a rich resource toward an enhanced mechanistic understanding of cellular reprogramming...
  56. doi request reprint Tandem fluorescent protein timers for in vivo analysis of protein dynamics
    Anton Khmelinskii
    Center for Molecular Biology of the University of Heidelberg ZMBH, DKFZ ZMBH Alliance, Heidelberg, Germany
    Nat Biotechnol 30:708-14. 2012
    ..Our experiments reveal the stable nature and asymmetric inheritance of nuclear pore complexes and identify regulators of N-end rule–mediated protein degradation...
  57. pmc Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
    Danni Yu
    Genome Biology Unit, European Molecular Biology Laboratory, Mayerhofstraße 1, Heidelberg 69117, Germany
    Bioinformatics 29:1275-82. 2013
    ..However, in experiments with small sample size, the per-gene estimates of the dispersion parameter are unreliable...
  58. pmc Data-driven hypothesis weighting increases detection power in genome-scale multiple testing
    Nikolaos Ignatiadis
    European Molecular Biology Laboratory, Heidelberg, Germany
    Nat Methods 13:577-80. 2016
    ..bioconductor.org/packages/IHW). IHW increases power while controlling the false discovery rate and is a practical approach to discovering associations in genomics, high-throughput biology and other large data sets. ..
  59. pmc The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances
    Orsolya Symmons
    Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Dev Cell 39:529-543. 2016
    ..In large genomes where genomic distances per se can limit regulatory interactions, this function of TADs could be as essential for gene expression as the formation of insulated neighborhoods...
  60. pmc SomaticSignatures: inferring mutational signatures from single-nucleotide variants
    Julian S Gehring
    European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany, Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, CA 94080, USA and
    Bioinformatics 31:3673-5. 2015
    ..It facilitates large-scale, cross-dataset estimation of mutational signatures, implements existing methods for pattern decomposition, supports extension through user-defined approaches and integrates with existing Bioconductor workflows...
  61. doi request reprint Enhancer loops appear stable during development and are associated with paused polymerase
    Yad Ghavi-Helm
    European Molecular Biology Laboratory, Genome Biology Unit, D 69117 Heidelberg, Germany
    Nature 512:96-100. 2014
    ..Our results indicate that the general topology governing enhancer contacts is conserved from flies to humans and suggest that transcription initiates from preformed enhancer-promoter loops through release of paused polymerase. ..
  62. 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...
  63. pmc A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes
    Taro Tsujimura
    Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS Genet 11:e1004897. 2015
    ..Altogether, these data highlight the prime role of the topological organization of the genome in long-distance regulation of gene expression. ..
  64. pmc Addressing accuracy and precision issues in iTRAQ quantitation
    Natasha A Karp
    European Bioinformatics Institute, European Molecular Biology Laboratory Outstation, Hinxton, UK
    Mol Cell Proteomics 9:1885-97. 2010
    ....
  65. 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...
  66. 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...
  67. 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...
  68. 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...
  69. 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...
  70. 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...
  71. 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...
  72. 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...
  73. 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
  74. ncbi request reprint Top-down standards will not serve systems biology
    John Quackenbush
    Nature 440:24. 2006
  75. 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...
  76. 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...