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FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context

By Malte Mader, Ronald Simon, Sascha Steinbiss and Stefan Kurtz
Topics: Research
Publisher: BioMed Central
OAI identifier: oai:pubmedcentral.nih.gov:3164613
Provided by: PubMed Central

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Citations

  1. (2009). (CgHExpreSS): a comprehensive analysis tool for the analysis of genomic alterations and their effects on the expression profile of the genome.
  2. A: An integrative genomic approach reveals coordinated expression of intronic
  3. (2009). AE: Genoviz Software Development Kit: Java tool kit for building genomics visualization applications.
  4. (2009). AE: The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics
  5. Affymetrix Genotyping Console. [http://www.affymetrix.com/browse/ level_seven_software_products_only.jsp?
  6. (2005). Ajax: A New Approach to Web Applications.
  7. (2004). AN: Hidden Markov models approach to the analysis of array CGH data.
  8. (2009). AnnotationSketch: a genome annotation drawing library. Bioinformatics
  9. Array Data Management System.
  10. (2005). arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays.
  11. (2010). Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Res
  12. (2004). Barillot E: Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics
  13. (2006). Barillot E: CAPweb: a bioinformatics CGH array Analysis Platform. Nucleic Acids Res
  14. (2006). Barillot E: VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles. Bioinformatics
  15. (2006). BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data. Bioinformatics
  16. (2005). BL: CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data. Bioinformatics
  17. (2005). Børresen-Dale AL: CGHExplorer: a program for analysis of array-CGH data. Bioinformatics
  18. (2011). Brazma A: ArrayExpress update-an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res
  19. (2004). Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. BMC Bioinformatics
  20. (2005). Chinnaiyan AM: Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science
  21. (2005). Chung YJ: ArrayCyGHt: a web application for analysis and visualization of array-CGH data. Bioinformatics
  22. (2004). Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics
  23. (2004). Cox AV: The Ensembl Web site: mechanics of a genome browser. Genome Res
  24. (2005). Denoising array-based comparative genomic hybridization data using wavelets. Biostatistics
  25. (2008). Eldar YC: A fast and flexible method for the segmentation of aCGH data. Bioinformatics
  26. (2007). HA: Visualization of genomic aberrations using Affymetrix SNP arrays. Bioinformatics
  27. (2002). Haussler D: The human genome browser at UCSC. Genome Res
  28. (2009). IH: JBrowse: a nextgeneration genome browser. Genome Res
  29. (2007). ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling. Nucleic Acids Res
  30. (2008). Lam WL: MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data.
  31. (2006). Lam WL: SIGMA: a system for integrative genomic microarray analysis of cancer genomes.
  32. (2008). Lam WL: SIGMA2: a system for the integrative genomic multidimensional analysis of cancer genomes, epigenomes, and transcriptomes.
  33. (2002). Lewis S: The generic genome browser: a building block for a model organism system database. Genome Res
  34. (1999). losses, and amplifications of genomic materials in primary gastric cancers analyzed by comparative genomic hybridization. Genes Chromosomes Cancer
  35. (2011). Mesirov JP: Integrative genomics viewer. Nat Biotechnol
  36. (2002). Microarray data normalization and transformation.
  37. (2004). MR: A census of human cancer genes. Nat Rev Cancer
  38. (2010). Pisano DG: waviCGH: a web application for the analysis and visualization of genomic copy number alterations.
  39. (2005). R: CGHPRO - a comprehensive data analysis tool for array CGH. BMC Bioinformatics
  40. (2009). RK: A flexible rank-based framework for detecting copy number aberrations from array data. Bioinformatics
  41. (2009). S: UTGB toolkit for personalized genome browsers. Bioinformatics
  42. (2011). Searle SMJ: Ensembl 2011. Nucleic Acids Res
  43. (1997). Sidransky D: Frequent inactivation of PTEN/MMAC1 in primary prostate cancer. Cancer Res
  44. (2005). SJL: SWARRAY: a dynamic programming solution for the identification of copynumber changes in genomic DNA using array comparative genome hybridization data. Nucleic Acids Res
  45. (2011). Soboleva A: NCBI GEO: archive for functional genomics data sets-10 years on. Nucleic Acids Res
  46. (2003). Speed T: Normalization of cDNA microarray data. Methods
  47. (2009). TG: SnoopCGH: software for visualizing comparative genomic hybridization data. Bioinformatics
  48. (2005). The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res
  49. (2011). The UniProt Consortium: Ongoing and future developments at the Universal Protein Resource.
  50. (2006). TM4 microarray software suite. Methods Enzymol
  51. (2004). Troyanskaya OG: Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics
  52. (2005). Troyanskaya OG: Visualization-based discovery and analysis of genomic aberrations in microarray data.
  53. (2010). Unwin A: SEURAT: visual analytics for the integrated analysis of microarray data.
  54. (2010). WL: Integrative genomic profiling of human prostate cancer. Cancer Cell