Literature DB >> 15201182

Breakpoint identification and smoothing of array comparative genomic hybridization data.

Kees Jong1, Elena Marchiori, Gerrit Meijer, A V D Vaart, Bauke Ylstra.   

Abstract

SUMMARY: We describe a tool, called aCGH-Smooth, for the automated identification of breakpoints and smoothing of microarray comparative genomic hybridization (array CGH) data. aCGH-Smooth is written in visual C++, has a user-friendly interface including a visualization of the results and user-defined parameters adapting the performance of data smoothing and breakpoint recognition. aCGH-Smooth can handle array-CGH data generated by all array-CGH platforms: BAC, PAC, cosmid, cDNA and oligo CGH arrays. The tool has been successfully applied to real-life data. AVAILABILITY: aCGH-Smooth is free for researchers at academic and non-profit institutions at http://www.few.vu.nl/~vumarray/.

Entities:  

Mesh：

Year:  2004        PMID： 15201182     DOI： 10.1093/bioinformatics/bth355

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  66 in total

1.  Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data.

Authors:  Weil R Lai; Mark D Johnson; Raju Kucherlapati; Peter J Park
Journal:  Bioinformatics       Date:  2005-08-04       Impact factor: 6.937

2.  High-resolution mapping identifies a commonly amplified 11q13.3 region containing multiple genes flanked by segmental duplications.

Authors:  Johan H Gibcus; Klaas Kok; Lorian Menkema; Mario A Hermsen; Mirjam Mastik; Philip M Kluin; Jacqueline E van der Wal; Ed Schuuring
Journal:  Hum Genet       Date:  2006-12-15       Impact factor: 4.132

3.  Generation and characterization of novel canine malignant mast cell line CL1.

Authors:  Tzu-Yin Lin; Rachael Thomas; Pei-Chien Tsai; Matthew Breen; Cheryl A London
Journal:  Vet Immunol Immunopathol       Date:  2008-10-11       Impact factor: 2.046

4.  MSB: a mean-shift-based approach for the analysis of structural variation in the genome.

Authors:  Lu-Yong Wang; Alexej Abyzov; Jan O Korbel; Michael Snyder; Mark Gerstein
Journal:  Genome Res       Date:  2008-11-26       Impact factor: 9.043

5.  Bayesian Frequentist hybrid Model wth Application to the Analysis of Gene Copy Number Changes.

Authors:  Ao Yuan; Guanjie Chen; Juan Xiong; Wenqing He; Charles Rotimi
Journal:  J Appl Stat       Date:  2011       Impact factor: 1.404

6.  YEATS4 is a novel oncogene amplified in non-small cell lung cancer that regulates the p53 pathway.

Authors:  Larissa A Pikor; William W Lockwood; Kelsie L Thu; Emily A Vucic; Raj Chari; Adi F Gazdar; Stephen Lam; Wan L Lam
Journal:  Cancer Res       Date:  2013-10-29       Impact factor: 12.701

7.  Integrative molecular characterization of head and neck cancer cell model genomes.

Authors:  Ivy F L Tsui; Cathie Garnis
Journal:  Head Neck       Date:  2010-09       Impact factor: 3.147

8.  Extensive genomic copy number variation in embryonic stem cells.

Authors:  Qi Liang; Nathalie Conte; William C Skarnes; Allan Bradley
Journal:  Proc Natl Acad Sci U S A       Date:  2008-11-06       Impact factor: 11.205

9.  Overlay tool for aCGHViewer: an analysis module built for aCGHViewer used to perform comparisons of data derived from different microarray platforms.

Authors:  Ken C Lo; Ganesh Shankar; Yaron Turpaz; Dione Bailey; Michael R Rossi; Tania Burkhardt; Ping Liang; John K Cowell
Journal:  Cancer Inform       Date:  2007-08-08

10.  Normalized, segmented or called aCGH data?

Authors:  Wessel N van Wieringen; Mark A van de Wiel; Bauke Ylstra
Journal:  Cancer Inform       Date:  2007-09-17
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