Literature DB >> 17038341

NMPP: a user-customized NimbleGen microarray data processing pipeline.

Xiangfeng Wang1, Hang He, Lei Li, Runsheng Chen, Xing Wang Deng, Songgang Li.   

Abstract

UNLABELLED: NMPP package is a bundle of user-customized tools based on established algorithms and methods to process self-designed NimbleGen microarray data. It features a command-line-based integrative processing procedure that comprises five major functional components, namely the raw microarray data parsing and integrating module, the array spatial effect smoothing and visualization module, the probe-level multi-array normalization module, the gene expression intensity summarization module and the gene expression status inference module. AVAILABILITY: http://plantgenomics.biology.yale.edu/nmpp

Entities:  

Mesh:

Year:  2006        PMID: 17038341     DOI: 10.1093/bioinformatics/btl525

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


  19 in total

1.  WUS and STM-based reporter genes for studying meristem development in poplar.

Authors:  Y Bao; P Dharmawardhana; R Arias; M B Allen; C Ma; Steven H Strauss
Journal:  Plant Cell Rep       Date:  2009-03-12       Impact factor: 4.570

2.  Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus.

Authors:  Eli Rodgers-Melnick; Shrinivasrao P Mane; Palitha Dharmawardhana; Gancho T Slavov; Oswald R Crasta; Steven H Strauss; Amy M Brunner; Stephen P Difazio
Journal:  Genome Res       Date:  2011-10-05       Impact factor: 9.043

3.  NTAP: for NimbleGen tiling array ChIP-chip data analysis.

Authors:  Kun He; Xueyong Li; Junli Zhou; Xing-Wang Deng; Hongyu Zhao; Jingchu Luo
Journal:  Bioinformatics       Date:  2009-05-25       Impact factor: 6.937

4.  The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer.

Authors:  Mark M Pomerantz; Nasim Ahmadiyeh; Li Jia; Paula Herman; Michael P Verzi; Harshavardhan Doddapaneni; Christine A Beckwith; Jennifer A Chan; Adam Hills; Matt Davis; Keluo Yao; Sarah M Kehoe; Heinz-Josef Lenz; Christopher A Haiman; Chunli Yan; Brian E Henderson; Baruch Frenkel; Jordi Barretina; Adam Bass; Josep Tabernero; José Baselga; Meredith M Regan; J Robert Manak; Ramesh Shivdasani; Gerhard A Coetzee; Matthew L Freedman
Journal:  Nat Genet       Date:  2009-06-28       Impact factor: 38.330

5.  Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays.

Authors:  Ranjit Kumar; Pratik Shah; Edwin Swiatlo; Shane C Burgess; Mark L Lawrence; Bindu Nanduri
Journal:  BMC Genomics       Date:  2010-06-03       Impact factor: 3.969

6.  Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa.

Authors:  Palitha Dharmawardhana; Amy M Brunner; Steven H Strauss
Journal:  BMC Genomics       Date:  2010-03-04       Impact factor: 3.969

7.  Broad spectrum microarray for fingerprint-based bacterial species identification.

Authors:  Frédérique Pasquer; Cosima Pelludat; Brion Duffy; Jürg E Frey
Journal:  BMC Biotechnol       Date:  2010-02-17       Impact factor: 2.563

8.  Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development.

Authors:  Sébastien Terrat; Eric Peyretaillade; Olivier Gonçalves; Eric Dugat-Bony; Fabrice Gravelat; Anne Moné; Corinne Biderre-Petit; Delphine Boucher; Julien Troquet; Pierre Peyret
Journal:  BMC Bioinformatics       Date:  2010-09-23       Impact factor: 3.169

9.  ARTADE2DB: improved statistical inferences for Arabidopsis gene functions and structure predictions by dynamic structure-based dynamic expression (DSDE) analyses.

Authors:  Kei Iida; Shuji Kawaguchi; Norio Kobayashi; Yuko Yoshida; Manabu Ishii; Erimi Harada; Kousuke Hanada; Akihiro Matsui; Masanori Okamoto; Junko Ishida; Maho Tanaka; Taeko Morosawa; Motoaki Seki; Tetsuro Toyoda
Journal:  Plant Cell Physiol       Date:  2011-01-12       Impact factor: 4.927

10.  An integrated approach for finding overlooked genes in Shigella.

Authors:  Junping Peng; Jian Yang; Qi Jin
Journal:  PLoS One       Date:  2011-04-05       Impact factor: 3.240

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