Literature DB >> 21257608

Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup.

Andrew T Magis1, John C Earls, Youn-Hee Ko, James A Eddy, Nathan D Price.   

Abstract

SUMMARY: The top-scoring pair (TSP) and top-scoring triplet (TST) algorithms are powerful methods for classification from expression data, but analysis of all combinations across thousands of human transcriptome samples is computationally intensive, and has not yet been achieved for TST. Implementation of these algorithms for the graphics processing unit results in dramatic speedup of two orders of magnitude, greatly increasing the searchable combinations and accelerating the pace of discovery. AVAILABILITY: http://www.igb.illinois.edu/labs/price/downloads/.

Entities:  

Mesh：

Year:  2011        PMID： 21257608      PMCID： PMC3051334          DOI： 10.1093/bioinformatics/btr033

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


  12 in total

1.  Knowledge-based analysis of microarray gene expression data by using support vector machines.

Authors:  M P Brown; W N Grundy; D Lin; N Cristianini; C W Sugnet; T S Furey; M Ares; D Haussler
Journal:  Proc Natl Acad Sci U S A       Date:  2000-01-04       Impact factor: 11.205

2.  Stem cell transcriptome profiling via massive-scale mRNA sequencing.

Authors:  Nicole Cloonan; Alistair R R Forrest; Gabriel Kolle; Brooke B A Gardiner; Geoffrey J Faulkner; Mellissa K Brown; Darrin F Taylor; Anita L Steptoe; Shivangi Wani; Graeme Bethel; Alan J Robertson; Andrew C Perkins; Stephen J Bruce; Clarence C Lee; Swati S Ranade; Heather E Peckham; Jonathan M Manning; Kevin J McKernan; Sean M Grimmond
Journal:  Nat Methods       Date:  2008-05-30       Impact factor: 28.547

3.  GPU-accelerated molecular modeling coming of age.

Authors:  John E Stone; David J Hardy; Ivan S Ufimtsev; Klaus Schulten
Journal:  J Mol Graph Model       Date:  2010-07-08       Impact factor: 2.518

4.  Classifying gene expression profiles from pairwise mRNA comparisons.

Authors:  Donald Geman; Christian d'Avignon; Daniel Q Naiman; Raimond L Winslow
Journal:  Stat Appl Genet Mol Biol       Date:  2004-08-30

Review 5.  Relative expression analysis for molecular cancer diagnosis and prognosis.

Authors:  James A Eddy; Jaeyun Sung; Donald Geman; Nathan D Price
Journal:  Technol Cancer Res Treat       Date:  2010-04

6.  Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks.

Authors:  J Khan; J S Wei; M Ringnér; L H Saal; M Ladanyi; F Westermann; F Berthold; M Schwab; C R Antonescu; C Peterson; P S Meltzer
Journal:  Nat Med       Date:  2001-06       Impact factor: 53.440

7.  Cell and tumor classification using gene expression data: construction of forests.

Authors:  Heping Zhang; Chang-Yung Yu; Burton Singer
Journal:  Proc Natl Acad Sci U S A       Date:  2003-03-17       Impact factor: 11.205

8.  Simple decision rules for classifying human cancers from gene expression profiles.

Authors:  Aik Choon Tan; Daniel Q Naiman; Lei Xu; Raimond L Winslow; Donald Geman
Journal:  Bioinformatics       Date:  2005-08-16       Impact factor: 6.937

9.  Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas.

Authors:  Nathan D Price; Jonathan Trent; Adel K El-Naggar; David Cogdell; Ellen Taylor; Kelly K Hunt; Raphael E Pollock; Leroy Hood; Ilya Shmulevich; Wei Zhang
Journal:  Proc Natl Acad Sci U S A       Date:  2007-02-21       Impact factor: 11.205

10.  The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations.

Authors:  Xue Lin; Bahman Afsari; Luigi Marchionni; Leslie Cope; Giovanni Parmigiani; Daniel Naiman; Donald Geman
Journal:  BMC Bioinformatics       Date:  2009-08-20       Impact factor: 3.169
View more
  5 in total

1.  Evolutionary approach for relative gene expression algorithms.

Authors:  Marcin Czajkowski; Marek Kretowski
Journal:  ScientificWorldJournal       Date:  2014-03-23

2.  Bridging cancer biology with the clinic: relative expression of a GRHL2-mediated gene-set pair predicts breast cancer metastasis.

Authors:  Xinan Yang; Prabhakaran Vasudevan; Vishwas Parekh; Aleks Penev; John M Cunningham
Journal:  PLoS One       Date:  2013-02-18       Impact factor: 3.240

3.  AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures.

Authors:  John C Earls; James A Eddy; Cory C Funk; Younhee Ko; Andrew T Magis; Nathan D Price
Journal:  BMC Bioinformatics       Date:  2013-03-05       Impact factor: 3.169

4.  The top-scoring 'N' algorithm: a generalized relative expression classification method from small numbers of biomolecules.

Authors:  Andrew T Magis; Nathan D Price
Journal:  BMC Bioinformatics       Date:  2012-09-11       Impact factor: 3.169

Review 5.  Discovering epistasis in large scale genetic association studies by exploiting graphics cards.

Authors:  Gary K Chen; Yunfei Guo
Journal:  Front Genet       Date:  2013-12-03       Impact factor: 4.599
  5 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.