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.refereed research


Genome Biology aims to provide the best possible service to authors and readers of primary research articles. The method section publishes peer-reviewed methods in all areas of molecular, cellular, organismal and population biology that are informed by genomics. All method articles are made available free to individuals through the web, and there are no restrictions on article length or on the types of information that can be included. The publication schedule is very fast, using electronic systems for article delivery, proofing and peer-review. For more details about how methods are published in Genome Biology, and for instructions for authors,see 'about refereed research'.
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Methods

Singular value decomposition-based regression identifies activation of endogenous signaling pathways in vivo

Method    
Zhandong Liu, Min Wang, James V Alvarez, Megan E Bonney, Chien-chung Chen, Celina D'cruz, Tien-chi Pan, Mahlet G Tadesse, Lewis A Chodosh
(18 December 2008)

Singular value decomposition regression can detect the activation of endogenous signaling pathways, allowing the identification of pathway cross-talk.

[Abstract] [Provisional PDF]

KEGG spider: interpretation of genomics data in the context of the global gene metabolic network

Method    
Alexey V Antonov, Sabine Dietmann, Hans W Mewes
(18 December 2008)

A web-based tool for interpretation of experimentally-derived gene lists that provides global models uniting genes from different metabolic pathways.

[Abstract] [Provisional PDF]

Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum

Method    
Kevin Brick, Junichi Watanabe, Elisabetta Pizzi
(18 December 2008)

A method is presented to computationally identify core promoters in the Plasmodium falciparum genome using only DNA physicochemical properties

[Abstract] [Provisional PDF]

Prioritizing functional modules mediating genetic perturbations and their phenotypic effects: a global strategy

Method    
Li Wang, Fengzhu Sun, Ting Chen
(16 December 2008)

A strategy is presented to prioritize the functional modules that mediate genetic perturbations and their phenotypic effects among candidate modules.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

Annotating genomes with massive-scale RNA-sequencing

Method    
France Denoeud, Jean-Marc Aury, Corinne Da Silva, Benjamin Noel, Odile Rogier, Massimo Delledonne, Michele Morgante, Giorgio Valle, Patrick Wincker, Claude Scarpelli, Olivier Jaillon, Francois Artiguenave
(16 December 2008)

A method for de novo genome annotation using high-throughput cDNA sequencing data

[Abstract] [Provisional PDF]

Whole genome transcriptome polymorphisms in Arabidopsis thaliana

Method    
Xu Zhang, Jake K Byrnes, Thomas S Gal, Wen-Hsiung Li, Justin O Borevitz
(24 November 2008)

New methods for detecting global patterns of gene expression and splicing variation in natural Arabidopsis thaliana populations.

[Abstract] [Full text] [PDF] [PubMed] [Related articles]

Boolean implication networks derived from large scale, whole genome microarray datasets

Method    
Debashis Sahoo, David L Dill, Andrew J Gentles, Robert Tibshirani, Sylvia K Plevritis
(30 October 2008)

A method for analysis of microarray data is presented that extracts statistically significant Boolean implication relationships between pairs of genes.

[Abstract] [Full text] [PDF] [PubMed] [Related articles]

A simple, fast, and accurate method of phylogenomic inference

Method    
Martin Wu, Jonathan A Eisen
(13 October 2008)

An automated pipeline for phylogenomic analysis (AMPHORA) is presented that overcomes existing limits to large-scale protein phylogenetic inference.

[Abstract] [Full text] [PDF] [PubMed] [Related articles]

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