Published in BMC Bioinformatics on October 10, 2017
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (2010) 53.23
Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics (2014) 44.23
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol (2013) 32.42
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol (2014) 27.48
Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics (2010) 26.76
HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics (2014) 23.22
WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics (2008) 18.58
A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol (2005) 17.23
The Sorghum bicolor genome and the diversification of grasses. Nature (2009) 14.62
An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets. PLoS One (2007) 9.60
InterProScan 5: genome-scale protein function classification. Bioinformatics (2014) 8.52
Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics (2008) 7.12
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics (2003) 3.24
HISAT: a fast spliced aligner with low memory requirements. Nat Methods (2015) 2.83
Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat Genet (2015) 2.51
Protein function prediction using local 3D templates. J Mol Biol (2005) 2.13
PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell (2011) 2.13
Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm. Plant Physiol (2009) 1.61
Biosynthesis of antinutritional alkaloids in solanaceous crops is mediated by clustered genes. Science (2013) 1.60
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol (2015) 1.53
Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays. PLoS One (2013) 1.40
Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol (2012) 1.30
Utilizing RNA-Seq data for de novo coexpression network inference. Bioinformatics (2012) 1.28
Towards revealing the functions of all genes in plants. Trends Plant Sci (2013) 1.24
Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice. Plant Physiol (2011) 1.21
Genevestigator transcriptome meta-analysis and biomarker search using rice and barley gene expression databases. Mol Plant (2008) 1.21
Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana. Bioinformatics (2013) 1.19
Guidance for RNA-seq co-expression network construction and analysis: safety in numbers. Bioinformatics (2015) 1.01
AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species. Nucleic Acids Res (2014) 0.98
PaGenBase: a pattern gene database for the global and dynamic understanding of gene function. PLoS One (2013) 0.88
Elucidating gene function and function evolution through comparison of co-expression networks of plants. Front Plant Sci (2014) 0.87