Title	Publication Date	Language	Citations
The RAST Server: Rapid Annotations using Subsystems Technology	2008/02/08	English	8,544
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons	2011/08/08	English	2,161
The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification evaluation	2020/01/02	English	2,015
Centering, scaling, and transformations: improving the biological information content of metabolomics data	2006/06/08	English	1,541
Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics	2018/06/19	English	1,056
The molecular portraits of breast tumors are conserved across microarray platforms	2006/04/27	English	928
Characterization of human plasma-derived exosomal RNAs by deep sequencing	2013/05/10	English	707
A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains	2007/02/01	English	683
A data-driven approach to preprocessing Illumina 450K methylation array data	2013/05/01	English	667
BioMart – biological queries made easy	2009/01/14	English	534
Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential	2015/11/17	English	479
WebMGA: a customizable web server for fast metagenomic sequence analysis	2011/09/07	English	477
MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress	2007/07/18	English	444
A universal DNA mini-barcode for biodiversity analysis	2008/05/12	English	440
Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing	2015/01/02	English	426
Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources?	2009/03/12	English	396
A genome-wide association study of seed protein and oil content in soybean	2014/01/02	English	393
Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma	2006/10/09	English	392
Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications	2008/12/01	English	386
Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis	2012/10/10	English	385
Selective extracellular vesicle-mediated export of an overlapping set of microRNAs from multiple cell types	2012/08/01	English	379
Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote	2004/10/12	English	368
Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay	2009/05/08	English	359
Correlations between RNA and protein expression profiles in 23 human cell lines	2009/08/07	English	347
Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi	2013/04/23	English	335
H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells	2012/08/24	English	334
High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome	2008/06/30	English	328
CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers	2015/03/25	English	327
De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)	2010/12/01	English	321
Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis	2006/12/01	English	318