Published in BMC Genomics on September 22, 2013
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The Influence of the Global Gene Expression Shift on Downstream Analyses. PLoS One (2016) 0.75
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Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol (2005) 31.06
Metagenomic analysis of the human distal gut microbiome. Science (2006) 29.76
Bacterial community variation in human body habitats across space and time. Science (2009) 24.84
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol (2007) 23.58
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res (2012) 19.48
Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell (2006) 18.83
Topographical and temporal diversity of the human skin microbiome. Science (2009) 15.96
Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One (2008) 14.63
Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol (2011) 13.24
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res (2007) 13.08
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Global diversity in the human salivary microbiome. Genome Res (2009) 5.16
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A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS One (2012) 4.35
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J Microbiol Methods (2009) 4.32
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Community-wide analysis of microbial genome sequence signatures. Genome Biol (2009) 3.96
Metagenomic signatures of 86 microbial and viral metagenomes. Environ Microbiol (2009) 3.30
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Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res (2003) 3.02
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Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data. BMC Bioinformatics (2006) 2.53
Alignment and clustering of phylogenetic markers--implications for microbial diversity studies. BMC Bioinformatics (2010) 2.01
DNACLUST: accurate and efficient clustering of phylogenetic marker genes. BMC Bioinformatics (2011) 1.66
Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome. Sci Rep (2012) 1.52
Comparison of metagenomic samples using sequence signatures. BMC Genomics (2012) 1.10
Assembly free comparative genomics of short-read sequence data discovers the needles in the haystack. Mol Ecol (2010) 1.03
Role of gut microbiota in Crohn's disease. Expert Rev Gastroenterol Hepatol (2009) 1.02
Retracted The microbiota in inflammatory bowel disease in different age groups. Dig Dis (2009) 0.99
Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data. Bioinformatics (2011) 0.99
A comprehensive evaluation of multicategory classification methods for microbiomic data. Microbiome (2013) 0.95
HabiSign: a novel approach for comparison of metagenomes and rapid identification of habitat-specific sequences. BMC Bioinformatics (2011) 0.94
Selecting age-related functional characteristics in the human gut microbiome. Microbiome (2013) 0.85
Prebiotics, probiotics and helminths: the 'natural' solution? Dig Dis (2009) 0.81
OTU analysis using metagenomic shotgun sequencing data. PLoS One (2012) 0.78
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics (2009) 14.83
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
Meta-analysis of genome-wide association studies identifies common variants associated with blood pressure variation in east Asians. Nat Genet (2011) 4.04
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics (2005) 3.69
MicroRNA identification based on sequence and structure alignment. Bioinformatics (2005) 2.52
Predicting features of breast cancer with gene expression patterns. Breast Cancer Res Treat (2007) 2.49
Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq. Bioinformatics (2010) 2.17
Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq. J Bioinform Comput Biol (2010) 1.78
Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases. Genome Res (2012) 1.59
CpG island methylation pattern in different human tissues and its correlation with gene expression. Biochem Biophys Res Commun (2009) 1.58
Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome. Sci Rep (2012) 1.52
Predicting methylation status of CpG islands in the human brain. Bioinformatics (2006) 1.38
Computing exact P-values for DNA motifs. Bioinformatics (2007) 1.33
The effect of GeneChip gene definitions on the microarray study of cancers. Bioessays (2006) 1.32
Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. Genomics (2008) 1.31
Primary transcripts and expressions of mammal intergenic microRNAs detected by mapping ESTs to their flanking sequences. Mamm Genome (2006) 1.21
Array comparative genome hybridization for tumor classification and gene discovery in mouse models of malignant melanoma. Cancer Res (2003) 1.12
Significance of gene ranking for classification of microarray samples. IEEE/ACM Trans Comput Biol Bioinform (2006) 1.10
Comparison of metagenomic samples using sequence signatures. BMC Genomics (2012) 1.10
Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes. BMC Bioinformatics (2012) 1.08
Prediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach. Proteins (2008) 1.07
A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data. Am J Hum Genet (2006) 1.04
The impact of very short alternative splicing on protein structures and functions in the human genome. Trends Genet (2004) 1.04
The effect of haplotype-block definitions on inference of haplotype-block structure and htSNPs selection. Mol Biol Evol (2004) 1.00
htSNPer1.0: software for haplotype block partition and htSNPs selection. BMC Bioinformatics (2005) 0.99
Opportunities and methods for studying alternative splicing in cancer with RNA-Seq. Cancer Lett (2012) 0.99
Identifying differentially spliced genes from two groups of RNA-seq samples. Gene (2012) 0.99
An overview of hepatocellular carcinoma study by omics-based methods. Acta Biochim Biophys Sin (Shanghai) (2009) 0.97
Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic. PLoS Comput Biol (2013) 0.97
Characterization and prediction of lysine (K)-acetyl-transferase specific acetylation sites. Mol Cell Proteomics (2011) 0.95
Histone methylation marks play important roles in predicting the methylation status of CpG islands. Biochem Biophys Res Commun (2008) 0.93
Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila. BMC Bioinformatics (2007) 0.91
Computational prediction of associations between long non-coding RNAs and proteins. BMC Genomics (2013) 0.90
Putative zinc finger protein binding sites are over-represented in the boundaries of methylation-resistant CpG islands in the human genome. PLoS One (2007) 0.90
Molecular classification of liver cirrhosis in a rat model by proteomics and bioinformatics. Proteomics (2004) 0.89
Evidence and characteristics of putative human alpha recombination hotspots. Hum Mol Genet (2004) 0.89
NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data. BMC Bioinformatics (2013) 0.89
Interaction between variants of two glycosyltransferase genes in IgA nephropathy. Kidney Int (2009) 0.86
OSCAR: one-class SVM for accurate recognition of cis-elements. Bioinformatics (2007) 0.86
Gene-set analysis identifies master transcription factors in developmental courses. Genomics (2009) 0.85
Symptom combinations associated with outcome and therapeutic effects in a cohort of cases with SARS. Am J Chin Med (2006) 0.84
Sequence alignment as hypothesis testing. J Comput Biol (2011) 0.83
Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. Nucleic Acids Res (2013) 0.83
Comparison of gene expression in hepatocellular carcinoma, liver development, and liver regeneration. Mol Genet Genomics (2010) 0.83
The fetal mouse is a sensitive genotoxicity model that exposes lentiviral-associated mutagenesis resulting in liver oncogenesis. Mol Ther (2012) 0.82
Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite. BMC Syst Biol (2011) 0.82
Multi-locus penetrance variance analysis method for association study in complex diseases. Hum Hered (2005) 0.82
Global network analysis of lipid-raft-related proteins reveals their centrality in the network and their roles in multiple biological processes. J Mol Biol (2010) 0.81
Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse. BMC Genomics (2008) 0.81
The effect of U1 snRNA binding free energy on the selection of 5' splice sites. Biochem Biophys Res Commun (2005) 0.81
Multi-locus association study of schizophrenia susceptibility genes with a posterior probability method. Sci China C Life Sci (2005) 0.80
Observations on novel splice junctions from RNA sequencing data. Biochem Biophys Res Commun (2011) 0.80
Common variants in the ATP2B1 gene are associated with hypertension and arterial stiffness in Chinese population. Mol Biol Rep (2012) 0.79
Prediction of transcription start sites based on feature selection using AMOSA. Comput Syst Bioinformatics Conf (2007) 0.79
Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma. BMC Bioinformatics (2013) 0.77
Network-based group variable selection for detecting expression quantitative trait loci (eQTL). BMC Bioinformatics (2011) 0.77
Predicting the fate of microRNA target genes based on sequence features. J Theor Biol (2009) 0.77
RNAseqViewer: visualization tool for RNA-Seq data. Bioinformatics (2013) 0.76
Observations on shifted cumulative regulation. Genome Biol (2011) 0.75
Prioritizing genes responsible for host resistance to influenza using network approaches. BMC Genomics (2013) 0.75
Finding distinct biclusters from background in gene expression matrices. Bioinformation (2007) 0.75
The Seventh Asia Pacific Bioinformatics Conference (APBC2009). BMC Bioinformatics (2009) 0.75
MYH9-related disease: description of a large Chinese pedigree and a survey of reported mutations. Acta Haematol (2014) 0.75
Sequence signatures of genes with accompanying antisense transcripts in Saccharomyces cerevisiae. Sci China Life Sci (2013) 0.75
Karyotyping of comparative genomic hybridization human metaphases by using support vector machines. Cytometry (2002) 0.75
Integrative data mining in systems biology: from text to network mining. Artif Intell Med (2007) 0.75
Short read mapping for exome sequencing. Methods Mol Biol (2013) 0.75