Published in BMC Bioinformatics on January 30, 2009
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
Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A (2004) 6.08
A dynamic programming algorithm for haplotype block partitioning. Proc Natl Acad Sci U S A (2002) 5.12
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
High-resolution human genome structure by single-molecule analysis. Proc Natl Acad Sci U S A (2010) 2.47
Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi. Genome Res (2007) 2.37
A single molecule scaffold for the maize genome. PLoS Genet (2009) 2.33
Distributional regimes for the number of k-word matches between two random sequences. Proc Natl Acad Sci U S A (2002) 2.20
Alignment-free sequence comparison (I): statistics and power. J Comput Biol (2009) 2.18
Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq. Bioinformatics (2010) 2.17
Alignment of optical maps. J Comput Biol (2006) 1.88
HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics (2004) 1.86
Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq. J Bioinform Comput Biol (2010) 1.78
Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. Genome Res (2004) 1.74
An algorithm for assembly of ordered restriction maps from single DNA molecules. Proc Natl Acad Sci U S A (2006) 1.63
Systematic discovery of functional modules and context-specific functional annotation of human genome. Bioinformatics (2007) 1.61
A graph-based approach to systematically reconstruct human transcriptional regulatory modules. Bioinformatics (2007) 1.59
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
Alignment-free sequence comparison (II): theoretical power of comparison statistics. J Comput Biol (2010) 1.52
Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome. Sci Rep (2012) 1.52
Estimating the repeat structure and length of DNA sequences using L-tuples. Genome Res (2003) 1.41
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
An Eulerian path approach to local multiple alignment for DNA sequences. Proc Natl Acad Sci U S A (2005) 1.21
Primary transcripts and expressions of mammal intergenic microRNAs detected by mapping ESTs to their flanking sequences. Mamm Genome (2006) 1.21
Haplotype reconstruction from SNP alignment. J Comput Biol (2004) 1.20
Refinement of optical map assemblies. Bioinformatics (2006) 1.17
Gene Aging Nexus: a web database and data mining platform for microarray data on aging. Nucleic Acids Res (2006) 1.14
Integrative analysis of many weighted co-expression networks using tensor computation. PLoS Comput Biol (2011) 1.12
New Generations: Sequencing Machines and Their Computational Challenges. J Comput Sci Technol (2010) 1.12
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
New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. Brief Bioinform (2013) 1.07
Prediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach. Proteins (2008) 1.07
New powerful statistics for alignment-free sequence comparison under a pattern transfer model. J Theor Biol (2011) 1.05
The impact of very short alternative splicing on protein structures and functions in the human genome. Trends Genet (2004) 1.04
A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data. Am J Hum Genet (2006) 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 Eulerian path approach to global multiple alignment for DNA sequences. J Comput Biol (2003) 0.98
Integrative missing value estimation for microarray data. BMC Bioinformatics (2006) 0.97
An overview of hepatocellular carcinoma study by omics-based methods. Acta Biochim Biophys Sin (Shanghai) (2009) 0.97
The power of detecting enriched patterns: an HMM approach. J Comput Biol (2010) 0.97
Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic. PLoS Comput Biol (2013) 0.97
Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data. Am J Hum Genet (2003) 0.96
An integrative network approach to map the transcriptome to the phenome. J Comput Biol (2009) 0.95
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
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
Molecular classification of liver cirrhosis in a rat model by proteomics and bioinformatics. Proteomics (2004) 0.89
Accuracy assessment of diploid consensus sequences. IEEE/ACM Trans Comput Biol Bioinform (2007) 0.88
OSCAR: one-class SVM for accurate recognition of cis-elements. Bioinformatics (2007) 0.86
Interaction between variants of two glycosyltransferase genes in IgA nephropathy. Kidney Int (2009) 0.86
Gene-set analysis identifies master transcription factors in developmental courses. Genomics (2009) 0.85
An integrative modular approach to systematically predict gene-phenotype associations. BMC Bioinformatics (2010) 0.85
Alignment-free supervised classification of metagenomes by recursive SVM. BMC Genomics (2013) 0.84
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
A geometric interpretation for local alignment-free sequence comparison. J Comput Biol (2013) 0.83
Multi-locus penetrance variance analysis method for association study in complex diseases. Hum Hered (2005) 0.82
Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite. BMC Syst Biol (2011) 0.82
The fetal mouse is a sensitive genotoxicity model that exposes lentiviral-associated mutagenesis resulting in liver oncogenesis. Mol Ther (2012) 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
The effect of U1 snRNA binding free energy on the selection of 5' splice sites. Biochem Biophys Res Commun (2005) 0.81
Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse. BMC Genomics (2008) 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
HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome. Bioinformatics (2009) 0.79
Prediction of transcription start sites based on feature selection using AMOSA. Comput Syst Bioinformatics Conf (2007) 0.79
Common variants in the ATP2B1 gene are associated with hypertension and arterial stiffness in Chinese population. Mol Biol Rep (2012) 0.79
A quantile method for sizing optical maps. J Comput Biol (2007) 0.78
On the length of the longest exact position match in a random sequence. IEEE/ACM Trans Comput Biol Bioinform (2007) 0.78
Network-based group variable selection for detecting expression quantitative trait loci (eQTL). BMC Bioinformatics (2011) 0.77
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
Predicting the fate of microRNA target genes based on sequence features. J Theor Biol (2009) 0.77
Normal and compound poisson approximations for pattern occurrences in NGS reads. J Comput Biol (2012) 0.76
RNAseqViewer: visualization tool for RNA-Seq data. Bioinformatics (2013) 0.76
Prioritizing genes responsible for host resistance to influenza using network approaches. BMC Genomics (2013) 0.75
Observations on shifted cumulative regulation. Genome Biol (2011) 0.75
Finding distinct biclusters from background in gene expression matrices. Bioinformation (2007) 0.75
Short read mapping for exome sequencing. Methods Mol Biol (2013) 0.75
MYH9-related disease: description of a large Chinese pedigree and a survey of reported mutations. Acta Haematol (2014) 0.75