Published in Bioinformatics on November 04, 2008
Statistical inferences for isoform expression in RNA-Seq. Bioinformatics (2009) 12.50
RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics (2009) 10.74
Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol (2010) 6.10
Quantitative comparison of immunohistochemical staining measured by digital image analysis versus pathologist visual scoring. Diagn Pathol (2012) 2.03
The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events. RNA Biol (2009) 1.57
Differential splicing using whole-transcript microarrays. BMC Bioinformatics (2009) 1.02
Evolution of alternative splicing in primate brain transcriptomes. Hum Mol Genet (2010) 0.99
The translational landscape of the splicing factor SRSF1 and its role in mitosis. Elife (2014) 0.89
Sudemycin E influences alternative splicing and changes chromatin modifications. Nucleic Acids Res (2014) 0.88
Development of multigene expression signature maps at the protein level from digitized immunohistochemistry slides. PLoS One (2012) 0.88
Role of HGF in obesity-associated tumorigenesis: C3(1)-TAg mice as a model for human basal-like breast cancer. Breast Cancer Res Treat (2013) 0.87
Hybridization modeling of oligonucleotide SNP arrays for accurate DNA copy number estimation. Nucleic Acids Res (2009) 0.85
Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays. BMC Bioinformatics (2010) 0.83
Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure. Nucleic Acids Res (2013) 0.82
ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking. BMC Bioinformatics (2013) 0.82
Genome wide array analysis indicates that an amyotrophic lateral sclerosis mutation of FUS causes an early increase of CAMK2N2 in vitro. Biochim Biophys Acta (2013) 0.81
Integrative genomics and transcriptomics analysis of human embryonic and induced pluripotent stem cells. BioData Min (2014) 0.81
Valproic acid causes proteasomal degradation of DICER and influences miRNA expression. PLoS One (2013) 0.80
A robust estimation of exon expression to identify alternative spliced genes applied to human tissues and cancer samples. BMC Genomics (2014) 0.77
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (2003) 100.88
Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A (2001) 68.44
SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics (2008) 39.08
SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics (2008) 24.32
Ensembl 2007. Nucleic Acids Res (2006) 20.10
Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A (2006) 13.68
A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev (2007) 5.83
MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA (2008) 5.78
Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol (2007) 5.53
Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. BMC Bioinformatics (2006) 3.44
Detection and measurement of alternative splicing using splicing-sensitive microarrays. Methods (2005) 3.21
Probe selection and expression index computation of Affymetrix Exon Arrays. PLoS One (2006) 3.03
Exon arrays provide accurate assessments of gene expression. Genome Biol (2007) 2.86
Alternative splicing events identified in human embryonic stem cells and neural progenitors. PLoS Comput Biol (2007) 2.71
Applications of DNA microarrays in biology. Annu Rev Biochem (2005) 2.58
Comparing whole genomes using DNA microarrays. Nat Rev Genet (2008) 2.27
Sequence dependence of cross-hybridization on short oligo microarrays. Nucleic Acids Res (2005) 1.82
Replacing cRNA targets with cDNA reduces microarray cross-hybridization. Nat Biotechnol (2006) 1.49
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation. BMC Bioinformatics (2007) 1.32
SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics (2008) 24.32
A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J Neurosci (2008) 17.27
An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol (2008) 13.96
Statistical inferences for isoform expression in RNA-Seq. Bioinformatics (2009) 12.50
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res (2010) 6.95
dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics (2004) 6.78
Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol (2010) 6.10
MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA (2008) 5.78
Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat Genet (2011) 5.73
TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics (2005) 5.68
Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell (2012) 5.62
Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet (2010) 5.44
The mitochondrial phosphatase PGAM5 functions at the convergence point of multiple necrotic death pathways. Cell (2012) 4.37
Identifiability of isoform deconvolution from junction arrays and RNA-Seq. Bioinformatics (2009) 4.32
Transitive functional annotation by shortest-path analysis of gene expression data. Proc Natl Acad Sci U S A (2002) 3.93
Comparative epidemiology of human infections with avian influenza A H7N9 and H5N1 viruses in China: a population-based study of laboratory-confirmed cases. Lancet (2013) 3.77
The bifunctional microRNA miR-9/miR-9* regulates REST and CoREST and is downregulated in Huntington's disease. J Neurosci (2008) 3.62
Clinical application of massively parallel sequencing-based prenatal noninvasive fetal trisomy test for trisomies 21 and 18 in 11,105 pregnancies with mixed risk factors. Prenat Diagn (2012) 3.54
Novel mechanisms of T-cell and dendritic cell activation revealed by profiling of psoriasis on the 63,100-element oligonucleotide array. Physiol Genomics (2003) 3.39
Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays. PLoS Comput Biol (2006) 3.39
ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis. Nucleic Acids Res (2003) 3.31
Functional annotation and network reconstruction through cross-platform integration of microarray data. Nat Biotechnol (2005) 3.30
Probe selection and expression index computation of Affymetrix Exon Arrays. PLoS One (2006) 3.03
ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci U S A (2009) 2.96
A gene regulatory network in mouse embryonic stem cells. Proc Natl Acad Sci U S A (2007) 2.94
Exon arrays provide accurate assessments of gene expression. Genome Biol (2007) 2.86
ASAP: the Alternative Splicing Annotation Project. Nucleic Acids Res (2003) 2.83
Assessing the impact of alternative splicing on domain interactions in the human proteome. J Proteome Res (2004) 2.71
Structure and activity of putative intronic miRNA promoters. RNA (2010) 2.50
Nonallele-specific silencing of mutant and wild-type huntingtin demonstrates therapeutic efficacy in Huntington's disease mice. Mol Ther (2009) 2.47
An ESRP-regulated splicing programme is abrogated during the epithelial-mesenchymal transition. EMBO J (2010) 2.42
Correlation of obesity and osteoporosis: effect of fat mass on the determination of osteoporosis. J Bone Miner Res (2008) 2.40
Evolutionary history of GS3, a gene conferring grain length in rice. Genetics (2009) 2.33
Diaphyseal bone formation in murine tibiae in response to knee loading. J Appl Physiol (1985) (2006) 2.32
How is mRNA expression predictive for protein expression? A correlation study on human circulating monocytes. Acta Biochim Biophys Sin (Shanghai) (2008) 2.19
Comprehensive comparison of three commercial human whole-exome capture platforms. Genome Biol (2011) 2.15
MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res (2012) 2.09
A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Res (2010) 2.07
Improving PacBio long read accuracy by short read alignment. PLoS One (2012) 2.06
Global analysis of alternative splicing differences between humans and chimpanzees. Genes Dev (2007) 2.00
Completely phased genome sequencing through chromosome sorting. Proc Natl Acad Sci U S A (2010) 1.96
Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation. Nucleic Acids Res (2004) 1.93
Risk factors for severe illness with 2009 pandemic influenza A (H1N1) virus infection in China. Clin Infect Dis (2011) 1.87
Assessing the conservation of mammalian gene expression using high-density exon arrays. Mol Biol Evol (2007) 1.81
Six2 and Wnt regulate self-renewal and commitment of nephron progenitors through shared gene regulatory networks. Dev Cell (2012) 1.75
Laparoscopy versus open distal gastrectomy for advanced gastric cancer: a systematic review and meta-analysis. Surg Laparosc Endosc Percutan Tech (2013) 1.72
A strategy for ZnO nanorod mediated multi-mode cancer treatment. Biomaterials (2010) 1.70
Human transcriptome array for high-throughput clinical studies. Proc Natl Acad Sci U S A (2011) 1.62
Novel functions of the phosphatidylinositol metabolic pathway discovered by a chemical genomics screen with wortmannin. Proc Natl Acad Sci U S A (2003) 1.61
Fast and accurate read alignment for resequencing. Bioinformatics (2012) 1.58
The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events. RNA Biol (2009) 1.57
Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation. Proc Natl Acad Sci U S A (2012) 1.54
Failure to vaccinate Medicare inpatients: a missed opportunity. Arch Intern Med (2002) 1.54
Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genet (2008) 1.52
Genome-wide determination of a broad ESRP-regulated posttranscriptional network by high-throughput sequencing. Mol Cell Biol (2012) 1.49
Depolarization and CaM kinase IV modulate NMDA receptor splicing through two essential RNA elements. PLoS Biol (2007) 1.49
Statistical Modeling of RNA-Seq Data. Stat Sci (2011) 1.49
Characterization of the human ESC transcriptome by hybrid sequencing. Proc Natl Acad Sci U S A (2013) 1.48
Noninvasive Fetal Trisomy (NIFTY) test: an advanced noninvasive prenatal diagnosis methodology for fetal autosomal and sex chromosomal aneuploidies. BMC Med Genomics (2012) 1.45
Identification of sequence variants in genetic disease-causing genes using targeted next-generation sequencing. PLoS One (2011) 1.44
Adenosine deamination in human transcripts generates novel microRNA binding sites. Hum Mol Genet (2009) 1.43
NOTCH1 mutations in T-cell acute lymphoblastic leukemia: prognostic significance and implication in multifactorial leukemogenesis. Clin Cancer Res (2006) 1.42
Expression of heat shock proteins and heat shock protein messenger ribonucleic acid in human prostate carcinoma in vitro and in tumors in vivo. Cell Stress Chaperones (2005) 1.41
Mechanism of intrauterine infection of hepatitis B virus. World J Gastroenterol (2004) 1.41
Comparison of patients hospitalized with influenza A subtypes H7N9, H5N1, and 2009 pandemic H1N1. Clin Infect Dis (2014) 1.40
Widespread establishment and regulatory impact of Alu exons in human genes. Proc Natl Acad Sci U S A (2011) 1.40
Noninvasive prenatal diagnosis of common fetal chromosomal aneuploidies by maternal plasma DNA sequencing. J Matern Fetal Neonatal Med (2012) 1.38
RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. Genome Res (2012) 1.36
Knee-loading modality drives molecular transport in mouse femur. Ann Biomed Eng (2006) 1.36
Kinetic resolution of 2-oxazolidinones via catalytic, enantioselective N-acylation. J Am Chem Soc (2006) 1.35
Analysis of factorial time-course microarrays with application to a clinical study of burn injury. Proc Natl Acad Sci U S A (2010) 1.33
Poultry market closures and human infection with influenza A(H7N9) virus, China, 2013-14. Emerg Infect Dis (2014) 1.29
Recombinatoric exploration of novel folded structures: a heteropolymer-based model of protein evolutionary landscapes. Proc Natl Acad Sci U S A (2002) 1.28
The substantial hospitalization burden of influenza in central China: surveillance for severe, acute respiratory infection, and influenza viruses, 2010-2012. Influenza Other Respir Viruses (2013) 1.28
A small-molecule inhibitor of Mps1 blocks the spindle-checkpoint response to a lack of tension on mitotic chromosomes. Curr Biol (2005) 1.26
Iso-migrastatin congeners from Streptomyces platensis and generation of a glutarimide polyketide library featuring the dorrigocin, lactimidomycin, migrastatin, and NK30424 scaffolds. J Am Chem Soc (2005) 1.25
Migrastatin and dorrigocins are shunt metabolites of iso-migrastatin. J Am Chem Soc (2005) 1.24
Extensive X-linked adaptive evolution in central chimpanzees. Proc Natl Acad Sci U S A (2012) 1.23
A method for noninvasive detection of fetal large deletions/duplications by low coverage massively parallel sequencing. Prenat Diagn (2013) 1.22
Isolation and transcriptional profiling of purified hepatic cells derived from human embryonic stem cells. Stem Cells (2008) 1.19
2,3-Dihydroimidazo[1,2-a]pyridines: a new class of enantioselective acyl transfer catalysts and their use in kinetic resolution of alcohols. J Am Chem Soc (2004) 1.19
Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer. Gigascience (2012) 1.18
Sexual function of premature ejaculation patients assayed with Chinese Index of Premature Ejaculation. Asian J Androl (2004) 1.17
Computational biology: toward deciphering gene regulatory information in mammalian genomes. Biometrics (2006) 1.16
A single cell level based method for copy number variation analysis by low coverage massively parallel sequencing. PLoS One (2013) 1.15
Massively parallel sequencing for chromosomal abnormality testing in trophectoderm cells of human blastocysts. Biol Reprod (2013) 1.14
Comparative linkage analysis and visualization of high-density oligonucleotide SNP array data. BMC Genet (2005) 1.14
Diversity of the vaginal microbiome correlates with preterm birth. Reprod Sci (2013) 1.13