Published in Genome Res on September 04, 2007
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res (2009) 3.83
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A spatial and temporal map of C. elegans gene expression. Genome Res (2010) 2.16
At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biol (2008) 1.62
Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags. BMC Biol (2008) 1.39
High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans. Genome Biol (2009) 1.36
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Res (2010) 1.35
Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays. Genome Biol (2010) 1.20
Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biol (2009) 1.19
On the potential for extinction by Muller's ratchet in Caenorhabditis elegans. BMC Evol Biol (2008) 1.12
Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays. BMC Genomics (2010) 1.12
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Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome. Genome Res (2009) 0.93
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FBN-1, a fibrillin-related protein, is required for resistance of the epidermis to mechanical deformation during C. elegans embryogenesis. Elife (2015) 0.90
Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans. Nucleic Acids Res (2009) 0.89
The Caenorhabditis elegans paxillin orthologue, PXL-1, is required for pharyngeal muscle contraction and for viability. Mol Biol Cell (2011) 0.88
Analysis of DNA strand-specific differential expression with high density tiling microarrays. BMC Bioinformatics (2010) 0.86
Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea. BMC Genomics (2012) 0.86
Genome-scale identification of Caenorhabditis elegans regulatory elements by tiling-array mapping of DNase I hypersensitive sites. BMC Genomics (2009) 0.85
The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression. Nucleic Acids Res (2011) 0.85
Bioinformatics in China: a personal perspective. PLoS Comput Biol (2008) 0.83
A differential sequencing-based analysis of the C. elegans noncoding transcriptome. RNA (2012) 0.82
Evolutionary conservation and functional roles of ncRNA. Front Genet (2012) 0.81
Identification of intermediate-size non-coding RNAs involved in the UV-induced DNA damage response in C. elegans. PLoS One (2012) 0.80
Seeing elegance in gene regulatory networks of the worm. Curr Opin Genet Dev (2011) 0.80
Analysis of antisense expression by whole genome tiling microarrays and siRNAs suggests mis-annotation of Arabidopsis orphan protein-coding genes. PLoS One (2010) 0.80
Microarray analysis of ncRNA expression patterns in Caenorhabditis elegans after RNAi against snoRNA associated proteins. BMC Genomics (2008) 0.80
An integrated approach for finding overlooked genes in Shigella. PLoS One (2011) 0.79
Computational prediction of Caenorhabditis box H/ACA snoRNAs using genomic properties of their host genes. RNA (2009) 0.77
Molecular profiling of mitochondrial dysfunction in Caenorhabditis elegans. Methods Mol Biol (2012) 0.77
Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans. Nucleic Acids Res (2010) 0.76
Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy. Protein Cell (2014) 0.75
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miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res (2006) 39.25
The ENCODE (ENCyclopedia Of DNA Elements) Project. Science (2004) 38.24
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science (2005) 16.82
Large-scale transcriptional activity in chromosomes 21 and 22. Science (2002) 14.01
A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci U S A (2006) 11.81
Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (2003) 11.62
Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res (2000) 10.40
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res (2004) 8.35
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nat Genet (2006) 6.20
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WormBase: a cross-species database for comparative genomics. Nucleic Acids Res (2003) 5.28
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res (2005) 3.82
Complex Loci in human and mouse genomes. PLoS Genet (2006) 3.74
Global analysis of dauer gene expression in Caenorhabditis elegans. Development (2003) 3.38
Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. Proc Natl Acad Sci U S A (2001) 3.30
Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc Natl Acad Sci U S A (2005) 3.21
Trans-splicing and polyadenylation of let-7 microRNA primary transcripts. RNA (2004) 3.18
NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res (2005) 3.16
RNAdb--a comprehensive mammalian noncoding RNA database. Nucleic Acids Res (2005) 2.84
TUF love for "junk" DNA. Cell (2006) 2.59
Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet (2005) 2.39
Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression. Genome Res (2005) 1.77
Genomics in C. elegans: so many genes, such a little worm. Genome Res (2005) 1.70
Evolution of small nucleolar RNAs in nematodes. Nucleic Acids Res (2006) 1.58
Design optimization methods for genomic DNA tiling arrays. Genome Res (2005) 1.53
Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. J Exp Zool B Mol Dev Evol (2006) 1.34
Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray. Nucleic Acids Res (2006) 1.03
C. elegans noncoding RNA genes. WormBook (2005) 1.02
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
Genome-wide analysis of estrogen receptor binding sites. Nat Genet (2006) 18.63
Erlotinib versus chemotherapy as first-line treatment for patients with advanced EGFR mutation-positive non-small-cell lung cancer (OPTIMAL, CTONG-0802): a multicentre, open-label, randomised, phase 3 study. Lancet Oncol (2011) 18.34
Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell (2006) 16.05
Mechanisms and functional implications of adult neurogenesis. Cell (2008) 14.50
Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell (2005) 14.32
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell (2008) 14.18
Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A (2006) 13.68
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
Structure of the novel ternary hydrides Li4Tt2D (Tt=Si and Ge). Acta Crystallogr B (2007) 10.58
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature (2010) 8.87
TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res (2006) 8.83
Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet (2009) 8.11
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature (2011) 7.43
RNA interference targeting Fas protects mice from fulminant hepatitis. Nat Med (2003) 7.37
Model-based analysis of two-color arrays (MA2C). Genome Biol (2007) 7.28
Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell (2009) 7.09
Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature (2005) 6.95
TreeFam: 2008 Update. Nucleic Acids Res (2007) 6.63
A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. Mol Cell (2007) 5.99
Nucleosome dynamics define transcriptional enhancers. Nat Genet (2010) 5.94
A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism. Science (2011) 5.91
Germline mutations in HOXB13 and prostate-cancer risk. N Engl J Med (2012) 5.49
Mili, a mammalian member of piwi family gene, is essential for spermatogenesis. Development (2004) 5.47
Chromatin structure analyses identify miRNA promoters. Genes Dev (2008) 5.40
High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol (2007) 5.24
Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res (2002) 4.92
Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods (2012) 4.89
PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev (2008) 4.83
In vivo antitumor activity of MEK and phosphatidylinositol 3-kinase inhibitors in basal-like breast cancer models. Clin Cancer Res (2009) 4.81
Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci U S A (2003) 4.74
Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature (2010) 4.64
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol (2009) 4.64
The JAK2/STAT3 signaling pathway is required for growth of CD44⁺CD24⁻ stem cell-like breast cancer cells in human tumors. J Clin Invest (2011) 4.41
CEAS: cis-regulatory element annotation system. Bioinformatics (2009) 4.26
Intercalated combination of chemotherapy and erlotinib for patients with advanced stage non-small-cell lung cancer (FASTACT-2): a randomised, double-blind trial. Lancet Oncol (2013) 4.20
Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome. J Proteome Res (2005) 4.13
Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol (2011) 4.13
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08
Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet (2012) 4.07
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature (2012) 4.00
A family cluster of infections by a newly recognized bunyavirus in eastern China, 2007: further evidence of person-to-person transmission. Clin Infect Dis (2011) 3.91
Changes in hippocampal connectivity in the early stages of Alzheimer's disease: evidence from resting state fMRI. Neuroimage (2006) 3.77
EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent. Science (2012) 3.74
Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat Genet (2012) 3.67
A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4. Nat Genet (2010) 3.63
Identifying ChIP-seq enrichment using MACS. Nat Protoc (2012) 3.60
Epidermal growth factor receptor mutations in plasma DNA samples predict tumor response in Chinese patients with stages IIIB to IV non-small-cell lung cancer. J Clin Oncol (2009) 3.58
8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC. Proc Natl Acad Sci U S A (2010) 3.37
Vandetanib plus docetaxel versus docetaxel as second-line treatment for patients with advanced non-small-cell lung cancer (ZODIAC): a double-blind, randomised, phase 3 trial. Lancet Oncol (2010) 3.30
A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury. Nat Med (2005) 3.26
Defining the roles of the periplasmic chaperones SurA, Skp, and DegP in Escherichia coli. Genes Dev (2007) 3.24
Cytoplasmic domain structures of Kir2.1 and Kir3.1 show sites for modulating gating and rectification. Nat Neurosci (2005) 3.22
Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk. Nat Genet (2012) 3.19
NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res (2005) 3.16
CEAS: cis-regulatory element annotation system. Nucleic Acids Res (2006) 3.15
Lipoprotein SmpA is a component of the YaeT complex that assembles outer membrane proteins in Escherichia coli. Proc Natl Acad Sci U S A (2007) 3.09
Imaging of Plasmodium liver stages to drive next-generation antimalarial drug discovery. Science (2011) 3.07
A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics (2005) 3.06
Gefitinib versus placebo as maintenance therapy in patients with locally advanced or metastatic non-small-cell lung cancer (INFORM; C-TONG 0804): a multicentre, double-blind randomised phase 3 trial. Lancet Oncol (2012) 2.98
Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis. Proc Natl Acad Sci U S A (2009) 2.95
Icotinib versus gefitinib in previously treated advanced non-small-cell lung cancer (ICOGEN): a randomised, double-blind phase 3 non-inferiority trial. Lancet Oncol (2013) 2.94
XPD and XRCC1 genetic polymorphisms are prognostic factors in advanced non-small-cell lung cancer patients treated with platinum chemotherapy. J Clin Oncol (2004) 2.93
Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell (2010) 2.92
Moesin controls cortical rigidity, cell rounding, and spindle morphogenesis during mitosis. Curr Biol (2008) 2.92
Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Res (2003) 2.90
Gait analysis using wearable sensors. Sensors (Basel) (2012) 2.90
Androgen receptor gene expression in prostate cancer is directly suppressed by the androgen receptor through recruitment of lysine-specific demethylase 1. Cancer Cell (2011) 2.86
Resolving new memories: a critical look at the dentate gyrus, adult neurogenesis, and pattern separation. Neuron (2011) 2.84
Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. Dev Cell (2010) 2.84
Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol (2013) 2.84
Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res (2004) 2.84
NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res (2011) 2.82
Synthesis and anticancer activity of thiosemicarbazones. Bioorg Med Chem Lett (2006) 2.78
Lynch syndrome (hereditary nonpolyposis colorectal cancer) diagnostics. J Natl Cancer Inst (2007) 2.77
One-year treatment with exenatide improves beta-cell function, compared with insulin glargine, in metformin-treated type 2 diabetic patients: a randomized, controlled trial. Diabetes Care (2009) 2.75
Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence. Mol Cell (2007) 2.74
Targeted ablation of connexin26 in the inner ear epithelial gap junction network causes hearing impairment and cell death. Curr Biol (2002) 2.72
Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics (2008) 2.66
Chromatin signature of embryonic pluripotency is established during genome activation. Nature (2010) 2.64