Published in Genome Res on December 01, 2004
Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters. Genome Res (2007) 2.12
Genome-wide promoter extraction and analysis in human, mouse, and rat. Genome Biol (2005) 1.64
Annotation of mammalian primary microRNAs. BMC Genomics (2008) 1.53
Ectopic expression of peripheral-tissue antigens in the thymic epithelium: probabilistic, monoallelic, misinitiated. Proc Natl Acad Sci U S A (2008) 1.41
Mapping of transcription start sites of human retina expressed genes. BMC Genomics (2007) 0.84
Melanocortin 3 receptor has a 5' exon that directs translation of apically localized protein from the second in-frame ATG. Mol Endocrinol (2014) 0.82
Mapping of the transcription start site (TSS) and identification of SNPs in the bovine neuropeptide Y (NPY) gene. BMC Genet (2008) 0.77
Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration. BMC Bioinformatics (2006) 0.75
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol (2000) 128.08
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
The sequence of the human genome. Science (2001) 101.55
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Prediction of complete gene structures in human genomic DNA. J Mol Biol (1997) 58.76
A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res (1998) 22.69
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science (2002) 20.59
Large-scale transcriptional activity in chromosomes 21 and 22. Science (2002) 14.01
Experimental annotation of the human genome using microarray technology. Nature (2001) 10.39
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res (2004) 8.35
Integrating genomic homology into gene structure prediction. Bioinformatics (2001) 7.92
CpG islands as gene markers in the human genome. Genomics (1992) 7.45
C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat Genet (2003) 7.25
Computational inference of homologous gene structures in the human genome. Genome Res (2001) 6.96
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Number of CpG islands and genes in human and mouse. Proc Natl Acad Sci U S A (1993) 6.79
Computational identification of promoters and first exons in the human genome. Nat Genet (2001) 5.88
Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans. Nat Genet (2001) 4.03
Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Res (2003) 3.50
Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome. Genome Res (2002) 1.78
CART classification of human 5' UTR sequences. Genome Res (2000) 1.75
Multiple variable first exons: a mechanism for cell- and tissue-specific gene regulation. Genome Res (2003) 1.71
Extra-long first-strand cDNA synthesis. Biotechniques (2002) 1.64
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics (2008) 39.08
ZOOM! Zillions of oligos mapped. Bioinformatics (2008) 29.78
Genome-wide in situ exon capture for selective resequencing. Nat Genet (2007) 19.97
A microRNA component of the p53 tumour suppressor network. Nature (2007) 19.25
Tumour evolution inferred by single-cell sequencing. Nature (2011) 19.13
The B73 maize genome: complexity, diversity, and dynamics. Science (2009) 18.73
Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet (2008) 18.28
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell (2007) 16.66
ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res (2003) 12.81
Prepublication data sharing. Nature (2009) 12.24
Role of transposable elements in heterochromatin and epigenetic control. Nature (2004) 10.51
Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol (2012) 10.31
De novo gene disruptions in children on the autistic spectrum. Neuron (2012) 9.69
Second-generation shRNA libraries covering the mouse and human genomes. Nat Genet (2005) 8.23
The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev (2002) 7.61
Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res (2009) 7.42
A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc Natl Acad Sci U S A (2003) 7.30
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary. Cell (2009) 6.39
A resource for large-scale RNA-interference-based screens in mammals. Nature (2004) 6.36
Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nat Methods (2008) 5.70
Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature (2012) 5.67
Regulating gene expression through RNA nuclear retention. Cell (2005) 5.58
An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer. Cell (2008) 5.47
A biochemical approach to identifying microRNA targets. Proc Natl Acad Sci U S A (2007) 5.16
Network-based global inference of human disease genes. Mol Syst Biol (2008) 5.01
An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Hum Mol Genet (2006) 4.56
Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nat Protoc (2009) 4.45
Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol (2007) 4.29
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice (N Y) (2013) 4.27
Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev (2008) 4.24
Critical roles for Dicer in the female germline. Genes Dev (2007) 4.23
Large-scale structure of genomic methylation patterns. Genome Res (2005) 4.11
Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell (2013) 3.81
Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol (2011) 3.51
The genome of Theobroma cacao. Nat Genet (2010) 3.47
Deregulation of scribble promotes mammary tumorigenesis and reveals a role for cell polarity in carcinoma. Cell (2008) 3.43
Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell (2011) 3.39
Maize genome sequencing by methylation filtration. Science (2003) 3.31
Updates to the RMAP short-read mapping software. Bioinformatics (2009) 3.18
A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J (2010) 3.18
Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res (2007) 3.13
High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res (2009) 3.08
Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis. Nat Methods (2004) 3.01
Direct coupling of the cell cycle and cell death machinery by E2F. Nat Cell Biol (2002) 3.00
Novel Foxo1-dependent transcriptional programs control T(reg) cell function. Nature (2012) 2.77
Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol Cell (2011) 2.77
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Res (2005) 2.73
An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. Nucleic Acids Res (2009) 2.69
A complete sequence of the T. tengcongensis genome. Genome Res (2002) 2.60
Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model. Cancer Cell (2009) 2.54
Topoisomerase levels determine chemotherapy response in vitro and in vivo. Proc Natl Acad Sci U S A (2008) 2.53
Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics (2004) 2.51
Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res (2003) 2.50
Targeted investigation of the Neandertal genome by array-based sequence capture. Science (2010) 2.49
DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Natl Acad Sci U S A (2006) 2.38
Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci U S A (2005) 2.36
Assembling genomic DNA sequences with PHRAP. Curr Protoc Bioinformatics (2007) 2.29
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res (2007) 2.16
Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol (2004) 2.12
Interacting models of cooperative gene regulation. Proc Natl Acad Sci U S A (2004) 2.09
Sorghum genome sequencing by methylation filtration. PLoS Biol (2005) 2.02
Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Res (2006) 2.00
A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics (2004) 1.94
High-resolution human core-promoter prediction with CoreBoost_HM. Genome Res (2008) 1.88
Cell-type-based analysis of microRNA profiles in the mouse brain. Neuron (2012) 1.85
Computational prediction of methylation status in human genomic sequences. Proc Natl Acad Sci U S A (2006) 1.83
Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics (2005) 1.81
Adaptively inferring human transcriptional subnetworks. Mol Syst Biol (2006) 1.81
Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics (2009) 1.80
The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Res (2013) 1.78
A comparative analysis of exome capture. Genome Biol (2011) 1.78
Differential methylation of genes and repeats in land plants. Genome Res (2005) 1.77
Genomic amplification and oncogenic properties of the KCNK9 potassium channel gene. Cancer Cell (2003) 1.76
Chaperonins facilitate KNOTTED1 cell-to-cell trafficking and stem cell function. Science (2011) 1.73
Loss of p53 impedes the antileukemic response to BCR-ABL inhibition. Proc Natl Acad Sci U S A (2006) 1.71
A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proc Natl Acad Sci U S A (2013) 1.70
Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Res (2005) 1.70
Current challenges in de novo plant genome sequencing and assembly. Genome Biol (2012) 1.69