Yijun Ruan

Interrogating the transcriptome.

Laboratory-acquired severe acute respiratory syndrome.

5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation.

Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003.

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

SARS transmission pattern in Singapore reassessed by viral sequence variation analysis.

Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation.

Transcriptome analysis of zebrafish embryogenesis using microarrays.

RNA viral community in human feces: prevalence of plant pathogenic viruses.

A global map of p53 transcription-factor binding sites in the human genome.

The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells.

Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes.

PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data.

Global mapping of c-Myc binding sites and target gene networks in human B cells.

A genomics approach to understanding host response during dengue infection.

Whole-genome cartography of estrogen receptor alpha binding sites.

Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs).

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.

Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes.

Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation.

Paired-end diTagging for transcriptome and genome analysis.

The use of multiple displacement amplification to amplify complex DNA libraries.

Biodiversity and biogeography of phages in modern stromatolites and thrombolites.

Functional metagenomic profiling of nine biomes.

Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells.

The airborne metagenome in an indoor urban environment.

Computational analysis and modeling of genome-scale avidity distribution of transcription factor binding sites in chip-pet experiments.

Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.

Tackling the epigenome in the pluripotent stem cells.

Evolution of the mammalian transcription factor binding repertoire via transposable elements.

ChIP-based methods for the identification of long-range chromatin interactions.

De-novo identification of PPARgamma/RXR binding sites and direct targets during adipogenesis.

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses.

Recent positive selection of a human androgen receptor/ectodysplasin A2 receptor haplotype and its relationship to male pattern baldness.

Metagenomic analysis of viruses in reclaimed water.

An oestrogen-receptor-alpha-bound human chromatin interactome.

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells.

Chromatin interaction analysis using paired-end tag sequencing.

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing.

A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence.

International network of cancer genome projects.

Multiplex parallel pair-end-ditag sequencing approaches in system biology.

Genome-wide analysis reveals methyl-CpG-binding protein 2-dependent regulation of microRNAs in a mouse model of Rett syndrome.

Integrative model of genomic factors for determining binding site selection by estrogen receptor-α.

Determination of transcription factor binding.

Genome-sequencing anniversary. Presenting the human genome: now in 3D!

Transcriptional consequences of genomic structural aberrations in breast cancer.

Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes.

Chromatin interaction networks and higher order architectures of eukaryotic genomes.

Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes.

CTCF-mediated functional chromatin interactome in pluripotent cells.

Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET).

Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.

A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer.

Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes.

Systematic evaluation of factors influencing ChIP-seq fidelity.