Yijun Ruan

Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore

Affiliated withAgency for Science, Technology and Research, Singapore National University of Singapore, Singapore

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 17	2012

Other Publications

Article	Year
Interrogating the transcriptome. Trends in biotechnology\| PubMed ID: 14690619	2004
Laboratory-acquired severe acute respiratory syndrome. The New England journal of medicine\| PubMed ID: 15103000	2004
5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 15272081	2004
Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003. BMC infectious diseases\| PubMed ID: 15347429	2004
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research\| PubMed ID: 15489334	2004
SARS transmission pattern in Singapore reassessed by viral sequence variation analysis. PLoS medicine\| PubMed ID: 15736999	2005
Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nature methods\| PubMed ID: 15782207	2005
Transcriptome analysis of zebrafish embryogenesis using microarrays. PLoS genetics\| PubMed ID: 16132083	2005
RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS biology\| PubMed ID: 16336043	2006
A global map of p53 transcription-factor binding sites in the human genome. Cell\| PubMed ID: 16413492	2006
The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nature genetics\| PubMed ID: 16518401	2006
Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes. Nucleic acids research\| PubMed ID: 16840528	2006
PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data. BMC bioinformatics\| PubMed ID: 16934139	2006
Global mapping of c-Myc binding sites and target gene networks in human B cells. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 17093053	2006
A genomics approach to understanding host response during dengue infection. Novartis Foundation symposium\| PubMed ID: 17319164	2006
Whole-genome cartography of estrogen receptor alpha binding sites. PLoS genetics\| PubMed ID: 17542648	2007
Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome research\| PubMed ID: 17568001	2007
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome research\| PubMed ID: 17568002	2007
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome research\| PubMed ID: 17568005	2007
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature\| PubMed ID: 17571346	2007
Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes. BMC cancer\| PubMed ID: 17594473	2007
Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation. Molecular cell\| PubMed ID: 17707233	2007
Paired-end diTagging for transcriptome and genome analysis. Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.]\| PubMed ID: 18265396	2007
The use of multiple displacement amplification to amplify complex DNA libraries. Nucleic acids research\| PubMed ID: 18285362	2008
Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature\| PubMed ID: 18311127	2008
Functional metagenomic profiling of nine biomes. Nature\| PubMed ID: 18337718	2008
Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell stem cell\| PubMed ID: 18371363	2007
The airborne metagenome in an indoor urban environment. PloS one\| PubMed ID: 18382653	2008
Computational analysis and modeling of genome-scale avidity distribution of transcription factor binding sites in chip-pet experiments. Genome informatics. International Conference on Genome Informatics\| PubMed ID: 18546507	2007
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell\| PubMed ID: 18555785	2008
Tackling the epigenome in the pluripotent stem cells. Journal of genetics and genomics = Yi chuan xue bao\| PubMed ID: 18640620	2008
Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome research\| PubMed ID: 18682548	2008
ChIP-based methods for the identification of long-range chromatin interactions. Journal of cellular biochemistry\| PubMed ID: 19247990	2009
De-novo identification of PPARgamma/RXR binding sites and direct targets during adipogenesis. PloS one\| PubMed ID: 19300518	2009
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome research\| PubMed ID: 19339662	2009
Recent positive selection of a human androgen receptor/ectodysplasin A2 receptor haplotype and its relationship to male pattern baldness. Human genetics\| PubMed ID: 19373488	2009
Metagenomic analysis of viruses in reclaimed water. Environmental microbiology\| PubMed ID: 19555373	2009
An oestrogen-receptor-alpha-bound human chromatin interactome. Nature\| PubMed ID: 19890323	2009
Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nature genetics\| PubMed ID: 20010836	2010
Chromatin interaction analysis using paired-end tag sequencing. Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.]\| PubMed ID: 20069536	2010
ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome biology\| PubMed ID: 20181287	2010
A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence. PLoS pathogens\| PubMed ID: 20368977	2010
International network of cancer genome projects. Nature\| PubMed ID: 20393554	2010
Multiplex parallel pair-end-ditag sequencing approaches in system biology. Wiley interdisciplinary reviews. Systems biology and medicine\| PubMed ID: 20836024	2010
Genome-wide analysis reveals methyl-CpG-binding protein 2-dependent regulation of microRNAs in a mouse model of Rett syndrome. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 20921386	2010
Integrative model of genomic factors for determining binding site selection by estrogen receptor-Î±. Molecular systems biology\| PubMed ID: 21179027	2010
Determination of transcription factor binding. Nature genetics\| PubMed ID: 21217639	2011
Genome-sequencing anniversary. Presenting the human genome: now in 3D! Science (New York, N.Y.)\| PubMed ID: 21350163	2011
Transcriptional consequences of genomic structural aberrations in breast cancer. Genome research\| PubMed ID: 21467264	2011
Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome research\| PubMed ID: 21467267	2011
Chromatin interaction networks and higher order architectures of eukaryotic genomes. Journal of cellular biochemistry\| PubMed ID: 21520242	2011
Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. PloS one\| PubMed ID: 21674005	2011
CTCF-mediated functional chromatin interactome in pluripotent cells. Nature genetics\| PubMed ID: 21685913	2011
Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 22113299	2012
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell\| PubMed ID: 22265404	2012
A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer. Nature medicine\| PubMed ID: 22426421	2012
Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes. Nature genetics\| PubMed ID: 22484628	2012
Systematic evaluation of factors influencing ChIP-seq fidelity. Nature methods\| PubMed ID: 22522655	2012