Yijun Ruan Genome Institute of Singapore Agency for Science, Technology and Research, Singapore Biography Publications Institution JoVE Articles Yijun Ruan has not added a biography. If you are Yijun Ruan and would like to personalize this page please email our Author Liaison for assistance. Publications Systematic Evaluation of Factors Influencing ChIP-seq Fidelity Nature Methods. Apr, 2012 | Pubmed ID: 22522655 Exome Sequencing of Gastric Adenocarcinoma Identifies Recurrent Somatic Mutations in Cell Adhesion and Chromatin Remodeling Genes Nature Genetics. Apr, 2012 | Pubmed ID: 22484628 A Common BIM Deletion Polymorphism Mediates Intrinsic Resistance and Inferior Responses to Tyrosine Kinase Inhibitors in Cancer Nature Medicine. 2012 | Pubmed ID: 22426421 Extensive Promoter-centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation Cell. Jan, 2012 | Pubmed ID: 22265404 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.). 2012 | Pubmed ID: 22113299 CTCF-mediated Functional Chromatin Interactome in Pluripotent Cells Nature Genetics. Jul, 2011 | Pubmed ID: 21685913 Broad Surveys of DNA Viral Diversity Obtained Through Viral Metagenomics of Mosquitoes PloS One. 2011 | Pubmed ID: 21674005 Chromatin Interaction Networks and Higher Order Architectures of Eukaryotic Genomes Journal of Cellular Biochemistry. Sep, 2011 | Pubmed ID: 21520242 Comprehensive Long-span Paired-end-tag Mapping Reveals Characteristic Patterns of Structural Variations in Epithelial Cancer Genomes Genome Research. May, 2011 | Pubmed ID: 21467267 Transcriptional Consequences of Genomic Structural Aberrations in Breast Cancer Genome Research. May, 2011 | Pubmed ID: 21467264 Genome-sequencing Anniversary. Presenting the Human Genome: Now in 3D! Science (New York, N.Y.). Feb, 2011 | Pubmed ID: 21350163 Determination of Transcription Factor Binding Nature Genetics. Jan, 2011 | Pubmed ID: 21217639 Integrative Model of Genomic Factors for Determining Binding Site Selection by Estrogen Receptor-α Molecular Systems Biology. Dec, 2010 | Pubmed ID: 21179027 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. Oct, 2010 | Pubmed ID: 20921386 Multiplex Parallel Pair-end-ditag Sequencing Approaches in System Biology Wiley Interdisciplinary Reviews. Systems Biology and Medicine. Mar-Apr, 2010 | Pubmed ID: 20836024 International Network of Cancer Genome Projects Nature. Apr, 2010 | Pubmed ID: 20393554 A Genomic Survey of Positive Selection in Burkholderia Pseudomallei Provides Insights into the Evolution of Accidental Virulence PLoS Pathogens. Apr, 2010 | Pubmed ID: 20368977 ChIA-PET Tool for Comprehensive Chromatin Interaction Analysis with Paired-end Tag Sequencing Genome Biology. 2010 | Pubmed ID: 20181287 Chromatin Interaction Analysis Using Paired-end Tag Sequencing Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [et Al.]. Jan, 2010 | Pubmed ID: 20069536 Preferential Associations Between Co-regulated Genes Reveal a Transcriptional Interactome in Erythroid Cells Nature Genetics. Jan, 2010 | Pubmed ID: 20010836 An Oestrogen-receptor-alpha-bound Human Chromatin Interactome Nature. Nov, 2009 | Pubmed ID: 19890323 Metagenomic Analysis of Viruses in Reclaimed Water Environmental Microbiology. Nov, 2009 | Pubmed ID: 19555373 Recent Positive Selection of a Human Androgen Receptor/ectodysplasin A2 Receptor Haplotype and Its Relationship to Male Pattern Baldness Human Genetics. Aug, 2009 | Pubmed ID: 19373488 Next-generation DNA Sequencing of Paired-end Tags (PET) for Transcriptome and Genome Analyses Genome Research. Apr, 2009 | Pubmed ID: 19339662 De-novo Identification of PPARgamma/RXR Binding Sites and Direct Targets During Adipogenesis PloS One. 2009 | Pubmed ID: 19300518 ChIP-based Methods for the Identification of Long-range Chromatin Interactions Journal of Cellular Biochemistry. May, 2009 | Pubmed ID: 19247990 Evolution of the Mammalian Transcription Factor Binding Repertoire Via Transposable Elements Genome Research. Nov, 2008 | Pubmed ID: 18682548 Tackling the Epigenome in the Pluripotent Stem Cells Journal of Genetics and Genomics = Yi Chuan Xue Bao. Jul, 2008 | Pubmed ID: 18640620 Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells Cell. Jun, 2008 | Pubmed ID: 18555785 The Airborne Metagenome in an Indoor Urban Environment PloS One. 2008 | Pubmed ID: 18382653 Functional Metagenomic Profiling of Nine Biomes Nature. Apr, 2008 | Pubmed ID: 18337718 Biodiversity and Biogeography of Phages in Modern Stromatolites and Thrombolites Nature. Mar, 2008 | Pubmed ID: 18311127 The Use of Multiple Displacement Amplification to Amplify Complex DNA Libraries Nucleic Acids Research. Mar, 2008 | Pubmed ID: 18285362 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. 2007 | Pubmed ID: 18546507 Whole-genome Mapping of Histone H3 Lys4 and 27 Trimethylations Reveals Distinct Genomic Compartments in Human Embryonic Stem Cells Cell Stem Cell. Sep, 2007 | Pubmed ID: 18371363 Paired-end DiTagging for Transcriptome and Genome Analysis Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [et Al.]. Jul, 2007 | Pubmed ID: 18265396 Genome-wide Mapping of RELA(p65) Binding Identifies E2F1 As a Transcriptional Activator Recruited by NF-kappaB Upon TLR4 Activation Molecular Cell. Aug, 2007 | Pubmed ID: 17707233 Pathway Aberrations of Murine Melanoma Cells Observed in Paired-End DiTag Transcriptomes BMC Cancer. 2007 | Pubmed ID: 17594473 Identification and Analysis of Functional Elements in 1% of the Human Genome by the ENCODE Pilot Project Nature. Jun, 2007 | Pubmed ID: 17571346 Mapping of Transcription Factor Binding Regions in Mammalian Cells by ChIP: Comparison of Array- and Sequencing-based Technologies Genome Research. Jun, 2007 | Pubmed ID: 17568005 Pseudogenes in the ENCODE Regions: Consensus Annotation, Analysis of Transcription, and Evolution Genome Research. Jun, 2007 | Pubmed ID: 17568002 Fusion Transcripts and Transcribed Retrotransposed Loci Discovered Through Comprehensive Transcriptome Analysis Using Paired-End DiTags (PETs) Genome Research. Jun, 2007 | Pubmed ID: 17568001 Whole-genome Cartography of Estrogen Receptor Alpha Binding Sites PLoS Genetics. Jun, 2007 | Pubmed ID: 17542648 A Genomics Approach to Understanding Host Response During Dengue Infection Novartis Foundation Symposium. 2006 | Pubmed ID: 17319164 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. Nov, 2006 | Pubmed ID: 17093053 PET-Tool: a Software Suite for Comprehensive Processing and Managing of Paired-End DiTag (PET) Sequence Data BMC Bioinformatics. 2006 | Pubmed ID: 16934139 Multiplex Sequencing of Paired-end Ditags (MS-PET): a Strategy for the Ultra-high-throughput Analysis of Transcriptomes and Genomes Nucleic Acids Research. 2006 | Pubmed ID: 16840528 The Oct4 and Nanog Transcription Network Regulates Pluripotency in Mouse Embryonic Stem Cells Nature Genetics. Apr, 2006 | Pubmed ID: 16518401 A Global Map of P53 Transcription-factor Binding Sites in the Human Genome Cell. Jan, 2006 | Pubmed ID: 16413492 RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses PLoS Biology. Jan, 2006 | Pubmed ID: 16336043 Transcriptome Analysis of Zebrafish Embryogenesis Using Microarrays PLoS Genetics. Aug, 2005 | Pubmed ID: 16132083 Gene Identification Signature (GIS) Analysis for Transcriptome Characterization and Genome Annotation Nature Methods. Feb, 2005 | Pubmed ID: 15782207 SARS Transmission Pattern in Singapore Reassessed by Viral Sequence Variation Analysis PLoS Medicine. Feb, 2005 | Pubmed ID: 15736999 The Status, Quality, and Expansion of the NIH Full-length CDNA Project: the Mammalian Gene Collection (MGC) Genome Research. Oct, 2004 | Pubmed ID: 15489334 Mutational Dynamics of the SARS Coronavirus in Cell Culture and Human Populations Isolated in 2003 BMC Infectious Diseases. Sep, 2004 | Pubmed ID: 15347429 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. Aug, 2004 | Pubmed ID: 15272081 Laboratory-acquired Severe Acute Respiratory Syndrome The New England Journal of Medicine. Apr, 2004 | Pubmed ID: 15103000 Interrogating the Transcriptome Trends in Biotechnology. Jan, 2004 | Pubmed ID: 14690619 Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation Yufen Goh*1, Melissa J. Fullwood*1,2,3, Huay Mei Poh1, Su Qin Peh1, Chin Thing Ong1, Jingyao Zhang1, Xiaoan Ruan1, Yijun Ruan1,3 1Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 2A*STAR-Duke-NUS Neuroscience Research Partnership, Singapore, 3Department of Biochemistry, National University of Singapore, Singapore JoVE 3770 Biology
Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation Yufen Goh*1, Melissa J. Fullwood*1,2,3, Huay Mei Poh1, Su Qin Peh1, Chin Thing Ong1, Jingyao Zhang1, Xiaoan Ruan1, Yijun Ruan1,3 1Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 2A*STAR-Duke-NUS Neuroscience Research Partnership, Singapore, 3Department of Biochemistry, National University of Singapore, Singapore JoVE 3770 Biology