PubRank

Yijun Ruan

Author PubWeight™ 438.10‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007 75.09
2 Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008 28.29
3 The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet 2006 20.76
4 A global map of p53 transcription-factor binding sites in the human genome. Cell 2006 20.65
5 International network of cancer genome projects. Nature 2010 20.35
6 Landscape of transcription in human cells. Nature 2012 20.18
7 The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 2012 15.41
8 An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 2009 12.16
9 Functional metagenomic profiling of nine biomes. Nature 2008 11.00
10 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res 2004 9.18
11 Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 2012 8.41
12 Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods 2005 7.87
13 Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell 2007 7.05
14 CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 2011 6.55
15 Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet 2009 6.39
16 Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet 2007 5.85
17 Global mapping of c-Myc binding sites and target gene networks in human B cells. Proc Natl Acad Sci U S A 2006 5.27
18 RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol 2006 4.93
19 A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer. Nat Med 2012 4.90
20 Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes. Nat Genet 2012 4.82
21 Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res 2007 4.59
22 Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes. Nucleic Acids Res 2006 4.51
23 Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res 2009 4.47
24 Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res 2007 3.82
25 Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res 2008 3.76
26 ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol 2010 3.24
27 The draft genome of sweet orange (Citrus sinensis). Nat Genet 2012 2.81
28 Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature 2008 2.70
29 Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res 2012 2.66
30 Transcriptome analysis of zebrafish embryogenesis using microarrays. PLoS Genet 2005 2.32
31 Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods 2012 2.31
32 Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation. Mol Cell 2007 2.05
33 Integrative model of genomic factors for determining binding site selection by estrogen receptor-α. Mol Syst Biol 2010 2.04
34 ChIP-based methods for the identification of long-range chromatin interactions. J Cell Biochem 2009 1.84
35 The airborne metagenome in an indoor urban environment. PLoS One 2008 1.81
36 Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. PLoS One 2011 1.75
37 Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Res 2011 1.67
38 A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence. PLoS Pathog 2010 1.65
39 5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation. Proc Natl Acad Sci U S A 2004 1.64
40 Metagenomic analysis of viruses in reclaimed water. Environ Microbiol 2009 1.51
41 DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. Nat Genet 2013 1.40
42 De-novo identification of PPARgamma/RXR binding sites and direct targets during adipogenesis. PLoS One 2009 1.39
43 PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data. BMC Bioinformatics 2006 1.38
44 Laboratory-acquired severe acute respiratory syndrome. N Engl J Med 2004 1.37
45 Whole-genome reconstruction and mutational signatures in gastric cancer. Genome Biol 2012 1.33
46 Genome-wide analysis reveals methyl-CpG-binding protein 2-dependent regulation of microRNAs in a mouse model of Rett syndrome. Proc Natl Acad Sci U S A 2010 1.33
47 Paired-end diTagging for transcriptome and genome analysis. Curr Protoc Mol Biol 2007 1.30
48 Transcriptional consequences of genomic structural aberrations in breast cancer. Genome Res 2011 1.30
49 Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003. BMC Infect Dis 2004 1.21
50 TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed. EMBO J 2012 1.21
51 ChIA-PET analysis of transcriptional chromatin interactions. Methods 2012 1.17
52 Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol 2012 1.14
53 SARS transmission pattern in Singapore reassessed by viral sequence variation analysis. PLoS Med 2005 1.11
54 BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation. Genome Biol 2012 1.09
55 Large-scale functional organization of long-range chromatin interaction networks. Cell Rep 2012 1.08
56 Chromatin interaction analysis using paired-end tag sequencing. Curr Protoc Mol Biol 2010 0.99
57 Transcriptional profiles of bovine in vivo pre-implantation development. BMC Genomics 2014 0.97
58 Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for mapping chromatin interactions and understanding transcription regulation. J Vis Exp 2012 0.91
59 Recent positive selection of a human androgen receptor/ectodysplasin A2 receptor haplotype and its relationship to male pattern baldness. Hum Genet 2009 0.90
60 Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons. PLoS One 2012 0.89
61 Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application. BMC Genomics 2014 0.84
62 Dissecting the chromatin interactome of microRNA genes. Nucleic Acids Res 2013 0.83
63 Computational analysis and modeling of genome-scale avidity distribution of transcription factor binding sites in chip-pet experiments. Genome Inform 2007 0.82
64 Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes. BMC Cancer 2007 0.81
65 Chromatin interaction networks and higher order architectures of eukaryotic genomes. J Cell Biochem 2011 0.81
66 Tackling the epigenome in the pluripotent stem cells. J Genet Genomics 2008 0.81
67 Determination of transcription factor binding. Nat Genet 2011 0.80
68 Targeted inactivation and identification of targets of the Gli2a transcription factor in the zebrafish. Biol Open 2013 0.80
69 Cross-enhancement of ANGPTL4 transcription by HIF1 alpha and PPAR beta/delta is the result of the conformational proximity of two response elements. Genome Biol 2014 0.78
70 A genomics approach to understanding host response during dengue infection. Novartis Found Symp 2006 0.77
71 The use of multiple displacement amplification to amplify complex DNA libraries. Nucleic Acids Res 2008 0.75
72 Path-preference cellular-automaton model for traffic flow through transit points and its application to the transcription process in human cells. Phys Rev E Stat Nonlin Soft Matter Phys 2012 0.75