Yi Chen

Bio: Yi Chen is an academic researcher from Chinese Academy of Sciences. The author has contributed to research in topics: Large Hadron Collider & Medicine. The author has an hindex of 217, co-authored 4342 publications receiving 293080 citations. Previous affiliations of Yi Chen include Rochester Institute of Technology & National Institutes of Health.

Evidence for associated production of a single top quark and W Boson in pp collisions at √s=7 TeV

Abstract: Evidence is presented for the associated production of a single top quark and W boson in pp collisions at √s=7 TeV with the CMS experiment at the LHC. The analyzed data correspond to an integrated luminosity of 4.9 fb^(-1). The measurement is performed using events with two leptons and a jet originated from a b quark. A multivariate analysis based on kinematic properties is utilized to separate the tt background from the signal. The observed signal has a significance of 4.0σ and corresponds to a cross section of 16_(-4)^(+5) pb, in agreement with the standard model expectation of 15.6±0.4_(-1.2)^(+1.0) pb.

Exome-based analysis for RNA epigenome sequencing data

Abstract: Motivation: Fragmented RNA immunoprecipitation combined with RNA sequencing enabled the unbiased study of RNA epigenome at a near single-base resolution; however, unique features of this new type of data call for novel computational techniques. Result: Through examining the connections of RNA epigenome sequencing data with two well-studied data types, ChIP-Seq and RNA-Seq, we unveiled the salient characteristics of this new data type. The computational strategies were discussed accordingly, and a novel data processing pipeline was proposed that combines several existing tools with a newly developed exome-based approach ‘exomePeak’ for detecting, representing and visualizing the post-transcriptional RNA modification sites on the transcriptome. Availability: The MATLAB package ‘exomePeak’ and additional details are available at http://compgenomics.utsa.edu/exomePeak/. Contact:[email protected] or [email protected] Supplementary information:Supplementary data are available at Bioinformatics online.

Skraup-Doebner-Von Miller quinoline synthesis revisited: reversal of the regiochemistry for gamma-aryl-beta,gamma-unsaturated alpha-ketoesters.

Abstract: A reversal of the standard regiochemistry of the Skraup-Doebner-Von Miller quinoline synthesis was observed when anilines were condensed with gamma-aryl-beta,gamma-unsaturated alpha-ketoesters in refluxing TFA. The reaction is proposed to involve 1,2-addition of the anilines to gamma-aryl-beta,gamma-unsaturated alpha-ketoesters to form Schiff's base adducts, followed by cyclization and oxidation. The products were unambiguously shown to the 2-carboxy-4-arylquinolines by spectroscopy and X-ray crystallographic analysis.

A fluorescent dye with large Stokes shift and high stability: synthesis and application to live cell imaging

Abstract: A fluorescent dye, 2,5-bis(6-amine-benzoxazol-2-yl)thiophene (BBTA), was synthesized by a two-step reaction from starting material 2,5-bis(benzoxazol-2-yl)thiophene (BBT). BBTA exhibited strong emission and large Stokes shift in solvent, and the largest Stokes shift (Δλ = 186 nm or Δν = 8572 cm−1) was obtained in buffer solution (PBS, pH = 7.2) with 5% (v/v) of polyethylene glycol monomethyl ether (mPEG550, MW = 550) as additive. Application of BBTA to live cell imaging showed that BBTA was clearly expressed in mitochondria with high contrast. Besides, BBTA showed low cytotoxicity and excellent photo-stability.

I and i

Abstract: There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality. Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

KEGG: Kyoto Encyclopedia of Genes and Genomes

Abstract: Kyoto Encyclopedia of Genes and Genomes (KEGG) is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules. The major component of KEGG is the PATHWAY database that consists of graphical diagrams of biochemical pathways including most of the known metabolic pathways and some of the known regulatory pathways. The pathway information is also represented by the ortholog group tables summarizing orthologous and paralogous gene groups among different organisms. KEGG maintains the GENES database for the gene catalogs of all organisms with complete genomes and selected organisms with partial genomes, which are continuously re-annotated, as well as the LIGAND database for chemical compounds and enzymes. Each gene catalog is associated with the graphical genome map for chromosomal locations that is represented by Java applet. In addition to the data collection efforts, KEGG develops and provides various computational tools, such as for reconstructing biochemical pathways from the complete genome sequence and for predicting gene regulatory networks from the gene expression profiles. The KEGG databases are daily updated and made freely available (http://www.genome.ad.jp/kegg/).

limma powers differential expression analyses for RNA-sequencing and microarray studies

Abstract: limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.

Atherosclerosis — An Inflammatory Disease

Abstract: Atherosclerosis is an inflammatory disease. Because high plasma concentrations of cholesterol, in particular those of low-density lipoprotein (LDL) cholesterol, are one of the principal risk factors for atherosclerosis,1 the process of atherogenesis has been considered by many to consist largely of the accumulation of lipids within the artery wall; however, it is much more than that. Despite changes in lifestyle and the use of new pharmacologic approaches to lower plasma cholesterol concentrations,2,3 cardiovascular disease continues to be the principal cause of death in the United States, Europe, and much of Asia.4,5 In fact, the lesions of atherosclerosis represent . . .