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.

Amine-modified random primers to label probes for DNA microarrays

Abstract: DNA microarrays have been used to study the expression of thousands of genes at the same time in a variety of cells and tissues1,2,3. The methods most commonly used to label probes for microarray studies require a minimum of 20 μg of total RNA or 2 μg of poly(A) RNA4,5. This has made it difficult to study small and rare tissue samples. RNA amplification techniques and improved labeling methods have recently been described6,7,8,9. These new procedures and reagents allow the use of less input RNA, but they are relatively time-consuming and expensive. Here we introduce a technique for preparing fluorescent probes that can be used to label as little as 1 μg of total RNA. The method is based on priming cDNA synthesis with random hexamer oligonucleotides, on the 5′ ends of which are bases with free amino groups. These amine-modified primers are incorporated into the cDNA along with aminoallyl nucleotides, and fluorescent dyes are then chemically added to the free amines. The method is simple to execute, and amine-reactive dyes are considerably less expensive than dye-labeled bases or dendrimers.

Search for top-squark pair production in final states with one lepton, jets, and missing transverse momentum using 36 fb−1 of s√=13 TeV pp collision data with the ATLAS detector

Abstract: The results of a search for the direct pair production of top squarks, the supersymmetric partner of the top quark, in final states with one isolated electron or muon, several energetic jets, and missing transverse momentum are reported. The analysis also targets spin-0 mediator models, where the mediator decays into a pair of dark-matter particles and is produced in association with a pair of top quarks. The search uses data from proton-proton collisions delivered by the Large Hadron Collider in 2015 and 2016 at a centre-of-mass energy of $ \sqrt{s}=13 $ TeV and recorded by the ATLAS detector, corresponding to an integrated luminosity of 36 fb$^{−1}$. A wide range of signal scenarios with different mass-splittings between the top squark, the lightest neutralino and possible intermediate supersymmetric particles are considered, including cases where the W bosons or the top quarks produced in the decay chain are off-shell. No significant excess over the Standard Model prediction is observed. The null results are used to set exclusion limits at 95% confidence level in several supersymmetry benchmark models. For pair-produced top-squarks decaying into top quarks, top-squark masses up to 940 GeV are excluded. Stringent exclusion limits are also derived for all other considered top-squark decay scenarios. For the spin-0 mediator models, upper limits are set on the visible cross-section.

Search for anomalous production of prompt same-sign lepton pairs and pair-produced doubly charged Higgs bosons with s =8 TeV pp collisions using the ATLAS detector

Abstract: A low-background inclusive search for new physics in events with same-sign dileptons is presented The search uses proton-proton collisions corresponding to 203 fb−1 of integrated luminosity taken in 2012 at a centre-of-mass energy of 8 TeV with the ATLAS detector at the LHC Pairs of isolated leptons with the same electric charge and large transverse momenta of the type e±e±, e±μ±, and μ±μ± are selected and their invariant mass distribution is examined No excess of events above the expected level of Standard Model background is found The results are used to set upper limits on the cross-sections for processes beyond the Standard Model Limits are placed as a function of the dilepton invariant mass within a fiducial region corresponding to the signal event selection criteria Exclusion limits are also derived for a specific model of doubly charged Higgs boson production

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 . . .