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Chao Xu

Bio: Chao Xu is an academic researcher from Chinese Academy of Sciences. The author has contributed to research in topics: Medicine & Computer science. The author has an hindex of 75, co-authored 845 publications receiving 20541 citations. Previous affiliations of Chao Xu include Structural Genomics Consortium & Harbin Institute of Technology.


Papers
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TL;DR: This protocol describes pathway enrichment analysis of gene lists from RNA-seq and other genomics experiments using g:Profiler, GSEA, Cytoscape and EnrichmentMap software, and describes innovative visualization techniques.
Abstract: Pathway enrichment analysis helps researchers gain mechanistic insight into gene lists generated from genome-scale (omics) experiments. This method identifies biological pathways that are enriched in a gene list more than would be expected by chance. We explain the procedures of pathway enrichment analysis and present a practical step-by-step guide to help interpret gene lists resulting from RNA-seq and genome-sequencing experiments. The protocol comprises three major steps: definition of a gene list from omics data, determination of statistically enriched pathways, and visualization and interpretation of the results. We describe how to use this protocol with published examples of differentially expressed genes and mutated cancer genes; however, the principles can be applied to diverse types of omics data. The protocol describes innovative visualization techniques, provides comprehensive background and troubleshooting guidelines, and uses freely available and frequently updated software, including g:Profiler, Gene Set Enrichment Analysis (GSEA), Cytoscape and EnrichmentMap. The complete protocol can be performed in ~4.5 h and is designed for use by biologists with no prior bioinformatics training.

958 citations

Journal ArticleDOI
TL;DR: These structural studies, together with transcriptome-wide identification of YTHDC1-binding sites and biochemical experiments, not only reveal the specific mode of m(6)A-YTH binding but also explain the preferential recognition of the GG(m( 6)A)C)C sequences by YTH DC1.
Abstract: N6-methyladenosine (m6A) is an abundant eukaryotic RNA modification that regulates mRNA stability. Biochemical analysis and crystallographic visualization of m6A-YTHDC1 interactions establish this YTH family member as an m6A reader and explain its RNA consensus sequence selectivity.

500 citations

Journal ArticleDOI
TL;DR: The identification, definition and architecture of the WD40 domains are discussed, and how post-translational modifications are recognized by the large versatile family of WD40 domain proteins are discussed.
Abstract: The WD40 domain exhibits a β-propeller architecture, often comprising seven blades. The WD40 domain is one of the most abundant domains and also among the top interacting domains in eukaryotic genomes. In this review, we will discuss the identification, definition and architecture of the WD40 domains. WD40 domain proteins are involved in a large variety of cellular processes, in which WD40 domains function as a protein-protein or protein-DNA interaction platform. WD40 domain mediates molecular recognition events mainly through the smaller top surface, but also through the bottom surface and sides. So far, no WD40 domain has been found to display enzymatic activity. We will also discuss the different binding modes exhibited by the large versatile family of WD40 domain proteins. In the last part of this review, we will discuss how post-translational modifications are recognized by WD40 domain proteins.

492 citations

Journal ArticleDOI
TL;DR: In this article, fluoroethylene carbonate (FEC) was used as an electrolyte additive, which significantly improved the cyclability of silicon-based electrodes and suppressed further salt degradation.
Abstract: Silicon as a negative electrode material for lithium-ion batteries has attracted tremendous attention due to its high theoretical capacity, and fluoroethylene carbonate (FEC) was used as an electrolyte additive, which significantly improved the cyclability of silicon-based electrodes in this study. The decomposition of the FEC additive was investigated by synchrotron-based X-ray photoelectron spectroscopy (PES) giving a chemical composition depth-profile. The reduction products of FEC were found to mainly consist of LiF and −CHF–OCO2-type compounds. Moreover, FEC influenced the lithium hexafluorophosphate (LiPF6) decomposition reaction and may have suppressed further salt degradation. The solid electrolyte interphase (SEI) formed from the decomposition of ethylene carbonate (EC) and diethyl carbonate (DEC), without the FEC additive present, covered surface voids and lead to an increase in polarization. However, in the presence of FEC, which degrades at a higher reduction potential than EC and DEC, instant...

473 citations

Journal ArticleDOI
TL;DR: A hydrolytically stable and radiation-resistant cationic metal-organic framework (MOF), SCU-101, exhibiting extremely fast removal kinetics, exceptional distribution coefficient, and high sorption capacity toward TcO4 is reported, capable of effectively separating T cO4- from Hanford low-level waste melter off-gas scrubber simulant stream.
Abstract: Effective and selective removal of 99TcO4– from aqueous solution is highly desirable for both waste partitioning and contamination remediation purposes in the modern nuclear fuel cycle, but is of significant challenge. We report here a hydrolytically stable and radiation-resistant cationic metal–organic framework (MOF), SCU-101, exhibiting extremely fast removal kinetics, exceptional distribution coefficient, and high sorption capacity toward TcO4–. More importantly, this material can selectively remove TcO4– in the presence of large excesses of NO3– and SO42–, as even 6000 times of SO42– in excess does not significantly affect the sorption of TcO4–. These superior features endow that SCU-101 is capable of effectively separating TcO4– from Hanford low-level waste melter off-gas scrubber simulant stream. The sorption mechanism is directly unraveled by the single crystal structure of TcO4–-incorporated SCU-101, as the first reported crystal structure to display TcO4– trapped in a sorbent material. A recogni...

336 citations


Cited by
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08 Dec 2001-BMJ
TL;DR: There is, I think, something ethereal about i —the square root of minus one, which seems an odd beast at that time—an intruder hovering on the edge of reality.
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 …

33,785 citations

01 May 1993
TL;DR: Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems.
Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

29,323 citations

01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations