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Search Results: 1 - 10 of 58825 matches for " Huanming Yang "
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Sequencing and analysis of the giant panda genome
HuanMing Yang
Science China Life Sciences , 2010, DOI: 10.1007/s11427-010-4046-9
Abstract:
Tree Matrix Algorithm of LDPC Codes  [PDF]
Huanming Zhang
Journal of Signal and Information Processing (JSIP) , 2014, DOI: 10.4236/jsip.2014.54020
Abstract: LDPC codes are finding increasing use in applications requiring reliable and highly efficient information transfer over bandwidth. An LDPC code is defined by a sparse parity-check matrix and can be described by a bipartite graph called Tanner graph. Loops in Tanner graph prevent the sum-product algorithm from converging. Further, loops, especially short loops, degrade the performance of LDPC decoder, because they affect the independence of the extrinsic information exchanged in the iterative decoding. This paper, by graph theory, deduces cut-node tree graph of LDPC code, and depicts it with matrix. On the basis of tree matrix algorithm, whole depictions of loops can be figured out, providing of foundation for further research of relations between loops and LDPC codes’ performance.
Novel Methods in the Study of the Breast Cancer Genome: Towards a Better Understanding of the Disease of Breast Cancer  [PDF]
Jian Li, Xue Lin, Nils Brünner, Huanming Yang, Lars Bolund
Journal of Cancer Therapy (JCT) , 2012, DOI: 10.4236/jct.2012.325101
Abstract: Rapidly developing sequencing technologies and bioinformatic approacheshave provided us with an unprecedented instrument allowing for an unbiased and exhaustive characterization of the cancer genome in genetic, epigenetic and transcriptomic dimensions. This review introduces recent excitingfindings and new methodologies in genomic breast cancer research. With this development, cancer genome research will illuminate new delicate interactionsbetween molecular networks and thereby unravelthe underlying biological mechanisms for cancer initiation and progression. It also holds promise for providing a molecular clock for the estimation of the temporal processes of tumorigenesis. These methods in combination with single cell sequencing will make it possible to construct a family tree elucidating the evolutionary lineage relationships between cell populations at single-cell resolution. The anticipatedrapid progress in genomic breast cancer research should lead to anenhanced understanding of breast cancer biology andguide us towardsnovel ways to ultimatelyprevent and cure breast cancer.
Codon Usage Patterns in Corynebacterium glutamicum: Mutational Bias, Natural Selection and Amino Acid Conservation
Guiming Liu,Jinyu Wu,Huanming Yang,Qiyu Bao
Comparative and Functional Genomics , 2010, DOI: 10.1155/2010/343569
Abstract: The alternative synonymous codons in Corynebacterium glutamicum, a well-known bacterium used in industry for the production of amino acid, have been investigated by multivariate analysis. As C. glutamicum is a GC-rich organism, G and C are expected to predominate at the third position of codons. Indeed, overall codon usage analyses have indicated that C and/or G ending codons are predominant in this organism. Through multivariate statistical analysis, apart from mutational selection, we identified three other trends of codon usage variation among the genes. Firstly, the majority of highly expressed genes are scattered towards the positive end of the first axis, whereas the majority of lowly expressed genes are clustered towards the other end of the first axis. Furthermore, the distinct difference in the two sets of genes was that the C ending codons are predominate in putatively highly expressed genes, suggesting that the C ending codons are translationally optimal in this organism. Secondly, the majority of the putatively highly expressed genes have a tendency to locate on the leading strand, which indicates that replicational and transciptional selection might be invoked. Thirdly, highly expressed genes are more conserved than lowly expressed genes by synonymous and nonsynonymous substitutions among orthologous genes fromthe genomes of C. glutamicum and C. diphtheriae. We also analyzed other factors such as the length of genes and hydrophobicity that might influence codon usage and found their contributions to be weak.
Codon Usage Patterns in Corynebacterium glutamicum: Mutational Bias, Natural Selection and Amino Acid Conservation
Guiming Liu,Jinyu Wu,Huanming Yang,Qiyu Bao
International Journal of Genomics , 2010, DOI: 10.1155/2010/343569
Abstract: The alternative synonymous codons in Corynebacterium glutamicum, a well-known bacterium used in industry for the production of amino acid, have been investigated by multivariate analysis. As C. glutamicum is a GC-rich organism, G and C are expected to predominate at the third position of codons. Indeed, overall codon usage analyses have indicated that C and/or G ending codons are predominant in this organism. Through multivariate statistical analysis, apart from mutational selection, we identified three other trends of codon usage variation among the genes. Firstly, the majority of highly expressed genes are scattered towards the positive end of the first axis, whereas the majority of lowly expressed genes are clustered towards the other end of the first axis. Furthermore, the distinct difference in the two sets of genes was that the C ending codons are predominate in putatively highly expressed genes, suggesting that the C ending codons are translationally optimal in this organism. Secondly, the majority of the putatively highly expressed genes have a tendency to locate on the leading strand, which indicates that replicational and transciptional selection might be invoked. Thirdly, highly expressed genes are more conserved than lowly expressed genes by synonymous and nonsynonymous substitutions among orthologous genes fromthe genomes of C. glutamicum and C. diphtheriae. We also analyzed other factors such as the length of genes and hydrophobicity that might influence codon usage and found their contributions to be weak. 1. Introduction It is well established that the codon usage patterns are generally not used with equal frequency. Grantham et al. firstly explained the phenomena of unequal usage and proposed the “genome hypothesis", stating that the biases are species specific [1], and multivariate analysis methods were used to analyze codon usage and amino acid composition [2–4]. As more and more complete genome sequences of diverse species are investigated, researchers have found that biased usage of synonymous codons may result from various factors. Some unicellular species have extremely biased compositions, where compositional constraints are the main factors in determining the codon usage variation among genes [5–7]. In contrast, both translational selection and compositional constraint operate on the codon usage variation in other organisms [8–14]. Moreover, in several bacteria, the replication and translational selection is responsible for the codon usage variation among genes [15–18]. In organisms, such as Escherichia coli [36], Drosophila
Preparing a re-sequencing DNA library of 2 cancer candidate genes using the ligation-by-amplification protocol by two PCR reactions
YeYang Su,Lin Lin,Geng Tian,Chen Chen,Tao Liu,Xingya Xu,XinPeng Qi,XiuQing Zhang,HuanMing Yang
Science China Life Sciences , 2009, DOI: 10.1007/s11427-009-0066-8
Abstract: To meet the needs of large-scale genomic/genetic studies, the next-generation massively parallelized sequencing technologies provide high throughput, low cost and low labor-intensive sequencing service, with subsequent bioinformatic software and laboratory methods developed to expand their applications in various types of research. PCR-based genomic/genetic studies, which have significant usage in association studies like cancer research, haven’t benefited much from those next-generation sequencing technologies, because the shortgun re-sequencing strategy used by such sequencing machines as the Illumina/Solexa Genome Analyzer may not be applied to direct re-sequencing of short-length target regions like those in PCR-based genomic/genetic studies. Although several methods have been proposed to solve this problem, including microarray-based genomic selections and selector-based technologies, they require advanced equipment and procedures which limit their applications in many laboratories. By contrast, we overcame such potential drawbacks by utilizing a ligation by amplification (LBA) protocol, a method using a pair of Universal Adapters to randomly ligate target regions in a two-step-PCR procedure, whose Long LBA products were easily fragmented and sequenced on the next-generation sequencing machine. In this concept-proven study, we chose the consensus coding sequences of two human cancer genes: BRCA1 and BRCA2 as target regions, specifically designed LBA primer pairs to amplify and randomly ligate them. 70 target sequences were successfully amplified and ligated into Long LBA products, which were then fragmented to construct DNA libraries for sequencing on both a conventional Sanger sequencer ABI 3730xl DNA Analyzer and the next-generation ‘synthesis by sequencing technology’ Illumina/Solexa Genome Analyzer. Bioinformatic analysis demonstrated the utility and efficiency (including the coverage and depth of each target sequence and the SNPs detection effectiveness) of using the LBA protocol in facilitating PCR-based re-sequencing and genetic-variant-detection studies on the next-generation sequencing machine, raising the prospect of various PCR-based genomic/genetic studies using this strategy.
Preparing a re-sequencing DNA library of 2 cancer candidate genes using the ligation-by-amplification protocol by two PCR reactions

SU YeYang,LIN Lin,TIAN Geng,CHEN Chen,LIU Tao,XU Xingya,QI XinPeng,ZHANG XiuQing &,YANG HuanMing,

中国科学C辑(英文版) , 2009,
Abstract: To meet the needs of large-scale genomic/genetic studies, the next-generation massively parallelized sequencing technologies provide high throughput, low cost and low labor-intensive sequencing service, with subsequent bioinformatic software and laboratory methods developed to expand their applications in various types of research. PCR-based genomic/genetic studies, which have significant usage in association studies like cancer research, haven’t benefited much from those next-generation sequencing technologies, because the shortgun re-sequencing strategy used by such sequencing machines as the Illumina/Solexa Genome Analyzer may not be applied to direct re-sequencing of short-length target regions like those in PCR-based genomic/genetic studies. Although several methods have been proposed to solve this problem, including microarray-based genomic selections and selector-based technologies, they require advanced equipment and procedures which limit their applications in many laboratories. By contrast, we overcame such potential drawbacks by utilizing a ligation by amplification (LBA) protocol, a method using a pair of Universal Adapters to randomly ligate target regions in a two-step-PCR procedure, whose Long LBA products were easily fragmented and sequenced on the next-generation sequencing machine. In this concept-proven study, we chose the consensus coding sequences of two human cancer genes: BRCA1 and BRCA2 as target regions, specifically designed LBA primer pairs to amplify and randomly ligate them. 70 target sequences were successfully amplified and ligated into Long LBA products, which were then fragmented to construct DNA libraries for sequencing on both a conventional Sanger sequencer ABI 3730xl DNA Analyzer and the next-generation ‘synthesis by sequencing technology’ Illumina/Solexa Genome Analyzer. Bioinformatic analysis demonstrated the utility and efficiency (including the coverage and depth of each target sequence and the SNPs detection effectiveness) of using the LBA protocol in facilitating PCR-based re-sequencing and genetic-variant-detection studies on the next-generation sequencing machine, raising the prospect of various PCR-based genomic/genetic studies using this strategy. National High-Tech Research & Development Program of China (Grant No.2006 AA02A301)
SELF-REACTION COEFFICIENTS OF Ca AND Mg IN LIQUID Sn
锡基稀溶液中Ca和Mg的自身作用系数

LIU Huanming,YANG Zupan,TIAN Yanwen The Steel Works No,Benxi Iron,Steel Company Northeast University of Technology,Shenyang LIU Huanming,assistant engineer,the Laboratory of Steel Works No,Benxi Iron,Steel Company,Benxi,Ltaoning,
刘焕明
,杨祖磐,田彦文

金属学报 , 1989,
Abstract: 在1500℃下以金属Sn作熔剂,石墨作还原剂,采用相同组成熔渣与不同组成的锡合金在CO-Ar混合气体条件下,使反应达到平衡,测定了锡基稀溶液中Ca,Ti和Mg的自身和相互作用系数。指出在用此法测定熔渣中组元的活度时,忽略Sn中元素的自身作用系数,将带来较大误差。
A New Scheme to Construct Orthogonal Channel Matrix for MIMO STBC by Givens Rotation  [PDF]
Huanming Zhang, Kaiyi Xian, Lijun Feng, Chaokang Hu
Journal of Signal and Information Processing (JSIP) , 2016, DOI: 10.4236/jsip.2016.71005
Abstract: This paper proposes a scheme to construct orthogonal channel matrix for full rate quasiorthogonal STBC based on givens rotation with lower bit error rate. The transmission diversity method rotates every single information symbol. The scheme can suppress channel noise and eliminate the interference term well. Simulation results show that the method can improve performance better than conventional algorithm without increasing decoding complexity.
ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun
Ruiqiang Li ,Jia Ye ,Songgang Li ,Jing Wang ,Yujun Han,Chen Ye,Jian Wang,Huanming Yang,Jun Yu,Gane Ka-Shu Wong ,Jun Wang
PLOS Computational Biology , 2005, DOI: 10.1371/journal.pcbi.0010043
Abstract: We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer recognizable in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences.
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