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检索条件"任意字段=第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学"

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CHASE:Discovery of Cancer Heterogeneity and Chromosomal Aberrations from SNP-array Experiments

CHASE:Discovery of Cancer Heterogeneity and Chromosomal Aber...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者：李骜 Hong Xial Yuanning Liu Minghui Wang School of Information Science and Technology University of Science and Technology of China Center for Biomedical Engineering Research University of Science and Technology of China

Background:With the advance of single nucleotide polymorphism(SNP) genotyping arrays,there is increasing interest in using this powerful technology for profiling chromosomal aberrations in ***,currently a critical issue hampering further applications of SNP-array in cancer research lies in the fact that cancer is often heterogeneous with multiple sub-clones that exhibit distinct biological characteristic including chromosomal *** addition,cancer heterogeneity is of great interest to oncologists as study on it may shed light on the origin of cancer and carcinogenesis. Methods:To address the issue of cancer heterogeneity,we developed a novel statistical model named CHASE(Cancer Heterogeneity and Chromosomal Aberrations from SNP-array Experiments) based on the framework of global parameter hidden Markov model(HMM).By quantitatively delineating the genomic similarity and discrepancy between two cancer sub-clones using global parameters representing the percentage of different sub-clones,we generated empirical emission probability density functions and incorporated them with the *** modeling fitting and parameter estimation,ECM algorithm was adopted in CHASE and formulas were derived for parameter updating. Results:Test on both simulated and real SNP-array data showed that CHASE can automatically determine cancer heterogeneity from the results of SNP-array experiment. For each cancer sub-clone,various kinds of chromosomal aberrations,such as amplification,deletion,LOH,etc,can be precisely discovered by *** example, by applying CHASE to breast cancer sample "BLCB1T45" that was manually identified as heterogeneous,we successfully identified two cancer sub-clones with two chromosomal regions exhibiting distinct chromosomal aberrations. Conclusions:To the best of our knowledge,CHASE is currently the most powerful computational methods that can discover cancer heterogeneity and chromosomal aberrations for each sub-clone from SNP-array data.

关键词： SNP-array cancer heterogeneity chromosomal aberration HMM

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CePa:Finding Significant Pathways through Network Centralities

CePa:Finding Significant Pathways through Network Centraliti...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者：顾祖光 Kun-Ming Cao Jin Wang The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology School of Life ScienceNanjing University

Background:Pathway analysis can assist researchers to understand biological aberrations at a systems ***,finding important pathways that underlie biological problems helps researchers to focus on the most relevant sets of *** resemble networks with complicated structures,but most of the existing pathway enrichment tools ignore topological information embedded within pathways,which limits their applicability. Methods:In the current analysis,we focus mainly on the centrality-based extension of the broadly applied Over-Representation Analysis method(ORA).The pathway score is defined as the summation of the weights of differentially affected nodes in the pathway,and the non-parametric null distribution of pathway score is generated through simulation from background *** the model,we weight the nodes by network *** the available centralities in network analysis,we defined one additional centrality,largest reach,to measure whether nodes stay in the upstream or downstream part of the pathway. Results:A systematic and extensible pathway enrichment method in which nodes are weighted by network centrality was *** demonstrate how choice of pathway structure and centrality measurement,as well as the presence of key genes, affects pathway *** emphasize two improvements of our method over current ***,allowing for the diversity of genes' characters and the difficulty of covering gene importance from all aspects,we set centrality as an optional parameter in the ***,nodes rather than genes form the basic unit of pathways,such that one node can be composed of several genes and one gene may reside in different nodes. By comparing our methodology to the original enrichment method using both simulation data and real-world data,we demonstrate the efficacy of our method in finding new pathways from biological perspective. Conclusions:Our method can benefit the systematic analysis of biological pathways and help

关键词： Pathway enrichment Network centrality Systems biology

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An Asynchronous Parallel Model for Genome Assembly

An Asynchronous Parallel Model for Genome Assembly

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Jintao Meng Shengzhong Feng Yanjie Wei Institute of Computing Technology Chinese Academy of Sciences Center for High Performance Computing Shenzhen Institutes of Advanced TechnologyChinese Academy of Sciences

Background:Current sequencing technology(Illumina Solexa,Applied Biosystems SoLiD,and Helicos Biosciences Heliscope etc.) allows one to read millions of 35 to 100 nucleotide sequences per *** to experimental errors,gaps,and genomic repeats,a much higher coverage depth of 50-fold to 300-fold is needed for accurate *** factors contribute to a 300-fold to 1000-fold increase in the number of reads,resulting in billions of reads to be processed,which significantly complicates the genome assembly problem. Methods:This paper first demonstrates a multi-step bi-directed graph for the problem of genome *** can be recovered by merging semi-extended edges to fullextended edges or *** a small world asynchronous parallel(SWAP) model is proposed to realize edge merging over a distributed one-step bi-directed *** model applies the Lock-Computation-Unlock scheme to each vertex's small ***,we implement an assembler named as Para-Assembler using the SWAP *** the number of processes p,the complexity of this problem is reduced to 0(n/p) parallel compute time, 0(n/p) communication round,and O(glog(g)/p) communication volume,here g is the length of genomes,and n is the number of nucleotide in all input reads. Results:Simulation results shows that Para-Assembler has a factor of 20 times speedup when the number of processors scales from 10 to 640. Conclusions:The proposed SWAP introduced local synchronization and global asynchronization mechanism to maximize the parallelism in the graph *** on SWAP model,we developed a new framework named as Para-assembler,and simulation results confirm its scalability over 640 *** Para-assembler can be used as basic computing framework for genome assembly.

关键词： parallel computing De Bruijn graph genome assembly

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Potential influences of the segments in 16S rRNA besides anti-SD sequence on gene translation initiation of ***

Potential influences of the segments in 16S rRNA besides ant...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Zhiqiang Ying Hong Li Xiaoqing Zhao School of Physical Science and Technology Inner Mongolia University

Background:Anti-SD(Shine Dalgarno) sequence of 16S rRNA is considered a key segment to regulate gene translation initiation by combined with SD sequence in prokaryotes. However,some analysis showed that other segments besides anti-SD sequence in 16S rRNA have potential affections to regulate gene translation *** segments and antiSD sequence are composed a net system to regulate translation *** the characters and functions of these potential segments is not *** will try to detect these potential segments and study their influence on translation initiation. Methods:We selected all of the mRNAs in *** genome as our date set and calculated the codon adaptation index(CAI) values of each *** value is considered an available parameter to characterize gene expression levels in *** is considered that high expressed genes have higher translation ***,1200 genes are selected according to gene expression levels,which are 400 genes with high expression levels,400 genes with low expression levels and 400 genes with middle expression levels by random selected from 3488 genes with middle CAI *** mRNA sequence was divided into three *** are upstream SD region,SD region and downstream AUG region.16S rRNA was divided into 27 loops segments and 38 helixes segments and anti-SD sequence according to its second structure. Smith-Waterman local alignment method is used to get the scores of optimal matched regions between the selected segments in 16S rRNA and three mRNA *** the correlation between the alignment scores and CAI values are calculated respectively by Spearman correlation analysis. Results:Spearman correlation analysis shows that the alignment scores between SD region and anti-SD region have positive correlation obviously with gene *** is to say the alignment score is available parameter to character the sequence affections. We find that there are six loops and 22 helixes combined with

关键词： E.coli 16S rRNA SD region sequence alignment gene expression

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Identification of gene-environment barcodes for complex human diseases

Identification of gene-environment barcodes for complex huma...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者：苏伟扬 Zhong Zhao Shaoqi Rao School of Public Health Sun Yat-sen University School of Mathematics and Computational Sciences Sun Yat-Sen University Institute of Medical Systems Biology and School of Public Health Guangdong Medical College

Background:It is widely recognized that the molecular etiology of complex human diseases is very sophisticated,involving a large number of genes,gene-gene and geneenvironment *** the underlying high order of multiple susceptible genes or genetic barcodes for complex diseases is always the great hope in biomedical domains,which has important implications in both early molecular diagnosis and personalized *** aim of this study was to assess the potential of high-dimension SNP data (and environmental factors) to be used to generate the multi-factorial patterns for accurately partitioning human populations. Materials and Methods:Two datasets of case-control for two cancers were analyzed. The data for nasopharyngeal carcinoma(NPC) contained 676 SNPs and 12 environmental variables,while the data for coronary heart disease(CHD),provided by The Wellcome Trust Case Control Consortium(WTCCC),contained only genome-wide *** reduce the following computational burden,Chi-square association analysis of single SNP loci was first performed to reduce the SNP ***,genetic algorithm(GA) and probabilistic neural network(PNN) were integrated to be used to identify the multi-dimension patterns of SNPs (and environmental factors).ROC curve was also used to assess their performances for partitioning human ***,The pathway analysis software,PathwayAssist,was used to explore the biological functions that the genetic barcodes were involved. Results:For NPC data,a barcode composing of 14 SNPs(in 10 genes) and four environmental factors was identified,with an accuracy of 78.49%and Youden index 52.98% for distinguishing between NPC patients and health *** for CHD data,6 barcodes (with no more than 100 SNPs in each barcode) were identified,with accuracies of all >89% and AUC(area under the ROC curve) of all >*** functional analysis of these barcodes demonstrated that these high-dimension barcodes were of sounding biological signif

关键词： complex human disease barcode SNP environments genetic algorithm probabilistic neural network

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Chemical Bioinformatics-From Evolution to Drug Discovery

Chemical Bioinformatics-From Evolution to Drug Discovery

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者：张红雨 National Key Laboratory of Crop Genetic Improvement Center for BioinformaticsHuazhong Agricultural University

In this omics era,informatics pervades the entire *** life consists of not only macromolecules(e.g.,DNA,RNA and proteins) but also small molecules(e.g., metabolites and metals),chemoinformatics,in addition to bioinformatics,should find important use in current life ***,the value of chemoinformatics was largely overlooked by *** the past decade,we were engaged in data mining by combinatorial use of chemoinformatics and bioinformatics,which was termed chemical bioinformatics. By using a train of thought "starting from small molecules and beginning with fundamental questions",we have performed a rather systematic research in this new *** major findings include:i) Based on the power-law distribution of small-molecule ligands in protein universe,we proposed a model for protein origin and evolution that the birth of new protein architectures was facilitated(induced and/ or selected) by binding of small-molecule ligands(including metals)(Ji et al.2007). ii) By using protein structures as molecular fossils and employing the geological age information of small molecules,we established the molecular clocks of protein folds and superfamilies,which were used to trace some critical events in evolutionary history of life and earth,such as the evolution of amino acid biosynthesis,the rise of oxygen,and the origin of aerobic metabolism(Wang et al.2011;Kim et al.2012;Zhang et al.2012). iii) By means of chemoinformatics,we revealed novel molecular links between oxygen rise and biological evolution,and found a chemical basis for the metabolic network organization(Zhu et al.2011;Jiang et al.2012).iv) Through a chemical genetic analysis, we revealed that natural products can hinder the evolution of antibiotic resistance by repairing the oxidative DNA ***,we proposed the concepts of "evolution inhibitor" and "evolution-inspired drug discovery" to help find anticancer, antioxidant and antibacterial drugs(Zhang et al.2010;Wang et a

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miRDeathDB:a database bridging microRNAs and the programmed cell death

miRDeathDB:a database bridging microRNAs and the programmed ...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Jianzhen Xu Yan-Hui Li College of Bioengineering Henan University of TechnologyZhengzhouChina 450001 Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences Ministry of EducationPeking University Health Science Center Scientific Data Center Computer Network Information CenterChinese Academy of Sciences

Background:MicroRNAs(miRNAs) are a class of small non-coding RNAs,which negatively regulate protein coding genes at the posttranscriptional *** tiny regulators have been associated to almost all known physiological and pathological *** defects in miRNAs have been implicated in the etiology of many forms of human diseases. Apoptosis,autophagy and programmed necrosis are three distinct yet intimately connected functional modules of programmed cell death(PCD).In the past few years,increasing evidences suggested that aberrant expression of miRNAs regulate different subroutines of *** the roles of miRNAs in PCD network has attracted interests of researchers from a wide range of ***,a knowledge depository,which integrates information for both miRNAs and their targets in PCD network,will be of great help. Methods:Based on PubMed search,we firstly collected literatures which reported the roles of miRNAs in PCD before April ***,these literatures were inspected manually and the miRNAs and their targets genes were *** criterion for selecting PCD associated miRNAs in miRDeathDB is *** morphological or biochemical data should be provided when the miRNAs(or their targets) are manipulated in cell death *** miRDeathDB(http://***/mirdeathdb/) was developed,which allows users to browse,search and analyze the PCD associated miRNAs. Results:In total,210 records covering 86 miRNAs and 95 protein coding genes were collected in five model species:humans(Homo sapiens),mice(Mus musculus),fruit flies (Drosophila melanogaster),rat(Rattus norvegicus) and African frog(Xenopus tropicalis). Users can search the database for both miRNAs and protein coding entries based on principal *** addition,users can browse and obtain full lists of miRNAs involved in PCD for any given *** data can be freely downloaded or accessed via our website for academic uses. Conclusions:miRDeathDB provides a valuab

关键词： microRNAs apoptosis autophagy necrosis

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Expression profiles of microRNAs from lactating and non-lactating bovine mammary glands

Expression profiles of microRNAs from lactating and non-lact...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Zhen Li Xiaolu Jin.Hongyun Liu Lijian Luo Jianxin Liu Institute of Dairy Science MOE Key Laboratory of Molecular Animal NutritionZhejiang University Laboratory of Functional Genomics College of Animal SciencesZhejiang University

Background:MicroRNAs(miRNAs) have been implicated in the regulation of milk protein synthesis and development of mammary gland(MG).However,the function of miRNAs in regulating lactation is ***,the elucidation of miRNA expression profiles in MG provides a crucial entry into the understanding of the mechanisms of lactation. Methods:In this study,parenchymal tissues were sampled from the MG of non- and lactating Holstein dairy *** small RNA was sequenced by Solexa sequencing and processed using ACGTlOl-miR program and UNAFold *** IDEG 6 was used to identify differentially expressed miRNAs.A custom-designed microarray assay including 523 miRNA probes was performed to analyze miRNA expression *** EGAN software was used to construct network between miRNAs,target genes and lactation. Results:Two miRNA libraries were constructed and *** were 885 premiRNAs encoding for 921 miRNAs,of which 884 were unique and 544(61.5%) were expressed in both *** them,284 were known as bovine miRNAs registered in the miRbase database;96 miRNAs were conserved among other mammalian;and 566 miRNAs were bovine-novel candidates.A custom-designed microarray assay was performed to analyze miRNA expression patterns in the MG of lactating and non-lactating dairy *** against non-lactating MG,a total of 226 miRNAs in the lactating MG showed significant differences in expression(P<0.01).Real-time quantitative PCR was used for validation of the sequencing results of selected 32 *** 50%of miRNAs were consistent with Solexa sequencing *** chromosome positions for all 885 pre-miRNAs were found that 800 premiRNAs matched with bta genome,and only 230 pre-miRNAs were grouped into 55 clusters. Using integrative miRNA target-prediction and network-analysis approaches an interaction network of lactation-related miRNAs and their putative targets was *** networks involved 37 miRNAs detected by this study and 15 target

关键词： bovine mammary gland lactation,miRNAs

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Complete Genome Sequence of Mycoplasma ovipneumoniae Strain Y98

Complete Genome Sequence of Mycoplasma ovipneumoniae Strain ...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Li Min Wang Jing Hao Xiujing Cui Juanjuan Zhang Simin Xie Qin Wang Yujiong Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources of Western China Ningxia University College of Life Science Ningxia University

Mycoplasma ovipneumoniae is the aetiologic agent of contagious pleuropneumonia,a respiratory disease of sheep and goats that is widespread in the country with developed sheep industry,especially in Asian and Africa,and caused important economic losses in the sheep ***,its pathogenesis is still not fully ***,we announce the complete genome sequence of *** Strain Y98(*** a standard strain,M. ovipneumoniae strain Y98 has been widely used in the study of the characterization of M. ovipneumoniae,but it's complete genome sequence has not been reported by *** accomplishment of the complete genome sequencing of strain Y98 will benefit studying M. ovipneumoniae pathogenic mechanism. Whole-genome sequencing was performed by sequencing side-synthesis Illumina Hiseq2000 high-throughput sequencing technology.2,454,900 Paired-end reads were produced with Hiseq 2000 system sequenced by using PCR-free library that contains 350 bp inserts,and 240X-fold average of genome were gotten.99.95%of reads were assembled into 98 contigs with SOAP de novo software,then contigs were collected into 92 scaffolds according to the relationship between Paired-end of reads. The total length genome of the entire *** strain Y98 is 1,021,486 bp with 29.21%GC *** total of 819 gene sequences were predicted by Glimmer 3.0 ,the length of gene region which accounted for 76.23%of the entire genome was 778,686 bp,the average length of gene was 950 bp.50.7%of gene sequences were annotated to KEGG database,and 45.2%were assigned to GO database.31 tRNA genes and 3 rRNA genes were also predicted. Compared with whole-genome sequence of *** SC01,*** Y98 is similar to the proteins that are highly similar to bacterial toxins,hemolysin A and hemolysin *** pathogenesis is still not fully clear,although they are also in other mycoplasma,such as ***,***,and ***. Weishurget *** ***

关键词： Mycoplasma ovipneumoniae Y98 Genome

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DiNuP:A Systematic Approach to Identify Regions of Differential Nucleosome Positioning

DiNuP:A Systematic Approach to Identify Regions of Different...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Kai Fu Qianzi Tang Jianxing Feng X.Shirley Liu Yong Zhang Department of Bioinformatics School of Life Science and TechnologyTongji University Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard School of Public Health44 Binney StreetBostonMA 02115USA

Background:With the rapid development of high-throughput sequencing technologies, the genome-wide profiling of nucleosome positioning has become increasingly affordable. Many future studies will investigate the dynamic behaviour of nucleosome positioning in cells that have different states or that are exposed to different ***,a robust method to effectively identify the regions of differential nucleosome positioning(RDNPs) has not been previously available. Methods:We use two sample K-S test to identify the sliding windows between samples that have different nucleosome positioning *** input samples may have different sequencing depth,we use re-sampling method to empirically estimate FDR as cutoff to identify reliable RDNPs from background *** addition,we integrated several parameters to describe physical properties of the identified RDNPs from various aspects. Evaluated by both simulation datasets and real biological datasets,we prove that our method has a high sensitivity and high specificity in the identification of different types of nucleosome positioning dynamics. Results:We describe a novel computational approach,DiNuP,that compares nucleosome profiles generated by high-throughput sequencing under various *** provides a statistical p-value for each identified RDNP based on the difference of read distributions. DiNuP also empirically estimates the false discovery rate(FDR) as a cutoff when two samples have different sequencing depths and differentiate reliable RDNPs from the background noise. Evaluation of DiNuP showed it to be both sensitive and specific for the detection of changes in nucleosome location,occupancy and *** that were identified using publicly available datasets revealed that nucleosome positioning dynamics are closely related to the epigenetic regulation of transcription. Conclusions:We develop an effective algorithm for the identification of differential nucleosome *** us

关键词： Nucleosome positioning chromatin dynamics Kolmogorov-Smirnov test

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