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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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Genome-wide protein structure prediction and structure-based function annotation

Genome-wide protein structure prediction and structure-based...

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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：张扬 Department of Computational Medicine and Bioinformatics Department of Biological ChemistryUniversity of MichiganAnn ArborMI 48109

The biological function of protein molecules is determined by the shape of their three-dimensional *** it possible to predict protein structure and function from the amino acid sequence? We developed a new algorithm,I-TASSER,which assembles atomic structure of proteins using fragments excised from unrelated experiment *** insights (***-binding affinity,enzyme classification and gene ontology) are then deduced by matching the predicted structure models with the known proteins in protein function libraries. The I-TASSER algorithm was ranked as the best for automated protein structure prediction in the communitywide CASP experiments of 2006,2008 and 2010;it was also ranked at the top for protein function annotation in CASP9 in 2010. In this talk,we first review the recent progress in computer-based protein structure prediction including the new developments in ab initio folding and atomic structure refinements since the CASP9 experiment,and show that the protein structure prediction problem can in principle be solved using the current PDB ***,we discuss the application of the developed methods to the structural and functional modeling of a number of genomes,including all G-protein coupled receptors(GPCRs) in the human genome,yielding models 90%of which are shown to have correct topology,and Marek's disease virus,the first success of the computational modeling of a complete viral ***,we demonstrate how the predicted I-TASSER structure models can be used to annotate the biological function of the proteins and screen drug candidates by matching their global topology and functional sites against the existing structure/function/binding databases.

关键词： Protein structure prediction protein function annotation G protein-coupled receptors

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A Stochastic Model of Bacterial Persister Formation

A Stochastic Model of Bacterial Persister Formation

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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： Ning Yin Jianfeng Pei Luhua Lai Center for Quantitative Biology Peking University College of Chemistry and Molecular Engineering Peking University

Background:Bacterial persisters are a tiny fraction of preexisting dormant cells inside bacterial *** isogenic with the rest of the population,persister cells exhibit a distinct phenotype,and are slow growing and generally antibiotics *** antibiotics treatment,persister cells survive while the normal growing cells ***,after treatment, persister cells can spontaneously switch to normal growing state and regenerate the whole bacterial ***,persisters represent a challenge for antibiotics treatment,and are responsible for several kinds of persistent infections such as *** set out to build a model to explain the nature of stochastic bacterial persister formation. Methods:The HipA-induced persister formation model was built based on previous models and recent experimental findings.A chemical reaction network composed of 7 species and 14 reactions with manually tuned parameters was then simulated using Gillespie algorithm to capture the stochastic nature of persister *** was then done on the stochastic time course from the simulation. Results:We have built a model for the expression dynamics of hipAB operon,which included the expression of hipAB operon,the oligomerization of the toxin HipA and antitoxin HipB,as well as the autoregulations in the *** simulation could correctly reproduce the bimodal distribution of HipA protein level,which corresponds to the two phenotypic states of *** bimodal distribution could be the result of cooperative positive feedback without bistability. Conclusions:We have constructed and simulated the HipA-induced *** persister formation process using stochastic simulations.A biomodal distribution representing normal state and persistence state could be reproduced from our *** model is still being improved to better describe experimental *** elucidation of persister formation mechanism could provide a starting point for

关键词： Bacterial persisters stochastic switching stochastic simulation

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Statistical power of three model-free metrics for detecting gene-gene interactions

Statistical power of three model-free metrics for detecting ...

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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： Su-Fen Qi Liang-Chang Xiu Shao-Qi Rao Yuan-Lin Ding Institute of Medical Systems Biology and School of Public Health Guangdong Medical College

Background:It is increasingly recognized that gene-gene interaction is an important genetic component for complex *** several metrics for detecting gene-gene interactions have been developed,there is dearth of knowledge regarding their statistical power under different scenarios of *** study thus aimed at systematic evaluation of the merits of three data mining metrics for detecting gene-gene interactions under various genetic models. Methods:In this article,we compared three different metrics of non-linear dependence between two genetic loci for detecting gene-gene *** three metrics were two-loci Fst,mutual information and linkage disequilibrium,*** generated case-control data by using simulation software genomeSIMLA based on 17 genetic models(including both epistatic and multiplicative interaction models).For each model,two different sets of disease allele frequencies and five different interaction effects were *** statistical power was computed from 500 simulated datasets. Results:In eight epistatic models,except for the model of recessive versus recessive, two-loci Fst and mutual information had higher statistical power than the linkagedisequilibrium based *** nine multiplicative models,two-loci Fst and mutual information also had higher statistical power. Conclusions:The evolution-based metric,Fst,and information-based metric, mutual information,are more powerful and robust statistic for detecting both epistatic and multiplicative gene-gene interactions.

关键词： Models of gene-gene interactions Evolutionary theory Case-control design

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A Wiki-based English-to-Chinese Scientific Nomenclature Dictionary

A Wiki-based English-to-Chinese Scientific Nomenclature Dict...

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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： Ming Tian Jian Sang Chao Xu Dong Zou Jiaya Wu Jingfa Xiao Xumin Wang Lin Dai Zhang Zhang School of Computer Science and Technology Beijing Institute of Technology Research Institute of Subtropical Forestry Chinese Academy of Forestry CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences

Background:Scientific nomenclature is a system of words used to name things in a particular ***,accurate translation of scientific nomenclature from English to Chinese is of critical significance,not only for effectively facilitating communications with overseas researchers,but also for efficiently disseminating knowledge among domestic people,especially students and young researchers in ***,among English nomenclature,some do not have unique or acknowledged translations in Chinese. Furthermore,a dynamically growing volume of scientific nomenclature poses additional challenges in English-to-Chinese *** is very often,for example,in life sciences that new nomenclature emerges with the rapid development of experimental technologies and the exploding number of related scientific studies. Methods:Here we develop a wiki-based English-to-Chinese Scientific Nomenclature Dictionary(ESND),aiming to exploit the power of the whole scientific community for nomenclature translation. Results:ESND provides a collaborative platform for collectively managing Englishto -Chinese scientific *** user can add a specific nomenclature when it is not *** addition,any user can make vote when there are multiple translations available for a given English nomenclature and thus most voted translations indicate wide acceptance by the scientific community. Conclusions:Based on the collective intelligence,ESND is capable of achieving accurate and comprehensive English-to-Chinese scientific nomenclature,laying a solid foundation for domestic scientific activities.

关键词： scientific nomenclature wiki English-to-Chinese ESND collective intelligence

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Quantifying authors' contributions in biological knowledge wikis

Quantifying authors' contributions in biological knowledge w...

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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： Ming Tian Jingfa Xiao Xumin Wang Lin Dai Zhang Zhang School of Computer Science and Technology Beijing Institute of Technology CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics.Chinese Academy of Sciences

Background:With the exponentially exploding volume of scientific literatures available, traditional expert curation becomes increasingly ineffective to keep biological knowledge upto -date,comprehensive and *** to this reason,several efforts have been devoted to building biological knowledge wikis(bio-wiki),aiming to harness collective intelligence for knowledge ***,extant bio-wikis have not achieved a substantial success,primarily due to no credit for authors' contributions and consequently inadequate participations from the scientific community. Methods:Sufficient participations in bio-wikis arc fundamentally vital in increasing knowledge coverage,improving knowledge accuracy and keeping knowledge up-to-date. To increase authors' participations from the scientific community and contribute knowledge by making edits in bio-wikis,we develop an algorithm,ScienceReward,to quantify authors' contributions by factoring edit quality as well as edit *** on quantitative contributions,ScienceReward ranks all contributed authors and provides explicit authorships for any wiki page. Results:ScienceReward provides a standard practice in bio-wikis for rewarding authors' contributions,helpful to encourage users' participations,improve knowledge reliability and increase collaborations in knowledge *** is implemented as an extension to MediaWiki,a bunch of codes for adding customized *** is easily installed and compatible to any MediaWiki-based system,possessing a broad scope for its application and providing a consistent appearance and functionality as Wikipedia. Conclusions:When contribution is appropriately measured and explicit authorship is duly rewarded as demonstrated in ScienceReward,bio-wikis bears significant promises in fully exploiting the power of the scientific community to integrate immense biological knowledge.

关键词： wiki contribution knowledge integration ScienceReward

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Predicting the subcellular localizatioon of chloroplast proteins using sequence and sequence-derived structural descriptors

Predicting the subcellular localizatioon of chloroplast prot...

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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： Cheng-Yan Wu Qian-Zhong Li Laboratory of Theoretiacl Biophysical School of Physical Science and TechnologyInner Mongoia University

Background:Chloroplast proteins are considered to be the functional unit of photosynthesis in the green plants and eukaryotic *** precise prediction of chloroplast proteins localization is very important for understanding the mechanism of photosynthesis and amino acid ***,developing a kind of fast and effective algorithm for predicting the chloroplast proteins localization is very necessary. Methods:According to Chou's PseACC,some novel custom-designed features are extracted,including amino acid sequence components optimized by mRMR(minimum Redundancy Maximum Relevance Feature Selection),the secondary structure,the sup- secondary structural motifs,pseudo-average chemical shift and reduced physicochemical *** increment of diversity is used to reduce the dimension of inputting vector. By using novel input features and combining the increment of diversity and support vector machine,an approach for predicting protein subchloropast location is ***,the leave-one-out test is employed to evaluate the prediction performance of our method for the datasets RWA737 and S60(with < 60%sequence identity) constructed by Du RF et al. Results:The overall predictive success rates for RWA737 and S60 by our method achieve 92.12%and 78.55%,respectively,in the leave-one-out *** results show that the prediction accuracies for RWA737 and S60 are about 2.43%and 11.37%higher than the results of SubChlo method,and is about 3%higher than the latest methods of BS-KNN for S60 dataset. Conclusions:The favorable predicting quality indicate that structural characters may be the important information parameters for describing chloroplast proteins and is helpful for predicting subcellular location of chloroplast proteins.

关键词： Chloroplast protein location Secondary structure Average chemical shift Increment of diversity(ID)

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Accurate Prediction of Protein Disordered Regions

Accurate Prediction of Protein Disordered Regions

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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： Qianqian Yang Tonghua Li Department of Chemistry Tongji University

Background:Intrinsically disordered proteins(IDPs) that do not possess stable secondary and tertiary structures are crucial for the function of numerous proteins. Even though these proteins lack intrinsic structure,they could bind to many different macromolecular partners when functioning in protein and protein *** their prevalence is implicated in a number of human *** prediction of disordered regions from protein sequence is a necessary prerequisite for the further understanding of principles and mechanisms of protein function,and is a key for the elaboration of a structural and functional hierarchy of *** prediction of IDPs has attracted the attention of many researchers,and a number of prediction methods have been *** of disorder play major roles in directing laboratory experiments that are leading to the discovery of disordered proteins,and thereby leading to a positive feedback loop in the investigation of these proteins. Methods:In this work,we propose a novel predictor,DRPred,which is based on a disorder position-specific scoring matrix(DPSSM).We develop a strategy to construct DPSSM which is generated by sequence alignment,and its element is disorder profiles. DRPred uses a database of disorder states of 35811 entries that is a non-redundant database contains amino acids and relative one of disorder,near-disorder and order information.A query is aligned against the database and resulting in *** training set is compiled by Pierre and *** contains 723 protein sequences with 215,612 residues,of which 13,909(6.5%) are *** approach utilizes a custom-designed set of features that are based on sequence profiles,predicted secondary structure,a structural position-specific scoring matrix(SPSSM),DPSSM,predicted shape string and its profiles. Results:The PDB723 set is used as the training in the classification algorithm of Conditional Random Fields(CRFs).Short and long disordered re

关键词： protein structure prediction disordered regions DPSSM CRFs

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Nucleosome positioning:mechanism;dynamics and computational challenges

Nucleosome positioning:mechanism;dynamics and computational ...

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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：张勇 School of Life Science and Technology Tongji University

Nucleosome positioning in vivo is influenced by DNA sequence,chromatin remodelers and fixed barriers,such as DNA-binding proteins,but the relative contribution of each one remains poorly *** DNA sequence is an unchanging factor,the recruitment of remodelers and barriers is closely related to the process of transcription in a cell status dependent manner. To study the effect of transcription on nucleosome positioning,we focused on the onset of zygotic transcription in zebrafish by deeply mapping nucleosome positions before and after maternal-zygotic transition(MZT).In the sample before MZT,we cannot observe the common nucleosomal pattern reported in other organisms,i.e.a clear nucleosome free region upstream transcription start site,flanking by a strong +1 and -1 ***,after the activation of zygotic transcription,nucleosome positioning is globally reshaped with the establishment of common nucleosomal pattern,together with clear nucleosome *** the genome-wide nucleosome profiles among the earliest developmental stages in vertebrate genomes,our results provide valuable insights in the reshaping of in vivo nucleosome profiles that play a role in the response to developmental signaling. We also developed a novel computational approach,DiNuP,that compares the nucleosome profiles generated by high-throughput sequencing between different conditions. Evaluation of DiNuP showed it to be both sensitive and specific for the detection of changes in nucleosome location,occupancy and *** identified from publicly available datasets revealed that nucleosome positioning dynamics are closely related to the epigenetic regulation of transcription. In addition,we generated whole-genome nucleosome positioning profiles for both wild type and mutant mouse ES cells with DNA methylation defects,aiming to reveal how DNA methylation can effect nucleosome *** research holds promise to provide a deeper insight into the crosstalk betwee

关键词： Nucleosome positioning:mechanism dynamics and computational challenges

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Analysis of synonymous codon usage in 11 Archaeal Virus genomes

Analysis of synonymous codon usage in 11 Archaeal Virus geno...

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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： Sen Li Jie Yang State Key Laboratory of Pharmaceutical Biotechnology School of Life ScienceNanjing University Department of Biochemistry Nanjing University

Recent studies of geothermally heated aquatic ecosystems have found widely divergent viruses with unusual *** Viruses isolated from these hot habitats usually have double-stranded DNA genomes,linear or circular,and can infect members of the Archaea *** this study,the codon usage bias and dinucleotide composition in the available complete Archaeal Virus genome sequences have been *** was found that there is a significant variation in codon usage bias among different Archaeal Virus species,which is mainly determined by the base *** outcome of correspondence analysis (COA) and Spearman's rank correlation analysis shows that codon usage of selected Archaeal Virus genes depends mainly on GC richness of genome,and the gene's function,albeit with smaller effects,also contributes to codon usage in this ***,this investigation reveals that aromaticity of each protein is also critical in affecting codon usage bias of these viral genes although it was less important than that of the mutational ***,the relative synonymous codon usage(RSCU) of 26 genes from these 11 Archaeal Virus genomes is analyzed using a hierarchical cluster *** result reveals that genes of genomes with similar GC content are classified into the same lineage,and gene function may play important role in determining the classification at the level of sublineage although other factors may also involve *** conclusions not only can offer an insight into the codon usage bias of Archaeal Virus,but also may help in the gene classification of Archaeal Viruses.

关键词： Archaeal Virus Synonymous codon usage Mutational bias Gene function Hierarchical cluster analysis

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MetaMHCIIpan:a consensus approach for pan-specific HLA-DR binding predictions

MetaMHCIIpan:a consensus approach for pan-specific HLA-DR bi...

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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： Lianming Zhang Linyuan Guo Shanfeng Zhu School of Computer Science and Shanghai Key Lab of Intelligent Information Processing Fudan University

Background:Binding of antigen peptides to Major Histocompatibility Complex ClassⅡ(MHC-Ⅱ,mainly HLA-DR for human) molecules is a core step in the adaptive immune *** identification of MHC-restricted peptides is of great importance for elucidating the underlying mechanism of immune recognition,as well as for developing effective cpitope-based vaccines and promising immunotherapies for many severe diseases. Due to extreme polymorphism of MHC-Ⅱalleles and the high cost of biochemical experiments,the development of computational methods for accurate prediction of binding peptides of MHC-Ⅱmolecules,particularly for the ones with few or no experimental data,has become a topic of increasing *** a few so called pan-specific methods have been developed to meet this need,including our newly proposed method,TEPITOPEpan,which can make prediction with decent accuracy for over 700 HLA-DR *** performance of these methods is however not good enough and should be improved. Methods:MetaMHCIIpan is a consensus method which integrates by AvgTanh the outputs of multiple pan-specific methods for predicting binding *** state-of-the-art pan-specific predictors and two leading normal allele-specific predictors are involved in this *** checking the performance of various combinations,an optimal one is selected as the default setting of MetaMHCIIpan. Results:Experimental results over three benchmark datasets showed MetaMHCIIpan with the default predictor combination,which outperformed all individual predictors in prediction accuracy,being statistically *** is freely available at http:// ***/Service/MetaMHCIIpan. Conclusions:MetaMHCIIpan utilizes diverse base predictors to achieve the current best performance in predict peptides binding to MHCⅡ,keeping a nice feature of pan-specific *** is,MetaMHCIIpan is applicable to any HLA-DR *** consensus method thus shows great potential for

关键词： Immunoinformatics MHC peptide binding prediction pan-specific

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