A Bayes random field approach for integrative large-scale regulatory network analysis [0.03%]
一种贝叶斯随机域方法在大规模调控网络分析中的应用
Yinyin Yuan,Chang-Tsun Li
Yinyin Yuan
We present a Bayes-Random Fields framework which is capable of integrating unlimited data sources for discovering relevant network architecture of large-scale networks. The random field potential function is designed to impose a cluster con...
MoRAine--a web server for fast computational transcription factor binding motif re-annotation [0.03%]
MoRAine--一个用于计算性转录因子结合基序再注释的web服务器
Jan Baumbach,Tobias Wittkop,Jochen Weile et al.
Jan Baumbach et al.
Background: A precise experimental identification of transcription factor binding motifs (TFBMs), accurate to a single base pair, is time-consuming and diffcult. For several databases, TFBM annotations are extracted from ...
Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks [0.03%]
整合分析可变剪接对蛋白质结构域互作网络的影响
Dorothea Emig,Melissa S Cline,Karsten Klein et al.
Dorothea Emig et al.
Proteins and their interactions are essential for the functioning of all organisms and for understanding biological processes. Alternative splicing is an important molecular mechanism for increasing the protein diversity in eukaryotic cells...
Data integration for spatio-temporal patterns of gene expression of zebrafish development: the GEMS database [0.03%]
斑马鱼发育过程中基因表达时空模式的数据整合：GEMS数据库
Mounia Belmamoune,Fons J Verbeek
Mounia Belmamoune
The Gene Expression Management System (GEMS) is a database system for patterns of gene expression. These patterns result from systematic whole-mount fluorescent in situ hybridization studies on zebrafish embryos. GEMS is an integrative plat...
Widespread existence of uncorrelated probe intensities from within the same probeset on Affymetrix GeneChips [0.03%]
阿菲米蒂斯基因芯片中来自同一探针集内无关的探针强度广泛存在
Olivia Sanchez-Graillet,Joanna Rowsell,William B Langdon et al.
Olivia Sanchez-Graillet et al.
We have developed a computational pipeline to analyse large surveys of Affymetrix GeneChips, for example NCBI's Gene Expression Omnibus. GEO samples data for many organisms, tissues and phenotypes. Because of this experimental diversity, an...
ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis [0.03%]
ReMatch：一个用于构造、存储和共享具有碳图的计量代谢模型以进行代谢通量分析的网络工具
Esa Pitkänen,Arto Akerlund,Ari Rantanen et al.
Esa Pitkänen et al.
ReMatch is a web-based, user-friendly tool that constructs stoichiometric network models for metabolic flux analysis, integrating user-developed models into a database collected from several comprehensive metabolic data resources, including...
David C Y Fung,Seok-Hee Hong,Dirk Koschützki et al.
David C Y Fung et al.
Biological data is often structured in the form of complex interconnected networks such as protein interaction and metabolic networks. In this paper, we investigate a new problem of visualising such overlapping biological networks. Two netw...
Conservation of the LexA repressor binding site in Deinococcus radiodurans [0.03%]
耐辐射球菌中LexA抑制物结合位点的保护作用
Feroz Khan,S P Singh,B N Mishra
Feroz Khan
The LexA protein is a transcriptional repressor of the bacterial SOS DNA repair system, which comprises a set of DNA repair and cellular survival genes that are induced in response to DNA damage. Its varied DNA binding motifs have been char...
WebStruct and VisualStruct: Web interfaces and visualization for Structure software implemented in a cluster environment [0.03%]
WebStruct和VisualStruct：用于集群环境中的结构软件的网络接口和可视化工具
B Jayashree,S Rajgopal,D Hoisington et al.
B Jayashree et al.
Structure, is a widely used software tool to investigate population genetic structure with multi-locus genotyping data. The software uses an iterative algorithm to group individuals into "K" clusters, representing possibly K genetically dis...
Towards the integration of computational systems biology and high-throughput data: supporting differential analysis of microarray gene expression data [0.03%]
计算系统生物学和高通量数据的整合：支持微阵列基因表达数据的差异分析
Nicola Segata,Enrico Blanzieri,Corrado Priami
Nicola Segata
The paradigmatic shift occurred in biology that led first to high-throughput experimental techniques and later to computational systems biology must be applied also to the analysis paradigm of the relation between local models and data to o...