检索结果-南通市图书馆

Reconstructing ancestral ranges in historical biogeography:properties and prospects

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Journal of Systematics and Evolution 2009年第5期47卷 369-382页

作者： Kristin S.LAMM Benjamin D.REDELINGS bioinformatics Research center North Carolina State University

Recent years have witnessed a proliferation of quantitative methods for biogeographic *** particular,novel parametric approaches represent exciting new opportunities for the study of range ***,we review a selection of current methods for biogeographic analysis and discuss their respective *** methods include generalized parsimony approaches,weighted ancestral area analysis,dispersal-vicariance analysis,the dispersal-extinction-cladogenesis model and other maximum likelihood approaches,and Bayesian stochastic mapping of ancestral ranges,including a novel approach to inferring range evolution in the context of island *** of these methods were developed specifically for problems of ancestral range reconstruction,whereas others were designed for more general problems of character state reconstruction and subsequently applied to the study of ancestral *** for reconstructing ancestral history on a phylogenetic tree differ not only in the types of ancestral range states that are allowed,but also in the various historical events that may change the ancestral *** explore how the form of allowed ancestral ranges and allowed transitions can both affect the outcome of ancestral range ***,we mention some promising avenues for future work in the development of model-based approaches to biogeographic analysis.

关键词： allopatry ancestral range ancestral state reconstruction biogeography dispersal historical biogeogra-phy review speciation statistics vicariance.

Structure of the 40S ribosomal subunit of Plasmodium falciparum by homology and de novo modeling

在线全文

同方期刊数据库

学校读者我要写书评

暂无评论

Acta Pharmaceutica Sinica B 2017年第1期7卷 97-105页

作者： Harrison Ndung'u Mwangi Peter Wagacha Peterson Mathenge Fredrick Sijenyi Francis Mulaa center for Biotechnology and bioinformatics Chiromo CampusUniversity of Nairobi.HEP Bioinformatics Consultants Ltd. Department of Computing Informatics University of Nairobi DNA Software Inc. Department of Biochemistry Riverside DriveChiromo CampusUniversity of Nairobi

Generation of three dimensional structures of macromolecules using in silico structural modeling technologies such as homology and de novo modeling has improved dramatically and increased the speed by which tertiary structures of organisms can be generated. This is especially the case if a homologous crystal structure is already available. High-resolution structures can be rapidly created using only their sequence information as input, a process that has the potential to increase the speed of scientific discovery. In this study, homology modeling and structure prediction tools such as RNA123 and SWISS–MODEL were used to generate the 40 S ribosomal subunit from Plasmodium falciparum. This structure was modeled using the published crystal structure from Tetrahymena thermophila, a homologous eukaryote. In the absence of the Plasmodium falciparum 40 S ribosomal crystal structure, the model accurately depicts a global topology, secondary and tertiary connections, and gives an overall root mean square deviation(RMSD) value of 3.9 ? relative to the template's crystal structure. Deviations are somewhat larger in areas with no homology between the templates. These results demonstrate that this approach has the power to identify motifs of interest in RNA and identify potential drug targets for macromolecules whose crystal structures are unknown. The results also show the utility of RNA homology modeling software for structure determination and lay the groundwork for applying thisapproach to larger and more complex eukaryotic ribosomes and other RNA-protein complexes. Structures generated from this study can be used in in silico screening experiments and lead to the determination of structures for targets/hit complexes.

关键词： Ribosome 40S subunit RNA structure Plasmodium falciparum 3D modeling De novo Homology

Microbial Dark Matter: from Discovery to Applications

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & bioinformatics 2022年第5期20卷 867-881页

作者： Yuguo Zha Hui Chong Pengshuo Yang Kang Ning MOE Key Laboratory of Molecular Biophysics Hubei Key Laboratory of Bioinformatics and Molecular-imagingCenter of Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan 430074China

With the rapid increase of the microbiome samples and sequencing data,more and more knowledge about microbial communities has been ***,there is still much more to learn about microbial communities,including billions of novel species and genes,as well as countless spatiotemporal dynamic patterns within the microbial communities,which together form the microbial dark *** this work,we summarized the dark matter in microbiome research and reviewed current data mining methods,especially artificial intelligence(AI)methods,for different types of knowledge discovery from microbial dark *** also provided case studies on using AI methods for microbiome data mining and knowledge *** summary,we view microbial dark matter not as a problem to be solved but as an opportunity for AI methods to explore,with the goal of advancing our understanding of microbial communities,as well as developing better solutions to global concerns about human health and the environment.

关键词： Microbiome Dark matter Artificial intelligence Knowledge discovery Application

The crossroads of receptor-mediated signaling and endocytosis in plants

在线全文

学校读者我要写书评

暂无评论

Journal of Integrative Plant Biology 2018年第9期60卷 827-840页

作者： Lucas Alves Neubus Claus Daniel V.Savatin Eugenia Russinova Department of Plant Biotechnology and bioinformatics Ghent University9052 GhentBelgium center for Plant Systems Biology VIB9052 GhentBelgium

Plants deploy numerous plasma membrane receptors to sense and rapidly react to environmental changes. Correct localization and adequate protein levels of the cell-surface receptors are critical for signaling activation and modulation of plant development and defense against pathogens. After ligand binding, receptors are internalized for degradation and signaling attenuation. However, one emerging notion is that the Iigand-induced endocytosis of reCeptor complexes is important for the signal duration, amplitude, and specificity. Recently, mutants of maior endocytosis players, including clathrin and dynamin, have been shown to display defects in activation of a subset of signal transduction pathways, implying that signaling in plants might not be solely restricted to the plasma membrane. Here, we summarize the up-to-date knowledge of receptor complex endocytosis and its effect on the signaling outcome, in the context of plant development and immunity.

关键词： The crossroads of receptor-mediated signaling and endocytosis in plants BRI PM

Identifying cancer genes from cancer mutation profiles by cancer functions

在线全文

学校读者我要写书评

暂无评论

Science China(Life Sciences) 2008年第6期51卷 569-574页

作者： LI YanHui1, GUO Zheng1,2, PENG ChunFang2, LIU Qing2, MA WenCai2, WANG Jing2, YAO Chen2, ZHANG Min2 & ZHU Jing1 1 bioinformatics Centre, School of Life Science, University of Electronic Science and Technology of China, Chengdu 610054, China 2 School of bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China 1. bioinformatics Centre School of Life Science University of Electronic Science and Technology of China Chengdu 610054 China 2. School of bioinformatics Science and Technology Harbin Medical University Harbin 150086 China

It is of great importance to identify new cancer genes from the data of large scale genome screenings of gene mutations in cancers. Considering the alternations of some essential functions are indispensable for oncogenesis, we define them as cancer functions and select, as their approximations, a group of detailed functions in GO (Gene Ontology) highly enriched with known cancer genes. To evaluate the efficiency of using cancer functions as features to identify cancer genes, we define, in the screened genes, the known protein kinase cancer genes as gold standard positives and the other kinase genes as gold standard negatives. The results show that cancer associated functions are more efficient in identifying cancer genes than the selection pressure feature. Furthermore, combining cancer functions with the number of non-silent mutations can generate more reliable positive predictions. Finally, with precision 0.42, we suggest a list of 46 kinase genes as candidate cancer genes which are annotated to cancer functions and carry at least 3 non-silent mutations.

关键词： mutation profile cancer gene Gene Ontology gene function prediction

Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data

在线全文

学校读者我要写书评

暂无评论

National Science Review 2016年第2期3卷 240-251页

作者： Yong Wang Rui Jiang Wing Hung Wong Department of Statistics Department of Biomedical Data ScienceBio-X ProgramStanford University Academy of Mathematics and Systems Science National Center for Mathematics and Interdisciplinary SciencesChinese Academy of Sciences MOE Key Laboratory of bioinformatics Bioinformatics Division and Center for Synthetic and Systems BiologyTNLISTDepartment of AutomationTsinghua University

Cell packs a lot of genetic and regulatory information through a structure known as chromatin,*** is wrapped around histone proteins and is tightly packed in a remarkable *** express a gene in a specific coding region,the chromatin would open up and DNA loop may be formed by interacting enhancers and ***,the mediator and cohesion complexes,sequence-specific transcription factors,and RNA polymerase Ⅱ are recruited and work together to elaborately regulate the expression *** is in pressing need to understand how the information,about when,where,and to what degree genes should be expressed,is embedded into chromatin structure and gene regulatory *** to large consortia such as Encyclopedia of DNA Elements(ENCODE) and Roadmap Epigenomic projects,extensive data on chromatin accessibility and transcript abundance are available across many tissues and cell *** rich data offer an exciting opportunity to model the causal regulatory ***,we will review the current experimental approaches,foundational data,computational problems,interpretive frameworks,and integrative models that will enable the accurate interpretation of regulatory ***,we will discuss the efforts to organize,analyze,model,and integrate the DNA accessibility data,transcriptional data,and functional genomic regions *** believe that these efforts will eventually help us understand the information flow within the cell and will influence research directions across many fields.

关键词： gene regulatory network open chromatin DNA accessibility transcription factor colocalization statistical model data integration

DeepCAPE: A Deep Convolutional Neural Network for the Accurate Prediction of Enhancers

在线全文

同方期刊数据库

学校读者我要写书评

暂无评论

Genomics, Proteomics & bioinformatics 2021年第4期19卷 565-577页

作者： Shengquan Chen Mingxin Gan Hairong Lv Rui Jiang Ministry of Education Key Laboratory of bioinformatics Bioinformatics Division at the Beijing National Research Center for Information Science and TechnologyCenter for Synthetic and Systems BiologyDepartment of AutomationTsinghua UniversityBeijing 100084China Department of Management Science and Engineering School of Economics and ManagementUniversity of Science and Technology BeijingBeijing 100083China

The establishment of a landscape of enhancers across human cells is crucial to deciphering the mechanism of gene regulation,cell differentiation,and disease ***-throughput experimental approaches,which contain successfully reported enhancers in typical cell lines,are still too costly and time-consuming to perform systematic identification of enhancers specific to different cell *** computational methods,capable of predicting regulatory elements purely relying on DNA sequences,lack the power of cell line-specific *** studies have suggested that chromatin accessibility of a DNA segment is closely related to its potential function in regulation,and thus may provide useful information in identifying regulatory *** by the aforementioned understanding,we integrate DNA sequences and chromatin accessibility data to accurately predict enhancers in a cell line-specific *** proposed Deep CAPE,a deep convolutional neural network to predict enhancers via the integration of DNA sequences and DNase-seq *** from the well-designed feature extraction mechanism and skip connection strategy,our model not only consistently outperforms existing methods in the imbalanced classification of cell line-specific enhancers against background sequences,but also has the ability to self-adapt to different sizes of ***,with the adoption of autoencoder,our model is capable of making cross-cell line *** further visualize kernels of the first convolutional layer and show the match of identified sequence signatures and known *** finally demonstrate the potential ability of our model to explain functional implications of putative disease-associated genetic variants and discriminate diseaserelated *** source code and detailed tutorial of Deep CAPE are freely available at https://***/Shengquan Chen/DeepCAPE.

关键词： Enhancer prediction Chromatin accessibility Data integration Transcription factor binding motif Disease-associated regulatory element

TCM network pharmacology:A new trend towards combining computational,experimental and clinical approaches

在线全文

学校读者我要写书评

暂无评论

Chinese Journal of Natural Medicines 2021年第1期19卷 1-11页

作者： WANG Xin WANG Zi-Yi ZHENG Jia-Hui LI Shao Institute for TCM-X MOE Key Laboratory of Bioinformatics/Bioinformatics DivisionBNRISTDepartment of AutomationTsinghua UniversityBeijing 100084China

Traditional Chinese medicine(TCM)is a precious treasure of the Chinese nation and has unique advantages in the prevention and treatment of *** holistic view of TCM coincides with the new generation of medical research paradigm characterized by network and *** gave birth to a new method featuring holistic and systematic"network target",a core theory and method of network *** is also an important research object of network *** network pharmacology,which aims to understand the network-based biological basis of complex diseases,TCM syndromes and herb treatments,plays a critical role in the origin and development process of network *** review introduces new progresses of TCM network pharmacology in recent years,including predicting herb targets,understanding biological foundation of diseases and syndromes,network regulation mechanisms of herbal formulae,and identifying disease and syndrome biomarkers based on biological *** studies show a trend of combining computational,experimental and clinical approaches,which is a promising direction of TCM network pharmacology research in the *** that TCM network pharmacology is still a young research field,it is necessary to further standardize the research process and evaluation indicators to promote its healthy development.

关键词： Network pharmacology Traditional Chinese medicine Network target Computation Experiment Clinical approach

OP-Synthetic： identification of optimal genetic manipulations for the overproduction of native and non-native metabolites

在线全文

学校读者我要写书评

暂无评论

Frontiers of Electrical and Electronic Engineering in China 2014年第3期9卷 100-109页

作者： Honglei Liu Yanda Li Xiaowo Wang MOE Key Laboratory of bioinformatics Bioinformatics Division and Center for Synthetic and Systems Biology TNLIST/Department of Automation Tsinghua University Beijing100084 China

Constraint-based flux analysis has been widely used in metabolic engineering to predict genetic optimization strategies. These methods seek to find genetic manipulations that maximally couple the desired metabolites with the cellular growth objective. However, such framework does not work well for overproducing chemicals that are not closely correlated with biomass, for example non-native biochemical production by introducing synthetic pathways into heterologous host cells. Here, we present a computational method called OP-Synthetic, which can identify effective manipulations （upregulation, downregulation and deletion of reactions） and produce a step-by-step optimization strategy for the overproduction of indigenous and non-native chemicals. We compared OP-Synthetic with several state-of-the-art computational approaches on the problems of succinate overproduction and N- acetylneuraminic acid synthetic pathway optimization in Escherichia coli. OP-Synthetic showed its advantage for efficiently handling multiple steps optimization problems on genome wide metabolic networks. And more importantly, the optimization strategies predicted by OP-Synthetic have a better match with existing engineered strains, especially for the engineering of synthetic metabolic pathways for non-native chemical production. OP- Synthetic is freely available at：http：//***/member/xwwang/OPSynthetic/.

关键词： metabolic network flux analysis optimization