检索结果-南通市图书馆

High-throughput experimental methods for investigating biomolecular condensates

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

Quantitative Biology 2021年第3期9卷 255-266页

作者： Taoyu Chen Qi Lei Minglei Shi Tingting Li Department of Biomedical Informatics School of Basic Medical SciencesPeking University Health Science CenterBeijing 100191China MOE Key Laboratory of bioinformatics Bioinformatics Division and Center for Synthetic&Systems BiologyTNLISTSchool of MedicineTsinghua UniversityBeijing 100084China

Background:The concept of biomolecular condensate was put forward recently to emphasize the ability of certain cellular compartments to concentrate molecules and comprise proteins and nucleic acids with specific biological functions,from ribosome genesis to RNA *** to their unique role in biological processes,it is crucial to investigate their compositions,which is a primary determinant of condensate ***:Since a wide range of macromolecules comprise biomolecular condensates,it is necessary for researchers to investigate them using high-throughput methodologies while low-throughput experiments are not efficient *** high-throughput methods usually purify interacting protein libraries from condensates before being scanned in mass *** is possible to extract organelles as a whole for specific condensates for further analysis,however,most condensates do not have a distinguishable marker or are sensitive to shear force to be extracted as a *** tagging allows a comprehensive view of interacting proteins of target molecule yet only proteins with strong bonds may be pulled *** labeling serves as a complementary method to label more dynamic proteins with weaker interactions,increasing sensitivity while decreasing ***-based fluorescent screening takes another path by scanning images automatically to illustrate the condensing state of biomolecules within membraneless organelles,which is a unique feature unlike the previous mass spectrometry-based ***:This review presents a rough glimpse into high-throughput methodologies for biomolecular condensate investigation to encourage usage of bioinformatic tools by researchers in relevant fields.

关键词： biomolecular condensates high-throughput phase separation interaction

Constructing a Boolean implication network to study the interactions between environmental factors and OTUs

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4期9卷 127-141页

作者： Congmin Zhu Rui Jiang Ting Chen MOE Key Laboratory of bioinformatics and bioinformatics division Center for Synthetic & Systems Biology TNLIST/ Department of Automation Tsinghua University Beijing 100084 China Computational and Molecular Biology Program University of Southern California Loa Angles CA 90089 USA

Mining relationships between microbes and the environment they live in are crucial to understand the intrinsic mechanisms that govern cycles of carbon, nitrogen and energy in a microbial community. Building upon next- generation sequencing technology, the selective capture of 16S rRNA genes has enabled the study of co-occurrence patterns of microbial species from the viewpoint of complex networks, yielding successful descriptions of phenomena exhibited in a microbial community. However, since the effects of such environmental factors as temperature or soil conditions on microbes are complex, reliance on the analysis of co-occurrence networks alone cannot elucidate such complicated effects underlying microbial communities. In this study, we apply a statistical method, which is called Boolean implications for metagenomic studies （BIMS） for extracting Boolean implications （IF-THEN relationships） to capture the effects of environmental factors on microbial species based on 16S rRNA sequencing data. We first demonstrate the power and effectiveness of BIMS through comprehensive simulation studies and then apply it to a 16S rRNA sequencing dataset of real marine microbes. Based on a total of 6,514 pairwise relationships identified at a low false discovery rate （FDR） of 0.01, we construct a Boolean implication network between operational taxonomic units （OTUs） and environmental factors. Relationships in this network are supported by literature, and, most importantly, they bring biological insights into the effects of environmental factors on microbes. We next apply BIMS to detect three-way relationships and show the possibility of using this strategy to explain more complex relationships within a microbial community.

关键词： Boolean implication metagenome marine OTUs environmental factors

A Data-Driven Clustering Recommendation Method for Single-Cell RNA-Sequencing Data

在线全文

学校读者我要写书评

暂无评论

Tsinghua Science and Technology 2021年第5期26卷 772-789页

作者： Yu Tian Ruiqing Zheng Zhenlan Liang Suning Li Fang-Xiang Wu Min Li the Hunan Provincial Key Lab on bioinformatics School of Computer Science and EngineeringCentral South UniversityHunan 410083China the division of Biomedical Engineering and Department of Mechanical Engineering University of SaskatchewanSKS7N5A9Canada

Recently,the emergence of single-cell RNA-sequencing(scRNA-seq)technology makes it possible to solve biological problems at the single-cell *** of the critical steps in cellular heterogeneity analysis is the cell type *** scRNA-seq clustering methods have been proposed to partition cells into *** all the methods,hierarchical clustering and spectral clustering are the most popular approaches in the downstream clustering analysis with different preprocessing strategies such as similarity learning,dropout imputation,and dimensionality *** this study,we carry out a comprehensive analysis by combining different strategies with these two categories of clustering methods on scRNA-seq datasets under different biological *** analysis results show that the methods with spectral clustering tend to perform better on datasets with continuous shapes in two-dimension,while those with hierarchical clustering achieve better results on datasets with obvious boundaries between clusters in *** by this finding,a new strategy,called QRS,is developed to quantitatively evaluate the latent representative shape of a dataset to distinguish whether it has clear boundaries or ***,a data-driven clustering recommendation method,called DDCR,is proposed to recommend hierarchical clustering or spectral clustering for scRNA-seq *** perform DDCR on two typical single cell clustering methods,SC3 and RAFSIL,and the results show that DDCR recommends a more suitable downstream clustering method for different scRNA-seq datasets and obtains more robust and accurate results.

关键词： single-cel RNA-sequencing(sc RNA-seq) cel ular heterogeneity cel type identification data latent shape clustering

Pharmacological manipulation of transcription factor protein-protein interactions:opportunities and obstacles

在线全文

学校读者我要写书评

暂无评论

Cell Regeneration 2015年第1期4卷 8-19页

作者： Frank Fontaine Jeroen Overman Mathias François division of Genomics of Development and Diseases Institute for Molecular BioscienceThe University of Queensland306 Carmody RoadSt LuciaQLD 4072Australia

Much research on transcription factor biology and their genetic pathways has been undertaken over the last30 years, especially in the field of developmental biology and cancer. Yet, very little is known about the molecularmodalities of highly dynamic interactions between transcription factors, genomic DNA, and protein *** breakthroughs such as RNA-seq (RNA-sequencing), ChIP-seq (chromatin immunoprecipitationsequencing), RIME (rapid immunoprecipitation mass spectrometry of endogenous proteins), and single-moleculeimaging will dramatically accelerate the discovery rate of their molecular mode of action in the next few *** a pharmacological viewpoint, conventional methods used to target transcription factor activity withmolecules mimicking endogenous ligands fail to achieve high specificity and are limited by a lack of identificationof new molecular targets. Protein-protein interactions are likely to represent one of the next major classes oftherapeutic targets. Transcription factors, known to act mostly via protein-protein interaction, may well be atthe forefront of this type of drug development. One hurdle in this field remains the difficulty to collate structuraldata into meaningful information for rational drug design. Another hurdle is the lack of chemical libraries meeting thestructural requirements of protein-protein interaction *** more attempts at modulating transcription factor activity are undertaken, valuable knowledge will be accumulatedon the modality of action required to modulate transcription and how these findings can be applied to developingtranscription factor drugs. Key discoveries will spawn into new therapeutic approaches not only as anticancer targetsbut also for other indications, such as those with an inflammatory component including neurodegenerative disorders,diabetes, and chronic liver and kidney diseases.

关键词： Transcription Screening Proteomics Interactome Pharmacology Specificity Cancer Genomics

A genome-wide survey of alternative translational initiation events in Homo sapiens

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

Science China(Life Sciences) 2007年第3期50卷 423-428页

作者： ZHANG Jing1, CAI Jun2 & LI YanDa1 1 bioinformatics division, TNLIST and Department of Automation, Tsinghua University, Beijing 100084, China 2 Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801,USA 1. bioinformatics division TNLIST and Department of Automation Tsinghua University Beijing 100084 China 2. Department of Bioengineering University of Illinois at Urbana-Champaign Urbana IL 61801 USA

Alternative translational initiation is an important mechanism to increase the diversity of gene products. Although some of alternative translational initiation events have been reported, such information remains anecdotal and does not allow for any generalizations. The number of the known alternative translational initiation genes is so few that we know little about its mechanism. There is a great demand to discover more alternative translational initiation genes. However, it is arduously time-consuming to discover novel alternative translational initiation genes by the experimental method. Therefore we systematically analyzed protein sequences available in public database and predicted 1237 protein clusters as potential alternative translational initiation events. We concluded that about 8%—10% of human genes have alternative translational initiation sites. The results significantly increased the number of alternative translation initiation events and indicated that alternative translation initiation is an important and general regulation mechanism in the cellular process.

关键词： ATI A genome-wide survey of alternative translational initiation events in Homo sapiens

Differential expression analyses for single-ce RNA-Seq： old questions on new data

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 2016年第4期4卷 243-260页

作者： Zhun Miao Xuegong Zhang MOE Key Laboratory of bioinformatics bioinformatics division and Center for Synthetic & Systems Biology TNLIST Department of Automation Tsinghua University Beijing 100084 China School of Life Sciences Tsinghua University Beijing 100084 China

Single-cell RNA sequencing （scRNA-seq） is an emerging technology that enables high resolution detection of heterogeneities between ceils. One important application of scRNA-seq data is to detect differential expression （DE） of genes. Currently, some researchers still use DE analysis methods developed for bulk RNA-Seq data on single-cell data, and some new methods for scRNA-seq data have also been developed. Bulk and single-cell RNA-seq data have different characteristics. A systematic evaluation of the two types of methods on scRNA-seq data is needed. Results： In this study, we conducted a series of experiments on scRNA-seq data to quantitatively evaluate 14 popular DE analysis methods, including both of traditional methods developed for bulk RNA-seq data and new methods specifically designed for scRNA-seq data. We obtained observations and recommendations for the methods under different situations. Conclusions： DE analysis methods should be chosen for scRNA-seq data with great caution with regard to different situations of data. Different strategies should be taken for data with different sample sizes and/or different strengths of the expected signals. Several methods for scRNA-seq data show advantages in some aspects, and DEGSeq tends to outperform other methods with respect to consistency, reproducibility and accuracy of predictions on scRNA-seq data.

关键词： single-cell RNA-Seq differential expression

Computational Identification of 99 Insect MicroRNAs Using Comparative Genomics

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

Tsinghua Science and Technology 2008年第4期13卷 425-432页

作者：何涛李非古槿李瑞强李飞 bioinformatics division Tsinghua National Laboratory for Information Science and Technology (TNLIST) Department of Automation Tsinghua University Beijing 100084 China Beijing Genomics Institute Chinese Academy of Sciences Beijing 100084 China bioinformatics division Tsinghua National Laboratory for Information Science and Technology (TNLIST) Department of Automation Tsinghua University Beijing 100084 China Department of Entomology College of Plant Pro-tection Nanjing Agricultural University Nanjing 210095 China

In recent years, much effort has been made in identifying microRNA （miRNA） genes from mammals insects, worms, plants, and viruses. Continuing the search for more miRNA genes is still important but difficult. This paper presents a computational strategy based on comparative genomics analysis. The algorithm was used to scan four invertebrate genomes, Drosophila melangoster, Bombyx mori, Apis mellifera, and Anopheles gambiae, which are either model organisms or medically/economically important insects. 99 new miRNA genes were predicted from the four insect species which can be grouped into 17 miRNA gene families, of which 10 of the miRNA families are insect-specific. Sequence similarity analysis showed that 16 of the newly predicted insect miRNAs belong to the K-box, GY-box, and Brd-box miRNA families which are important participators in Notch-related pathways. To test the validity of the algorithm, 39 predicted insect miRNA genes from D. melangoster and A. mellifera were selected for further biological validation. 34 （87%） predicted miRNA genes＇ transcripts were successfully detected by reverse transcription-polymerase chain reaction experiments. Thus, this strategy can be used to efficiently screen for miRNA genes conserved cross species.

关键词： microRNA (miRNA) insect comparative genomics reverse transcription-polymerase chain reaction

In Memory of Vladimir ***(1952–2019)

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & bioinformatics 2019年第5期17卷 473-474页

作者： Zhang Zhang Jun Yu Frank Eisenhaber Xin Gao Takashi Gojobori Beijing Institute of Genomics Chinese Academy of SciencesBeijing 100101China bioinformatics Institute Agency for ScienceTechnology and Research(A*STAR)Singapore 138671Singapore Computational bioscience Research Center King Abdullah University of Science and Technology(KAUST)Thuwal 23955Saudi Arabia

Professor Vladimir ***,a world-renowned pioneer in bioinformatics and associate editor-in-chief of Genomics Proteomics&bioinformatics(GPB)since 2015,passed away on31 October 2019 in Jeddah,Saudi *** joined the editorial board of GPB in 2012 and had been devoting his precious time and efforts to handling and reviewing manuscripts and providing many valuable instructions and suggestions in improving journal quality and readership as well.

关键词： bioinformatics Memory suggestions

Predictive models for mild cognitive impairment to Alzheimer's disease conversion

在线全文

学校读者我要写书评

暂无评论

Neural Regeneration Research 2021年第9期16卷 1766-1767页

作者： Konstantina Skolariki Graciella Muniz Terrera Samuel O.Danso bioinformatics and Human Electrophysiology Laboratory Ionian UniversityCorfuGreece Centre for Dementia Prevention University of EdinburghUK division of Neuroimaging Centre for Clinical Brain Sciences and Edinburgh ImagingUniversity of EdinburghScotlandUK

Alzheimer's disease(AD) is an irreversible and progressive neurodegenerative disease as well as the most common form of dementia. It usually affects the older population, but early onset AD is still possible(Ritchie e... 详细信息

关键词： Alzheimer al. impairment