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基因组蛋白质组与生物信息学报（英文版）
基因组蛋白质组与生物信息学报（英文版）

杨焕明；于军

双月刊

1672-0229

journal@cspg.net

010-84097425

100101

北京市朝阳区北辰西路1-7号中国科学院北京基因组研究所

基因组蛋白质组与生物信息学报（英文版）/Journal Genomics、Proteomics & BioinformaticsCSCDCSTPCD北大核心SCI
查看更多>>Genomics, Proteomics & Bioinformatics (《基因组蛋白质组与生物信息学报》，简称GPB)创刊于2003年，是由中国科学院北京基因组研究所主办、科学出版社出版的国家级英文学术期刊，由杨焕明教授、于军教授担任主编，汪建教授、贺福初院士担任副主编。 本刊主要刊载基因组学、蛋白质组学、生物信息学及其相关领域的研究进展、综述、研究论文、实验技术与方法、研究快讯等高质量的稿件，突出刊物的学术性、前沿性、指导性和实用性。 本刊读者对象为基础医学、生命科学、农学、计算机科学领域的科研与教学人员、研究生等，以及数学、物理学领域对生物科学有兴趣的研究者。 GPB (ISSN 1672-0229，CN11-4926/Q)现为季刊，面向国内外发行，邮发代号80-113。2004年国内定价每期45元，全年180元。 欢迎赐稿和订阅! 联系人：张欣 《基因组蛋白质组与生物信息学报》编辑部 北京空港科技创业园B区6号 101300 Tel: 010-80485179 Fax: 010-80498676 E-mail：editor@genomics.org.cn Http：
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    What Has Genomics Taught An Evolutionary Biologist?

    Jianzhi Zhang
    1-12页
    查看更多>>摘要：Genomics,an interdisciplinary field of biology on the structure,function,and evolution of genomes,has revolutionized many subdisciplines of life sciences,including my field of evolution-ary biology,by supplying huge data,bringing high-throughput technologies,and offering a new approach to biology.In this review,I describe what I have learned from genomics and highlight the fundamental knowledge and mechanistic insights gained.I focus on three broad topics that are central to evolutionary biology and beyond—variation,interaction,and selection—and use pri-marily my own research and study subjects as examples.In the next decade or two,I expect that the most important contributions of genomics to evolutionary biology will be to provide genome sequences of nearly all known species on Earth,facilitate high-throughput phenotyping of natural variants and systematically constructed mutants for mapping genotype-phenotype-fitness land-scapes,and assist the determination of causality in evolutionary processes using experimental evo-lution.
      原文链接:
    • 万方数据
    • 维普

    Integration of Computational Analysis and Spatial Transcriptomics in Single-cell Studies

    Ran WangGuangdun PengPatrick P.L.TamNaihe Jing...
    13-23页
    查看更多>>摘要：Recent advances of single-cell transcriptomics technologies and allied computational methodologies have revolutionized molecular cell biology.Meanwhile,pioneering explorations in spatial transcriptomics have opened up avenues to address fundamental biological questions in health and diseases.Here,we review the technical attributes of single-cell RNA sequencing and spa-tial transcriptomics,and the core concepts of computational data analysis.We further highlight the challenges in the application of data integration methodologies and the interpretation of the biolog-ical context of the findings.
      原文链接:
    • 万方数据
    • 维普

    Computational Approaches and Challenges in Spatial Transcriptomics

    Shuangsang FangBichao ChenYong ZhangHaixi Sun...
    24-47页
    查看更多>>摘要：The development of spatial transcriptomics(ST)technologies has transformed genetic research from a single-cell data level to a two-dimensional spatial coordinate system and facilitated the study of the composition and function of various cell subsets in different environments and organs.The large-scale data generated by these ST technologies,which contain spatial gene expres-sion information,have elicited the need for spatially resolved approaches to meet the requirements of computational and biological data interpretation.These requirements include dealing with the explosive growth of data to determine the cell-level and gene-level expression,correcting the inner batch effect and loss of expression to improve the data quality,conducting efficient interpretation and in-depth knowledge mining both at the single-cell and tissue-wide levels,and conducting multi-omics integration analysis to provide an extensible framework toward the in-depth under-standing of biological processes.However,algorithms designed specifically for ST technologies to meet these requirements are still in their infancy.Here,we review computational approaches to these problems in light of corresponding issues and challenges,and present forward-looking insights into algorithm development.
      原文链接:
    • 万方数据
    • 维普

    Computational Methods for Single-cell DNA Methylome Analysis

    Waleed IqbalWanding Zhou
    48-66页
    查看更多>>摘要：Dissecting intercellular epigenetic differences is key to understanding tissue heterogene-ity.Recent advances in single-cell DNA methylome profiling have presented opportunities to resolve this heterogeneity at the maximum resolution.While these advances enable us to explore frontiers of chromatin biology and better understand cell lineage relationships,they pose new chal-lenges in data processing and interpretation.This review surveys the current state of computational tools developed for single-cell DNA methylome data analysis.We discuss critical components of single-cell DNA methylome data analysis,including data preprocessing,quality control,imputa-tion,dimensionality reduction,cell clustering,supervised cell annotation,cell lineage reconstruc-tion,gene activity scoring,and integration with transcriptome data.We also highlight unique aspects of single-cell DNA methylome data analysis and discuss how techniques common to other single-cell omics data analyses can be adapted to analyze DNA methylomes.Finally,we discuss existing challenges and opportunities for future development.
      原文链接:
    • 万方数据
    • 维普

    A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences,Bulk RNA-seq,and Single-cell RNA-seq

    Wenbin YeQiwei LianCongting YeXiaohui Wu...
    67-83页
    查看更多>>摘要：Alternative polyadenylation(APA)plays important roles in modulating mRNA stability,translation,and subcellular localization,and contributes extensively to shaping eukaryotic tran-scriptome complexity and proteome diversity.Identification of poly(A)sites(pAs)on a genome-wide scale is a critical step toward understanding the underlying mechanism of APA-mediated gene regulation.A number of established computational tools have been proposed to predict pAs from diverse genomic data.Here we provided an exhaustive overview of computational approaches for predicting pAs from DNA sequences,bulk RNA sequencing(RNA-seq)data,and single-cell RNA sequencing(scRNA-seq)data.Particularly,we examined several representative tools using bulk RNA-seq and scRNA-seq data from peripheral blood mononuclear cells and put forward operable suggestions on how to assess the reliability of pAs predicted by different tools.We also proposed practical guidelines on choosing appropriate methods applicable to diverse scenarios.Moreover,we discussed in depth the challenges in improving the performance of pA prediction and bench-marking different methods.Additionally,we highlighted outstanding challenges and opportunities using new machine learning and integrative multi-omics techniques,and provided our perspective on how computational methodologies might evolve in the future for non-3'untranslated region,tissue-specific,cross-species,and single-cell pA prediction.
      原文链接:
    • 万方数据
    • 维普

    Gut Microbiome in Colorectal Cancer:Clinical Diagnosis and Treatment

    Yali LiuHarry Cheuk-Hay LauWing Yin ChengJun Yu...
    84-96页
    查看更多>>摘要：Colorectal cancer(CRC)is one of the most frequently diagnosed cancers and the leading cause of cancer-associated deaths.Epidemiological studies have shown that both genetic and envi-ronmental risk factors contribute to the development of CRC.Several metagenomic studies of CRC have identified gut dysbiosis as a fundamental risk factor in the evolution of colorectal malignancy.Although enormous efforts and substantial progresses have been made in understanding the rela-tionship between human gut microbiome and CRC,the precise mechanisms involved remain elusive.Recent data have shown a direct causative role of the gut microbiome in DNA damage,inflamma-tion,and drug resistance in CRC,suggesting that modulation of gut microbiome could act as a powerful tool in CRC prevention and therapy.Here,we provide an overview of the relationship between gut microbiome and CRC,and explore relevant mechanisms of colorectal tumorigenesis.We next highlight the potential of bacterial species as clinical biomarkers,as well as their roles in therapeutic response.Factors limiting the clinical translation of gut microbiome and strategies for resolving current challenges are further discussed.
      原文链接:
    • 万方数据
    • 维普

    Application of Microbiome in Forensics

    Jun ZhangWenli LiuHalimureti SimayijiangPing Hu...
    97-107页
    查看更多>>摘要：Recent advances in next-generation sequencing technologies and improvements in bioinformatics have expanded the scope of microbiome analysis as a forensic tool.Microbiome research is concerned with the study of the compositional profile and diversity of microbial flora as well as the interactions between microbes,hosts,and the environment.It has opened up many new possibilities for forensic analysis.In this review,we discuss various applications of microbiome in forensics,including identification of individuals,geolocation inference,and post-mortem interval(PMI)estimation.
      原文链接:
    • 万方数据
    • 维普

    Computational Tools and Resources for CRISPR/Cas Genome Editing

    Chao LiWen ChuRafaqat Ali GillShifei Sang...
    108-126页
    查看更多>>摘要：The past decade has witnessed a rapid evolution in identifying more versatile clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein(Cas)nucle-ases and their functional variants,as well as in developing precise CRISPR/Cas-derived genome editors.The programmable and robust features of the genome editors provide an effective RNA-guided platform for fundamental life science research and subsequent applications in diverse scenar-ios,including biomedical innovation and targeted crop improvement.One of the most essential principles is to guide alterations in genomic sequences or genes in the intended manner without undesired off-target impacts,which strongly depends on the efficiency and specificity of single guide RNA(sgRNA)-directed recognition of targeted DNA sequences.Recent advances in empirical scor-ing algorithms and machine learning models have facilitated sgRNA design and off-target predic-tion.In this review,we first briefly introduce the different features of CRISPR/Cas tools that should be taken into consideration to achieve specific purposes.Secondly,we focus on the computer-assisted tools and resources that are widely used in designing sgRNAs and analyzing CRISPR/Cas-induced on-and off-target mutations.Thirdly,we provide insights into the limita-tions of available computational tools that would help researchers of this field for further optimiza-tion.Lastly,we suggest a simple but effective workflow for choosing and applying web-based resources and tools for CRISPR/Cas genome editing.
      原文链接:
    • 万方数据
    • 维普

    The Jasmine(Jasminum sambac)Genome Provides Insight into the Biosynthesis of Flower Fragrances and Jasmonates

    Gang ChenSalma MostafaZhaogeng LuRan Du...
    127-149页
    查看更多>>摘要：Jasminum sambac(jasmine flower),a world-renowned plant appreciated for its excep-tional flower fragrance,is of cultural and economic importance.However,the genetic basis of its fragrance is largely unknown.Here,we present the first de novo genome assembly of J.sambac with 550.12 Mb(scaffold N50=40.10 Mb)assembled into 13 pseudochromosomes.Terpene synthase(TPS)genes associated with flower fragrance are considerably amplified in the form of gene clusters through tandem duplications in the genome.Gene clusters within the salicylic acid/benzoic acid/theobromine(SABATH)and benzylalcohol O-acetyltransferase/anthocyanin O-hydroxycinnamoyltransferases/anthranilate N-hydroxycinnamoyl/benzoyltransferase/deacetyl-vindoline 4-O-acetyltransferase(BAHD)superfamilies were identified to be related to the biosyn-thesis of phenylpropanoid/benzenoid compounds.Several key genes involved in jasmonate biosyn-thesis were duplicated,causing an increase in copy numbers.In addition,multi-omics analyses identified various aromatic compounds and many genes involved in fragrance biosynthesis path-ways.Furthermore,the roles of JsTPS3 in β-ocimene biosynthesis,as well as JsAOC1 and JsAOS in jasmonic acid biosynthesis,were functionally validated.The genome assembled in this study for J.sambac offers a basic genetic resource for studying floral scent and jasmonate biosynthesis,and provides a foundation for functional genomic research and variety improvements in Jasminum.
      原文链接:
    • 万方数据
    • 维普

    Gut Microbiome Variation Along A Lifestyle Gradient Reveals Threats Faced by Asian Elephants

    Chengbo ZhangZhenghan LianBo XuQingzhong Shen...
    150-163页
    查看更多>>摘要：The gut microbiome is closely related to host nutrition and health.However,the relation-ships between gut microorganisms and host lifestyle are not well characterized.In the absence of confounding geographic variation,we defined clear patterns of variation in the gut microbiomes of Asian elephants(AEs)in the Wild Elephant Valley,Xishuangbanna,China,along a lifestyle gra-dient(completely captive,semicaptive,semiwild,and completely wild).A phylogenetic analysis using the 16S rRNA gene sequences highlighted that the microbial diversity decreased as the degree of captivity increased.Furthermore,the results showed that the bacterial taxon WCHB1-41_c was substantially affected by lifestyle variations.qRT-PCR analysis revealed a paucity of genes related to butyrate production in the gut microbiome of AEs with a completely wild lifestyle,which may be due to the increased unfavorable environmental factors.Overall,these results demonstrate the dis-tinct gut microbiome characteristics among AEs with a gradient of lifestyles and provide a basis for designing strategies to improve the well-being or conservation of this important animal species.
      原文链接:
    • 万方数据
    • 维普