《Genomics, Proteomics & Bioinformatics》

作品数：1260被引量：3248H指数：22
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《Genomics, Proteomics & Bioinformatics》
主办单位：中国科学院北京基因组研究所（国家生物信息中心）
最新期次：2024年5期更多>>
发文主题：BIOINFORMATICSPROTEOMICSSINGLE-CELLGENOMICSJOURNAL更多>>
发文领域：生物学医药卫生农业科学文化科学更多>>
发文基金：国家自然科学基金国家重点基础研究发展计划国家高技术研究发展计划中国博士后科学基金更多>>
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RNA 5-Methylcytosine Modification:Regulatory Molecules,Biological Functions,and Human Diseases
《Genomics, Proteomics & Bioinformatics》2024年第5期11-26,共16页Yanfang Lu Liu Yang Qi Feng Yong Liu Xiaohui Sun Dongwei Liu Long Qiao Zhangsuo Liu 
supported by grants from the China Postdoctoral Science Foundation(Grant No.2021TQ0297);the Key Scientific Research Projects of Higher Education Institutions in Henan Province(Grant No.22A320060);the Henan Provincial Natural Science Foundation(Grant No.242300421479);the Henan Provincial Medical Science and Technology Research Projectt(Grant No.LHGJ20190115),China。
RNA methylation modifications influence gene expression,and disruptions of these processes are often associated with various human diseases.The common RNA methylation modification 5-methylcytosine(m^(5)C),which is dyn...
关键词：Biological process Human disease RNA methylation m^(5)C m^(5)C regulator 
Multiome-wide Association Studies:Novel Approaches for Understanding Diseases
《Genomics, Proteomics & Bioinformatics》2024年第5期27-43,共17页Mengting Shao Kaiyang Chen Shuting Zhang Min Tian Yan Shen Chen Cao Ning Gu 
supported by the National Natural Science Foundation of China(Grant Nos.62102068,62231013,61821002,81971750,81701833);the National Key R&D Program of China(Grant No.2017YFA0104300).
The rapid development of multiome(transcriptome,proteome,cistrome,imaging,and regulome)-wide association study methods have opened new avenues for biologists to understand the susceptibility genes underlying complex d...
关键词：Complex disease Gene-based association study Genome-wide association study Multiome Transcriptome-wide association study 
Bioinformatic Resources for Exploring Human-virus Protein-protein Interactions Based on Binding Modes
《Genomics, Proteomics & Bioinformatics》2024年第5期45-59,共15页Huimin Chen Jiaxin Liu Gege Tang Gefei Hao Guangfu Yang 
supported by the National Natural Science Foundation of China(Grant No.32125033).
Historically,there have been many outbreaks of viral diseases that have continued to claim millions of lives.Research on human-virus protein-protein interactions(PPIs)is vital to understanding the principles of human-...
关键词：Artificial intelligence Bioinformatic resource Protein-protein docking Protein-protein interaction Viral pandemic 
Centromere Landscapes Resolved from Hundreds of Human Genomes
《Genomics, Proteomics & Bioinformatics》2024年第5期61-71,共11页Shenghan Gao Yimeng Zhang Stephen J. Bush Bo Wang Xiaofei Yang Kai Ye 
supported by the National Key R&D Program of China(Grant No.2022YFC3400300);the National Natural Science Foundation of China(Grant Nos.32125009,32400520,32422019,62172325,32070663,32200510);the Natural Science Foundation of Shaanxi Province(Grant No.2024JC-JCQN-28);the Fundamental Research Funds for the Central Universities(Grant No.xzy012024088);China.
High-fidelity(HiFi)sequencing has facilitated the assembly and analysis of the most repetitive region of the genome,the centromere.Nevertheless,our current understanding of human centromeres is based on a relatively s...
关键词：Centromere sequence Genome evolution High-fidelity sequencing technology Higher order repeat annotation Human population 
RAG-seq:NSR-primed and Transposase Tagmentation-mediated Strand-specific Total RNA Sequencing in Single Cells
《Genomics, Proteomics & Bioinformatics》2024年第5期73-84,共12页Ping Xu Zhiheng Yuan Xiaohua Lu Peng Zhou Ding Qiu Zhenghao Qiao Zhongcheng Zhou Li Guan Yongkang Jia Xuan He Ling Sun Youzhong Wan Ming Wang Yang Yu 
supported in part by grants from the National Natural Science Foundation of China(Grant Nos.81921003 and 32170605 to YY,Grant No.32100473 to LG);the Ministry of Science and Technology of China(Grant Nos.2019YFA0508903 and 2017YFA0504200 to YY);the Jilin Province Health Research Special Fund for Outstanding Talented Person(Grant No.2023SCZ58 to YW);YY was additionally supported by the start-up fund from Guangzhou Women and Children's Medical Center.
Single-cell RNA sequencing(scRNA-seq)has transformed our understanding of cellular diversity with unprecedented resolution.However,many current methods are limited in capturing full-length transcripts and discerning s...
关键词：Antisense transcript FULL-LENGTH Mouse early embryonic development Single-cell RNA sequencing Strand-specific 
Identify Non-mutational p53 Functional Deficiency in Human Cancers
《Genomics, Proteomics & Bioinformatics》2024年第5期85-98,共14页Qianpeng Li Yang Zhang Sicheng Luo Zhang Zhang Ann L.Oberg David E.Kozono Hua Lu Jann N.Sarkaria Lina Ma Liguo Wang 
supported by the National Institutes of Health(Grant No.U10-CA180882-07)and the Mayo Clinic Center for Individualized Medicine,USA,as well as the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDB38030400);the Youth Innovation Promotion Association of Chinese Academy of Sciences(Grant No.2019104),China.
An accurate assessment of p53's functional statuses is critical for cancer genomic medicine.However,there is a significant challenge in identifying tumors with non-mutational p53 inactivation which is not detectable t...
关键词：CANCER Composite expression DNA mutation Machine learning p53 deficiency 
Enhancing Variant Calling in Whole-exome Sequencing Data Using Population-matched Reference Genomes
《Genomics, Proteomics & Bioinformatics》2024年第5期99-107,共9页Shuming Guo Zhuo Huang Yanming Zhang Yukun He Xiangju Chen Wenjuan Wang Lansheng Li Yu Kang Zhancheng Gao Jun Yu Zhenglin Du Yanan Chu 
supported by grants from the National Key R&DäProgram of China(Grant No.2021YFC 2301000);the National Science Foundation of China(Grant No.32371537);the Linfen Soft Science Research Project(Grant No.2126);the National and Provincial Key Clinical Specialty Capacity Building Project 2020(Department of the Respiratory Medicine);the Peking University People's Hospital Scientific Research Development Funds(Grant No.RDGS2022-11),China.
Whole-exome sequencing(WES)data are frequently used for cancer diagnosis and genome-wide association studies(GWAS),based on high-coverage read mapping,informative variant calling,and high-quality reference genomes.The...
关键词：Population-specific reference genome T2T-YAO TUMOR Variant calling Whole-exome sequencing 
Virus Infection Induces Immune Gene Activation with CTCF-anchored Enhancers and Chromatin Interactions in Pig Genome
《Genomics, Proteomics & Bioinformatics》2024年第5期109-120,共12页Jianhua Cao Ruimin Ren Xiaolong Li Xiaoqian Zhang Yan Sun Xiaohuan Tian Ru Liu Xiangdong Liu Yijun Ruan Guoliang Li Shuhong Zhao 
supported by the National Key R&D Program of China(Grant No.2021YFF1000601);the Hubei Provincial Natural Science Foundation(Grant No.2023AFB1085);the Wuhan Science and Technology Major Project on Key Techniques of Biological Breeding and Breeding of New Varieties(Grant No.2022021302024853);the National Natural Science Foundation of China(Grant Nos.31772563,31790414,and 31771402);the Fundamental Research Funds for the Central Universities(Grant No.2662014PY067).
Chromatin organization is important for gene transcription in pig genome.However,its three-dimensional(3D)structure and dynamics are much less investigated than those in human.Here,we applied the long-read chromatin i...
关键词：CTCF ChIA-PET CHROMATIN Immunity PIG 
The Genome Architecture of the Copepod Eurytemora carolleeae-the Highly Invasive Atlantic Clade of the Eurytemoraaffinis Species Complex
《Genomics, Proteomics & Bioinformatics》2024年第5期121-136,共16页Zhenyong Du Gregory Gelembiuk Wynne Moss Andrew Tritt Carol Eunmi Lee 
funded by the National Science Foundation(Grant Nos.OCE-1658517 and NSF DEB-2055356);the French National Research Agency(Grant No.ANR-19-MPGA-0004)(Macron's"Make Our Planet Great Again"award)to Carol E.Lee.Karyotype visualization was performed by David Stern,Jesse Hunter,and Kim Oxendine at the Wisconsin State Laboratory of Hygiene,Department of Pediatrics,University of Wisconsin School of Medicine and Public Health.
Copepods are among the most abundant organisms on the planet and play critical functions in aquatic ecosystems.Among copepods,populations of the Eurytemora affinis species complex are numerically dominant in many coas...
关键词：ARTHROPOD CRUSTACEA Genome architecture Invasion OSMOREGULATION 
MitoSort:Robust Demultiplexing of Pooled Single-cell Genomic Data Using Endogenous Mitochondrial Variants
《Genomics, Proteomics & Bioinformatics》2024年第5期137-150,共14页Zhongjie Tang Weixing Zhang Peiyu Shi Sijun Li Xinhui Li Yueming Li Yicong Xu Yaqing Shu Zheng Hu Jin Xu 
supported by the National Key R&D Program of China(Grant No.2021YFA1102100);the National Natural Science Foundation of China(Grant Nos.32070644,32293190,32293191)to JX,and the Guangzhou Key Research and Development Program(Grant No.2023B03J1347)to YS and JX.
Multiplexing across donors has emerged as a popular strategy to increase throughput,reduce costs,overcome technical batch effects,and improve doublet detection in single-cell genomic studies.To eliminate additional ex...
关键词：DEMULTIPLEXING Doublet detection MitoSort Mitochondrial genome variant Single-cell genomics 
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