GENOMIC

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TransCell:In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning
《Genomics, Proteomics & Bioinformatics》2024年第2期157-170,共14页Shan-Ju Yeh Shreya Paithankar Ruoqiao Chen Jing Xing Mengying Sun Ke Liu Jiayu Zhou Bin Chen 
supported by the National Institute of Health(Grant Nos.R01GM134307 and K01 ES028047);the MSU Global Impact Initiative,USA.
Gene expression profiling of new or modified cell lines becomes routine today;however,obtaining comprehensive molecular characterization and cellular responses for a variety of cell lines,including those derived from ...
关键词：GENOMICS TRANSCRIPTOMICS Cancer dependency Drug repurposing Transfer learning 
Genomic Epidemiology of Carbapenemaseproducing Klebsiella pneumoniae in China被引量：4
《Genomics, Proteomics & Bioinformatics》2022年第6期1154-1167,共14页Cuidan Li Xiaoyuan Jiang Tingting Yang Yingjiao Ju Zhe Yin Liya Yue Guannan Ma Xuebing Wang Ying Jing Xinhua Luo Shuangshuang Li Xue Yang Fei Chen Dongsheng Zhou 
supported by the National Natural Science Foundation of China(Grant No.31770870);the National Science and Technology Major Projects of China(Grant No.2018ZX10302-301-004-003).
The rapid spread of carbapenemase-producing Klebsiella pneumoniae(cpKP)poses serious threats to public health;however,the underlying genetic basis for its dissemination is still unknown.We conducted a comprehensive ge...
关键词：Klebsiella pneumoniae Drug resistance CARBAPENEMASE PLASMID Genomic epidemiology 
Genomic Shift in Population Dynamics of mcr-1-positive Escherichia coli in Human Carriage被引量：1
《Genomics, Proteomics & Bioinformatics》2022年第6期1168-1179,共12页Yingbo Shen Rong Zhang Dongyan Shao Lu Yang Jiayue Lu Congcong Liu Xueyang Wang Junyao Jiang Boxuan Wang Congming Wu Julian Parkhill Yang Wang Timothy R.Walsh George F.Gao Zhangqi Shen 
This work was supported in part by the grants from the Guangdong Laboratory for Lingnan Modern Agriculture Project,China(Grant No.NT2021006);the National Natural Science Foundation of China(Grant Nos.81861138051,32002335,32141001,and 31761133004);the National Postdoctoral Program for Innovative Talents,China(Grant No.BX20190359);the UK MRC DETER-XDR-China-HUB(Grant No.MR/S013768/1).
Emergence of the colistin resistance gene,mcr-1,has attracted worldwide attention.Despite the prevalence of mcr-1-positive Escherichia coli(MCRPEC)strains in human carriage showing a significant decrease between 2016 ...
关键词：COLISTIN mcr-1 Escherichia coli GENOMICS Human 
Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant被引量：2
《Genomics, Proteomics & Bioinformatics》2022年第1期60-69,共10页Wentai Ma Jing Yang Haoyi Fu Chao Su Caixia Yu Qihui Wang Ana Tereza Ribeiro de Vasconcelos Georgii A.Bazykin Yiming Bao Mingkun Li 
funded by the National Natural Science Foundation of China(Grant No.82161148009);the Strategic Priority Research Program of Chinese Academy of Sciences(Grant No.XDB38030400);the Capital Health Development and Research Special Programme(Grant No.20211G-3012);the Conselho Nacional de Desenvolvimento Cientifico e Tecnológico(CNPq)-NGS-BRICS-n°:440931/2020-7;the Russian Foundation for Basic Research(RFBR)(Grant No.20-54-80014)。
A new variant of concern for SARS-CoV-2,Omicron(B.1.1.529),was designated by the World Health Organization on November 26,2021.This study analyzed the viral genome sequencing data of 108 samples collected from patient...
关键词：Omicron GENOMICS MUTATION Variant of concern SARS-CoV-2 
BrcaSeg:A Deep Learning Approach for Tissue Quantification and Genomic Correlations of Histopathological Images
《Genomics, Proteomics & Bioinformatics》2021年第6期1032-1042,共11页Zixiao Lu Xiaohui Zhan Yi Wu Jun Cheng Wei Shao Dong Ni Zhi Han Jie Zhang Qianjin Feng Kun Huang 
supported by Indiana University Precision Health Initiative to KH and JZ;the NSFC-Guangdong Joint Fund of China (Grant No. U1501256) to QF;Shenzhen Peacock Plan (Grant No. KQTD2016053112051497) to XZ and ND.
Epithelial and stromal tissues are components of the tumor microenvironment and play a major role in tumor initiation and progression.Distinguishing stroma from epithelial tissues is critically important for spatial c...
关键词：Whole-slide tissue image Computational pathology Deep learning Integrative genomics Breast cancer 
Genomic Epidemiology of SARS-CoV-2 in Pakistan被引量：2
《Genomics, Proteomics & Bioinformatics》2021年第5期727-740,共14页Shuhui Song Cuiping Li Lu Kang Dongmei Tian Nazish Badar Wentai Ma Shilei Zhao Xuan Jiang Chun Wang Yongqiao Sun Wenjie Li Meng Lei Shuangli Li Qiuhui Qi Aamer Ikram Muhammad Salman Massab Umair Huma Shireen Fatima Batool Bing Zhang Hua Chen Yun-Gui Yang Amir Ali Abbasi Mingkun Li Yongbiao Xue Yiming Bao 
supported by grants from the National Key R&D Program of China(Grant Nos.2021YFC0863300,2020YFC0848900,and 2016YFE0206600);the National Natural Science Foundation of China(Grant No.82161148009);the Strategic Priority Research Program of Chinese Academy of Sciences,China(Grant Nos.XDA19090116 and XDB38060100);the Open Biodiversity and Health Big Data Programme of International Union of Biological Sciences,International Partnership Program of Chinese Academy of Sciences(Grant No.153F11KYSB20160008);the Professional Association of the Alliance of International Science Organizations(Grant No.ANSO-PA-2020-07);the Youth Innovation Promotion Association of Chinese Academy of Sciences(Grant No.2017141)。
COVID-19 has swept globally and Pakistan is no exception.To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan,we performed the largest genomic epidemiology study of COVID-19 in Paki...
关键词：SARS-CoV-2 VIRUS Molecular evolution Haplotype network Pakistan 
Integrating Genomic and Transcriptomic Data to Reveal Genetic Mechanisms Underlying Piao Chicken Rumpless Trait被引量：2
《Genomics, Proteomics & Bioinformatics》2021年第5期787-799,共13页Yun-Mei Wang Saber Khederzadeh Shi-Rong Li Newton Otieno Otecko David M.Irwin Mukesh Thakur Xiao-Die Ren Ming-Shan Wang Dong-Dong Wu Ya-Ping Zhang 
supported by the National Natural Science Foundation of China(Grant Nos.31771415 and 31801054);the Bureau of Science and Technology of Yunnan Province,China(Grant No.2015FA026);the Youth Innovation Promotion Association,Chinese Academy of Sciences;the support of the CAS-TWAS President’s Fellowship Program for Doctoral Candidates。
Piao chicken,a rare Chinese native poultry breed,lacks primary tail structures,such as pygostyle,caudal vertebra,uropygial gland,and tail feathers.So far,the molecular mechanisms underlying tail absence in this breed ...
关键词：Comparative transcriptomics Population genomics Rumplessness Vertebra development Artificial selection 
GAPIT Version 3: Boosting Power and Accuracy for Genomic Association and Prediction被引量：27
《Genomics, Proteomics & Bioinformatics》2021年第4期629-640,共12页Jiabo Wang Zhiwu Zhang 
partially funded by National Science Foundation,the United States(Grant Nos.DBI 1661348 and ISO 2029933);the United States Department of Agriculture–National Institute of Food and Agriculture,the United States(Hatch Project No.1014919,Grant Nos.2018-70005-28792,2019-67013-29171,and 2020-67021-32460);the Washington Grain Commission,the United States(Endowment and Grant Nos.126593 and 134574);Sichuan Science and Technology Program,China(Grant Nos.2021YJ0269 and 2021YJ0266);the Program of Chinese National Beef Cattle and Yak Industrial Technology System,China(Grant No.CARS-37);Fundamental Research Funds for the Central Universities,China(Southwest Minzu University,Grant No.2020NQN26)。
Genome-wide association study(GWAS)and genomic prediction/selection(GP/GS)are the two essential enterprises in genomic research.Due to the great magnitude and complexity of genomic and phenotypic data,analytical metho...
关键词：GWAS Genomic selection SOFTWARE R GAPIT 
G9a/GLP-sensitivity of H3K9me2 Demarcates Two Types of Genomic Compartments
《Genomics, Proteomics & Bioinformatics》2020年第4期359-370,共12页Zixiang Yan Luzhang Ji Xiangru Huo Qianfeng Wang Yuwen Zhang Bo Wen 
supported by the National Key R&D Program of China(Grant No.2018YFC1003500 awarded to BW);the National Natural Science Foundation of China(Grant No.31771435 awarded to BW)
In the nucleus, chromatin is folded into hierarchical architecture that is tightly linked to various nuclear functions. However, the underlying molecular mechanisms that confer these architectures remain incompletely ...
关键词：H3K9me2 G9a/GLP Chromatin organization 3D genome Genomic compartment 
SR4R:An Integrative SNP Resource for Genomic Breeding and Population Research in Rice被引量：6
《Genomics, Proteomics & Bioinformatics》2020年第2期173-185,共13页Jun Yan Dong Zou Chen Li Zhang Zhang Shuhui Song Xiangfeng Wang 
supported by the National Natural Science Foundation of China(Grant No.31871706);the Department of Agriculture of Guangdong Province(2018-36);Science and Technology Program of Guangdong Province(Grant No.2019B030316006);The Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDA24040201);the Youth Innovation Promotion Association of the Chinese Academy of Sciences(Grant No.2017141)
The information commons for rice(IC4 R)database is a collection of 18 million single nucleotide polymorphisms(SNPs)identified by resequencing of 5152 rice accessions.Although IC4 R offers ultra-high density rice varia...
关键词：RICE SNP Database HAPMAP Panel 
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