SPECIFICITY

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Computational Tools and Resources for CRISPR/Cas Genome Editing
《Genomics, Proteomics & Bioinformatics》2023年第1期108-126,共19页Chao Li Wen Chu Rafaqat Ali Gill Shifei Sang Yuqin Shi Xuezhi Hu Yuting Yang Qamar U.Zaman Baohong Zhang 
We greatly appreciate Dr.Jeffrey McKinnon for his thoughtful proofreading and wonderful suggestion on this manuscript.We also greatly appreciate the scientific community for making huge progress in this field.We have tried to cite as many references as possible.However,due to the page limitation,there may be some important works not cited here;we apologize for this.The work in Dr.Baohong Zhang’s Laboratory is supported in part by Cotton Incorporated and the National Science Foundation,the United States(Grant No.1658709);This work was also supported by the National Natural Science Foundation of China(Grant No.31700316);the Fundamental Research Funds for the Central Nonprofit Scientific Institution(Grant No.1610172018009);the Natural Science Foundation of Hubei Province,China(Grant No.2018CFB543).
The past decade has witnessed a rapid evolution in identifying more versatile clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein(Cas)nucleases and their functional variants,as ...
关键词：Genome editing Efficiency and specificity CRISPR/Cas9 sgRNA Computational tool Algorithm 
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from A Data-driven Perspective
《Genomics, Proteomics & Bioinformatics》2023年第1期164-176,共13页Jianlei Gu Jiawei Dai Hui Lu Hongyu Zhao 
We thank Dr.Yongkun Wang from the Network and Information Center at Shanghai Jiao Tong University(SJTU)for his support in high-performance computing.We thank Ph.D.Candidate Wei Liu from Yale University for her support in the acquisition of physiological trait-related genes.HL is supported by the National Key R&D Program of China(Grant No.2018YFC0910500);JG and JD are supported by the SJTU-Yale Collaborative Research Seed Fund and Neil Shen’s SJTU Medical Research Fund,China.JG and HL are partially supported by the Shanghai Municipal Commission of Health and Family Planning,China(Grant No.2018ZHYL0223);the Science and Technology Commission of Shanghai Municipality(STCSM),China(Grant No.17DZ2251200).
Comprehensive characterization of spatial and temporal gene expression patterns in humans is critical for uncovering the regulatory codes of the human genome and understanding the molecular mechanisms of human disease...
关键词：Ubiquitous expression Housekeeping gene Disallowed gene Expression specificity Expression variability 
Specificity of mRNA Folding and Its Association with Evolutionarily Adaptive mRNA Secondary Structures
《Genomics, Proteomics & Bioinformatics》2021年第6期882-900,共19页Gongwang Yu Hanbing Zhu Xiaoshu Chen Jian-Rong Yang 
supported by the National Key Technology R&D Program of China(Grant Nos.2017YFA0103504 to XC,2018ZX10301402 to JRY);the National Natural Science Foundation of China(Grant Nos.31671320,31871320,and 81830103 to JRY);the start-up grants from the“100 Top Talents Program”of Sun Yat-sen University,China(Grant Nos.50000-18821112 to XC,50000-18821117 to JRY).
The secondary structure is a fundamental feature of both non-coding RNAs(ncRNAs)and messenger RNAs(mRNAs).However,our understanding of the secondary structures of mRNAs,especially those of the coding regions,remains e...
关键词：Evolutionary genomics RNA secondary structure RNA folding specificity RNA alternative folding Ribosome density 
GPS 5.0: An Update on the Prediction of Kinase-specific Phosphorylation Sites in Proteins被引量：6
《Genomics, Proteomics & Bioinformatics》2020年第1期72-80,共9页Chenwei Wang Haodong Xu Shaofeng Lin Wankun Deng Jiaqi Zhou Ying Zhang Ying Shi Di Peng Yu Xue 
Special Project on Precision Medicine under the National Key R&D Program of China(Grant Nos.2017YFC0906600 and 2018YFC0910500);National Natural Science Foundation of China(Grant Nos.31671360,81701567,and 31801095);National Program for Support of Top-Notch Young Professionals,Changjiang Scholars Program of China;supported by the program for HUST Academic Frontier Youth Team,Fundamental Research Funds for the Central Universities,China(Grant Nos.2017KFXKJC001 and 2019kfy RCPY043);China Postdoctoral Science Foundation(Grant Nos.2018M642816 and 2018M632870)
In eukaryotes,protein phosphorylation is specifically catalyzed by numerous protein kinases(PKs),faithfully orchestrates various biological processes,and reversibly determines cellular dynamics and plasticity.Here we ...
关键词：Protein phosphorylation Protein kinase Group-based Prediction System Kinase-specific phosphorylation site Dual-specificity kinase 
Paralog-divergent Features May Help Reduce Off-target Effects of Drugs:Hints from Glucagon Subfamily Analysis
《Genomics, Proteomics & Bioinformatics》2017年第4期246-254,共9页Zhining Sa Jingqi Zhou Yangyun Zou Zhixi Su Xun Gu 
supported by a grant from the National Natural Science Foundation of China(Grant No.31571355 and 31301034);supported by Fudan University,China;Iowa State University,United States
Side effects from targeted drugs remain a serious conccrn. One reason is the nonselective binding of a drug to unintended proteins such as its paralogs, which arc highly homologous in sequences and have similar struct...
关键词：PARALOG Functional divergence Functional site Drug specificity Evolutionary conservation 
Relative Specificity:All Substrates Are Not Created Equal
《Genomics, Proteomics & Bioinformatics》2014年第1期1-7,共7页Yan Zeng 
partly supported by the National Institutes of Health(Grant Nos.5P50-DA011806-12 and R01DA031202)
A biological molecule,e.g.,an enzyme,tends to interact with its many cognate substrates,targets,or partners differentially.Such a property is termed relative specificity and has been proposed to regulate important phy...
关键词：Relative specificity Biochemical activity SUBSTRATES Biological systems 
Adaptive Evolution of cry Genes in Bacillus thuringiensis:Implications for Their Specificity Determination被引量：1
《Genomics, Proteomics & Bioinformatics》2007年第2期102-110,共9页Jin-Yu Wu Fang-Qing Zhao Jie Bai Gang Deng Song Qin Qi-Yu Bao 
This work was supported by the National Natural Science Foundation of China(No.30571009).
The cry gene family, produced during the late exponential phase of growth in Bacillus thuringiensis, is a large, still-growing family of homologous genes, in which each gene encodes a protein with strong specific acti...
关键词：adaptive evolution Bacillus thuringiensis Cry protein maximum likelihood method 
Prediction of GPCR-G Protein Coupling Specificity Using Features of Sequences and Biological Functions
《Genomics, Proteomics & Bioinformatics》2006年第4期238-244,共7页Toshihide Ono Haretsugu Hishigaki 
Understanding the coupling specificity between G protein-coupled receptors （GPCRs） and specific classes of G proteins is important for further elucidation of receptor functions within a cell. Increasing information ...
关键词：GPCR G protein coupling specificity NLP C4.5 text mining 
Predicting the Coupling Specificity of G-protein Coupled Receptors to G-proteins by Support Vector Machines
《Genomics, Proteomics & Bioinformatics》2005年第4期247-251,共5页Cui-Ping Guan Zhen-Ran Jiang Yan-Hong Zhou 
supported by the National Natural Science Foundation of China(No.90203011 and 30370354);the Ministry of Education of China(No.505010 and CG2003-GA002).
G-protein coupled receptors （GPCRs） represent one of the most important classes of drug targets for pharmaceutical industry and play important roles in cellular signal transduction. Predicting the coupling specifici...
关键词：GPCR G-PROTEIN SVM coupling specificity 
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