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Journal of Genetics and Genomics, Yi Chuan Xue Bao

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https://www.readbyqxmd.com/read/28529074/bioinformaticians-wrestling-with-the-big-biomedical-data
#1
EDITORIAL
Yu Xue, Xiu-Jie Wang
No abstract text is available yet for this article.
May 18, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28529082/rice-expression-database-red-an-integrated-rna-seq-derived-gene-expression-database-for-rice
#2
Lin Xia, Dong Zou, Jian Sang, Xingjian Xu, Hongyan Yin, Mengwei Li, Shuangyang Wu, Songnian Hu, Lili Hao, Zhang Zhang
Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community. Here, we present RED (Rice Expression Database; http://expression.ic4r.org), an integrated database of rice gene expression profiles derived entirely from RNA-Seq data. RED features a comprehensive collection of 284 high-quality RNA-Seq experiments, integrates a large number of gene expression profiles and covers a wide range of rice growth stages as well as various treatments. Based on massive expression profiles, RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene(s) of interest...
May 4, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28529081/sysfinder-a-customized-platform-for-search-comparison-and-assisted-design-of-appropriate-animal-models-based-on-systematic-similarity
#3
Shuang Yang, Guoqing Zhang, Wan Liu, Zhen Wang, Jifeng Zhang, Dongshan Yang, Y Eugene Chen, Hong Sun, Yixue Li
Animal models are increasingly gaining values by cross-comparisons of response or resistance to clinical agents used for patients. However, many disease mechanisms and drug effects generated from animal models are not transferable to human. To address these issues, we developed SysFinder (http://lifecenter.sgst.cn/SysFinder), a platform for scientists to find appropriate animal models for translational research. SysFinder offers a "topic-centered" approach for systematic comparisons of human genes, whose functions are involved in a specific scientific topic, to the corresponding homologous genes of animal models...
May 4, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28527662/cmgene-a-literature-based-database-and-knowledge-resource-for-cancer-metastasis-genes
#4
LETTER
Yining Liu, Zhe Li, Jiachun Lu, Min Zhao, Hong Qu
No abstract text is available yet for this article.
May 4, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28533016/drodvir-a-resource-for-exploring-the-virome-diversity-in-rodents
#5
Lihong Chen, Bo Liu, Zhiqiang Wu, Qi Jin, Jian Yang
Emerging zoonotic diseases have received tremendous interests in recent years, as they pose a significant threat to human health, animal welfare, and economic stability. A high proportion of zoonoses originate from wildlife reservoirs. Rodents are the most numerous, widespread, and diverse group of mammals on the earth and are reservoirs for many zoonotic viruses responsible for significant morbidity and mortality. A better understanding of virome diversity in rodents would be of importance for researchers and professionals in the field...
May 3, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28529077/plmd-an-updated-data-resource-of-protein-lysine-modifications
#6
Haodong Xu, Jiaqi Zhou, Shaofeng Lin, Wankun Deng, Ying Zhang, Yu Xue
Post-translational modifications (PTMs) occurring at protein lysine residues, or protein lysine modifications (PLMs), play critical roles in regulating biological processes. Due to the explosive expansion of the amount of PLM substrates and the discovery of novel PLM types, here we greatly updated our previous studies, and presented a much more integrative resource of protein lysine modification database (PLMD). In PLMD, we totally collected and integrated 284,780 modification events in 53,501 proteins across 176 eukaryotes and prokaryotes for up to 20 types of PLMs, including ubiquitination, acetylation, sumoylation, methylation, succinylation, malonylation, glutarylation, glycation, formylation, hydroxylation, butyrylation, propionylation, crotonylation, pupylation, neddylation, 2-hydroxyisobutyrylation, phosphoglycerylation, carboxylation, lipoylation and biotinylation...
May 3, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28529076/admetnet-the-knowledge-base-of-pharmacokinetics-and-toxicology-network
#7
LETTER
Quan Xu, Ke Liu, Xingming Lin, Yangmei Qin, Linshan Chen, Jiao Cheng, Mindong Zhong, Qiushun He, Yinbo Li, Tingwu Wang, Jianbo Pan, Menglu Peng, Lixia Yao, Zhiliang Ji
No abstract text is available yet for this article.
May 3, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28529075/mtd-a-database-of-micrornas-affecting-therapeutic-effects-of-drugs
#8
LETTER
Xiao Chen, Wen-Bin Xie, Pei-Pei Xiao, Xing-Ming Zhao, Hong Yan
No abstract text is available yet for this article.
May 3, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28529079/virusmap-a-visualization-database-for-the-influenza-a-virus
#9
LETTER
Yubin Xie, Xiaotong Luo, Zhihao He, Yueyuan Zheng, Zhixiang Zuo, Qi Zhao, Yanyan Miao, Jian Ren
No abstract text is available yet for this article.
April 29, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28529078/hcsgd-an-integrated-database-of-human-cellular-senescence-genes
#10
Qiongye Dong, Hongqing Han, Xuehui Liu, Lei Wei, Wei Zhang, Zhen Zhao, Michael Q Zhang, Xiaowo Wang
Cellular senescence is an irreversible cell cycle arrest program in response to various exogenous and endogenous stimuli like telomere dysfunction and DNA damage. It has been widely accepted as an anti-tumor program and is also found closely related to embryo development, tissue repair, organismal aging and age-related degenerative diseases. In the past decades, numerous efforts have been made to uncover the gene regulatory mechanisms of cellular senescence. There is a strong demand to integrate these data from various resources into one open platform...
April 29, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28325554/inscuteable-maintains-type-i-neuroblast-lineage-identity-via-numb-notch-signaling-in-the-drosophila-larval-brain
#11
Huanping An, Wanzhong Ge, Yongmei Xi, Xiaohang Yang
In the Drosophila larval brain, type I and type II neuroblasts (NBs) undergo a series of asymmetric divisions which give rise to distinct progeny lineages. The intermediate neural progenitors (INPs) exist only in type II NB lineages. In this study, we reveal a novel function of Inscuteable (Insc) that acts to maintain type I NB lineage identity. In insc type I NB clones of mosaic analyses with a repressible cell marker (MARCM), the formation of extra Deadpan (Dpn)(+) NB-like and GMC-like cells is observed. The lack of Insc leads to the defective localization and segregation of Numb during asymmetric cell division...
March 6, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28427862/molecular-evolution-of-pancreatic-ribonuclease-gene-rnase1-in-rodentia
#12
LETTER
Da-Tian Lang, Xiao-Ping Wang, Lei Wang, Li Yu
No abstract text is available yet for this article.
April 20, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28416245/a-simple-and-efficient-method-for-crispr-cas9-induced-mutant-screening
#13
Yufeng Hua, Chun Wang, Jian Huang, Kejian Wang
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system provides a technological breakthrough in mutant generation. Several methods such as the polymerase chain reaction (PCR)/restriction enzyme (RE) assay, T7 endonuclease I (T7EI) assay, Surveyor nuclease assay, PAGE-based genotyping assay, and high-resolution melting (HRM) analysis-based assay have been developed for screening CRISPR/Cas9-induced mutants. However, these methods are time- and labour-intensive and may also be sequence-limited or require very expensive equipment...
April 20, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28412228/temperature-effect-on-crispr-cas9-mediated-genome-editing
#14
Guanghai Xiang, Xingying Zhang, Chenrui An, Chen Cheng, Haoyi Wang
Zinc-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR-Cas9) are the most commonly used genome editing tools. Previous studies demonstrated that hypothermia treatment increased the mutation rates induced by ZFNs and TALENs in mammalian cells. Here, we characterize the effect of different culture temperatures on CRISPR-Cas9 mediated genome editing and find that the genome editing efficiency of CRISPR-Cas9 is significantly hampered by hypothermia treatment, unlike ZFN and TALEN...
April 20, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28412226/expression-profiling-based-clustering-of-healthy-subjects-recapitulates-classifications-defined-by-clinical-observation-in-chinese-medicine
#15
Ruoxi Yu, Dan Liu, Yin Yang, Yuanyuan Han, Lingru Li, Luyu Zheng, Ji Wang, Yan Zhang, Yingshuai Li, Qian-Fei Wang, Qi Wang
Differences between healthy subjects and associated disease risks are of substantial interest in clinical medicine. Based on clinical presentations, Traditional Chinese Medicine (TCM) classifies healthy people into nine constitutions: Balanced, Qi, Yang or Yin deficiency, Phlegm-dampness, Damp-heat, Blood stasis, Qi stagnation, and Inherited special constitutions. In particular, Yang and Yin deficiency constitutions exhibit cold and heat aversion, respectively. However, the intrinsic molecular characteristics of unbalanced phenotypes remain unclear...
April 20, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28411033/significant-differences-of-function-and-expression-of-micrornas-between-ground-state-and-serum-cultured-pluripotent-stem-cells
#16
Ying Yan, Xi Yang, Ting-Ting Li, Kai-Li Gu, Jing Hao, Qiang Zhang, Yangming Wang
Serum- and 2i-cultured embryonic stem cells (ESCs) show different epigenetic landscapes and transcriptomic profiles. The difference in the function and expression of microRNAs (miRNAs) between these two states remains unclear. Here, we showed that 2i- and serum-cultured ESCs exhibited distinctive miRNA expression profiles with >100 miRNAs differentially expressed, and the expression changes were largely due to transcriptional regulation. We further characterized the function of miRNAs differentially expressed under two conditions and found that ESCs exhibited higher degree of dependency on miRNAs for rapid proliferation; since Dgcr8(-/-) or Dicer1(-/-) but not wild-type ESCs showed slower growth rate and more accumulation in the G1 phase under 2i than serum condition...
April 20, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28411032/a-2-bp-insertion-c-67_68inscc-in-mc1r-causes-recessive-white-coat-color-in-bama-miniature-pigs
#17
LETTER
Qitao Jia, Chunwei Cao, Hai Tang, Ying Zhang, Qiantao Zheng, Xiao Wang, Rui Zhang, Xianlong Wang, Ailing Luo, Hong Wei, Anming Meng, Qi Zhou, Hongmei Wang, Jianguo Zhao
No abstract text is available yet for this article.
April 20, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28325553/metabolomics-through-the-lens-of-precision-cardiovascular-medicine
#18
REVIEW
Sin Man Lam, Yuan Wang, Bowen Li, Jie Du, Guanghou Shui
Metabolomics, which targets at the extensive characterization and quantitation of global metabolites from both endogenous and exogenous sources, has emerged as a novel technological avenue to advance the field of precision medicine principally driven by genomics-oriented approaches. In particular, metabolomics has revealed the cardinal roles that the environment exerts in driving the progression of major diseases threatening public health. Herein, the existent and potential applications of metabolomics in two key areas of precision cardiovascular medicine will be critically discussed: 1) the use of metabolomics in unveiling novel disease biomarkers and pathological pathways; 2) the contribution of metabolomics in cardiovascular drug development...
March 20, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28302421/identification-and-analysis-of-intermediate-size-noncoding-rnas-in-the-rhesus-macaque-fetal-brain
#19
LETTER
Liyuan Zhu, Xiaochao Tan, Wei Liu, Fengbiao Mao, Chao Wu, Junjie Zhou, Xiao Liu, Shuaiyao Lu, Kaili Ma, Bin Yin, Jianjun Luo, Jiangang Yuan, Boqin Qiang, Runsheng Chen, Xiaozhong Peng
No abstract text is available yet for this article.
March 20, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28302420/a-cryptic-mitochondrial-dna-link-between-north-european-and-west-african-dogs
#20
Adeniyi C Adeola, Sheila C Ommeh, Jiao-Jiao Song, S Charles Olaogun, Oscar J Sanke, Ting-Ting Yin, Guo-Dong Wang, Shi-Fang Wu, Zhong-Yin Zhou, Jacqueline K Lichoti, Bernard R Agwanda, Philip M Dawuda, Robert W Murphy, Min-Sheng Peng, Ya-Ping Zhang
Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA (mtDNA) D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe and West Asia. All Kenyan dogs can be assigned to one of three haplogroups (matrilines; clades): A, B, and C, while Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D...
March 20, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
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