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Journal of Genetics and Genomics, Yi Chuan Xue Bao

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https://www.readbyqxmd.com/read/30174135/mid1ip1b-modulates-apical-reorientation-of-non-centrosomal-microtubule-organizing-center-in-epithelial-cells
#1
Xin Zhou, Chun Xiao, Yu Li, Yanna Shang, Dongqin Yin, Siying Li, Bo Xiang, Ran Lu, Yi Ji, Yang Wu, Wentong Meng, Hongyan Zhu, Jin Liu, Huozhen Hu, Xianming Mo, Hong Xu
In most kinds of animal cells, the centrosome serves as the main microtubule organizing center (MTOC) that nucleates microtubule arrays throughout the cytoplasm to maintain cell structure, cell division and intracellular transport. Whereas in epithelial cells, non-centrosomal MTOCs are established in the apical domain for generating asymmetric microtubule fibers and cilia in epithelial cells for the organ morphogenesis during embryonic development. However, the mechanism by which MTOCs localize to the apical domain in epithelial cells remains largely unknown...
August 24, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30174134/genome-wide-variants-of-eurasian-facial-shape-differentiation-and-a-prospective-model-of-dna-based-face-prediction
#2
Lu Qiao, Yajun Yang, Pengcheng Fu, Sile Hu, Hang Zhou, Shouneng Peng, Jingze Tan, Yan Lu, Haiyi Lou, Dongsheng Lu, Sijie Wu, Jing Guo, Li Jin, Yaqun Guan, Sijia Wang, Shuhua Xu, Kun Tang
It is a long-standing question as to which genes define the characteristic facial features among different ethnic groups. In this study, we use Uyghurs, an ancient admixed population to query the genetic bases why Europeans and Han Chinese look different. Facial traits were analyzed based on high-dense 3D facial images; numerous biometric spaces were examined for divergent facial features between European and Han Chinese, ranging from inter-landmark distances to dense shape geometrics. Genome-wide association studies (GWAS) were conducted on a discovery panel of Uyghurs...
August 16, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30172581/overexpression-of-the-nuclear-protein-gene-atduf4-increases-organ-size-in-arabidopsis-thaliana-and-brassica-napus
#3
LETTER
Guang-Xia Chen, Xi Cao, Zhao-Xia Ma, Yu Tang, Yue-Juan Zeng, Li-Qun Chen, De Ye, Xue-Qin Zhang
No abstract text is available yet for this article.
August 16, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30172582/efficient-and-fast-identification-of-differentially-methylated-regions-using-whole-genome-bisulfite-sequencing-data
#4
LETTER
Dinh Diep, Kun Zhang
No abstract text is available yet for this article.
August 9, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30174136/prpf4-is-essential-for-cell-survival-and-posterior-lateral-line-primordium-migration-in-zebrafish
#5
Yixia Wang, Yanchao Han, Pengfei Xu, Shihui Ding, Guangyuan Li, Hongbin Jin, Yaping Meng, Anming Meng, Shunji Jia
Prpf4 (pre-mRNA processing factor 4), a key component of spliceosome, plays critical roles in pre-mRNA splicing and its mutations result in retinitis pigmentosa due to photoreceptor defects. In this study, we characterized a zebrafish prpf4t243 mutant harboring a Tol2 transposon-based gene trap cassette in the third intron of the prpf4 gene. Cells in the brain and spinal cord gradually undergo p53-dependent apoptosis after 28 hpf in prpf4t243 mutants, suggesting that a widespread function of prpf4 in neural cell survival...
August 7, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30057342/characterizing-functional-consequences-of-dna-copy-number-alterations-in-breast-and-ovarian-tumors-by-spacemap
#6
Christopher J Conley, Umut Ozbek, Pei Wang, Jie Peng
We propose a novel conditional graphical model - spaceMap - to construct gene regulatory networks from multiple types of high dimensional omic profiles. A motivating application is to characterize the perturbation of DNA copy number alterations (CNAs) on downstream protein levels in tumors. Through a penalized multivariate regression framework, spaceMap jointly models high dimensional protein levels as responses and high dimensional CNAs as predictors. In this setup, spaceMap infers an undirected network among proteins together with a directed network encoding how CNAs perturb the protein network...
July 26, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30055875/a-comparison-of-next-generation-sequencing-analysis-methods-for-cancer-xenograft-samples
#7
REVIEW
Wentao Dai, Jixiang Liu, Quanxue Li, Wei Liu, Yi-Xue Li, Yuan-Yuan Li
The application of next-generation sequencing (NGS) technology in cancer is influenced by the quality and purity of tissue samples. This issue is especially critical for patient-derived xenograft (PDX) models, which have proven to be by far the best preclinical tool for investigating human tumor biology, because the sensitivity and specificity of NGS analysis in xenograft samples would be compromised by the contamination of mouse DNA and RNA. This definitely affects downstream analyses by causing inaccurate mutation calling and gene expression estimates...
July 25, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30054214/the-drugpattern-tool-for-drug-set-enrichment-analysis-and-its-prediction-for-beneficial-effects-of-oxldl-on-type-2-diabetes
#8
Chuanbo Huang, Weili Yang, Junpei Wang, Yuan Zhou, Bin Geng, Georgios Kararigas, Jichun Yang, Qinghua Cui
Enrichment analysis methods, e.g., gene set enrichment analysis, represent one class of important bioinformatical resources for mining patterns in biomedical datasets. However, tools for inferring patterns and rules of a list of drugs are limited. In this study, we developed a web-based tool, DrugPattern, for drug set enrichment analysis. We first collected and curated 7019 drug sets, including indications, adverse reactions, targets, pathways, etc. from public databases. For a list of interested drugs, DrugPattern then evaluates the significance of the enrichment of these drugs in each of the 7019 drug sets...
July 24, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30055873/phopepmass-a-database-and-search-tool-assisting-human-phosphorylation-peptide-identification-from-mass-spectrometry-data
#9
Menghuan Zhang, Hui Cui, Lanming Chen, Ying Yu, Michael O Glocker, Lu Xie
Protein phosphorylation, one of the most important protein post-translational modifications, is involved in various biological processes, and the identification of phosphorylation peptides (phosphopeptides) and their corresponding phosphorylation sites (phosphosites) will facilitate the understanding of the molecular mechanism and function of phosphorylation. Mass spectrometry (MS) provides a high-throughput technology that enables the identification of large numbers of phosphosites. PhoPepMass is designed to assist human phosphopeptide identification from MS data based on a specific database of phophopeptide masses and a multivariate hypergeometric matching algorithm...
July 19, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30057343/mcenet-a-database-for-maize-conditional-co-expression-network-and-network-characterization-collaborated-with-multi-dimensional-omics-levels
#10
Tian Tian, Qi You, Hengyu Yan, Wenying Xu, Zhen Su
Maize (Zea mays) is the most widely grown grain crop in the world, playing important roles in agriculture and industry. However, the functions of maize genes remain largely unknown. High-quality genome-wide transcriptome datasets provide important biological knowledge which has been widely and successfully used in plants not only by measuring gene expression levels but also by enabling co-expression analysis for predicting gene functions and modules related to agronomic traits. Recently, thousands of maize transcriptomic data are available across different inbred lines, development stages, tissues, and treatments, or even across different tissue sections and cell lines...
July 18, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30054216/iresfinder-identifying-rna-internal-ribosome-entry-site-in-eukaryotic-cell-using-framed-k-mer-features
#11
LETTER
Jian Zhao, Jing Wu, Tianyi Xu, Qichang Yang, Junhao He, Xiaofeng Song
No abstract text is available yet for this article.
July 18, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30054215/vcsra-a-fast-and-accurate-multiple-sequence-alignment-algorithm-with-a-high-degree-of-parallelism
#12
LETTER
Dong Dong, Wenhe Su, Wenqiang Shi, Quan Zou, Shaoliang Peng
No abstract text is available yet for this article.
July 17, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30054217/systematic-identification-and-annotation-of-multiple-variant-compound-effects-at-transcription-factor-binding-sites-in-human-genome
#13
Si-Jin Cheng, Shuai Jiang, Fang-Yuan Shi, Yang Ding, Ge Gao
Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites (TFBSs) are one of the most important cis-regulatory elements. While multiple tools have been developed to assess functional effects of genetic variants at TFBSs, they usually assume that each variant works in isolation and neglect the potential "interference" among multiple variants within the same TFBS. In this study, we presented COPE-TFBS (Context-Oriented Predictor for variant Effect on Transcription Factor Binding Site), a novel method that considers sequence context to accurately predict variant effects on TFBSs...
July 7, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30055874/lncpipe-a-nextflow-based-pipeline-for-identification-and-analysis-of-long-non-coding-rnas-from-rna-seq-data
#14
LETTER
Qi Zhao, Yu Sun, Dawei Wang, Hongwan Zhang, Kai Yu, Jian Zheng, Zhixiang Zuo
No abstract text is available yet for this article.
July 6, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30115328/omics-tools-for-the-needle-out-of-haystack
#15
EDITORIAL
Zhiwei Cao, Xiu-Jie Wang, Shihua Zhang
No abstract text is available yet for this article.
July 20, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30049619/fgwas-an-r-package-for-genome-wide-association-analysis-with-longitudinal-phenotypes
#16
LETTER
Zhong Wang, Nating Wang, Rongling Wu, Zuoheng Wang
No abstract text is available yet for this article.
July 20, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/29983245/wocea-the-visualization-of-functional-enrichment-results-in-word-clouds
#17
LETTER
Wanshan Ning, Shaofeng Lin, Jiaqi Zhou, Yaping Guo, Ying Zhang, Di Peng, Wankun Deng, Yu Xue
No abstract text is available yet for this article.
July 20, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/30170984/construction-and-application-of-oligo-based-fish-karyotype-of-haynaldia-villosa
#18
LETTER
Haojie Sun, Jingjing Song, Jia Lei, Xinying Song, Keli Dai, Jin Xiao, Chunxia Yuan, Shengmin An, Haiyan Wang, Xiue Wang
No abstract text is available yet for this article.
June 21, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/29941353/advances-in-the-development-of-molecular-genetic-tools-for-mycobacterium-tuberculosis
#19
REVIEW
Chiranjibi Chhotaray, Yaoju Tan, Julius Mugweru, Md Mahmudul Islam, H M Adnan Hameed, Shuai Wang, Zhili Lu, Changwei Wang, Xinjie Li, Shouyong Tan, Jianxiong Liu, Tianyu Zhang
Mycobacterium tuberculosis, a clinically relevant Gram-positive bacterium of great clinical relevance, is a lethal pathogen owing to its complex physiological characteristics and development of drug resistance. Several molecular genetic tools have been developed in the past few decades to study this microorganism. These tools have been instrumental in understanding how M. tuberculosis became a successful pathogen. Advanced molecular genetic tools have played a significant role in exploring the complex pathways involved in M...
June 18, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/29929848/the-caudal-dorsal-artery-generates-hematopoietic-stem-and-progenitor-cells-via-the-endothelial-to-hematopoietic-transition-in-zebrafish
#20
Yandong Zhan, Youkui Huang, Jingying Chen, Zigang Cao, Jianbo He, Jingjing Zhang, Honghui Huang, Hua Ruan, Lingfei Luo, Li Li
Zebrafish hematopoietic stem and progenitor cells (HSPCs) originate from the hemogenic endothelium of the ventral wall of the dorsal aorta (DA) through the endothelial-to-hematopoietic transition (EHT) from approximately 30 to 60 hours post fertilization (hpf). However, whether other artery sites can generate HSPCs de novo remains unclear. In this study, using live imaging and lineage tracing, we found that the caudal dorsal artery (CDA) in the caudal hematopoietic tissue directly gave rise to HSPCs through EHT...
June 8, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
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