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Genomics, Proteomics & Bioinformatics

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https://read.qxmd.com/read/30771506/rice-genomics-over-the-past-two-decades-and-into-the-future
#1
REVIEW
Shuhui Song, Dongmei Tian, Zhang Zhang, Songnian Hu, Jun Yu
Domestic rice (Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct field applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we briefly review its achievements over the past two decades and present the potential for its bright future...
February 13, 2019: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30743052/an-exome-seq-based-tool-for-mapping-and-selection-of-candidate-genes-in-maize-deletion-mutants
#2
Shangang Jia, Kyla Morton, Chi Zhang, David Holding
Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by gamma-irradiation showed clear segregation for the kernel phenotypes in B73 × Mo17 F2 ears. To better understand the functional genomics of kernel development, we developed a mapping and gene identification pipeline, bulked segregant exome sequencing (BSEx-seq), to map mutants with kernel phenotypes including opaque endosperm and reduced kernel size...
February 8, 2019: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30743051/a-time-for-celebration-40th-anniversary-of-gsc-and-15th-anniversary-of-big-cas
#3
EDITORIAL
Jun Yu
No abstract text is available yet for this article.
February 8, 2019: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30710789/progress-and-challenges-for-live-cell-imaging-of-genomic-loci-using-crispr-based-platforms
#4
REVIEW
Xiaotian Wu, Shiqi Mao, Yachen Ying, Christopher J Krueger, Antony K Chen
Chromatin conformation, localization, and dynamics are crucial regulators of cellular behaviors. Although fluorescence in situ hybridization-based techniques have been widely utilized for investigating chromatin architectures in healthy and diseased states, the requirement for cell fixation precludes the comprehensive dynamic analysis necessary to fully understand chromatin activities. This has spurred the development and application of a variety of imaging methodologies for visualizing single chromosomal loci in the native cellular context...
January 30, 2019: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30639696/integration-of-a-deep-learning-classifier-with-a-random-forest-approach-for-predicting-malonylation-sites
#5
Zhen Chen, Ningning He, Yu Huang, Wen Tao Qin, Xuhan Liu, Lei Li
As a newly-identified protein post-translational modification, malonylation is involved in a variety of biological functions. Recognizing malonylation sites in substrates represents an initial but crucial step in elucidating the molecular mechanisms underlying protein malonylation. In this study, we constructed a deep learning (DL) network classifier based on long short-term memory (LSTM) with word embedding (LSTMWE ) for the prediction of mammalian malonylation sites. LSTMWE performs better than traditional classifiers developed with common pre-defined feature encodings or a DL classifier based on LSTM with a one-hot vector...
January 10, 2019: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30639122/discovery-of-novel-androgen-receptor-ligands-by-structure-based-virtual-screening-and-bioassays
#6
Wenfang Zhou, Mojie Duan, Weitao Fu, Jinping Pang, Qin Tang, Huiyong Sun, Lei Xu, Shan Chang, Dan Li, Tingjun Hou
Androgen receptor (AR) is a ligand-activated transcription factor that plays a pivotal role in the development and progression of many severe diseases such as prostate cancer, muscle atrophy, and osteoporosis. Binding of ligands to AR triggers the conformational changes in AR that may affect the recruitment of coactivators and downstream response of AR signaling pathway. Therefore, AR ligands have great potential to treat these diseases. In this study, we searched for novel AR ligands by performing a docking-based virtual screening (VS) on the basis of the crystal structure of the AR ligand binding domain (LBD) in complex with its agonist...
January 9, 2019: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30597257/recent-advances-in-function-based-metagenomic-screening
#7
REVIEW
Tanyaradzwa Rodgers Ngara, Houjin Zhang
Metagenomes from uncultured microorganisms are rich resources for novel enzyme genes. The methods used to screen the metagenomic libraries fall into two categories, which are based on sequence or function of the enzymes. The sequence-based approaches rely on the known sequences of the target gene families. In contrast, the function-based approaches do not involve the incorporation of metagenomic sequencing data and, therefore, may lead to the discovery of novel gene sequences with desired functions. In this review, we discuss the function-based screening strategies that have been used in the identification of enzymes from metagenomes...
December 28, 2018: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30594646/from-basic-research-to-molecular-breeding-chinese-scientists-play-a-central-role-in-boosting-world-rice-production
#8
Ding Tang, Zhukuan Cheng
On November 18, 2018, the Future Science Prize Awarding Ceremony was held in Beijing. In the area of life science, Professors Jiayang Li, Longping Yuan, and Qifa Zhang shared the prize for their pioneering contributions in producing high-yield, superior-quality rice through systematic study of molecular mechanisms associated with specific rice features and application of novel approaches in rice breeding. The Future Science Prize is also touted as "China's Nobel Prize", fully affirming their achievements in rice basic research and breeding...
December 27, 2018: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30583062/rgaat-a-reference-based-genome-assembly-and-annotation-tool-for-new-genomes-and-upgrade-of-known-genomes
#9
Wanfei Liu, Shuangyang Wu, Qiang Lin, Shenghan Gao, Feng Ding, Xiaowei Zhang, Hasan Awad Aljohi, Jun Yu, Songnian Hu
The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of version-dependent annotation files and other compatible public dataset for downstream analysis. To handle these tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool (RGAAT), a flexible toolkit for resequencing-based consensus building and annotation update...
December 21, 2018: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30578915/tels-a-novel-computational-framework-for-identifying-motif-signatures-of-transcribed-enhancers
#10
Dimitrios Kleftogiannis, Haitham Ashoor, Vladimir B Bajic
In mammalian cells, transcribed enhancers (TrEns) play important roles in the initiation of gene expression and maintenance of gene expression levels in a spatiotemporal manner. One of the most challenging questions is how the genomic characteristics of enhancers relate to enhancer activities. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers' DNA code in a more systematic way. To address this problem, we developed a novel computational framework, Transcribed Enhancer Landscape Search (TELS), aimed at identifying predictive cell type/tissue-specific motif signatures of TrEns...
December 19, 2018: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30578914/machine-learning-models-for-genetic-risk-assessment-of-infants-with-non-syndromic-orofacial-cleft
#11
Shi-Jian Zhang, Peiqi Meng, Jieni Zhang, Peizeng Jia, Jiuxiang Lin, Xiangfeng Wang, Feng Chen, Xiaoxing Wei
The isolated type of orofacial cleft, termed non-syndromic cleft lip with or without cleft palate (NSCL/P), is the second most common birth defect in China, with Asians having the highest incidence in the world. NSCL/P involves multiple genes and complex interactions between genetic and environmental factors, imposing difficulty for the genetic assessment of the unborn fetus carrying multiple NSCL/P-susceptible variants. Although genome-wide association studies (GWAS) have uncovered dozens of single nucleotide polymorphism (SNP) loci in different ethnic populations, the genetic diagnostic effectiveness of these SNPs requires further experimental validation in Chinese populations before a diagnostic panel or a predictive model covering multiple SNPs can be built...
December 19, 2018: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30578913/tica-transcriptional-interaction-and-coregulation-analyzer
#12
Stefano Perna, Pietro Pinoli, Stefano Ceri, Limsoon Wong
Transcriptional regulation is critical to cellular processes of all organisms. Regulatory mechanisms often involve more than one transcription factor (TF) from different families, binding together and attaching to the DNA as a single complex. However, only a fraction of the regulatory partners of each TF is currently known. In this paper, we present the Transcriptional Interaction and Coregulation Analyzer (TICA), a novel methodology for predicting heterotypic physical interaction of TFs. TICA employs a data-driven approach to infer interaction phenomena from chromatin immunoprecipitation and sequencing (ChIP-seq) data...
December 19, 2018: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30576740/vasc-dimension-reduction-and-visualization-of-single-cell-rna-seq-data-by-deep-variational-autoencoder
#13
Dongfang Wang, Jin Gu
Single-cell RNA sequencing (scRNA-seq) is a powerful technique to analyze the transcriptomic heterogeneities at the single cell level. It is an important step for studying cell sub-populations and lineages, with an effective low-dimensional representation and visualization of the original scRNA-Seq data. At the single cell level, the transcriptional fluctuations are much larger than the average of a cell population, and the low amount of RNA transcripts will increase the rate of technical dropout events. Therefore, scRNA-seq data are much noisier than traditional bulk RNA-seq data...
December 18, 2018: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30553884/gitar-an-open-source-tool-for-analysis-and-visualization-of-hi-c-data
#14
Riccardo Calandrelli, Qiuyang Wu, Jihong Guan, Sheng Zhong
Interactions between chromatin segments play a large role in functional genomic assays and developments in genomic interaction detection methods have shown interacting topological domains within the genome. Among these methods, Hi-C plays a key role. Here, we present the Genome Interaction Tools and Resources (GITAR), a software to perform a comprehensive Hi-C data analysis, including data preprocessing, normalization, and visualization, as well as analysis of topologically-associated domains (TADs). GITAR is composed of two main modules: (1) HiCtool, a Python library to process and visualize Hi-C data, including TAD analysis; and (2) processed data library, a large collection of human and mouse datasets processed using HiCtool...
December 13, 2018: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30553883/-development-of-the-third-generation-hybrid-rice-in-china
#15
Haiyang Wang, Xing Wang Deng
Rice is a major cereal crop for China. The development of the "three-line" hybrid rice system based on cytoplasmic male sterility in the 1970s (first-generation) and the "two-line" hybrid rice system based on photoperiod- and thermo-sensitive genic male-sterile lines (second-generation) in the 1980s has contributed significantly to rice yield increase and food security in China. Here we describe the development and implementation of the "third-generation" hybrid rice breeding system that is based on a transgenic approach to propagate and utilize stable recessive nuclear male sterile lines, and as such, the male sterile line and hybrid rice produced using such a system is non-transgenic...
December 13, 2018: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30550857/polyphyly-in-16s-rrna-based-lvtree-versus-monophyly-in-whole-genome-based-cvtree
#16
Guanghong Zuo, Ji Qi, Bailin Hao
We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequence analysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genome-based phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes by using the CVTree method, which is based on whole-genome information...
December 11, 2018: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30528693/a-scientist-guerilla-fighter-in-the-frontiers-of-bioinformatics-in-memory-of-bailin-hao
#17
EDITORIAL
Jun Yu
No abstract text is available yet for this article.
December 6, 2018: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30529286/rnf126-quenches-rnf168-function-in-the-dna-damage-response
#18
Lianzhong Zhang, Zhenzhen Wang, Ruifeng Shi, Xuefei Zhu, Jiahui Zhou, Bin Peng, Xingzhi Xu
DNA damage response (DDR) is essential for maintaining genome stability and protecting cells from tumorigenesis. Ubiquitin and ubiquitin-like modifications play an important role in DDR, from signaling DNA damage to mediating DNA repair. In this report, we found that the E3 ligase ring finger protein 126 (RNF126) was recruited to UV laser micro-irradiation-induced stripes in a RNF8-dependent manner. RNF126 directly interacted with and ubiquitinated another E3 ligase, RNF168. Overexpression of wild type RNF126, but not catalytically-inactive mutant RNF126 (CC229/232AA), diminished ubiquitination of H2A histone family member X (H2AX), and subsequent bleomycin-induced focus formation of total ubiquitin FK2, TP53-binding protein 1 (53BP1), and receptor-associated protein 80 (RAP80)...
December 4, 2018: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30472416/ancestrypainter-a-graphic-program-for-displaying-ancestry-composition-of-populations-and-individuals
#19
Qidi Feng, Dongsheng Lu, Shuhua Xu
Ancestry composition of populations and individuals has been extensively investigated in recent years due to advances in the genotyping and sequencing technologies. As the number of populations and individuals used for ancestry inference increases remarkably, say more than 100 populations or 1000 individuals, it is usually challenging to present the ancestry composition in a traditional way using a rectangular graph. To address this issue, we developed a program, AncestryPainter, which can illustrate the ancestry composition of populations and individuals with a rounded and nice-looking graph to save space...
November 22, 2018: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30268932/the-genome-of-opium-poppy-reveals-evolutionary-history-of-morphinan-pathway
#20
Yiheng Hu, Ran Zhao, Peng Xu, Yuannian Jiao
No abstract text is available yet for this article.
September 28, 2018: Genomics, Proteomics & Bioinformatics
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