Genomics, Proteomics and Bioinformatics 
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This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.Machine Learning Models for Genetic Risk Assessment of Infants with Non-syndromic Orofacial Cleft
In this study, we collected blood samples from control and NSCL/P infants in Han and Uyghur Chinese populations to validate the diagnostic effectiveness of 43 candidate SNPs previously detected using GWAS. We then built predictive models with the validated SNPs using different machine learning algorithms and evaluated their prediction performance. Our results showed that logistic regression had the best performance for risk assessment according to the area under curve. Notably, defective variants in MTHFR and RBP4, two genes involved in folic acid and vitamin A biosynthesis, were found to have high contributions to NSCL/P ...
Source: Genomics, Proteomics and Bioinformatics - December 19, 2018 Category: Bioinformatics Source Type: research
TICA: Transcriptional Interaction and Coregulation Analyzer
We present our method and test it on ENCODE ChIP-seq datasets, using three cell lines as reference including HepG2, GM12878, and K562. TICA positive predictions on ENCODE ChIP-seq data are strongly enriched when compared to protein complex (CORUM) and functional interaction (BioGRID) databases. We also compare TICA against both motif/ChIP-seq based methods for physical TF−TF interaction prediction and published literature. Based on our results, TICA offers significant specificity (average 0.902) while maintaining a good recall (average 0.284) with respect to CORUM, providing a novel technique for fast analysis of regulat...
Source: Genomics, Proteomics and Bioinformatics - December 19, 2018 Category: Bioinformatics Source Type: research
Development of the “Third-Generation” Hybrid Rice in China
Publication date: Available online 13 December 2018Source: Genomics, Proteomics & BioinformaticsAuthor(s): Haiyang Wang, Xing Wang DengAbstractRice 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 bre...
Source: Genomics, Proteomics and Bioinformatics - December 14, 2018 Category: Bioinformatics Source Type: research
GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data
Publication date: Available online 13 December 2018Source: Genomics, Proteomics & BioinformaticsAuthor(s): Riccardo Calandrelli, Qiuyang Wu, Jihong Guan, Sheng ZhongAbstractInteractions 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 anal...
Source: Genomics, Proteomics and Bioinformatics - December 14, 2018 Category: Bioinformatics Source Type: research
Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree
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. And many such genera, which are polyphyletic in 16S rRNA-based trees, are well resolved as monophyletic clusters by CVTree. We believe that with genome sequencing of prokaryotes becoming a commonplace, genome-based phylogeny is doomed to play a definitive role in the construction of a natural and objective taxonomy. (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - December 12, 2018 Category: Bioinformatics Source Type: research
A Scientist Guerilla Fighter in the Frontiers of Bioinformatics —In Memory of Bailin Hao
Publication date: Available online 6 December 2018Source: Genomics, Proteomics & BioinformaticsAuthor(s): Jun Yu (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - December 7, 2018 Category: Bioinformatics Source Type: research
RNF126 Quenches RNF168 Function in the DNA Damage Response
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). Interestingly, both RNF126 overexpression and RNF126 downregulation compromise...
Source: Genomics, Proteomics and Bioinformatics - December 5, 2018 Category: Bioinformatics Source Type: research
AncestryPainter: A Graphic Program for Displaying Ancestry Composition of Populations and Individuals
Publication date: Available online 22 November 2018Source: Genomics, Proteomics & BioinformaticsAuthor(s): Qidi Feng, Dongsheng Lu, Shuhua XuAbstractAncestry 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, AncestryPaint...
Source: Genomics, Proteomics and Bioinformatics - November 23, 2018 Category: Bioinformatics Source Type: research
TSNAdb: A Database for Tumor-specific Neoantigens from Immunogenomics Data Analysis
In this study, we developed a comprehensive tumor-specific neoantigen database (TSNAdb v1.0), based on pan-cancer immunogenomic analyses of somatic mutation data and human leukocyte antigen (HLA) allele information for 16 tumor types with 7748 tumor samples from The Cancer Genome Atlas (TCGA) and The Cancer Immunome Atlas (TCIA). We predicted binding affinities between mutant/wild-type peptides and HLA class I molecules by NetMHCpan v2.8/v4.0, and presented detailed information of 3,707,562/1,146,961 potential neoantigens generated by somatic mutations of all tumor samples. Moreover, we employed recurrent mutations in comb...
Source: Genomics, Proteomics and Bioinformatics - October 4, 2018 Category: Bioinformatics Source Type: research
HCCDB: A Database of Hepatocellular Carcinoma Expression Atlas
Publication date: Available online 25 September 2018Source: Genomics, Proteomics & BioinformaticsAuthor(s): Qiuyu Lian, Shicheng Wang, Guchao Zhang, Dongfang Wang, Guijuan Luo, Jing Tang, Lei Chen, Jin GuAbstractHepatocellular carcinoma (HCC) is highly heterogeneous in nature and has been one of the most common cancer types worldwide. To ensure repeatability of identified gene expression patterns and comprehensively annotate the transcriptomes of HCC, we carefully curated 15 public HCC expression datasets that cover around 4000 clinical samples and developed the database HCCDB to serve as a one-stop online resource for exp...
Source: Genomics, Proteomics and Bioinformatics - October 4, 2018 Category: Bioinformatics Source Type: research
PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System
In this study, we curated 2444 public pathogenesis-related gene expression samples from the model plant Arabidopsis and three major crops (maize, rice, and wheat). We organized the data into a user-friendly database termed as PlaD. Currently, PlaD contains three key features. First, it provides large-scale curated data related to plant defense responses, including gene expression and gene functional annotation data. Second, it provides the visualization of condition-specific expression profiles. Third, it allows users to search co-regulated genes under the infections of various pathogens. Using PlaD, we conducted a large-s...
Source: Genomics, Proteomics and Bioinformatics - October 4, 2018 Category: Bioinformatics Source Type: research
DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning
In this study, we aimed to develop a computational tool for predicting nitration and nitrosylation sites in proteins. We first constructed four types of encoding features, including positional amino acid distributions, sequence contextual dependencies, physicochemical properties, and position-specific scoring features, to represent the modified residues. Based on these encoding features, we established a predictor called DeepNitro using deep learning methods for predicting protein nitration and nitrosylation. Using n-fold cross-validation, our evaluation shows great AUC values for DeepNitro, 0.65 for tyrosine nitration, 0....
Source: Genomics, Proteomics and Bioinformatics - October 4, 2018 Category: Bioinformatics Source Type: research
GAAD: A Gene and Autoimmiune Disease Association Database
Publication date: Available online 27 September 2018Source: Genomics, Proteomics & BioinformaticsAuthor(s): Guanting Lu, Xiaowen Hao, Wei-Hua Chen, Shijie MuAbstractAutoimmune diseases (ADs) arise from an abnormal immune response of the body against substances and tissues normally present in the body. More than a hundred of ADs have been described in the literature so far. Although their etiology remains largely unclear, various types of ADs tend to share more associated genes with other types of ADs than with non-AD types. Here we present GAAD, a gene and AD association database. In GAAD, we collected 44,762 associations ...
Source: Genomics, Proteomics and Bioinformatics - October 4, 2018 Category: Bioinformatics Source Type: research
The Genome of Opium Poppy Reveals Evolutionary History of Morphinan Pathway
Publication date: Available online 28 September 2018Source: Genomics, Proteomics & BioinformaticsAuthor(s): Yiheng Hu, Ran Zhao, Peng Xu, Yuannian Jiao (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - October 4, 2018 Category: Bioinformatics Source Type: research
Bioinformatics Commons: The Cornerstone of Life and Health Sciences
Publication date: Available online 28 September 2018Source: Genomics, Proteomics & BioinformaticsAuthor(s): Zhang Zhang, Yu Xue, Fangqing Zhao (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - October 4, 2018 Category: Bioinformatics Source Type: research
