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Xiang Cheng, Xuan Xiao, Kuo-Chen Chou
Many efforts have been made in predicting the subcellular localization of eukaryotic proteins, but most of the existing methods have the following two limitations: (1) their coverage scope is less than ten locations and hence many organelles in an eukaryotic cell cannot be covered, and (2) they can only be used to deal with single-label systems in which each of the constituent proteins has one and only one location. Actually, proteins with multiple locations are particularly interesting since they may have some exceptional functions very important for in-depth understanding the biological process in a cell and for selecting drug target as well...
August 14, 2017: Genomics
Kyungmun Kim, Ju Hyeon Kim, Young Ho Kim, Seong-Eui Hong, Si Hyeock Lee
Perturbation of normal behaviors in honey bee colonies by any external factor can immediately reduce the colony's capacity for brood rearing, which can eventually lead to colony collapse. To investigate the effects of brood-rearing suppression on the biology of honey bee workers, gene-set enrichment analysis of the transcriptomes of worker bees with or without suppressed brood rearing was performed. When brood rearing was suppressed, pathways associated with both protein degradation and synthesis were simultaneously over-represented in both nurses and foragers, and their overall pathway representation profiles resembled those of normal foragers and nurses, respectively...
August 10, 2017: Genomics
Yue Wang, Tingting Xu, Weiyi He, Xiujing Shen, Qian Zhao, Jianlin Bai, Minsheng You
Long non-coding RNAs (lncRNAs) are of particular interest because of their contributions to many biological processes. Here, we present the genome-wide identification and characterization of putative lncRNAs in a global insect pest, Plutella xylostella. A total of 8096 lncRNAs were identified and classified into three groups. The average length of exons in lncRNAs was longer than that in coding genes and the GC content was lower than that in mRNAs. Most lncRNAs were flanked by canonical splice sites, similar to mRNAs...
August 5, 2017: Genomics
M Dashtban, Mohammadali Balafar, Prashanth Suravajhala
Identifying the informative genes has always been a major step in microarray data analysis. The complexity of various cancer datasets makes this issue still challenging. In this paper, a novel Bio-inspired Multi-objective algorithm is proposed for gene selection in microarray data classification specifically in the binary domain of feature selection. The presented method extends the traditional Bat Algorithm with refined formulations, effective multi-objective operators, and novel local search strategies employing social learning concepts in designing random walks...
August 3, 2017: Genomics
Guiqi Bi, Yunxiang Mao, Qikun Xing, Min Cao
Organelle phylogenomic analysis requires precisely constructed multi-gene alignment matrices concatenated by pre-aligned single gene datasets. For non-bioinformaticians, it can take days to weeks to manually create high-quality multi-gene alignments comprising tens or hundreds of homologous genes. Here, we describe a new and highly efficient pipeline, HomBlocks, which uses a homologous block searching method to construct multi-gene alignments. This approach can automatically recognize locally collinear blocks among organelle genomes and excavate phylogenetically informative regions to construct multi-gene alignment in a few hours...
August 2, 2017: Genomics
Niaz Ahmad, Zahid Mukhtar
An alarming increase in the human population necessitates doubling the world food production in the next few decades. Although a number of possible biotechnological measures are under consideration, central to these efforts is the development of transgenic crops to produce more food, and the traits with which plants could better adapt to adverse environmental conditions in a changing climate. The emergence of new tools for the introduction of foreign genes into plants has increased both our knowledge and the capacity to develop transgenic plants...
August 1, 2017: Genomics
Huiling Liu, Siddiq Ur Rahman, Yuanhui Mao, Xiaodong Xu, Shiheng Tao
Codon bias at the 5' terminal of coding sequence (CDS) is known to be distinct from the rest of the CDS. A number of events occur in this short region to regulate early translation elongation and co-translational translocation. In the genes encoding secretory proteins, there is a special signal sequence which has a higher occurrence of rare codons. In this study, we analyzed codon bias of secretory genes in several eukaryotes. The results showed that secretory genes in the species except mammals had a higher occurrence of rare codons in the 5' terminal of CDS, and the bias was greater than the same region of non-secretory genes...
August 1, 2017: Genomics
Emmanuel Quansah, Nathaniel W McGregor
There is a high burden of mental and neurological disorders in Africa. Nevertheless, there appears to be an under-representation of African ancestry populations in large-scale genomic studies. Here, we evaluated the extent of under-representation of Africans in neurogenomic studies in the GWAS Catalog. We found 569 neurogenomic studies, of which 88.9% were exclusively focused on people with European ancestry and the remaining 11.1% having African ancestry cases included. In terms of population, only 1.2% of the total populations involved in these 569 GWAS studies were of African descent...
August 1, 2017: Genomics
Qian Cong, Jinhui Shen, Wenlin Li, Dominika Borek, Zbyszek Otwinowski, Nick V Grishin
Sequencing complete genomes of all major phylogenetic groups of organisms opens unprecedented opportunities to study evolution and genetics. We report draft genomes of Calephelis nemesis and Calephelis virginiensis, representatives of the family Riodinidae. They complete the genomic coverage of butterflies at the family level. At 809 and 855 Mbp, respectively, they become the largest available Lepidoptera genomes. Comparison of butterfly genomes shows that the divergence between Riodinidae and Lycaenidae dates to the time when other families started to diverge into subfamilies...
July 27, 2017: Genomics
Vipavee Chanroj, Ratchanee Rattanawong, Thitaporn Phumichai, Sithichoke Tangphatsornruang, Kittipat Ukoskit
Latex yield and growth are the key complex traits in commercial rubber production. The present study is the first to report genome-wide association mapping of latex yield and girth, for 170 Amazonian accessions grown in a suboptimal area characterized by limited rainfall and a lengthy dry season. Targeted sequence enrichment to capture gene transcripts generated 14,155 high quality filtered single nucleotide polymorphisms (SNPs) of which 94.3% resided in coding regions. The rapid decay of linkage disequilibrium over physical and genetic distance found in the accessions was comparable to those previously reported for several outcrossing species...
July 24, 2017: Genomics
Bo Weng, Maoliang Ran, Bin Chen, Changqing He, Lianhua Dong, Fuzhi Peng
A comprehensive and systematic understanding of the roles of lncRNAs in the postnatal development of the pig testis has still not been achieved. In the present study, we obtained more than one billion clean reads and identified 15,528 lncRNA transcripts; these transcripts included 5032 known and 10,496 novel porcine lncRNA transcripts and corresponded to 10,041 lncRNA genes. Pairwise comparisons identified 449 known and 324 novel lncRNAs that showed differential expression patterns. GO and KEGG pathway enrichment analyses revealed that the targeted genes were involved in metabolic pathways regulating testis development and spermatogenesis, such as the TGF-beta pathway, the PI3K-Akt pathway, the Wnt/β-catenin pathway, and the AMPK pathway...
July 23, 2017: Genomics
Ronan F O'Toole, Sanjay S Gautam
The genome sequence of Mycobacterium tuberculosis strain H37Rv is an important and valuable reference point in the study of M. tuberculosis phylogeny, molecular epidemiology, and drug-resistance mutations. However, it is becoming apparent that use of H37Rv as a sole reference genome in analysing clinical isolates presents some limitations to fully investigating M. tuberculosis virulence. Here, we examine the presence of single locus variants and the absence of entire genes in H37Rv with respect to strains that are responsible for cases and outbreaks of tuberculosis...
July 22, 2017: Genomics
Pan Zhang, Brian D Lehmann, David C Samuels, Shilin Zhao, Ying-Yong Zhao, Yu Shyr, Yan Guo
We hypothesize that the relative mitochondria copy number (MTCN) can be estimated by comparing the abundance of mitochondrial DNA to nuclear DNA reads using high throughput sequencing data. To test this hypothesis, we examined relative MTCN across 13 breast cancer cell lines using the RT-PCR based NovaQUANT Human Mitochondrial to Nuclear DNA Ratio Kit as the gold standard. Six distinct computational approaches were used to estimate the relative MTCN in order to compare to the RT-PCR measurements. The results demonstrate that relative MTCN correlates well with the RT-PCR measurements using exome sequencing data, but not RNA-seq data...
July 19, 2017: Genomics
Hoda Mirsafian, Adiratna Mat Ripen, Wai-Mun Leong, Thamilvaani Manaharan, Saharuddin Bin Mohamad, Amir Feisal Merican
Differential gene and transcript expression pattern of human primary monocytes from healthy young subjects were profiled under different sequencing depths (50M, 100M, and 200M reads). The raw data consisted of 1.3 billion reads generated from RNA sequencing (RNA-Seq) experiments. A total of 17,657 genes and 75,392 transcripts were obtained at sequencing depth of 200M. Total splice junction reads showed an even more significant increase. Comparative analysis of the expression patterns of immune-related genes revealed a total of 217 differentially expressed (DE) protein-coding genes and 50 DE novel transcripts, in which 40 DE protein-coding genes were related to the immune system...
July 18, 2017: Genomics
Inti A Pagnuco, Juan I Pastore, Guillermo Abras, Marcel Brun, Virginia L Ballarin
It is usually assumed that co-expressed genes suggest co-regulation in the underlying regulatory network. Determining sets of co-expressed genes is an important task, based on some criteria of similarity. This task is usually performed by clustering algorithms, where the genes are clustered into meaningful groups based on their expression values in a set of experiment. In this work, we propose a method to find sets of co-expressed genes, based on cluster validation indices as a measure of similarity for individual gene groups, and a combination of variants of hierarchical clustering to generate the candidate groups...
July 8, 2017: Genomics
Amnah Siddiqa, Elisa Cirillo, Samar H K Tareen, Amjad Ali, Martina Kutmon, Lars Eijssen, Jamil Ahmad, Chris T Evelo, Susan L Coort
ANGPTL8 (Angiopoietin-like protein 8) is a newly identified hormone emerging as a novel drug target for treatment of diabetes mellitus and dyslipidemia due to its unique metabolic nature. With increasing number of studies targeting the regulation of ANGPTL8, integration of their findings becomes indispensable. This study has been conducted with the aim to collect, analyze, integrate and visualize the available knowledge in the literature about ANGPTL8 and its regulation. We utilized this knowledge to construct a regulatory pathway of ANGPTL8 which is available at WikiPathways, an open source pathways database...
July 3, 2017: Genomics
Fang-Fang Jia, Lu-Ji Zhang, Xue-Hui Pang, Xin-Xi Gu, Amro Abdelazez, Yu Liang, Si-Rui Sun, Xiang-Chen Meng
Lactobacillus plantarum KLDS1.0391 is a probiotic strain isolated from the traditional fermented dairy products and identified to produce bacteriocin against Gram-positive and Gram-negative bacteria. Previous studies showed that the strain has a high resistance to gastrointestinal stress and has a high adhesion ability to the intestinal epithelial cells (Caco-2). We reported the entire genome sequence of this strain, which contains a circular 2,886,607-bp chromosome and three circular plasmids. Genes, which are related to the biosynthesis of bacteriocins, the stress resistance to gastrointestinal tract environment and adhesive performance, were identified...
July 1, 2017: Genomics
Biswanath Chowdhury, Gautam Garai
Sequence alignment is an active research area in the field of bioinformatics. It is also a crucial task as it guides many other tasks like phylogenetic analysis, function, and/or structure prediction of biological macromolecules like DNA, RNA, and Protein. Proteins are the building blocks of every living organism. Although protein alignment problem has been studied for several decades, unfortunately, every available method produces alignment results differently for a single alignment problem. Multiple sequence alignment is characterized as a very high computational complex problem...
June 29, 2017: Genomics
S Huang, B Yang, B J Chen, N Bliim, U Ueberham, T Arendt, M Janitz
Circular RNAs (circRNAs) are a recently discovered form of RNA that has been found to regulate mammalian transcription. CircRNAs are covalently closed, single-stranded transcripts produced from precursor mRNA. While initially circRNAs were considered to be splicing artefacts, next-generation RNA sequencing of non-polyadenylated transcriptomes has recently shown that the expression of circRNAs is widespread and over 20% of expressed genes in examined cells and tissues can produce these transcripts. Until now thousands of circRNAs have been discovered in organisms ranging from Drosophila melanogaster to Homo sapiens...
June 26, 2017: Genomics
Maria Chiara Pelleri, Elena Gennari, Chiara Locatelli, Allison Piovesan, Maria Caracausi, Francesca Antonaros, Alessandro Rocca, Costanza Maria Donati, Letizia Conti, Pierluigi Strippoli, Marco Seri, Lorenza Vitale, Guido Cocchi
Among Down syndrome (DS) children, 40-50% have congenital heart disease (CHD). Although trisomy 21 is not sufficient to cause CHD, three copies of at least part of chromosome 21 (Hsa21) increases the risk for CHD. In order to establish a genotype-phenotype correlation for CHD in DS, we built an integrated Hsa21 map of all described partial trisomy 21 (PT21) cases with sufficient indications regarding presence or absence of CHD (n=107), focusing on DS PT21 cases. We suggest a DS CHD candidate region on 21q22...
June 22, 2017: Genomics
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