journal
MENU ▼
Read by QxMD icon Read
search

Genomics

journal
https://www.readbyqxmd.com/read/28192179/genome-inside-genome-ngs-based-identification-and-assembly-of-endophytic-sphingopyxis-granuli-and-pseudomonas-aeruginosa-genomes-from-rice-genomic-reads
#1
Battu Latha, Mettu Madhavi Reddy, Burragoni Sravanthi Goud, Kayalvili Ulaganathan, Kandasamy Ulaganathan
The interactions between crop plants and the endophytic bacteria colonizing them are poorly understood and experimental methods were found to be inadequate to meet the complexities associated with the interaction. Moreover, research onendophytic bacteria was focused at host plant species level and not at cultivar level which is essential for understanding the role played by themon the productivity of specific crop genotype. High throughput genomics offers valuable tools for identification, characterization of endophytic bacteria and understand their interaction with host plants...
February 10, 2017: Genomics
https://www.readbyqxmd.com/read/28192178/identification-and-characterization-of-the-expression-profile-of-the-micrornas-in-the-amazon-species-colossoma-macropomum-by-next-generation-sequencing
#2
Fátima Gomes, Luciana Watanabe, Sérgio Nozawa, Layanna Oliveira, Jedson Cardoso, João Vianez, Márcio Nunes, Horacio Schneider, Iracilda Sampaio
Colossoma macropomum is a resistant species native of Amazonas and Orinoco river basins. It is regarded as the second largest finfish of Solimões and Amazon rivers, representing a major fishery resource in Amazonas and an important species in tropical aquaculture. MicroRNAs are non-coding endogenous riboregulators of nearly 22 nucleotides that play a key role in post-transcriptional gene regulation of several organisms. We analyzed samples of liver and skin from specimens of C. macropomum using next generation sequencing...
February 10, 2017: Genomics
https://www.readbyqxmd.com/read/28189763/analysis-of-steric-effects-in-damid-profiling-of-transcription-factor-target-genes
#3
Mirana Ramialison, Ashley J Waardenberg, Nicole Schonrock, Tram Doan, Danielle de Jong, Romaric Bouveret, Richard P Harvey
DNA adenine methyltransferase identification (DamID) is an enzymatic technology for detecting DNA regions targeted by chromatin-associated proteins. Proteins are fused to bacterial DNA adenine methyltransferase (Dam) and expressed in cultured cells or whole organisms. Here, we used DamID to detect DNA regions bound by the cardiac-restricted transcription factors (TFs) NKX2-5 and SRF, and ubiquitously-expressed co-factors ELK1 and ELK4. We compared targets bound by these TFs as N- and C-terminal fusions with Dam, for both wild type (WT) NKX2-5 and mutant proteins mimicking those found in congenital heart disease...
February 8, 2017: Genomics
https://www.readbyqxmd.com/read/28188908/hive-heptagon-a-sensible-variant-calling-algorithm-with-post-alignment-quality-controls
#4
Vahan Simonyan, Konstantin Chumakov, Eric Donaldson, Konstantinos Karagiannis, Phuc VinhNguyen Lam, Hayley Dingerdissen, Alin Voskanian
: Advances in high-throughput sequencing (HTS) technologies have greatly increased the availability of genomic data and potential discovery of clinically significant genomic variants. However, numerous issues still exist with the analysis of these data, including data complexity, the absence of formally agreed upon best practices, and inconsistent reproducibility. Toward a more robust and reproducible variant-calling paradigm, we propose a series of selective noise filtrations and post-alignment quality control (QC) techniques that may reduce the rate of false variant calls...
February 7, 2017: Genomics
https://www.readbyqxmd.com/read/28163131/evaluation-of-genome-wide-genotyping-concordance-between-tumor-tissues-and-peripheral-blood
#5
Wei Shao, Yuqiu Ge, Gaoxiang Ma, Mulong Du, Haiyan Chu, Fulin Qiang, Meiling Wang, Zhengdong Zhang
Tumor tissues were potential resources in cancer susceptibility studies. To assess the genotyping concordance between tumor tissues and peripheral blood, we conducted this study in a large sample size and genome-wide scale. Genome-wide genotypes of human colon adenocarcinoma (COAD) retrieved from The Cancer Genome Atlas (TCGA) was analyzed. A total of 387 pairs of matched fresh frozen tumor tissues and peripheral blood samples passed the quality control processes. High concordant rate (94.85% with no-calls and 97...
February 2, 2017: Genomics
https://www.readbyqxmd.com/read/28159597/gene-selection-for-microarray-cancer-classification-using-a-new-evolutionary-method-employing-artificial-intelligence-concepts
#6
M Dashtban, Mohammadali Balafar
Gene selection is a demanding task for microarray data analysis. The diverse complexity of different cancers makes this issue still challenging. In this study, a novel evolutionary method based on genetic algorithms and artificial intelligence is proposed to identify predictive genes for cancer classification. A filter method was first applied to reduce the dimensionality of feature space followed by employing an integer-coded genetic algorithm with dynamic-length genotype, intelligent parameter settings, and modified operators...
January 31, 2017: Genomics
https://www.readbyqxmd.com/read/28131802/improvements-and-impacts-of-grch38-human-reference-on-high-throughput-sequencing-data-analysis
#7
Yan Guo, Yulin Dai, Hui Yu, Shilin Zhao, David C Samuels, Yu Shyr
Analyses of high throughput sequencing data starts with alignment against a reference genome, which is the foundation for all re-sequencing data analyses. Each new release of the human reference genome has been augmented with improved accuracy and completeness. It is presumed that the latest release of human reference genome, GRCh38 will contribute more to high throughput sequencing data analysis by providing more accuracy. But the amount of improvement has not yet been quantified. We conducted a study to compare the genomic analysis results between the GRCh38 reference and its predecessor GRCh37...
January 26, 2017: Genomics
https://www.readbyqxmd.com/read/28119109/widespread-pre-translational-regulation-of-the-inclusion-of-signal-peptides-in-human-proteins
#8
Philippe Balthazar, Daniel C Tucunduva, Mikael-Jonathan Luce, Michelle S Scott
Signal peptides (SP) are cleavable N-terminal protein motifs used co-translationally for entry of nascent polypeptides into the secretory pathway. Their co-translational cleavage prevents their extensive post-translational regulation and flexibility in their usage is made possible by the control of their inclusion at a pre-translational level. To characterize this regulation on a transcriptome scale, we analyzed the level and mechanisms of inclusion of the 3298 most likely human SP-encoding genes, 47% of which alternatively express their SP...
January 21, 2017: Genomics
https://www.readbyqxmd.com/read/27974244/a-new-method-to-analyze-protein-sequence-similarity-using-dynamic-time-warping
#9
Hou Wenbing, Pan Qiuhui, Peng Qianying, He Mingfeng
Sequences similarity analysis is one of the major topics in bioinformatics. It helps researchers to reveal evolution relationships of different species. In this paper, we outline a new method to analyze the similarity of proteins by Discrete Fourier Transform (DFT) and Dynamic Time Warping (DTW). The original symbol sequences are converted to numerical sequences according to their physico-chemical properties. We obtain the power spectra of sequences from DFT and extend the spectra to the same length to calculate the distance between different sequences by DTW...
December 11, 2016: Genomics
https://www.readbyqxmd.com/read/27940149/close-genetic-relationships-between-a-spousal-pair-with-autism-affected-children-and-high-minor-allele-content-in-cases-in-autism-associated-snps
#10
Zuobin Zhu, Xitong Lu, Dejian Yuan, Shi Huang
Parents of children affected with autism spectrum disorders (ASD) often have mild forms of autistic-like characteristics. Past studies have focused on searching for individual genetic risk loci of ASD. Here we studied the overall properties of the genomes of ASD trios by using previously published genome-wide data for common SNPs. The pairwise genetic distance (PGD) between a spousal pair with ASD-affected children was found smaller than that of a random pair selected among the spouses in the ASD trios, and spousal relatedness correlated with severe forms of ASD...
January 2017: Genomics
https://www.readbyqxmd.com/read/27913251/unmapped-reads-from-cattle-rnaseq-data-a-source-for-missing-and-misassembled-sequences-in-the-reference-assemblies-and-for-detection-of-pathogens-in-the-host
#11
Tahir Usman, Frieder Hadlich, Wiebke Demasius, Rosemarie Weikard, Christa Kühn
Usually, reads from transcriptome sequencing data unmapped to the target species' reference genome are disregarded. A recent RNAseq project on the new fatal disease Bovine Neonatal Pancytopenia had indicated an unexplained immune response signature to a double-stranded RNA virus. To unravel its background, contigs were de novo assembled from unmapped RNAseq reads and aligned against the bovine genome assemblies and multispecies NCBI databases. Lack of genuine virus sequence contigs rejected the hypothesis of a live virus being causal for the unexplained immune response...
January 2017: Genomics
https://www.readbyqxmd.com/read/27913250/identification-of-non-coding-and-coding-rnas-in-porcine-endometrium
#12
Yueying Wang, Tao Hu, Lihang Wu, Xiaoran Liu, Songyi Xue, Minggang Lei
One of the most critical periods of embryonic loss in pig is day 12 of pregnancy, when implantation begins. Here, we analyzed the gene expression on day 12 of pregnancy and non-pregnancy in the porcine endometrium using RNA sequencing (RNA-seq). 237 mRNAs, 34 lncRNAs and 1 miRNA were significantly differentially expressed between the two groups. Further functional analyses were conducted to identify these differentially expressed transcripts. The results demonstrated that they participate in various biological processes, such as cell adhesion, binding, nucleic and metabolic processes...
January 2017: Genomics
https://www.readbyqxmd.com/read/27913249/comparison-of-the-transcriptomic-profile-of-hepatic-human-induced-pluripotent-stem-like-cells-cultured-in-plates-and-in-a-3d-microscale-dynamic-environment
#13
Eric Leclerc, Keiichi Kimura, Marie Shinohara, Mathieu Danoy, Morgane Le Gall, Taketomo Kido, Atsushi Miyajima, Teruo Fujii, Yasuyuki Sakai
We have compared the transcriptomic profiles of human induced pluripotent stem cells after their differentiation in hepatocytes like cells in plates and microfluidic biochips. The biochips provided a 3D and dynamic support during the cell differentiation when compared to the 2D static cultures in plates. The microarray have demonstrated the up regulation of important pathway related to liver development and maturation during the culture in biochips. Furthermore, the results of the transcriptomic profile, coupled with immunostaining, and RTqPCR analysis have shown typical biomarkers illustrating the presence of responders of biliary like cells, hepatocytes like cells, and endothelial like cells...
January 2017: Genomics
https://www.readbyqxmd.com/read/27867104/identification-of-transcripts-involved-in-digestion-detoxification-and-immune-response-from-transcriptome-of-empoasca-vitis-hemiptera-cicadellidae-nymphs
#14
En-Si Shao, Gui-Fang Lin, Sijun Liu, Xiao-Li Ma, Ming-Feng Chen, Li Lin, Song-Qing Wu, Li Sha, Zhao-Xia Liu, Xiao-Hua Hu, Xiong Guan, Ling-Ling Zhang
Tea production has been significantly impacted by the false-eye leafhopper, Empoasca vitis (Göthe), around Asia. To identify the key genes which are responsible for nutrition absorption, xenobiotic metabolism and immune response, the transcriptome of either alimentary tracts or bodies minus alimentary tract of E. vitis was sequenced and analyzed. Over 31 million reads were obtained from Illumina sequencing. De novo sequence assembly resulted in 52,182 unigenes with a mean size of 848nt. The assembled unigenes were then annotated using various databases...
January 2017: Genomics
https://www.readbyqxmd.com/read/27856224/tid-standalone-software-for-mining-putative-drug-targets-from-bacterial-proteome
#15
Reena Gupta, Dibyabhaba Pradhan, Arun Kumar Jain, Chandra Shekhar Rai
TiD is a standalone application, which relies on basic assumption that a protein must be essential for pathogens survival and non-homologous with host to qualify as putative target. With an input bacterial proteome, TiD removes paralogous proteins, picks essential ones, and excludes proteins homologous with host organisms. The targets illustrate non-homology with at least 40 out of 84 gut microbes, considered safe for human. TiD classifies proposed targets as known, novel and virulent. Users can perform pathway analysis, choke point analysis, interactome analysis, subcellular localization and functional annotations through web servers cross-referenced with the application...
January 2017: Genomics
https://www.readbyqxmd.com/read/27851990/genetic-variants-associated-with-primary-open-angle-glaucoma-in-indian-population
#16
REVIEW
Sunil Kumar, Manzoor Ahmad Malik, Sooraj K, Ramanjit Sihota, Jasbir Kaur
Glaucoma is a very common disorder of the eye wherein the disturbance of the structural or functional integrity of the optic nerve causes characteristic atrophic changes in the optic nerve, which may lead to specific visual field defects over time. Primary open angle glaucoma (POAG) is most frequent among the three principle glaucoma subtypes. With well-established role of genes like Myocilin (MYOC), Optineurin (OPTN) and WD repeat Domain 36, (WDR36), at least 29 genetic loci have been found till date to be linked to POAG...
January 2017: Genomics
https://www.readbyqxmd.com/read/27816578/distinctive-gene-expression-profile-in-women-with-history-of-postpartum-depression
#17
Anna Landsman, Rafael Aidelman, Yoav Smith, Matthew Boyko, Chaya Greenberger
Postpartum depression (PPD) is a disease which incorporates a variety of depressive states differing in nature and severity. To assist in the understanding of the pathogenesis of the disease, we aimed to ascertain a molecular mechanism underlying PPD development. We applied microarray technology to characterize gene expression of euthymic women with a history of PPD and compared the results with healthy controls. Our study demonstrated that women who considered euthymic on a clinical level, in fact, had an altered molecular profile when compared to participants with no PPD history...
January 2017: Genomics
https://www.readbyqxmd.com/read/27856225/correlations-of-vdr-and-vdbp-genetic-polymorphisms-with-susceptibility-to-adolescent-idiopathic-scoliosis-and-efficacy-of-brace-treatment
#18
Yu Wang, Zhi-Qiang Cui, Tian-Bao Luo, Long Liu
OBJECTIVE: This paper aimed to elucidate the correlations of VDR and VDBP polymorphisms with susceptibility to adolescent idiopathic scoliosis (AIS) and efficacy of brace treatment. METHODS: AIS patients and healthy controls were enrolled. Lumbar spine bone mineral density (LSBMD) and femoral neck bone mineral density (FNBMD) were detected by dual energy X-ray absorptiometry. VDR and VDBP polymorphisms were detected by PCR-RFLP. Efficacy of brace treatment was evaluated by Cobb measurement...
December 2016: Genomics
https://www.readbyqxmd.com/read/27829169/slc44a2-single-nucleotide-polymorphisms-isoforms-and-expression-association-with-severity-of-meniere-s-disease
#19
Thankam S Nair, Pavan K Kommareddi, Maria M Galano, Danielle M Miller, Bala Naveen Kakaraparthi, Steven A Telian, H Alex Arts, Hussam El-Kashlan, Alyse Kilijanczyk, Amy Anne D Lassig, Martin P Graham, Susan G Fisher, Stefan W Stoll, Rajan P Nair, James T Elder, Thomas E Carey
SLC44A2 was discovered as the target of an antibody that causes hearing loss. Knockout mice develop age related hearing loss, loss of sensory cells and spiral ganglion neurons. SLC44A2 has polymorphic sites implicated in human disease. Transfusion related acute lung injury (TRALI) is linked to rs2288904 and genome wide association studies link rs2288904 and rs9797861 to venous thromboembolism (VTE), coronary artery disease and stroke. Here we report linkage disequilibrium of rs2288904 with rs3087969 and the association of these SLC44A2 SNPs with Meniere's disease severity...
December 2016: Genomics
https://www.readbyqxmd.com/read/27826049/methylation-status-of-homeobox-genes-in-common-human-cancers
#20
REVIEW
Maria Fernanda Setúbal Destro Rodrigues, Carina Magalhães Esteves, Flávia Caló Aquino Xavier, Fabio Daumas Nunes
Approximately 300 homeobox loci were identified in the euchromatic regions of the human genome, of which 235 are probable functional genes and 65 are likely pseudogenes. Many of these genes play important roles in embryonic development and cell differentiation. Dysregulation of homeobox gene expression is a frequent occurrence in cancer. Accumulating evidence suggests that as genetics disorders, epigenetic modifications alter the expression of oncogenes and tumor suppressor genes driving tumorigenesis and perhaps play a more central role in the evolution and progression of this disease...
December 2016: Genomics
journal
journal
29719
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"