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Genomics

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https://www.readbyqxmd.com/read/28442363/the-global-expression-profiling-in-esophageal-squamous-cell-carcinoma
#1
Fuqiang Dai, Longyong Mei, Shenglan Meng, Zheng Ma, Wei Guo, Jinghai Zhou, Jingge Zhang
Esophageal squamous cell carcinoma (ESCC) is the dominant subtype of esophageal cancer worldwide. This study aimed to explore the aberrant global expression profiling and construct regulatory network in ESCC for understanding tumorigenesis of ESCC. The expression pattern of long non-coding RNA (lncRNA), microRNA (miRNA) and mRNA was measured by RNA-sequencing in ESCC. Differentially expressed lncRNAs/miRNAs/mRNAs (DELs/DEMs/DEMIs) were identified in ESCC. DEMIs-DEMs network was constructed; hsa-miR-424-5p and hsa-miR-450b-5p were the hub miRNAs in the network, which negatively regulated 19 and 17 DEMs...
April 22, 2017: Genomics
https://www.readbyqxmd.com/read/28438488/whole-genome-sequencing-predicts-novel-human-disease-models-in-rhesus-macaques
#2
Benjamin N Bimber, Ranjani Ramakrishnan, Rita Cervera-Juanes, Ravi Madhira, Samuel M Peterson, Robert B Norgren, Betsy Ferguson
Rhesus macaques are an important pre-clinical model of human disease. To advance our understanding of genomic variation that may influence disease, we surveyed genome-wide variation in 21 rhesus macaques. We employed best-practice variant calling, validated with Mendelian inheritance. Next, we used alignment data from our cohort to detect genomic regions likely to produce inaccurate genotypes, potentially due to either gene duplication or structural variation between individuals. We generated a final dataset of >16 million high confidence variants, including 13 million in Chinese-origin rhesus macaques, an increasingly important disease model...
April 21, 2017: Genomics
https://www.readbyqxmd.com/read/28438487/processdriver-a-computational-pipeline-to-identify-copy-number-drivers-and-associated-disrupted-biological-processes-in-cancer
#3
Brittany Baur, Serdar Bozdag
Copy number amplifications and deletions that are recurrent in cancer samples harbor genes that confer a fitness advantage to cancer tumor proliferation and survival. One important challenge in computational biology is to separate the causal (i.e., driver) genes from passenger genes in large, aberrated regions. We propose a computational pipeline, called ProcessDriver, that prioritizes candidate drivers by relating cis genes within the copy number aberration to dysregulated trans genes and biological processes...
April 21, 2017: Genomics
https://www.readbyqxmd.com/read/28435088/improving-prediction-accuracy-using-decision-tree-based-meta-strategy-and-multi-threshold-sequential-voting-exemplified-by-mirna-target-prediction
#4
Bi Zhao, Bin Xue
Lots of computational predictors have been developed for fast and large-scale analysis of biological data. However, many of them were developed long time ago when training datasets or sets of input features were rather small. Consequently, the utility of these predictors in much large datasets, which are very common in nowadays, need to be examined carefully. In addition, with the rapid development of scientific research, the expectation on the prediction accuracy of computational predictors is continuously uplifting...
April 20, 2017: Genomics
https://www.readbyqxmd.com/read/28435087/the-complete-mitochondrial-genome-of-clostera-anachoreta-lepidoptera-notodontidae-and-phylogenetic-implications-for-noctuoidea-species
#5
Xiao-Yu Zhu, Zhao-Zhe Xin, Ying Wang, Hua-Bin Zhang, Dai-Zhen Zhang, Zheng-Fei Wang, Chun-Lin Zhou, Bo-Ping Tang, Qiu-Ning Liu
In this study, the complete mitochondrial genome (mitogenome) of Clostera anachoreta (Lepidoptera: Notodontidae) was sequenced. It comprises 15,456 base pairs (bp), including 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNA), 22 transfer RNAs (tRNA) and one non-coding control region (CR), as found in other lepidopterans. Gene order is identical to that of typical lepidopterans. There are 15 intergenic spacers ranging from 1 to 49bp, and 9 overlapping regions ranging from 1 to 8bp, occurring throughout the genome...
April 20, 2017: Genomics
https://www.readbyqxmd.com/read/28365388/comparative-analysis-of-mbd-seq-and-medip-seq-and-estimation-of-gene-expression-changes-in-a-rodent-model-of-schizophrenia
#6
Jennifer L Neary, Stephanie M Perez, Kara Peterson, Daniel J Lodge, Melanie A Carless
We conducted a comparative study of multiplexed affinity enrichment sequence methodologies (MBD-seq and MeDIP-seq) in a rodent model of schizophrenia, induced by in utero methylazoxymethanol acetate (MAM) exposure. We also examined related gene expression changes using a pooled sample approach. MBD-seq and MeDIP-seq identified 769 and 1771 differentially methylated regions (DMRs) between F2 offspring of MAM-exposed rats and saline control rats, respectively. The assays showed good concordance, with ~56% of MBD-seq-detected DMRs being identified by or proximal to MeDIP-seq DMRs...
March 29, 2017: Genomics
https://www.readbyqxmd.com/read/28347827/computational-prediction-of-functional-abortive-rna-in-e-coli
#7
Jeremy I Marcus, Soha Hassoun, Nikhil U Nair
Failure by RNA polymerase to break contacts with promoter DNA results in release of bound RNA and re-initiation of transcription. These abortive RNAs were assumed to be non-functional but have recently been shown to affect termination in bacteriophage T7. Little is known about the functional role of these RNA in other genetic models. Using a computational approach, we investigated whether abortive RNA could exert function in E. coli. Fragments generated from 3780 transcription units were used as query sequences within their respective transcription units to search for possible binding sites...
March 24, 2017: Genomics
https://www.readbyqxmd.com/read/28315383/genetic-equidistance-at-nucleotide-level
#8
Dejian Yuan, Shi Huang
The genetic equidistance phenomenon shows complex taxa to be all approximately equidistant to a less complex species in amino acid percentage identity. The overlooked mystery was re-interpreted by the maximum genetic diversity hypothesis (MGD). Here, we studied 14 proteomes and their coding DNA sequences (CDS) to see if the equidistance phenomenon also holds at the CDS level. We found that the outgroup taxon was equidistant to the two more complex taxa species. When two sister taxa were compared to human as the outgroup, the more complex taxon was closer to human, confirming species complexity to be the primary determinant of MGD...
March 14, 2017: Genomics
https://www.readbyqxmd.com/read/28286147/evaluation-and-assessment-of-read-mapping-by-multiple-next-generation-sequencing-aligners-based-on-genome-wide-characteristics
#9
Subazini Thankaswamy-Kosalai, Partho Sen, Intawat Nookaew
Massive data produced due to the advent of next-generation sequencing (NGS) technology is widely used for biological researches and medical diagnosis. The crucial step in NGS analysis is read alignment or mapping which is computationally intensive and complex. The mapping bias tends to affect the downstream analysis, including detection of polymorphisms. In order to provide guidelines to the biologist for suitable selection of aligners; we have evaluated and benchmarked 5 different aligners (BWA, Bowtie2, NovoAlign, Smalt and Stampy) and their mapping bias based on characteristics of 5 microbial genomes...
March 9, 2017: Genomics
https://www.readbyqxmd.com/read/28286146/altered-gene-expression-in-late-onset-alzheimer-s-disease-due-to-snps-within-3-utr-microrna-response-elements
#10
Jyoti Roy, Bibekanand Mallick
Late-onset Alzheimer's disease (LOAD) is a progressive and fatal neurodegenerative disease found in people older than 65years of age. Disease etiology is complex, as susceptibility has been linked to multiple gene variants conferred by single nucleotide polymorphisms (SNPs). However, the molecular mechanisms by which SNPs contribute to LOAD pathogenesis have not been extensively studied, particularly for SNPs within the 3' untranslated regions (3'UTRs), the hubs for microRNA binding. Therefore, we screened for SNPs within the 3'UTRs of LOAD-associated genes that may create or destroy microRNA response elements (MREs) and thus alter gene expression...
March 9, 2017: Genomics
https://www.readbyqxmd.com/read/28263792/a-genomic-approach-to-susceptibility-and-pathogenesis-leads-to-identifying-potential-novel-therapeutic-targets-in-androgenetic-alopecia
#11
R Dey-Rao, A A Sinha
We studied genome-wide gene expression from bald and haired scalp of individuals to evaluate pathogenic mechanisms underlying the development and progression of androgenetic alopecia (AGA). Unbiased analyses revealed a "bald pathology" based signature. Ontology enrichment analyses of the differentially expressed genes (DEGs) underscored apoptosis, cell proliferation, perturbed neurological pathways, and WNT signaling as central drivers of the hair loss process. Interactome analysis uncovered several known and novel key transcriptional regulators potentially affecting disease pathogenesis both within and "hidden" from the dataset...
March 2, 2017: Genomics
https://www.readbyqxmd.com/read/28235564/candidate-novel-long-noncoding-rnas-micrornas-and-putative-drugs-for-parkinson-s-disease-using-a-robust-and-efficient-genome-wide-association-study
#12
Zahra Mortezaei, Hossein Lanjanian, Ali Masoudi-Nejad
Parkinson's disease (PD) is a neurodegenerative disorder with serious symptoms of which, are not clearly demonstrated at the beginning stages of the disease, making treatment challenging. Understanding the genetic causes of PD can be useful for determining its mechanisms and proposing treatments and preventive methods. For different populations with different genetic backgrounds and lifestyles, genome-wide association studies (GWASs) represent a crucial approach for genetic analysis. In this study, a robust and efficient GWAS without dimensionality reduction applied to evaluate heritability and genetic causes of PD in the German and US populations...
February 21, 2017: Genomics
https://www.readbyqxmd.com/read/28215993/microrna-profiling-analysis-revealed-different-cellular-senescence-mechanisms-in-human-mesenchymal-stem-cells-derived-from-different-origin
#13
Xianhui Meng, Mengying Xue, Peng Xu, Feihu Hu, Bo Sun, Zhongdang Xiao
Mesenchymal stem cells (MSCs) from human umbilical cord (UC) and cord blood (CB) share many common properties and exhibit promising clinical potential. Cellular senescence, which induces the loss of stem cells characters and disrupts their therapeutic functions, has been demonstrated to be under the regulation of microRNAs (miRNAs). In this study, we compared the miRNA profiles in early and late passage UCMSCs and CBMSCs based on deep sequencing. 224 and 170 miRNAs were significantly altered in UCMSCs and CBMSCs respectively...
February 12, 2017: Genomics
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
#14
Latha Battu, Mettu Madhavi Reddy, Burragoni Sravanthi Goud, Kayalvili Ulaganathan, Ulaganathan Kandasamy
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 on endophytic bacteria was focused at host plant species level and not at cultivar level which is essential for understanding the role played by them on 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
#15
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
#16
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
#17
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 8, 2017: Genomics
https://www.readbyqxmd.com/read/28163131/evaluation-of-genome-wide-genotyping-concordance-between-tumor-tissues-and-peripheral-blood
#18
Wei Shao, Yuqiu Ge, Gaoxiang Ma, Mulong Du, Haiyan Chu, Fulin Qiang, Zhengdong Zhang, Meilin Wang
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
#19
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...
February 1, 2017: Genomics
https://www.readbyqxmd.com/read/28131802/improvements-and-impacts-of-grch38-human-reference-on-high-throughput-sequencing-data-analysis
#20
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
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