journal
MENU ▼
Read by QxMD icon Read
search

Genomics

journal
https://www.readbyqxmd.com/read/29935224/irspot-sf-prediction-of-recombination-hotspots-by-incorporating-sequence-based-features-into-chou-s-pseudo-components
#1
Md Abdullah Al Maruf, Swakkahr Shatabda
Recombination hotspots in a genome are unevenly distributed. Hotspots are regions in a genome that show higher rates of meiotic recombinations. Computational methods for recombination hotspot prediction often use sophisticated features that are derived from physico-chemical or structure based properties of nucleotides. In this paper, we propose iRSpot-SF that uses sequence based features which are computationally cheap to generate. Four feature groups are used in our method: k-mer composition, gapped k-mer composition, TF-IDF of k-mers and reverse complement k-mer composition...
June 20, 2018: Genomics
https://www.readbyqxmd.com/read/29908320/exploring-the-multi-drug-resistance-in-escherichia-coli-o157-h7-by-gene-interaction-network-a-systems-biology-approach
#2
Sravan Kumar Miryala, Sudha Ramaiah
In the present study, we have constructed an interaction network of 29 antibiotic resistant genes along with 777 interactions in E. coli O157:H7. Gene ontology analysis reveals that 94, 89 and 67 genes have roles in the cellular process, biological process and molecular function respectively. Gene complexes related to tripartite efflux pumps mdtEF-tolC and ABC family efflux pump macAB-tolC play key roles in multidrug efflux systems. It is noteworthy to mention that, 19 genes are involved in multi-efflux pumps and they play a significant role in multidrug resistance (MDR); while 18 genes are vital for fatty acid synthesis...
June 13, 2018: Genomics
https://www.readbyqxmd.com/read/29902512/quality-and-concordance-of-genotyping-array-data-of-12-064-samples-from-5840-cancer-patients
#3
Mingsheng Guo, Wei Yue, David C Samuels, Hui Yu, Jing He, Ying-Yong Zhao, Yan Guo
Genotyping arrays characterize genome-wide SNPs for a study cohort and were the primary technology behind genome wide association studies over the last decade. The Cancer Genome Atlas (TCGA) is one of the largest cancer consortium studies, and it collected genotyping data for all of its participants. Using TCGA SNP data genotyped using the Affymetrix 6.0 SNP array from 12,064 samples, we conducted a comprehensive comparisons across DNA sources (tumor tissue, normal tissue, and blood) and sample storage protocols (formalin-fixed paraffin-embedded (FFPE) vs...
June 11, 2018: Genomics
https://www.readbyqxmd.com/read/29885984/transcriptogenomics-identification-and-characterization-1-of-rna-editing-sites-in-human-primary-monocytes-using-high-depth-next-generation-sequencing-data
#4
Wai-Mun Leong, Adiratna Mat Ripen, Hoda Mirsafian, Saharuddin Bin Mohamad, Amir Feisal Merican
High-depth next generation sequencing data provide valuable insights into the number and distribution of RNA editing events. Here, we report the RNA editing events at cellular level of human primary monocyte using high-depth whole genomic and transcriptomic sequencing data. We identified over a ten thousand putative RNA editing sites and 69% of the sites were A-to-I editing sites. The sites enriched in repetitive sequences and intronic regions. High-depth sequencing datasets revealed that 90% of the canonical sites were edited at lower frequencies (<0...
June 7, 2018: Genomics
https://www.readbyqxmd.com/read/29879492/identification-of-six-novel-susceptibility-loci-for-dyslipidemia-using-longitudinal-exome-wide-association-studies-in-a-japanese-population
#5
Yoshiki Yasukochi, Jun Sakuma, Ichiro Takeuchi, Kimihiko Kato, Mitsutoshi Oguri, Tetsuo Fujimaki, Hideki Horibe, Yoshiji Yamada
Recent genome-wide association studies have identified various dyslipidemia-related genetic variants. However, most studies were conducted in a cross-sectional manner. We thus performed longitudinal exome-wide association studies of dyslipidemia in a Japanese population. We used ~244,000 genetic variants and clinical data of 6022 Japanese individuals who had undergone annual health checkups for several years. After quality control, the association of dyslipidemia-related phenotypes with 24,691 single nucleotide polymorphisms (SNPs) was tested using the generalized estimating equation model...
June 4, 2018: Genomics
https://www.readbyqxmd.com/read/29879491/exploring-the-selective-vulnerability-in-alzheimer-disease-using-tissue-specific-variant-analysis
#6
S Akila Parvathy Dharshini, Y-H Taguchi, M Michael Gromiha
The selective vulnerability of distinct regions of the brain is a critical factor in neurodegenerative disorders. In Alzheimer's disease (AD), neurons in hippocampus situated in medial temporal lobe are immensely damaged. Identifying tissue-specific variants is essential in order to perceive the selective vulnerability in AD. In current work, we aligned mRNA-seq data with HG19/HG38 genomic assembly and identified specific variations present in temporal, frontal and other lobes of the AD using sequence alignment map tools...
June 4, 2018: Genomics
https://www.readbyqxmd.com/read/29864461/correlations-of-il-23r-gene-polymorphism-with-clinicopathological-characteristics-and-prognosis-of-hepatocellular-carcinoma-patients-after-interventional-therapy
#7
Xin Pan, Gang Wang
In this study, we summarized the association of IL-23R gene polymorphisms with hepatocellular carcinoma (HCC). A total of 270 HCC patients were selected as HCC group, and 251 healthy individuals served as the control group. PCR-RFLP was performed to detect IL-23R gene polymorphism, including rs17375018 and rs11805303. Survival rate and risk factors of HCC were identified. The findings suggested that IL-23R rs17375018 was correlated with genetic susceptibility to HCC, and GC haplotype was closely linked with the risk factors of HCC...
June 1, 2018: Genomics
https://www.readbyqxmd.com/read/29860032/the-p53-signaling-pathway-and-colorectal-cancer-interactions-between-downstream-p53-target-genes-and-mirnas
#8
Martha L Slattery, Lila E Mullany, Roger K Wolff, Lori C Sakoda, Wade S Samowitz, Jennifer S Herrick
INTRODUCTION: We examined expression of genes in the p53-signaling pathway. We determine if genes that have significantly different expression in carcinoma tissue compared to normal mucosa also have significantly differentially expressed miRNAs. We utilize a sample of 217 CRC cases. METHODS: We focused on fold change (FC) > 1.50 or <0.67 for genes and miRNAs, that were statistically significant after adjustment for multiple comparisons. We evaluated the linear association between the differential expression of miRNA and mRNA...
May 31, 2018: Genomics
https://www.readbyqxmd.com/read/29860031/potential-of-cell-free-dna-as-a-screening-marker-for-parasite-infections-in-dog
#9
Shirin Akter, Ryo Nakao, Yuhei Imasato, Mohammad Zahangir Alam, Ken Katakura
Parasitic infections are common in stray dogs and accurate knowledge of parasite communities in dogs would provide insight into the epidemiology of parasitic diseases. In this study, we used Illumina sequencing technology to evaluate cell-free DNA (cfDNA) as a marker for screening of parasitic infections in dogs. Plasma samples from 14 stray dogs captured in Bangladesh were used in the experiments. An average of 2.3 million reads was obtained for each sample. BLASTn analysis identified 150 reads with high similarity with parasites from 19 different genera...
May 31, 2018: Genomics
https://www.readbyqxmd.com/read/29859262/functional-annotation-of-the-genome-unravels-probiotic-potential-of-bacillus-coagulans-hs243
#10
N G Kapse, A S Engineer, V Gowdaman, S Wagh, P K Dhakephalkar
Spore forming Bacillus species are widely used as probiotics for human dietary supplements and in animal feeds. However, information on genetic basis of their probiotic action is obscure. Therefore, the present investigation was undertaken to elucidate probiotic traits of B. coagulans HS243 through its genome analysis. Genome mining revealed the presence of an arsenal of marker genes attributed to genuine probiotic traits. In silico analysis of HS243 genome revealed the presence of multi subunit ATPases, ADI pathway genes, chologlycine hydrolase, adhesion proteins for surviving and colonizing harsh gastric transit...
May 30, 2018: Genomics
https://www.readbyqxmd.com/read/29857119/quality-control-and-integration-of-genotypes-from-two-calling-pipelines-for-whole-genome-sequence-data-in-the-alzheimer-s-disease-sequencing-project
#11
Adam C Naj, Honghuang Lin, Badri N Vardarajan, Simon White, Daniel Lancour, Yiyi Ma, Michael Schmidt, Fangui Sun, Mariusz Butkiewicz, William S Bush, Brian W Kunkle, John Malamon, Najaf Amin, Seung Hoan Choi, Kara L Hamilton-Nelson, Sven J van der Lee, Namrata Gupta, Daniel C Koboldt, Mohamad Saad, Bowen Wang, Alejandro Q Nato, Harkirat K Sohi, Amanda Kuzma, Li-San Wang, L Adrienne Cupples, Cornelia van Duijn, Sudha Seshadri, Gerard D Schellenberg, Eric Boerwinkle, Joshua C Bis, Josée Dupuis, William J Salerno, Ellen M Wijsman, Eden R Martin, Anita L DeStefano
The Alzheimer's Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants (indels) was performed centrally using GATK-HaplotypeCaller and Atlas V2. The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each pipeline, and developed and implemented a novel protocol, termed "consensus calling," to combine genotype calls from both pipelines into a single high-quality set...
May 29, 2018: Genomics
https://www.readbyqxmd.com/read/29857118/genome-sequence-of-the-endophytic-strain-enterobacter-sp-j49-a-potential-biofertilizer-for-peanut-and-maize
#12
Liliana Mercedes Ludueña, Maria Soledad Anzuay, Jorge Guillermo Angelini, Matthew McIntosh, Anke Becker, Oliver Rupp, Alexander Goesmann, Jochen Blom, Adriana Fabra, Tania Taurian
Enterobacter sp. J49 is a plant growth promoting endophytic strain that promotes the growth of peanut and maize crops. This strain promotes plant growth by different mechanisms with the supply of soluble phosphorus being one of the most important. Enterobacter sp. J49 not only increases the phosphorus content in the plant but also in the soil favoring the nutrition of other plants usually used in rotation with these crops. The aims of this study were to analyze the genome sequence of Enterobacter sp. J49 in order to deepen our knowledge regarding its plant growth promoting traits and to establish its phylogenetic relationship with other species of Enterobacter genus...
May 29, 2018: Genomics
https://www.readbyqxmd.com/read/29852216/gene-co-expression-network-analysis-for-identifying-genetic-markers-in-parkinson-s-disease-a-three-way-comparative-approach
#13
Gincy George, Sachidanand Singh, Sowmya Bekshe Lokappa, Jobin Varkey
Parkinson's disease (PD) is a neurodegenerative disorder involving progressive deterioration of dopaminergic neurons. Although few genetic markers for familial PD are known, the etiology of sporadic PD remains poorly understood. Microarray data was analysed for induced pluripotent stem cells (iPSCs) derived from PD patients and mature neuronal cells (mDA) differentiated from these iPSCs. Combining expression and semantic similarity, a highly-correlated PD interactome was constructed that included interactions of established Parkinson's disease marker genes...
May 28, 2018: Genomics
https://www.readbyqxmd.com/read/29842950/ploc-mgpos-predict-subcellular-localization-of-gram-positive-bacterial-proteins-by-quasi-balancing-training-dataset-and-pseaac
#14
Xuan Xiao, Xiang Cheng, Genqiang Chen, Qi Mao, Kuo-Chen Chou
Knowledge of protein subcellular localization is vitally important for both basic research and drug development. With the avalanche of protein sequences emerging in the post-genomic age, it is highly desired to develop computational tools for timely and effectively identifying their subcellular localization purely based on the sequence information alone. Recently, a predictor called "pLoc-mGpos" was developed for identifying the subcellular localization of Gram-positive bacterial proteins. Its performance is overwhelmingly better than that of the other predictors for the same purpose, particularly in dealing with multi-label systems in which some proteins, called "multiplex proteins", may simultaneously occur in two or more subcellular locations...
May 26, 2018: Genomics
https://www.readbyqxmd.com/read/29842949/evaluation-of-computational-techniques-for-predicting-non-synonymous-single-nucleotide-variants-pathogenicity
#15
Marwa S Hassan, A A Shaalan, M I Dessouky, Abdelaziz E Abdelnaiem, Mahmoud ElHefnawi
The human genetic diseases associated with many factors, one of these factors is the non-synonymous Single Nucleotide Variants (nsSNVs) cause single amino acid change with another resulting in protein function change leading to disease. Many computational techniques have been released to expect the impacts of amino acid alteration on protein function and classify mutations as pathogenic or neutral. Here in this article, we assessed the performance of eight techniques; FATHMM, SIFT, Provean, iFish, Mutation Assessor, PANTHER, SNAP2, and PON- P2 using a VaribenchSelectedPure dataset of 2144 pathogenic variants and 3777 neutral variants extracted from the free standard database "Varibench...
May 26, 2018: Genomics
https://www.readbyqxmd.com/read/29842948/gb2sequin-a-file-converter-preparing-custom-genbank-files-for-database-submission
#16
Pascal Lehwark, Stephan Greiner
The typical wet lab user often annotates smaller sequences in the GenBank format, but resulting files are not accepted for database submission by NCBI. This makes submission of such annotations a cumbersome task. Here we present "GB2sequin" an easy-to-use web application that converts custom annotations in the GenBank format into the NCBI direct submission format Sequin. Additionally, the program generates a "five-column, tab-delimited feature table" and a FASTA file. Those are required for submission through BankIt or the update of an existing GenBank entry...
May 26, 2018: Genomics
https://www.readbyqxmd.com/read/29842947/use-of-partial-least-squares-improves-the-efficacy-of-removing-unwanted-variability-in-differential-expression-analyses-based-on-rna-seq-data
#17
Sutirtha Chakraborty
RNA-Seq technology has revolutionized the face of gene expression profiling by generating read count data measuring the transcript abundances for each queried gene on multiple experimental subjects. But on the downside, the underlying technical artefacts and hidden biological profiles of the samples generate a wide variety of latent effects that may potentially distort the actual transcript/gene expression signals. Standard normalization techniques fail to correct for these hidden variables and lead to flawed downstream analyses...
May 26, 2018: Genomics
https://www.readbyqxmd.com/read/29802977/metahmm-a-webserver-for-identifying-novel-genes-with-specified-functions-in-metagenomic-samples
#18
Balázs Szalkai, Vince Grolmusz
The fast and affordable sequencing of large clinical and environmental metagenomic datasets opens up new horizons in medical and biotechnological applications. It is believed that today we have described only about 1% of the microorganisms on the Earth, therefore, metagenomic analysis mostly deals with unknown species in the samples. Microbial communities in extreme environments may contain genes with high biotechnological potential, and clinical metagenomes, related to diseases, may uncover still unknown pathogens and pathological mechanisms in known diseases...
May 23, 2018: Genomics
https://www.readbyqxmd.com/read/29792923/high-throughput-sequencing-identifies-chilling-responsive-genes-in-sweetpotato-ipomoea-batatas-lam-during-storage
#19
Zeyi Xie, Zhilin Zhou, Hongmin Li, Jingjing Yu, Jiaojiao Jiang, Zhonghou Tang, Daifu Ma, Baohong Zhang, Yonghua Han, Zongyun Li
Sweetpotato (Ipomoea batatas L.) is a globally important economic food crop. It belongs to Convolvulaceae family and origins in the tropics; however, sweetpotato is sensitive to cold stress during storage. In this study, we performed transcriptome sequencing to investigate the sweetpotato response to chilling stress during storage. A total of 110,110 unigenes were generated via high-throughput sequencing. Differentially expressed genes (DEGs) analysis showed that 18,681 genes were up-regulated and 21,983 genes were down-regulated in low temperature condition...
May 21, 2018: Genomics
https://www.readbyqxmd.com/read/29775785/integration-of-mirna-weighted-gene-co-expression-network-and-mirna-mrna-co-expression-analyses-reveals-potential-regulatory-functions-of-mirnas-in-calf-rumen-development
#20
Duy N Do, Pier-Luc Dudemaine, Bridget E Fomenky, Eveline M Ibeagha-Awemu
This study aimed to explore the roles of microRNAs (miRNAs) in calf rumen development during early life. Rumen tissues were collected from 16 calves (8 at pre-weaning and 8 at post-weaning) for miRNA-sequencing, differential expression (DE), miRNA weighted gene co-expression network (WGCNA) and miRNA-mRNA co-expression analyses. 295 miRNAs were identified. Bta-miR-143, miR-26a, miR-145 and miR-27b were the most abundantly expressed. 122 miRNAs were significantly DE between the pre- and post-weaning periods and the most up- and down-regulated miRNAs were bta-miR-29b and bta-miR-493, respectively...
May 21, 2018: 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"