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https://www.readbyqxmd.com/read/28227225/integration-of-snps-fmri-methylation-data-with-sparse-multi-cca-for-schizophrenia-study
#1
Wenxing Hu, Dongdong Lin, Vince D Calhoun, Yu-Ping Wang, Wenxing Hu, Dongdong Lin, Vince D Calhoun, Yu-Ping Wang, Vince D Calhoun, Yu-Ping Wang, Wenxing Hu, Dongdong Lin
Schizophrenia (SZ) is a complex mental disorder associated with genetic variations, brain development and activities, and environmental factors. There is an increasing interest in combining genetic, epigenetic and neuroimaging datasets to explore different level of biomarkers for the correlation and interaction between these diverse factors. Sparse Multi-Canonical Correlation Analysis (sMCCA) is a powerful tool that can analyze the correlation of three or more datasets. In this paper, we propose the sMCCA model for imaging genomics study...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226770/a-multiscale-model-based-analysis-of-the-multi-tissue-interplay-underlying-blood-glucose-regulation-in-type-i-diabetes
#2
Federico Wadehn, Stephan Schaller, Thomas Eissing, Markus Krauss, Lars Kupfer, Federico Wadehn, Stephan Schaller, Thomas Eissing, Markus Krauss, Lars Kupfer, Federico Wadehn, Markus Krauss, Lars Kupfer, Stephan Schaller, Thomas Eissing
A multiscale model for blood glucose regulation in diabetes type I patients is constructed by integrating detailed metabolic network models for fat, liver and muscle cells into a whole body physiologically-based pharmacokinetic/pharmacodynamic (pBPK/PD) model. The blood glucose regulation PBPK/PD model simulates the distribution and metabolization of glucose, insulin and glucagon on an organ and whole body level. The genome-scale metabolic networks in contrast describe intracellular reactions. The developed multiscale model is fitted to insulin, glucagon and glucose measurements of a 48h clinical trial featuring 6 subjects and is subsequently used to simulate (in silico) the influence of geneknockouts and drug-induced enzyme inhibitions on whole body blood glucose levels...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226412/rage-polymorphisms-and-oxidative-stress-levels-in-hashimoto-s-thyroiditis
#3
Maria Giannakou, Katerina Saltiki, Emily Mantzou, Eleni Loukari, Georgios Philippou, Konstantinos Terzidis, Kiriaki Lili, Charalampos Stavrianos, Miltiades Kyprianou, Maria Alevizaki
BACKGROUND: Polymorphisms of the receptor for advanced glycation end products (RAGE) gene have been studied in various autoimmune disorders, but not in Hashimoto's thyroiditis. Also, increased oxidative stress has been described in patients with Hashimoto's thyroiditis. The aim of the present study was to investigate the possible role of two common RAGE polymorphisms (-429T>C, -374T>A) in Hashimoto's thyroiditis; in parallel we studied oxidative stress levels. MATERIALS AND METHODS: 300 consecutive euthyroid women were examined and classified into three groups: Hashimoto's thyroiditis with treatment (n=96), Hashimoto's thyroiditis without treatment (n=109) and controls (n=95)...
February 22, 2017: European Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28226268/recent-progress-in-diatom-genomics-and-epigenomics
#4
REVIEW
Leila Tirichine, Achal Rastogi, Chris Bowler
Diatoms are one of the most diverse and successful groups of phytoplankton at the base of the food chain, sustaining life in the ocean and performing vital biogeochemical functions. The last fifteen years have witnessed the comprehensive analysis of several diatom genomes, revealing that they bear traces of their endosymbiotic origins from algal and heterotrophic ancestors, as well as significant gene transfer from bacteria. Their chimeric genomes are further regulated by a range of chromatin-based processes that are characteristic of both plant and animal genomes...
February 19, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28225946/the-intellectual-developmental-disorders-mexico-study-situational-diagnosis-burden-genomics-and-intervention-proposal
#5
Eduardo Lazcano-Ponce, Gregorio Katz, Rocío Rodríguez-Valentín, Filipa de Castro, Betania Allen-Leigh, María Elena Márquez-Caraveo, Miguel Ángel Ramírez-García, Eduardo Arroyo-García, María Elena Medina-Mora, Gustavo Ángeles, José Edmundo Urquieta-Salomón, Luis Salvador-Carulla
Objective: This study aims to generate evidence on intellectual development disorders (IDD) in Mexico. Materials and methods: IDD disease burden will be estimated with a probabilistic model, using population-based surveys. Direct and indirect costs of catastrophic expenses of families with a member with an IDD will be evaluated. Genomic characterization of IDD will include: sequencing participant exomes and performing bioinformatics analyses to identify de novo or inherited variants through trio analysis; identifying genetic variants associated with IDD, and validating randomly selected variants by polymerase chain reaction (PCR) and sequencing or real-time quantitative PCR (qPCR)...
November 2016: Salud Pública de México
https://www.readbyqxmd.com/read/28225828/systematic-analysis-of-non-structural-protein-features-for-the-prediction-of-ptm-function-potential-by-artificial-neural-networks
#6
Henry M Dewhurst, Matthew P Torres
Post-translational modifications (PTMs) provide an extensible framework for regulation of protein behavior beyond the diversity represented within the genome alone. While the rate of identification of PTMs has rapidly increased in recent years, our knowledge of PTM functionality encompasses less than 5% of this data. We previously developed SAPH-ire (Structural Analysis of PTM Hotspots) for the prioritization of eukaryotic PTMs based on function potential of discrete modified alignment positions (MAPs) in a set of 8 protein families...
2017: PloS One
https://www.readbyqxmd.com/read/28225791/characterization-of-long-noncoding-rna-and-messenger-rna-signatures-in-melanoma-tumorigenesis-and-metastasis
#7
Siqi Wang, Wenliang Fan, Bing Wan, Mengqi Tu, Feng Jin, Fang Liu, Haibo Xu, Ping Han
The incidence of melanoma, the most aggressive and life-threatening form of skin cancer, has significantly risen over recent decades. Therefore, it is essential to identify the mechanisms that underlie melanoma tumorigenesis and metastasis and to explore novel and effective melanoma treatment strategies. Accumulating evidence s uggests that aberrantly expressed long noncoding RNAs (lncRNAs) have vital functions in multiple cancers. However, lncRNA functions in melanoma tumorigenesis and metastasis remain unclear...
2017: PloS One
https://www.readbyqxmd.com/read/28225788/molecular-detection-and-genotyping-of-enteroviruses-from-csf-samples-of-patients-with-suspected-sepsis-like-illness-and-or-aseptic-meningitis-from-2012-to-2015-in-west-bank-palestine
#8
Kamal Dumaidi, Amer Al-Jawabreh
BACKGROUND: Human enteroviruses (HEVs) are the most frequently reported cause of aseptic meningitis with or without CSF pleocytosis in childhood. Rapid detection and genotype of HEVs is essential to determine the causative agent and variant causing sepsis-like illness and/or aseptic meningitis. AIM: To investigate the molecular epidemiology of enteroviruses (EVs) among patients with sepsis-like illness and/or aseptic meningitis admitted to three major hospitals in West Bank, Palestine from 2012 to 2015...
2017: PloS One
https://www.readbyqxmd.com/read/28225089/the-hidden-perils-of-read-mapping-as-a-quality-assessment-tool-in-genome-sequencing
#9
B Lehri, A M Seddon, A V Karlyshev
This article provides a comparative analysis of the various methods of genome sequencing focusing on verification of the assembly quality. The results of a comparative assessment of various de novo assembly tools, as well as sequencing technologies, are presented using a recently completed sequence of the genome of Lactobacillus fermentum 3872. In particular, quality of assemblies is assessed by using CLC Genomics Workbench read mapping and Optical mapping developed by OpGen. Over-extension of contigs without prior knowledge of contig location can lead to misassembled contigs, even when commonly used quality indicators such as read mapping suggest that a contig is well assembled...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28225085/aidp-a-novel-n-acyl-homoserine-lactonase-gene-from-antarctic-planococcus-sp
#10
Wah Seng See-Too, Robson Ee, Yan-Lue Lim, Peter Convey, David A Pearce, Wai-Fong Yin, Kok-Gan Chan
Planococcus is a Gram-positive halotolerant bacterial genus in the phylum Firmicutes, commonly found in various habitats in Antarctica. Quorum quenching (QQ) is the disruption of bacterial cell-to-cell communication (known as quorum sensing), which has previously been described in mesophilic bacteria. This study demonstrated the QQ activity of a psychrotolerant strain, Planococcus versutus strain L10.15(T), isolated from a soil sample obtained near an elephant seal wallow in Antarctica. Whole genome analysis of this bacterial strain revealed the presence of an N-acyl homoserine lactonase, an enzyme that hydrolyzes the ester bond of the homoserine lactone of N-acyl homoserine lactone (AHLs)...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28225033/rapid-and-reliable-detection-of-nonsyndromic-hearing-loss-mutations-by-multicolor-melting-curve-analysis
#11
Xudong Wang, Yongjun Hong, Peihong Cai, Ning Tang, Ying Chen, Tizhen Yan, Yinghua Liu, Qiuying Huang, Qingge Li
Hearing loss is a common birth defect worldwide. The GJB2, SLC26A4, MT-RNR1 and MT-TS1 genes have been reported as major pathogenic genes in nonsyndromic hearing loss. Early genetic screening is recommended to minimize the incidence of hearing loss. We hereby described a multicolor melting curve analysis (MMCA)-based assay for simultaneous detection of 12 prevalent nonsyndromic hearing loss-related mutations. The three-reaction assay could process 30 samples within 2.5 h in a single run on a 96-well thermocycler...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28224923/high-throughput-sequencing-reveals-modulation-of-micrornas-in-vigna-mungo-upon-mungbean-yellow-mosaic-india-virus-inoculation-highlighting-stress-regulation
#12
Anirban Kundu, Sujay Paul, Avishek Dey, Amita Pal
MicroRNAs (miRNAs) are 20-24 nucleotides long non-coding RNAs known to play important regulatory roles during biotic and abiotic stresses by controlling gene expression. Blackgram (Vigna mungo), an economically important grain legume is highly susceptible to pathogenic begomovirus Mungbean Yellow Mosaic India Virus (MYMIV) and resulting in high yield loss. In this study two different leaf-small-RNA libraries were prepared from the pooled RNA at three different time points of resistant V. mungo inbred line VM84 inoculated either with viruliferous or non-viruliferous whiteflies carrying MYMIV and performed high-throughput Illumina sequencing...
April 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28224759/genomic-variants-at-20p11-associated-with-body-fat-mass-in-the-european-population
#13
Yu-Fang Pei, Hai-Gang Ren, Lu Liu, Xiao Li, Chen Fang, Yun Huang, Wen-Zhu Hu, Wei-Wen Kong, An-Ping Feng, Xin-Yi You, Wen Zhao, Hui Shen, Qing Tian, Yong-Hong Zhang, Hong-Wen Deng, Lei Zhang
OBJECTIVE: Body fat mass (BFM) is more homogeneous and accurate than body total mass in measuring obesity but has rarely been studied. Aiming to uncover the genetic basis of fat-induced obesity, a genome-wide association meta-analysis of BFM, after adjustment by body lean mass, was performed in the European population. METHODS: Three samples of European ancestry were included in the meta-analysis: the Framingham Heart Study (N = 6,004), the Kansas City osteoporosis study (N = 2,207), and the Omaha osteoporosis study (N = 968)...
February 22, 2017: Obesity
https://www.readbyqxmd.com/read/28224712/a-novel-astrovirus-associated-with-encephalitis-and-ganglionitis-in-domestic-sheep
#14
F Pfaff, K Schlottau, S Scholes, A Courtenay, B Hoffmann, D Höper, M Beer
In June 2013, a 4-year-old Welsh Mountain ewe and in March 2014 a 10-day-old lamb of the same breed and the same flock presented progressive neurological signs including depressed sensorium, tremor, and unusual behaviour. Neuropathological examination of the brain and spinal cord detected non-suppurative polioencephalomyelitis and dorsal root ganglionitis, characteristic of a neurotropic viral agent in both sheep. Metagenomic analysis of different tissue samples from both animals identified a novel Ovine Astrovirus (OvAstV)...
February 22, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/28224650/androgen-receptor-splice-variants-are-not-substrates-of-nonsense-mediated-decay
#15
Atinuke S Ajiboye, David Esopi, Srinivasan Yegnasubramanian, Samuel R Denmeade
BACKGROUND: Androgen receptor (AR) splice variants have been clinically associated with progressive cancer, castration-resistance, and resistance to AR antagonists and androgen synthesis inhibitors. AR variants can be generated by genomic alterations and alternative splicing, and their expression is androgen-regulated. There has been a suggestion that AR variants bearing premature termination codons and coding for truncated proteins should be regulated by the nonsense-mediated decay (NMD) mRNA surveillance pathway, suggesting that either the NMD pathway is dysfunctional in variant-expressing cell lines or that variants are somehow able to evade degradation by NMD...
February 22, 2017: Prostate
https://www.readbyqxmd.com/read/28224622/slc2a3-single-nucleotide-polymorphism-and-duplication-influence-cognitive-processing-and-population-specific-risk-for-attention-deficit-hyperactivity-disorder
#16
Sören Merker, Andreas Reif, Georg C Ziegler, Heike Weber, Ute Mayer, Ann-Christine Ehlis, Annette Conzelmann, Stefan Johansson, Clemens Müller-Reible, Indrajit Nanda, Thomas Haaf, Reinhard Ullmann, Marcel Romanos, Andreas J Fallgatter, Paul Pauli, Tatyana Strekalova, Charline Jansch, Alejandro Arias Vasquez, Jan Haavik, Marta Ribasés, Josep Antoni Ramos-Quiroga, Jan K Buitelaar, Barbara Franke, Klaus-Peter Lesch
BACKGROUND: Attention-deficit/hyperactivity disorder (ADHD) is a common, highly heritable neurodevelopmental disorder with profound cognitive, behavioral, and psychosocial impairments with persistence across the life cycle. Our initial genome-wide screening approach for copy number variants (CNVs) in ADHD implicated a duplication of SLC2A3, encoding glucose transporter-3 (GLUT3). GLUT3 plays a critical role in cerebral glucose metabolism, providing energy for the activity of neurons, which, in turn, moderates the excitatory-inhibitory balance impacting both brain development and activity-dependent neural plasticity...
February 22, 2017: Journal of Child Psychology and Psychiatry, and Allied Disciplines
https://www.readbyqxmd.com/read/28224499/finding-rna-protein-interaction-sites-using-hmms
#17
Tao Wang, Jonghyun Yun, Yang Xie, Guanghua Xiao
RNA-binding proteins play important roles in the various stages of RNA maturation through binding to its target RNAs. Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) has made it possible to identify the targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Several Hidden Markov model-based (HMM) approaches have been suggested to identify protein-RNA binding sites from CLIP-Seq datasets. In this chapter, we describe how HMM can be applied to analyze CLIP-Seq datasets, including the bioinformatics preprocessing steps to extract count information from the sequencing data before HMM and the downstream analysis steps following peak-calling...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28224497/hidden-markov-models-in-population-genomics
#18
Julien Y Dutheil
With the advent of sequencing techniques population genomics took a major shift. The structure of data sets has evolved from a sample of a few loci in the genome, sequenced in dozens of individuals, to collections of complete genomes, virtually comprising all available loci. Initially sequenced in a few individuals, such genomic data sets are now reaching and even exceeding the size of traditional data sets in the number of haplotypes sequenced. Because all loci in a genome are not independent, this evolution of data sets is mirrored by a methodological change...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28224251/complete-genome-sequence-of-sunflower-ring-blotch-virus-a-new-potyvirus-infecting-sunflower-in-argentina
#19
Dariel Cabrera Mederos, Nicolás Bejerman, Verónica Trucco, Soledad de Breuil, Sergio Lenardon, Fabián Giolitti
The complete genome sequence of sunflower ring blotch virus (SuRBV), a previously undescribed potyvirus infecting sunflower in Argentina, is reported. The SuRBV genome comprises 9555 nucleotides (nt) and encodes a polyprotein of 3061 amino acids, flanked by 5' and 3' untranslated regions of 117 and 255 nt, respectively. Phylogenetic analysis showed that SuRBV belongs to the potato virus Y (PVY) subgroup and clusters together with sunflower chlorotic mottle virus and bidens mosaic virus. Percentage nucleotide identity between the whole genomes of SuRBV and BiMV was 70...
February 21, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28224116/persistence-of-functional-protein-domains-in-mycoplasma-species-and-their-role-in-host-specificity-and-synthetic-minimal-life
#20
Tjerko Kamminga, Jasper J Koehorst, Paul Vermeij, Simen-Jan Slagman, Vitor A P Martins Dos Santos, Jetta J E Bijlsma, Peter J Schaap
Mycoplasmas are the smallest self-replicating organisms and obligate parasites of a specific vertebrate host. An in-depth analysis of the functional capabilities of mycoplasma species is fundamental to understand how some of simplest forms of life on Earth succeeded in subverting complex hosts with highly sophisticated immune systems. In this study we present a genome-scale comparison, focused on identification of functional protein domains, of 80 publically available mycoplasma genomes which were consistently re-annotated using a standardized annotation pipeline embedded in a semantic framework to keep track of the data provenance...
2017: Frontiers in Cellular and Infection Microbiology
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