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Genomics, Proteomics & Bioinformatics

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https://www.readbyqxmd.com/read/28024918/t-cell-repertoire-diversity-is-decreased-in-type-1-diabetes-patients
#1
Yin Tong, Zhoufang Li, Hua Zhang, Ligang Xia, Meng Zhang, Ying Xu, Zhanhui Wang, Michael W Deem, Xiaojuan Sun, Jiankui He
Type 1 diabetes mellitus (T1D) is an immune-mediated disease. The autoreactive T cells in T1D patients attack and destroy their own pancreatic cells. In order to systematically investigate the potential autoreactive T cell receptors (TCRs), we used a high-throughput immune repertoire sequencing technique to profile the spectrum of TCRs in individual T1D patients and controls. We sequenced the T cell repertoire of nine T1D patients, four type 2 diabetes (T2D) patients, and six nondiabetic controls. The diversity of the T cell repertoire in T1D patients was significantly decreased in comparison with T2D patients (P=7...
December 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28007607/reading-and-interpreting-the-histone-acylation-code
#2
EDITORIAL
Jelly H M Soffers, Xuanying Li, Susan M Abmayr, Jerry L Workman
No abstract text is available yet for this article.
December 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27998811/plant-proteins-are-smaller-because-they-are-encoded-by-fewer-exons-than-animal-proteins
#3
Obed Ramírez-Sánchez, Paulino Pérez-Rodríguez, Luis Delaye, Axel Tiessen
Protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. We found remarkable differences in protein length, exon structure, and domain count among different phylogenetic lineages. While eukaryotic proteins have an average size of 472 amino acid residues (aa), average protein sizes in plant genomes are smaller than those of animals and fungi. Proteins unique to plants are ∼81aa shorter than plant proteins conserved among other eukaryotic lineages...
December 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27965104/identification-of-risk-pathways-and-functional-modules-for-coronary-artery-disease-based-on-genome-wide-snp-data
#4
Xiang Zhao, Yi-Zhao Luan, Xiaoyu Zuo, Ye-Da Chen, Jiheng Qin, Lv Jin, Yiqing Tan, Meihua Lin, Naizun Zhang, Yan Liang, Shao-Qi Rao
Coronary artery disease (CAD) is a complex human disease, involving multiple genes and their nonlinear interactions, which often act in a modular fashion. Genome-wide single nucleotide polymorphism (SNP) profiling provides an effective technique to unravel these underlying genetic interplays or their functional involvements for CAD. This study aimed to identify the susceptible pathways and modules for CAD based on SNP omics. First, the Wellcome Trust Case Control Consortium (WTCCC) SNP datasets of CAD and control samples were used to assess the joint effect of multiple genetic variants at the pathway level, using logistic kernel machine regression model...
December 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27965103/biological-databases-for-hematology-research
#5
REVIEW
Qian Zhang, Nan Ding, Lu Zhang, Xuetong Zhao, Yadong Yang, Hongzhu Qu, Xiangdong Fang
With the advances of genome-wide sequencing technologies and bioinformatics approaches, a large number of datasets of normal and malignant erythropoiesis have been generated and made public to researchers around the world. Collection and integration of these datasets greatly facilitate basic research and clinical diagnosis and treatment of blood disorders. Here we provide a brief introduction of the most popular omics data resources of normal and malignant hematopoiesis, including some integrated web tools, to help users get better equipped to perform common analyses...
December 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27888152/an-improved-methodology-to-overcome-key-issues-in-human-fecal-metagenomic-dna-extraction
#6
Jitendra Kumar, Manoj Kumar, Shashank Gupta, Vasim Ahmed, Manu Bhambi, Rajesh Pandey, Nar Singh Chauhan
Microbes are ubiquitously distributed in nature, and recent culture-independent studies have highlighted the significance of gut microbiota in human health and disease. Fecal DNA is the primary source for the majority of human gut microbiome studies. However, further improvement is needed to obtain fecal metagenomic DNA with sufficient amount and good quality but low host genomic DNA contamination. In the current study, we demonstrate a quick, robust, unbiased, and cost-effective method for the isolation of high molecular weight (>23kb) metagenomic DNA (260/280 ratio >1...
December 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27744061/precision-medicine-what-challenges-are-we-facing
#7
Yu Xue, Eric-Wubbo Lameijer, Kai Ye, Kunlin Zhang, Suhua Chang, Xiaoyue Wang, Jianmin Wu, Ge Gao, Fangqing Zhao, Jian Li, Chunsheng Han, Shuhua Xu, Jingfa Xiao, Xuerui Yang, Xiaomin Ying, Xuegong Zhang, Wei-Hua Chen, Yun Liu, Zhang Zhang, Kun Huang, Jun Yu
No abstract text is available yet for this article.
October 12, 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27744060/broad-h3k4me3-as-a-novel-epigenetic-signature-for-normal-development-and-disease
#8
Jie Lu, Kaifu Chen
No abstract text is available yet for this article.
October 12, 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27729266/pharmacogenomics-of-drug-metabolizing-enzymes-and-transporters-relevance-to-precision-medicine
#9
Shabbir Ahmed, Zhan Zhou, Jie Zhou, Shu-Qing Chen
The interindividual genetic variations in drug metabolizing enzymes and transporters influence the efficacy and toxicity of numerous drugs. As a fundamental element in precision medicine, pharmacogenomics, the study of responses of individuals to medication based on their genomic information, enables the evaluation of some specific genetic variants responsible for an individual's particular drug response. In this article, we review the contributions of genetic polymorphisms to major individual variations in drug pharmacotherapy, focusing specifically on the pharmacogenomics of phase-I drug metabolizing enzymes and transporters...
October 8, 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27746286/cancer-precision-medicine-in-china
#10
Hui Li
No abstract text is available yet for this article.
October 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27746285/construction-and-analysis-of-functional-networks-in-the-gut-microbiome-of-type-2-diabetes-patients
#11
Lianshuo Li, Zicheng Wang, Peng He, Shining Ma, Jie Du, Rui Jiang
Although networks of microbial species have been widely used in the analysis of 16S rRNA sequencing data of a microbiome, the construction and analysis of a complete microbial gene network are in general problematic because of the large number of microbial genes in metagenomics studies. To overcome this limitation, we propose to map microbial genes to functional units, including KEGG orthologous groups and the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) orthologous groups, to enable the construction and analysis of a microbial functional network...
October 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27646134/oxford-nanopore-minion-sequencing-and-genome-assembly
#12
REVIEW
Hengyun Lu, Francesca Giordano, Zemin Ning
The revolution of genome sequencing is continuing after the successful second-generation sequencing (SGS) technology. The third-generation sequencing (TGS) technology, led by Pacific Biosciences (PacBio), is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the MinION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies (ONT)...
October 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27693548/toward-personalized-intervention-for-alzheimer-s-disease
#13
Xing Peng, Peiqi Xing, Xiuhui Li, Ying Qian, Fuhai Song, Zhouxian Bai, Guangchun Han, Hongxing Lei
Alzheimer's disease (AD) remains to be a grand challenge for the international community despite over a century of exploration. A key factor likely accounting for such a situation is the vast heterogeneity in the disease etiology, which involves very complex and divergent pathways. Therefore, intervention strategies shall be tailored for subgroups of AD patients. Both demographic and in-depth information is needed for patient stratification. The demographic information includes primarily APOE genotype, age, gender, education, environmental exposure, life style, and medical history, whereas in-depth information stems from genome sequencing, brain imaging, peripheral biomarkers, and even functional assays on neurons derived from patient-specific induced pluripotent cells (iPSCs)...
September 28, 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27497711/computational-cardiology-a-new-discipline-of-translational-research
#14
EDITORIAL
Benjamin Meder, Hugo A Katus, Andreas Keller
No abstract text is available yet for this article.
August 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27477449/personalized-computer-simulation-of-diastolic-function-in-heart-failure
#15
Ali Amr, Elham Kayvanpour, Farbod Sedaghat-Hamedani, Tiziano Passerini, Viorel Mihalef, Alan Lai, Dominik Neumann, Bogdan Georgescu, Sebastian Buss, Derliz Mereles, Edgar Zitron, Andreas E Posch, Maximilian Würstle, Tommaso Mansi, Hugo A Katus, Benjamin Meder
The search for a parameter representing left ventricular relaxation from non-invasive and invasive diagnostic tools has been extensive, since heart failure (HF) with preserved ejection fraction (HF-pEF) is a global health problem. We explore here the feasibility using patient-specific cardiac computer modeling to capture diastolic parameters in patients suffering from different degrees of systolic HF. Fifty eight patients with idiopathic dilated cardiomyopathy have undergone thorough clinical evaluation, including cardiac magnetic resonance imaging (MRI), heart catheterization, echocardiography, and cardiac biomarker assessment...
August 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27475404/the-role-of-quality-control-in-targeted-next-generation-sequencing-library-preparation
#16
Rouven Nietsch, Jan Haas, Alan Lai, Daniel Oehler, Stefan Mester, Karen S Frese, Farbod Sedaghat-Hamedani, Elham Kayvanpour, Andreas Keller, Benjamin Meder
Next-generation sequencing (NGS) is getting routinely used in the diagnosis of hereditary diseases, such as human cardiomyopathies. Hence, it is of utter importance to secure high quality sequencing data, enabling the identification of disease-relevant mutations or the conclusion of negative test results. During the process of sample preparation, each protocol for target enrichment library preparation has its own requirements for quality control (QC); however, there is little evidence on the actual impact of these guidelines on resulting data quality...
August 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27475403/absent-micrornas-in-different-tissues-of-patients-with-acquired-cardiomyopathy
#17
Christine S Siegismund, Maria Rohde, Uwe Kühl, Felicitas Escher, Heinz Peter Schultheiss, Dirk Lassner
MicroRNAs (miRNAs) can be found in a wide range of tissues and body fluids, and their specific signatures can be used to determine diseases or predict clinical courses. The miRNA profiles in biological samples (tissue, serum, peripheral blood mononuclear cells or other body fluids) differ significantly even in the same patient and therefore have their own specificity for the presented condition. Complex profiles of deregulated miRNAs are of high interest, whereas the importance of non-expressed miRNAs was ignored...
August 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27431744/comparative-gene-expression-analysis-of-mouse-and-human-cardiac-maturation
#18
Hideki Uosaki, Y-H Taguchi
Understanding how human cardiomyocytes mature is crucial to realizing stem cell-based heart regeneration, modeling adult heart diseases, and facilitating drug discovery. However, it is not feasible to analyze human samples for maturation due to inaccessibility to samples while cardiomyocytes mature during fetal development and childhood, as well as difficulty in avoiding variations among individuals. Using model animals such as mice can be a useful strategy; nonetheless, it is not well-understood whether and to what degree gene expression profiles during maturation are shared between humans and mice...
August 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27224515/comparison-of-cox-model-methods-in-a-low-dimensional-setting-with-few-events
#19
Francisco M Ojeda, Christian Müller, Daniela Börnigen, David-Alexandre Trégouët, Arne Schillert, Matthias Heinig, Tanja Zeller, Renate B Schnabel
Prognostic models based on survival data frequently make use of the Cox proportional hazards model. Developing reliable Cox models with few events relative to the number of predictors can be challenging, even in low-dimensional datasets, with a much larger number of observations than variables. In such a setting we examined the performance of methods used to estimate a Cox model, including (i) full model using all available predictors and estimated by standard techniques, (ii) backward elimination (BE), (iii) ridge regression, (iv) least absolute shrinkage and selection operator (lasso), and (v) elastic net...
August 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27132144/a-biobank-for-long-term-and-sustainable-research-in-the-field-of-congenital-heart-disease-in-germany
#20
REVIEW
Thomas Pickardt, Eva Niggemeyer, Ulrike M M Bauer, Hashim Abdul-Khaliq
Congenital heart disease (CHD) is the most frequent birth defect (0.8%-1% of all live births). Due to the advance in prenatal and postnatal early diagnosis and treatment, more than 90% of these patients survive into adulthood today. However, several mid- and long-term morbidities are dominating the follow-up of these patients. Due to the rarity and heterogeneity of the phenotypes of CHD, multicenter registry-based studies are required. The CHD-Biobank was established in 2009 with the aim to collect DNA from patients and their parents (trios) or from affected families, as well as cardiovascular tissues from patients undergoing corrective heart surgery for cardiovascular malformations...
August 2016: Genomics, Proteomics & Bioinformatics
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