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clinical bioinformatics

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https://www.readbyqxmd.com/read/29909209/circular-rna-in-invasive-and-recurrent-clinical-nonfunctioning-pituitary-adenomas-expression-profiles-and-bioinformatic-analysis
#1
Jianpeng Wang, Dong Wang, Dehong Wan, Qingxia Ma, Qian Liu, Jiye Li, Zhaojian Li, Yang Gao, Guohui Jiang, Leina Ma, Jia Liu, Chuzhong Li
BACKGROUND: The invasion and recurrence of clinical nonfunctioning pituitary adenomas (NFA) often lead to surgical treatment failure. Circular RNAs (circRNAs) are a novel class of RNAs whose 3' and 5' ends are joined together and have been shown to play important roles in cancer development. Up to now, the roles of circRNAs remain unclear in invasive and recurrent NFA. METHODS: We detected and summarized the circRNA expression pattern in 75 NFA tissues from 10 non-invasive cases and 65 invasive cases and 9 pairs NFA tumor tissues from 9 recurrent cases by circRNA microarrays...
June 14, 2018: World Neurosurgery
https://www.readbyqxmd.com/read/29907797/a-comprehensive-iterative-approach-is-highly-effective-in-diagnosing-individuals-who-are-exome-negative
#2
Vandana Shashi, Kelly Schoch, Rebecca Spillmann, Heidi Cope, Queenie K-G Tan, Nicole Walley, Loren Pena, Allyn McConkie-Rosell, Yong-Hui Jiang, Nicholas Stong, Anna C Need, David B Goldstein
PURPOSE: Sixty to seventy-five percent of individuals with rare and undiagnosed phenotypes remain undiagnosed after exome sequencing (ES). With standard ES reanalysis resolving 10-15% of the ES negatives, further approaches are necessary to maximize diagnoses in these individuals. METHODS: In 38 ES negative patients an individualized genomic-phenotypic approach was employed utilizing (1) phenotyping; (2) reanalyses of FASTQ files, with innovative bioinformatics; (3) targeted molecular testing; (4) genome sequencing (GS); and (5) conferring of clinical diagnoses when pathognomonic clinical findings occurred...
June 15, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29905358/-molecular-understanding-of-hearing-how-does-this-matter-to-the-hearing-impaired
#3
Tobias Moser
This review addresses the advances of our molecular understanding of hearing and how this benefits the hearing impaired. Classical biochemical methods usually fall short in contributing to the analysis of the molecular mechanisms of hearing e. g. in the cochlea, the auditory part of the inner ear, due to the scarcity of the cells of interest. Genetics, molecular cell biology, and physiology, on the other hand, have elucidated the intricate molecular and cellular mechanisms that bring about the outstanding performance of the auditory system...
March 2018: Laryngo- Rhino- Otologie
https://www.readbyqxmd.com/read/29901616/a-novel-dmd-splicing-mutation-found-in-a-family-responsible-for-x-linked-dilated-cardiomyopathy-with-hyper-ckemia
#4
Jin Tang, Xueqin Song, Guang Ji, Hongran Wu, Shuyan Sun, Shan Lu, Yuan Li, Chi Zhang, Huiqing Zhang
This study was aimed to detect a new mutation responsible for X-linked dilated cardiomyopathy with hyper-CKemia.We studied a proband who presented with cardiac symptoms with hyper-CKemia, but no clinical skeletal involvement in physical examination, laboratory tests, electromyography, echocardiography, and magnetic resonance imaging (MRI) of cardiac muscles. Muscle biopsy for histopathology and immunohistochemistry for accessing sarcolemma changes. The next-generation sequencing and bioinformatics analysis were performed on the patient and Sanger sequencing was confirmed on the other 6 unaffected families...
June 2018: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29901177/microrna%C3%A2-574-inhibits-cell-proliferation-and-invasion-in-glioblastoma-multiforme-by-directly-targeting-zinc-finger-e%C3%A2-box%C3%A2-binding-homeobox-1
#5
Youyan Mao, Fangmeng Wei, Chenghong Wei, Chengjun Wei
Accumulated evidence has demonstrated that dysregulation of microRNAs (miRNAs) contributes to tumourigenesis and tumour development of glioblastoma multiforme (GBM). Therefore, miRNAs may be promising candidates in the development of prognosis biomarkers and effective therapeutic targets for patients with GBM. A number of studies have reported that miRNA‑574 (miR‑574) is aberrantly expressed in multiple types of human cancers. However, the expression pattern, biological functions and molecular mechanism of miR‑574 in GBM are yet to be elucidated...
May 31, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29901159/system-analysis-of-teratozoospermia-mrna-profile-based-on-integrated-bioinformatics-tools
#6
Tiancheng Zhang, Jun Wu, Caihua Liao, Zhong Ni, Jufen Zheng, Fudong Yu
mRNA has an important role in spermatogenesis and the maintenance of fertility, and may act as a potential biomarker for the clinical diagnosis of infertility. In the present study, potential biomarkers associated with teratozoospermia were screened through systemic bioinformatics analysis. Initially, genome‑wide expression profiles were downloaded from the Gene Expression Omnibus and primary analysis was conducted using R software, which included preprocessing of raw microarray data, transformation between probe ID and gene symbol and identification of differentially expressed genes...
May 31, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29901144/expression-of-vitamin-d-receptor-in-bronchial-asthma-and-its-bioinformatics-prediction
#7
Lishen Shan, Xinyuan Kang, Fen Liu, Xuxu Cai, Xiaohua Han, Yunxiao Shang
Vitamin D receptors (VDRs) are associated with the occurrence and development of asthma. The aim of the present study was to analyze the secondary structure and B‑cell and T‑cell epitopes of VDR using online prediction software and aid in the future development of a highly efficient epitope‑based vaccine against asthma. Blood samples were collected from peripheral blood of asthmatic children. Reverse transcription quantitative‑polymerase chain reaction (RT‑qPCR) was performed to detect the expression of VDR in the peripheral blood...
June 13, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29901134/identification-and-functional-analysis-of-differentially-expressed-genes-associated-with-cerebral-ischemia-reperfusion-injury-through-bioinformatics-methods
#8
Xiaoli Shao, Wangxiao Bao, Xiaoqin Hong, Huihua Jiang, Zhi Yu
Cerebral ischemia/reperfusion (I/R) injury results in detrimental complications. However, little is known about the underlying molecular mechanisms involved in the reperfusion stage. The aim of the present study was to identify a gene expression profile associated with cerebral ischemia/reperfusion injury. The GSE23160 dataset, which comprised data from sham control samples and post‑I/R injury brain tissues that were obtained using a middle cerebral artery occlusion (MCAO) model at 2, 8 and 24 h post‑reperfusion, was downloaded from the Gene Expression Omnibus database...
June 6, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29898651/mutational-signatures-in-cancer-musica-a-web-application-to-implement-mutational-signatures-analysis-in-cancer-samples
#9
Marcos Díaz-Gay, Maria Vila-Casadesús, Sebastià Franch-Expósito, Eva Hernández-Illán, Juan José Lozano, Sergi Castellví-Bel
BACKGROUND: Mutational signatures have been proved as a valuable pattern in somatic genomics, mainly regarding cancer, with a potential application as a biomarker in clinical practice. Up to now, several bioinformatic packages to address this topic have been developed in different languages/platforms. MutationalPatterns has arisen as the most efficient tool for the comparison with the signatures currently reported in the Catalogue of Somatic Mutations in Cancer (COSMIC) database. However, the analysis of mutational signatures is nowadays restricted to a small community of bioinformatic experts...
June 14, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29897414/conics-integrates-scrna-seq-with-dna-sequencing-to-map-gene-expression-to-tumor-sub-clones
#10
Sören Müller, Ara Cho, Siyuan J Liu, Daniel A Lim, Aaron Diaz
Motivation: Single-cell RNA-sequencing (scRNA-seq) has enabled studies of tissue composition at unprecedented resolution. However, the application of scRNA-seq to clinical cancer samples has been limited, partly due to a lack of scRNA-seq algorithms that integrate genomic mutation data. Results: To address this, we present. CONICS: COpy-Number analysis In single-Cell RNA-Sequencing. CONICS is a software tool for mapping gene expression from scRNA-seq to tumor clones and phylogenies, with routines enabling: the quantitation of copy-number alterations in scRNA-seq, robust separation of neoplastic cells from tumor-infiltrating stroma, inter-clone differential-expression analysis, and intra-clone co-expression analysis...
April 20, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29897412/mirnacancermap-an-integrative-web-server-inferring-mirna-regulation-network-for-cancer
#11
Yin Tong, Beibei Ru, Jiangwen Zhang
Summary: MicroRNAs play critical roles in oncogenesis by targeting a few key regulators or a large cohort of genes impinging on downstream signaling pathways. Conversely, miRNA activity is also titrated by ceRNA such as lncRNA with sponge effect. Web-based server, miRNACancerMap, aims to unravel lncRNA-miRNA-mRNA tripartite complexity to predict the function and clinical relevance of miRNA with network perspective. In conjunction with large-scale data and information integration, miRNACancerMap implements various algorithms and pipelines to construct dynamic miRNA-centered network with rigorous Systems Biology approaches and the state-of-the-art visualization tool...
April 20, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29897411/comorbidity-an-r-package-for-the-systematic-analysis-of-disease-comorbidities
#12
Alba Gutiérrez-Sacristán, Àlex Bravo, Alexia Giannoula, Miguel A Mayer, Ferran Sanz, Laura I Furlong
Motivation: The study of comorbidities is a major priority due to their impact on life expectancy, quality of life and healthcare cost. The availability of electronic health records for data mining offers the opportunity to discover disease associations and comorbidity patterns from the clinical history of patients gathered during routine medical care. This opens the need for analytical tools for detection of disease comorbidities, including the investigation of their underlying genetic basis...
April 20, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29896738/-immune-dysregulation-polyendocrinopathy-enteropathy-x-linked-syndrome-in-two-cases
#13
Qiong Zhu, Ke Yuan, Chunlin Wang, Yanlan Fang, Jianfang Zhu, Li Liang
OBJECTIVE: To report on two cases affected with immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome (IPEX). METHODS: Two unrelated Chinese infants affected with IPEX were investigated. Case 1 was a 4-month-old boy with neonatal diabetes and severe enteropathy. Case 2 was a 6-day newborn boy with neonatal diabetes and ketoacidosis. DNA samples of the two infants and their parents were sequenced for FOXP3 gene mutations. Suspected mutations were verified among 100 unrelated healthy controls...
June 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/29896303/mmp1-par1-sp-nk1r-paracrine-loop-modulates-early-perineural-invasion-of-pancreatic-cancer-cells
#14
Chumei Huang, Yaqing Li, Yubo Guo, Zuoquan Zhang, Guoda Lian, Yinting Chen, Jian Li, Yonghui Su, Jiajia Li, Kege Yang, Shaojie Chen, Hong Su, Kaihong Huang, Linjuan Zeng
The molecular mechanism of perineural invasion (PNI) is unclear, and insufficient detection during early-stage PNI in vivo hampers its investigation. We aimed to identify a cytokine paracrine loop between pancreatic ductal adenocarcinoma (PDAC) cells and nerves and established a noninvasive method to monitor PNI in vivo . Methods: A Matrigel/ dorsal root ganglia (DRG) system was used to observe PNI in vitro , and a murine sciatic nerve invasion model was established to examine PNI in vivo . PNI was assessed by MRI with iron oxide nanoparticle labeling ...
2018: Theranostics
https://www.readbyqxmd.com/read/29895573/the-mutation-associated-neoantigen-functional-expansion-of-specific-t-cells-manafest-assay-a-sensitive-platform-for-monitoring-antitumor-immunity
#15
Ludmila Danilova, Valsamo Anagnostou, Justina X Caushi, John-William Sidhom, Haidan Guo, Hok Yee Chan, Prerna Suri, Ada J Tam, Jiajia Zhang, Margueritta El Asmar, Kristen A Marrone, Jarushka Naidoo, Julie R Brahmer, Patrick M Forde, Alexander S Baras, Leslie Cope, Victor E Velculescu, Drew Pardoll, Franck Housseau, Kellie N Smith
Mutation-associated neoantigens (MANAs) are a target of antitumor T-cell immunity. Sensitive, simple, and standardized assays are needed to assess the repertoire of functional MANA-specific T cells in oncology. Assays analyzing in vitro cytokine production such as ELISpot and intracellular cytokine staining (ICS) have been useful but have limited sensitivity in assessing tumor-specific T-cell responses and do not analyze antigen-specific T-cell repertoires. The FEST (Functional Expansion of Specific T cells) assay described herein integrates TCR sequencing of short-term, peptide-stimulated cultures with a bioinformatic platform to identify antigen-specific clonotypic amplifications...
June 12, 2018: Cancer Immunology Research
https://www.readbyqxmd.com/read/29891014/hsa_circ_0046264-up-regulated-brca2-to-suppress-lung-cancer-through-targeting-hsa-mir-1245
#16
Liu Yang, Jun Wang, Yaodong Fan, Kun Yu, Baowei Jiao, Xiaosan Su
OBJECTIVE: Lung cancer had been leading mounts of deaths worldwide. Advances in genes microarray had helped human further understand genes and identify novel circular RNAs. This study aimed at investigating the biological functions and molecular mechanisms of hsa_circ_0046264 in lung cancer which may be helpful in lung cancer early diagnosis and clinical treatment. METHODS: Gene microarray data screened the differential gene of hsa_circ_0046264 and its downstream genes were found by bioinformatics analysis and verified by luciferase reporter assay...
June 11, 2018: Respiratory Research
https://www.readbyqxmd.com/read/29887958/analysis-of-differentially-expressed-genes-clinical-value-and-biological-pathways-in-prostate-cancer
#17
Zhaohui He, Fucai Tang, Zechao Lu, Yucong Huang, Hanqi Lei, Zhibiao Li, Guohua Zeng
The present study aimed to investigate the gene expression changes in prostate cancer (PC) and screen the hub genes and associated pathways of PC progression. The authors employed integrated analysis of GSE46602 downloaded from the Gene Expression Omnibus and The Cancer Genome Atlas databases to identify 484 consensual differentially expressed genes (DEGs) in PC, when compared with adjacent normal tissue samples. Functional annotation and pathway analysis were performed. The protein-protein interaction (PPI) networks and module were constructed...
2018: American Journal of Translational Research
https://www.readbyqxmd.com/read/29887852/differentially-expressed-genes-in-osteomyelitis-induced-by-staphylococcus-aureus-infection
#18
Peisheng Chen, Zilong Yao, Ganming Deng, Yilong Hou, Siwei Chen, Yanjun Hu, Bin Yu
Osteomyelitis (OM) is a complicated and serious disease and its underlying molecular signatures of disease initiation and progression remain unclear. Staphylococcus aureus (S. aureus) is the most common causative agent of OM. Previous study of Banchereau et al. has established a link between whole blood transcription profiles and clinical manifestations in patients infected with S. aureus . However, the differentially expressed genes (DEGs) in OM induced by S. aureus infection have not been intensively investigated...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29885652/mir-1-3p-that-correlates-with-left-ventricular-function-of-hcm-can-serve-as-a-potential-target-and-differentiate-hcm-from-dcm
#19
Mengmeng Li, Xiao Chen, Liang Chen, Kai Chen, Jianye Zhou, Jiangping Song
BACKGROUND: MicroRNAs (miRNAs) are non-coding RNAs that function as regulators of gene expression and thereby contribute to the complex disease phenotypes. Hypertrophic cardiomyopathy (HCM) and Dilated cardiomyopathy (DCM) can cause sudden cardiac death and eventually develop into heart failure. However, they have different clinical and pathophysiological phenotype and the expressional spectrum of miRNAs in left ventricles of HCM and DCM has never been compared before. METHODS: This study selected 30 human left ventricular heart samples belonged to three diagnostic groups (Control, HCM, DCM)...
June 9, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29883261/muscle-mirnaome-shows-suppression-of-chronic-inflammatory-mirnas-with-both-prednisone-and-vamorolone
#20
Alyson A Fiorillo, Christopher B Tully, Jesse M Damsker, Kanneboyina Nagaraju, Eric P Hoffman, Christopher R Heier
Corticosteroids are highly prescribed and effective anti-inflammatory drugs, but the burden of side effects with chronic use significantly detracts from patient quality of life, particularly in children. Developing safer steroids amenable to long-term use is an important goal for treatment of chronic inflammatory diseases such as Duchenne muscular dystrophy (DMD). We have developed vamorolone (VBP15), a first-in-class dissociative glucocorticoid receptor (GR) ligand that shows the anti-inflammatory efficacy of corticosteroids without key steroid side effects in animal models...
June 8, 2018: Physiological Genomics
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