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https://www.readbyqxmd.com/read/28650175/bioactive-peptide-natural-products-as-lead-structures-for-medicinal-use
#1
Tam Dang, Roderich D Süssmuth
The need for new drugs for the treatment of various diseases is enormous. From the previous century until the present, numerous peptide and peptide-derived natural products have been isolated from bacteria and fungi. Hence, microorganisms play a pivotal role as sources for novel drugs with an emphasis on anti-infective agents. Various disciplines from biology, chemistry, and medicine are involved in early stages of the search for peptide natural products including taxonomy, microbiology, bioanalytics, bioinformatics, and medicinal chemistry...
June 26, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28639162/bacterial-genome-sequencing-in-clinical-microbiology-a-pathogen-oriented-review
#2
REVIEW
F Tagini, G Greub
In recent years, whole-genome sequencing (WGS) has been perceived as a technology with the potential to revolutionise clinical microbiology. Herein, we reviewed the literature on the use of WGS for the most commonly encountered pathogens in clinical microbiology laboratories: Escherichia coli and other Enterobacteriaceae, Staphylococcus aureus and coagulase-negative staphylococci, streptococci and enterococci, mycobacteria and Chlamydia trachomatis. For each pathogen group, we focused on five different aspects: the genome characteristics, the most common genomic approaches and the clinical uses of WGS for (i) typing and outbreak analysis, (ii) virulence investigation and (iii) in silico antimicrobial susceptibility testing...
June 21, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28636311/insights-into-integrated-lead-generation-and-target-identification-in-malaria-and-tuberculosis-drug-discovery
#3
John Okombo, Kelly Chibale
New, safe and effective drugs are urgently needed to treat and control malaria and tuberculosis, which affect millions of people annually. However, financial return on investment in the poor settings where these diseases are mostly prevalent is very minimal to support market-driven drug discovery and development. Moreover, the imminent loss of therapeutic lifespan of existing therapies due to evolution and spread of drug resistance further compounds the urgency to identify novel effective drugs. However, the advent of new public-private partnerships focused on tropical diseases and the recent release of large data sets by pharmaceutical companies on antimalarial and antituberculosis compounds derived from phenotypic whole cell high throughput screening have spurred renewed interest and opened new frontiers in malaria and tuberculosis drug discovery...
June 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28630587/the-most-common-technologies-and-tools-for-functional-genome-analysis
#4
Evelina Gasperskaja, Vaidutis Kučinskas
Since the sequence of the human genome is complete, the main issue is how to understand the information written in the DNA sequence. Despite numerous genome-wide studies that have already been performed, the challenge to determine the function of genes, gene products, and also their interaction is still open. As changes in the human genome are highly likely to cause pathological conditions, functional analysis is vitally important for human health. For many years there have been a variety of technologies and tools used in functional genome analysis...
2017: Acta medica Lituanica
https://www.readbyqxmd.com/read/28609000/the-role-of-informatics-in-patient-centered-care-and-personalized-medicine
#5
Matthew G Hanna, Liron Pantanowitz
The practice of cytopathology has dramatically changed due to advances in genomics and information technology. Cytology laboratories have accordingly become increasingly dependent on pathology informatics support to meet the emerging demands of precision medicine. Pathology informatics deals with information technology in the laboratory, and the impact of this technology on workflow processes and staff who interact with these tools. This article covers the critical role that laboratory information systems, electronic medical records, and digital imaging plays in patient-centered personalized medicine...
June 2017: Cancer
https://www.readbyqxmd.com/read/28589363/tracking-b-cell-repertoires-and-clonal-histories-in-normal-and-malignant-lymphocytes
#6
Nicola J Weston-Bell, Graeme Cowan, Surinder S Sahota
Methods for tracking B-cell repertoires and clonal history in normal and malignant B-cells based on immunoglobulin variable region (IGV) gene analysis have developed rapidly with the advent of massive parallel next-generation sequencing (mpNGS) protocols. mpNGS permits a depth of analysis of IGV genes not hitherto feasible, and presents challenges of bioinformatics analysis, which can be readily met by current pipelines. This strategy offers a potential resolution of B-cell usage at a depth that may capture fully the natural state, in a given biological setting...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28589117/xmrv-and-public-health-the-retroviral-genome-is-not-a-suitable-template-for-diagnostic-pcr-and-its-association-with-myalgic-encephalomyelitis-chronic-fatigue-syndrome-appears-unreliable
#7
Simona Panelli, Lorenzo Lorusso, Alessandro Balestrieri, Giuseppe Lupo, Enrica Capelli
A few years ago, a highly significant association between the xenotropic murine leukemia virus-related virus (XMRV) and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), a complex debilitating disease of poorly understood etiology and no definite treatment, was reported in Science, raising concern for public welfare. Successively, the failure to reproduce these findings, and the suspect that the diagnostic PCR was vitiated by laboratory contaminations, led to the retraction of the paper. Notwithstanding, XMRV continued to be the subject of researches and public debates...
2017: Frontiers in Public Health
https://www.readbyqxmd.com/read/28588568/food-safety-in-the-age-of-next-generation-sequencing-bioinformatics-and-open-data-access
#8
REVIEW
Eduardo N Taboada, Morag R Graham, João A Carriço, Gary Van Domselaar
Public health labs and food regulatory agencies globally are embracing whole genome sequencing (WGS) as a revolutionary new method that is positioned to replace numerous existing diagnostic and microbial typing technologies with a single new target: the microbial draft genome. The ability to cheaply generate large amounts of microbial genome sequence data, combined with emerging policies of food regulatory and public health institutions making their microbial sequences increasingly available and public, has served to open up the field to the general scientific community...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28586063/myc-and-hsa%C3%A2-mirna%C3%A2-423%C3%A2-5p-as-biomarkers-in-nasopharyngeal-carcinoma-revealed-by-mirna%C3%A2-mrna%C3%A2-pathway-network-integrated-analysis
#9
Huan Tian, Shicai Chen, Caiyun Zhang, Meng Li, Hongliang Zheng
The present study was performed to identify the dysregulated microRNAs (miRNAs/miRs) and mRNAs, and enriched pathways involved in nasopharyngeal carcinoma (NPC) through the establishment of an miRNA‑mRNA‑pathways network. mRNA and miRNA expression profiles were collected from the European Molecular Biology Laboratory‑European Bioinformatics Institute. Differentially expressed genes and differentially expressed miRNA were selectively screened using the metaDE package. Following prediction of the risk genes and pathway pairs involved in NPC, an miRNA‑mRNA‑pathway network was constructed by merging the miRNA‑mRNA pairs, the mRNA‑pathway pairs and the mRNA‑mRNA pairs...
June 6, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28586052/a-novel-approach-to-select-differential-pathways-associated-with-hypertrophic-cardiomyopathy-based-on-gene-co%C3%A2-expression-analysis
#10
Xiao-Min Chen, Ming-Jun Feng, Cai-Jie Shen, Bin He, Xian-Feng Du, Yi-Bo Yu, Jing Liu, Hui-Min Chu
The present study was designed to develop a novel method for identifying significant pathways associated with human hypertrophic cardiomyopathy (HCM), based on gene co‑expression analysis. The microarray dataset associated with HCM (E‑GEOD‑36961) was obtained from the European Molecular Biology Laboratory‑European Bioinformatics Institute database. Informative pathways were selected based on the Reactome pathway database and screening treatments. An empirical Bayes method was utilized to construct co‑expression networks for informative pathways, and a weight value was assigned to each pathway...
July 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28584262/genome-wide-profiling-and-differential-expression-of-microrna-in-rat-pluripotent-stem-cells
#11
Vladimir V Sherstyuk, Sergey P Medvedev, Evgeniy A Elisaphenko, Evgeniya A Vaskova, Maxim T Ri, Yuri V Vyatkin, Olga V Saik, Dmitry N Shtokalo, Evgeniy A Pokushalov, Suren M Zakian
MicroRNAs (miRNAs) constitute a class of small noncoding RNAs that plays an important role in the post-transcriptional regulation of gene expression. Much evidence has demonstrated that miRNAs are involved in regulating the human and mouse pluripotency. Nevertheless, to our knowledge, miRNAs in the pluripotent stem cells of one of the most commonly used model organisms - the Rattus norvegicus have not been studied. In the present study, we performed deep sequencing of small RNA molecules in the embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells of laboratory rats...
June 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28582538/breakpoint-surveyor-a-pipeline-for-structural-variant-visualization
#12
Matthew A Wyczalkowski, Kristine M Wylie, Song Cao, Michael D McLellan, Jennifer Flynn, Mo Huang, Kai Ye, Xian Fan, Ken Chen, Michael C Wendl, Li Ding
Summary: BreakPoint Surveyor (BPS) is a computational pipeline for the discovery, characterization, and visualization of complex genomic rearrangements, such as viral genome integration, in paired-end sequence data. BPS facilitates interpretation of structural variants by merging structural variant breakpoint predictions, gene exon structure, read depth, and RNA-Seq expression into a single comprehensive figure. Availability: Source code and sample data freely available for download at https://github...
June 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28582485/compass-the-completely-arbitrary-sequence-simulator
#13
Andrew Low, Nicolas Rodrigue, Alex Wong
Summary: Simulated sequence alignments are frequently used to test bioinformatics tools, but current sequence simulators are limited to defined state spaces. Here, we present the COMPletely Arbitrary Sequence Simulator (COMPASS), which is able to simulate the evolution of absolutely any discrete state space along a tree, for any form of time-reversible model. Availability and Implementation: COMPASS is implemented in Python 2.7, and is freely available for all platforms with the Supplemetary Information, as well as at http://labs...
June 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28578698/dictyexpress-a-web-based-platform-for-sequence-data-management-and-analytics-in-dictyostelium-and-beyond
#14
Miha Stajdohar, Rafael D Rosengarten, Janez Kokosar, Luka Jeran, Domen Blenkus, Gad Shaulsky, Blaz Zupan
BACKGROUND: Dictyostelium discoideum, a soil-dwelling social amoeba, is a model for the study of numerous biological processes. Research in the field has benefited mightily from the adoption of next-generation sequencing for genomics and transcriptomics. Dictyostelium biologists now face the widespread challenges of analyzing and exploring high dimensional data sets to generate hypotheses and discovering novel insights. RESULTS: We present dictyExpress (2.0), a web application designed for exploratory analysis of gene expression data, as well as data from related experiments such as Chromatin Immunoprecipitation sequencing (ChIP-Seq)...
June 2, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28562486/diagnostics-and-laboratory-role-in-outbreaks
#15
Francesca Lee
PURPOSE OF REVIEW: The review describes the investigative benefits of traditional and novel molecular epidemiology techniques, while acknowledging the limitations faced by clinical laboratories seeking to implement these methods. RECENT FINDINGS: Pulse-field gel electrophoresis and other traditional techniques remain powerful tools in outbreak investigations and continue to be used by multiple groups. Newer techniques such as matrix-assisted laser desorption/ionization-time of flight mass-spectrometry and whole genome sequencing show great promise...
May 29, 2017: Current Opinion in Infectious Diseases
https://www.readbyqxmd.com/read/28557600/integration-of-technical-bioinformatic-and-variant-assessment-approaches-in-the-validation-of-a-targeted-next-generation-sequencing-panel-for-myeloid-malignancies
#16
Mariam Thomas, Mahadeo A Sukhai, Tong Zhang, Roozbeh Dolatshahi, Djamel Harbi, Swati Garg, Maksym Misyura, Trevor Pugh, Tracy L Stockley, Suzanne Kamel-Reid
CONTEXT: - Detection of variants in hematologic malignancies is increasingly important because of a growing number of variants impacting diagnosis, prognosis, and treatment response, and as potential therapeutic targets. The use of next-generation sequencing technologies to detect variants in hematologic malignancies in a clinical diagnostic laboratory setting allows for efficient identification of routinely tested markers in multiple genes simultaneously, as well as the identification of novel and rare variants in other clinically relevant genes...
June 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/28550117/comparative-exploration-of-multidimensional-flow-cytometry-software-a-model-approach-evaluating-t-cell-polyfunctional-behavior
#17
Timothy T Spear, Michael I Nishimura, Patricia E Simms
Advancement in flow cytometry reagents and instrumentation has allowed for simultaneous analysis of large numbers of lineage/functional immune cell markers. Highly complex datasets generated by polychromatic flow cytometry require proper analytical software to answer investigators' questions. A problem among many investigators and flow cytometry Shared Resource Laboratories (SRLs), including our own, is a lack of access to a flow cytometry-knowledgeable bioinformatics team, making it difficult to learn and choose appropriate analysis tool(s)...
May 26, 2017: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/28546994/sdha-related-tumorigenesis-a-new-case-series-and-literature-review-for-variant-interpretation-and-pathogenicity
#18
Ruth T Casey, David B Ascher, Eleanor Rattenberry, Louise Izatt, Katrina A Andrews, Helen L Simpson, Benjamen Challis, Soo-Mi Park, Venkata R Bulusu, Fiona Lalloo, Douglas E V Pires, Hannah West, Graeme R Clark, Philip S Smith, James Whitworth, Thomas G Papathomas, Phillipe Taniere, Rosina Savisaar, Laurence D Hurst, Emma R Woodward, Eamonn R Maher
PURPOSE: To evaluate the role of germline SDHA mutation analysis by (1) comprehensive literature review, (2) description of novel germline SDHA mutations and (3) in silico structural prediction analysis of missense substitutions in SDHA. PATIENTS AND METHODS: A systematic literature review and a retrospective review of the molecular and clinical features of patients identified with putative germline variants in UK molecular genetic laboratories was performed. To evaluate the molecular consequences of SDHA missense variants, a novel model of the SDHA/B/C/D complex was generated and the structural effects of missense substitutions identified in the literature, our UK novel cohort and a further 32 "control missense variants" were predicted by the mCSM computational platform...
May 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28544613/qtl-and-systems-genetics-analysis-of-mouse-grooming-and-behavioral-responses-to-novelty-in-an-open-field
#19
Anna Delprato, Marie-Paule Algéo, Brice Bonheur, Jason A Bubier, Lu Lu, Robert W Williams, Elissa J Chesler, Wim E Crusio
The open field is a classic test used to assess exploratory behavior, anxiety, and locomotor activity in rodents. Here we mapped quantitative trait loci (QTLs) underlying behaviors displayed in an open field, using a panel of 53 BXD recombinant inbred mouse strains with deep replication (10 per strain and sex). The use of these strains permits the integration and comparison of data obtained in different laboratories, and also offers the possibility to study trait covariance by exploiting powerful bioinformatics tools and resources...
May 24, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/28542189/mir-277-4989-regulate-transcriptional-landscape-during-juvenile-to-adult-transition-in-the-parasitic-helminth-schistosoma-mansoni
#20
Anna V Protasio, Stijn van Dongen, Julie Collins, Leonor Quintais, Diogo M Ribeiro, Florian Sessler, Martin Hunt, Gabriel Rinaldi, James J Collins, Anton J Enright, Matthew Berriman
Schistosomes are parasitic helminths that cause schistosomiasis, a disease affecting circa 200 million people, primarily in underprivileged regions of the world. Schistosoma mansoni is the most experimentally tractable schistosome species due to its ease of propagation in the laboratory and the high quality of its genome assembly and annotation. Although there is growing interest in microRNAs (miRNAs) in trematodes, little is known about the role these molecules play in the context of developmental processes...
May 2017: PLoS Neglected Tropical Diseases
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