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https://www.readbyqxmd.com/read/28820135/bioinformatic-analyses-of-whole-genome-sequence-data-in-a-public-health-laboratory
#1
Kelly F Oakeson, Jennifer Marie Wagner, Michelle Mendenhall, Andreas Rohrwasser, Robyn Atkinson-Dunn
The ability to generate high-quality sequence data in a public health laboratory enables the identification of pathogenic strains, the determination of relatedness among outbreak strains, and the analysis of genetic information regarding virulence and antimicrobial-resistance genes. However, the analysis of whole-genome sequence data depends on bioinformatic analysis tools and processes. Many public health laboratories do not have the bioinformatic capabilities to analyze the data generated from sequencing and therefore are unable to take full advantage of the power of whole-genome sequencing...
September 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28818599/a-new-cost-and-time-effective-method-for-multilocus-microsatellite-typing-mlmt-studies-application-of-leishmania-tropica-isolates-and-clinical-samples-from-turkey
#2
Mehmet Karakuş, Bahtiyar Yılmaz, Yusuf Özbel, Seray Töz
Molecular techniques are widely used in the field of parasitology to identify the genetic profile of the microbiological agents. Microsatellite typing studies are comprised of the amplification of polymorphic markers to analyze the fragment sizes using bioinformatics tools. Current methods need fluorescently labeled primers and size markers to obtain fragment peaks in ABI PRISM® systems and due to low discrimination power of gel-electrophoresis, it is not possible to differentiate primer-dimers from small fragments In the present study, we designed a new method for fragment analysis studies, which reduce the time by eliminating the classical PCR, the gel-electrophoresis and the preparation steps of fragment analysis...
August 14, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28811505/identification-and-quantification-of-plasma-free-salusin-%C3%AE-an-endogenous-parasympathomimetic-peptide
#3
Kazumi Fujimoto, Akinori Hayashi, Yoshio Kodera, Tatsuya Saito, Takuya Toki, Akifumi Ogawa, Yuji Kamata, Koji Takano, Hideki Katakami, Masayoshi Shichiri
Salusin-β is an endogenous parasympathomimetic proatherosclerotic peptide. Salusin-β was initially predicted from bioinformatic analyses and later immunologically detected in human biofluids. However, elucidation of salusin-β bioactivity has faced enormous challenges because of its unique physicochemical characteristics that cause it to strongly adhere to laboratory apparatus materials. In the strictest sense, the discovery of bioactive peptides is not complete until their exact native sequences have been confirmed in the peripheral circulation...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28809012/comparative-genomics-as-a-foundation-for-evo-devo-studies-in-birds
#4
Phil Grayson, Simon Y W Sin, Timothy B Sackton, Scott V Edwards
Developmental genomics is a rapidly growing field, and high-quality genomes are a useful foundation for comparative developmental studies. A high-quality genome forms an essential reference onto which the data from numerous assays and experiments, including ChIP-seq, ATAC-seq, and RNA-seq, can be mapped. A genome also streamlines and simplifies the development of primers used to amplify putative regulatory regions for enhancer screens, cDNA probes for in situ hybridization, microRNAs (miRNAs) or short hairpin RNAs (shRNA) for RNA interference (RNAi) knockdowns, mRNAs for misexpression studies, and even guide RNAs (gRNAs) for CRISPR knockouts...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28782984/review-of-clinical-next-generation-sequencing
#5
Sophia Yohe, Bharat Thyagarajan
CONTEXT: - Next-generation sequencing (NGS) is a technology being used by many laboratories to test for inherited disorders and tumor mutations. This technology is new for many practicing pathologists, who may not be familiar with the uses, methodology, and limitations of NGS. OBJECTIVE: - To familiarize pathologists with several aspects of NGS, including current and expanding uses; methodology including wet bench aspects, bioinformatics, and interpretation; validation and proficiency; limitations; and issues related to the integration of NGS data into patient care...
August 7, 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/28781745/developing-a-strategy-for-computational-lab-skills-training-through-software-and-data-carpentry-experiences-from-the-elixir-pilot-action
#6
Aleksandra Pawlik, Celia W G van Gelder, Aleksandra Nenadic, Patricia M Palagi, Eija Korpelainen, Philip Lijnzaad, Diana Marek, Susanna-Assunta Sansone, John Hancock, Carole Goble
Quality training in computational skills for life scientists is essential to allow them to deliver robust, reproducible and cutting-edge research. A pan-European bioinformatics programme, ELIXIR, has adopted a well-established and progressive programme of computational lab and data skills training from Software and Data Carpentry, aimed at increasing the number of skilled life scientists and building a sustainable training community in this field. This article describes the Pilot action, which introduced the Carpentry training model to the ELIXIR community...
2017: F1000Research
https://www.readbyqxmd.com/read/28774779/extensive-and-functional-overlap-of-the-stat6-and-rxr-cistromes-in-the-active-enhancer-repertoire-of-human-cd14-monocyte-derived-differentiating-macrophages
#7
REVIEW
Zsolt Czimmerer, Zsuzsanna S Nagy, Gergely Nagy, Attila Horvath, Timea Silye-Cseh, Agnes Kriston, David Jonas, Sascha Sauer, Laszlo Steiner, Bence Daniel, Jean-Francois Deleuze, Laszlo Nagy
Macrophages are able to differentiate into classically polarized (M1) or alternatively polarized (M2) states upon encountering pro-inflammatory cytokines such as interferon (IFN) γ or anti-inflammatory cytokines such as interleukin (IL) -4/IL-13, respectively. Moreover, macrophages are known to regulate lipid metabolism via multiple members of the nuclear hormone receptor family, including the retinoid X receptors (RXR). It has been also documented that cytokines are able to modulate macrophage responses to lipid signals but the nature of these interactions and the underlying mechanisms of these processes especially at the level of the chromatinized genome are not well understood...
July 31, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28764323/lipidccs-prediction-of-collision-cross-section-values-for-lipids-with-high-precision-to-support-ion-mobility-mass-spectrometry-based-lipidomics
#8
Zhiwei Zhou, Jia Tu, Xin Xiong, Xiaotao Shen, Zheng-Jiang Zhu
The use of collision cross-section (CCS) values derived from ion mobility-mass spectrometry (IM-MS) has been proven to facilitate lipid identifications. Its utility is restricted by the limited available CCS values. Recently, the machine-learning algorithm based prediction (e.g., MetCCS) is reported to generate CCS values in a large-scale. However, the prediction precision is not sufficient to differentiate lipids due to their high structural similarities and subtle differences on CCS values. To address this challenge, we developed a new approach, namely, LipidCCS, to precisely predict lipid CCS values...
August 1, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28763882/-analysis-of-a-chinese-charcot-marie-tooth-disease-type-2d-pedigree
#9
B Sun, Y R Li, Z H Chen, L Ling, Y T Ren, W X Liu, F Cui, F Yang, C Q Pu, X S Huang
Objective: To achieve definite diagnosis in a clinically diagnosed Charcot-Marie-Tooth disease (CMT) pedigree and broaden the mutational diversity of CMT-related mutations in Chinese Han population. Methods: Patients clinically diagnosed with CMT were recruited from Department of Neurology, Chinese PLA General Hospital between December, 2012 to June, 2016. Clinical examination, laboratory tests, nerve conduction studies, and molecular and bioinformatics analyses were performed on a clinically diagnosed CMT pedigree...
July 18, 2017: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://www.readbyqxmd.com/read/28760933/genetic-evidence-for-erythrocyte-receptor-glycophorin-b-expression-levels-defining-a-dominant-plasmodium-falciparum-invasion-pathway-into-human-erythrocytes
#10
Selasi Dankwa, Mudit Chaand, Usheer Kanjee, Rays H Y Jiang, Luis V Nobre, Jonathan M Goldberg, Amy K Bei, Mischka A Moechtar, Christof Grüring, Ambroise D Ahouidi, Daouda Ndiaye, Tandakha N Dieye, Souleymane Mboup, Michael P Weekes, Manoj T Duraisingh
Plasmodium falciparum, the parasite that causes the deadliest form of malaria, has evolved multiple proteins known as invasion ligands that bind to specific erythrocyte receptors to facilitate invasion of human erythrocytes. The EBA-175/glycophorin A (GPA) and Rh5/basigin ligand-receptor interactions, referred to as invasion pathways, have been the subject of intense study. In this study, we focused on the lesser characterized sialic acid-containing receptors glycophorin B (GPB) and glycophorin C (GPC). Through bioinformatic analysis, we identified extensive variation in glycophorin B transcript (GYPB) levels in individuals from Benin, suggesting selection from malaria pressure...
July 31, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28756964/key-features-of-invasive-pneumococcal-isolates-recovered-in-lima-peru-determined-through-whole-genome-sequencing
#11
Paulina Hawkins, Erik Mercado, Sopio Chochua, Maria E Castillo, Isabel Reyes, Eduardo Chaparro, Rebecca Gladstone, Stephen D Bentley, Robert F Breiman, Benjamin J Metcalf, Bernard Beall, Theresa J Ochoa, Lesley McGee
Before PCV7 introduction, invasive pneumococcal disease (IPD) was responsible for approximately 12,000-18,000 deaths annually among children <5years in Latin America. In Peru, PCV7 was introduced in 2009. We used whole genome sequencing to deduce key features of invasive strains collected in Lima, Peru from 2006 to 2011. We sequenced 212 IPD isolates from 16 hospitals in Lima pre (2006-2009; n=133) and post (2010-2011; n=79) PCV7 introduction; 130 (61.3%) isolates were from children≤5years old. CDC's Streptococcus lab bioinformatics pipeline revealed serotypes, sequence types (STs), pilus genes, PBP types and other resistance determinants...
July 22, 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/28751759/a-comparative-study-of-germline-brca1-and-brca2-mutation-screening-methods-in-use-in-20-european-clinical-diagnostic-laboratories
#12
Gillian Ellison, Andrew Wallace, Alexander Kohlmann, Simon Patton
BACKGROUND: Thousands of clinically relevant variations in BRCA1 and BRCA2 have been discovered and this poses a significant challenge with respect to the accurate detection, analysis turn-around time, characterisation and interpretation of these sequence variants. METHODS: We evaluated the performance of different BRCA1/2 gene testing practices in routine diagnostic use in 20 European laboratories, with a focus on next-generation sequencing-based strategies as this is the technical approach implemented by or under adoption by most European clinical laboratories...
July 27, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28747151/comparative-analysis-of-targeted-long-read-sequencing-approaches-for-characterization-of-a-plant-s-immune-receptor-repertoire
#13
Michael Giolai, Pirita Paajanen, Walter Verweij, Kamil Witek, Jonathan D G Jones, Matthew D Clark
BACKGROUND: The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments. Selective breeding of crops has led to a reduction in genetic diversity, and wild relatives are a key source of new genetic resistance to pathogens, usually via NLR immune receptor-encoding genes. Recent studies have demonstrated how crop NLR repertoires can be targeted for sequencing on Illumina or PacBio (RenSeq) and the specific gene conveying pathogen resistance identified...
July 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28730077/proteomic-profiling-of-early-degenerative-retina-of-rcs-rats
#14
Zhi-Hong Zhu, Yan Fu, Chuan-Huang Weng, Cong-Jian Zhao, Zheng-Qin Yin
AIM: To identify the underlying cellular and molecular changes in retinitis pigmentosa (RP). METHODS: Label-free quantification-based proteomics analysis, with its advantages of being more economic and consisting of simpler procedures, has been used with increasing frequency in modern biological research. Dystrophic RCS rats, the first laboratory animal model for the study of RP, possess a similar pathological course as human beings with the diseases. Thus, we employed a comparative proteomics analysis approach for in-depth proteome profiling of retinas from dystrophic RCS rats and non-dystrophic congenic controls through Linear Trap Quadrupole - orbitrap MS/MS, to identify the significant differentially expressed proteins (DEPs)...
2017: International Journal of Ophthalmology
https://www.readbyqxmd.com/read/28718274/-microbiome-and-next-generation-sequencing
#15
REVIEW
A Suárez Moya
The human microbiome is an internal ecosystem that refers to the community of microorganisms that populate the human body. These microorganisms are essential to support his health, because the interaction between the host immune system and microorganisms, provide the host with protection against pathogens, and contributes to the preservation of health. Bacteriological culture has been the basis for traditional microbiology; however, most of the bacterial forms observed in nature cannot be isolated with laboratory culture methods...
July 17, 2017: Revista Española de Quimioterapia: Publicación Oficial de la Sociedad Española de Quimioterapia
https://www.readbyqxmd.com/read/28717418/a-novel-community-driven-software-for-functional-enrichment-analysis-of-extracellular-vesicles-data
#16
Mohashin Pathan, Shivakumar Keerthikumar, David Chisanga, Riccardo Alessandro, Ching-Seng Ang, Philip Askenase, Arsen O Batagov, Alberto Benito-Martin, Giovanni Camussi, Aled Clayton, Federica Collino, Dolores Di Vizio, Juan Manuel Falcon-Perez, Pedro Fonseca, Pamali Fonseka, Simona Fontana, Yong Song Gho, An Hendrix, Esther Nolte-'t Hoen, Nunzio Iraci, Kenneth Kastaniegaard, Thomas Kislinger, Joanna Kowal, Igor V Kurochkin, Tommaso Leonardi, Yaxuan Liang, Alicia Llorente, Taral R Lunavat, Sayantan Maji, Francesca Monteleone, Anders Øverbye, Theocharis Panaretakis, Tushar Patel, Héctor Peinado, Stefano Pluchino, Simona Principe, Goran Ronquist, Felix Royo, Susmita Sahoo, Cristiana Spinelli, Allan Stensballe, Clotilde Théry, Martijn J C van Herwijnen, Marca Wauben, Joanne L Welton, Kening Zhao, Suresh Mathivanan
Bioinformatics tools are imperative for the in depth analysis of heterogeneous high-throughput data. Most of the software tools are developed by specific laboratories or groups or companies wherein they are designed to perform the required analysis for the group. However, such software tools may fail to capture "what the community needs in a tool". Here, we describe a novel community-driven approach to build a comprehensive functional enrichment analysis tool. Using the existing FunRich tool as a template, we invited researchers to request additional features and/or changes...
2017: Journal of Extracellular Vesicles
https://www.readbyqxmd.com/read/28716001/variant-ranker-a-web-tool-to-rank-genomic-data-according-to-functional-significance
#17
John Alexander, Dimitris Mantzaris, Marianthi Georgitsi, Petros Drineas, Peristera Paschou
BACKGROUND: The increasing volume and complexity of high-throughput genomic data make analysis and prioritization of variants difficult for researchers with limited bioinformatics skills. Variant Ranker allows researchers to rank identified variants and determine the most confident variants for experimental validation. RESULTS: We describe Variant Ranker, a user-friendly simple web-based tool for ranking, filtering and annotation of coding and non-coding variants...
July 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28710621/rna-seq-based-comparative-transcriptomics-rna-preparation-and-bioinformatics
#18
Antonio Rodríguez-García, Alberto Sola-Landa, Carlos Barreiro
The major transcriptome analysis is the determination of differentially expressed genes across experimental conditions. For this, the next-generation sequencing of RNA (RNA-seq) is an increasingly cost-effective technology for the analysis of transcriptomes with several advantages over gene expression microarrays, such as its higher sensitivity and accuracy, broader dynamic range, and the ability to detect novel transcripts, including noncoding RNA molecules, at nucleotide-level resolution. Although these advantages, many microbiology laboratories have not yet applied RNA-seq analyses to their investigations...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28692806/microrna-155-3p-mediates-tnf-%C3%AE-inhibited-cementoblast-differentiation
#19
X Wang, H Sun, H Liao, C Wang, C Jiang, Y Zhang, Z Cao
Periodontitis is a prevalent and chronic inflammatory disease that is interrelated with systemic health. Periodontitis can be promoted by tumor necrosis factor α (TNF-α). Cementum, a vital part of the periodontium, is a bone-like mineralized tissue that is produced by cementoblasts. Our laboratory previously revealed that TNF-α inhibits cementoblast differentiation and mineralization. However, how TNF-α modulates cementoblast differentiation and mineralization remains largely unknown. MicroRNA-155 (miR-155) is induced and regulates TNF-α-inhibited osteogenic differentiation...
July 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28690805/evaluating-hybridization-capture-with-rad-probes-as-a-tool-for-museum-genomics-with-historical-bird-specimens
#20
Ethan B Linck, Zachary R Hanna, Anna Sellas, John P Dumbacher
Laboratory techniques for high-throughput sequencing have enhanced our ability to generate DNA sequence data from millions of natural history specimens collected prior to the molecular era, but remain poorly tested at shallower evolutionary time scales. Hybridization capture using restriction site-associated DNA probes (hyRAD) is a recently developed method for population genomics with museum specimens. The hyRAD method employs fragments produced in a restriction site-associated double digestion as the basis for probes that capture orthologous loci in samples of interest...
July 2017: Ecology and Evolution
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