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https://www.readbyqxmd.com/read/28550117/comparative-exploration-of-multidimensional-flow-cytometry-software-a-model-approach-evaluating-t-cell-polyfunctional-behavior
#1
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
#2
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
#3
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
#4
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 23, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28540697/in-silico-pcr-tools-for-a-fast-primer-probe-and-advanced-searching
#5
Ruslan Kalendar, Alexandr Muterko, Malika Shamekova, Kabyl Zhambakin
The polymerase chain reaction (PCR) is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. The principle of this technique has been further used and applied in plenty of other simple or complex nucleic acid amplification technologies (NAAT). In parallel to laboratory "wet bench" experiments for nucleic acid amplification technologies, in silico or virtual (bioinformatics) approaches have been developed, among which in silico PCR analysis. In silico NAAT analysis is a useful and efficient complementary method to ensure the specificity of primers or probes for an extensive range of PCR applications from homology gene discovery, molecular diagnosis, DNA fingerprinting, and repeat searching...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28538739/multiplex-pcr-method-for-minion-and-illumina-sequencing-of-zika-and-other-virus-genomes-directly-from-clinical-samples
#6
Joshua Quick, Nathan D Grubaugh, Steven T Pullan, Ingra M Claro, Andrew D Smith, Karthik Gangavarapu, Glenn Oliveira, Refugio Robles-Sikisaka, Thomas F Rogers, Nathan A Beutler, Dennis R Burton, Lia Laura Lewis-Ximenez, Jaqueline Goes de Jesus, Marta Giovanetti, Sarah C Hill, Allison Black, Trevor Bedford, Miles W Carroll, Marcio Nunes, Luiz Carlos Alcantara, Ester C Sabino, Sally A Baylis, Nuno R Faria, Matthew Loose, Jared T Simpson, Oliver G Pybus, Kristian G Andersen, Nicholas J Loman
Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28535295/bioinformatic-analysis-of-bacteria-and-host-cell-dual-rna-sequencing-experiments
#7
James W Marsh, Regan J Hayward, Amol C Shetty, Anup Mahurkar, Michael S Humphrys, Garry S A Myers
Bacterial pathogens subvert host cells by manipulating cellular pathways for survival and replication; in turn, host cells respond to the invading pathogen through cascading changes in gene expression. Deciphering these complex temporal and spatial dynamics to identify novel bacterial virulence factors or host response pathways is crucial for improved diagnostics and therapeutics. Dual RNA sequencing (dRNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell...
May 23, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28534892/minimizing-next-generation-sequencing-errors-for-hiv-drug-resistance-testing
#8
José A Fernández-Caballero, Natalia Chueca, Eva Poveda, Federico García
Next-generation sequencing prototypes for the routine diagnosis of resistance to antiretrovirals approved for the treatment of HIV infection are now being used in many clinical diagnostic laboratories. As some of the next-generation sequencing platforms may be a source of errors, it is necessary to improve the currently available protocols and implement bioinformatic tools that may help to correctly identify the presence of resistance mutations with clinical impact. Several studies have addressed these issues in recent years...
May 23, 2017: AIDS Reviews
https://www.readbyqxmd.com/read/28520987/proteosign-an-end-user-online-differential-proteomics-statistical-analysis-platform
#9
Georgios Efstathiou, Andreas N Antonakis, Georgios A Pavlopoulos, Theodosios Theodosiou, Peter Divanach, David C Trudgian, Benjamin Thomas, Nikolas Papanikolaou, Michalis Aivaliotis, Oreste Acuto, Ioannis Iliopoulos
Profiling of proteome dynamics is crucial for understanding cellular behavior in response to intrinsic and extrinsic stimuli and maintenance of homeostasis. Over the last 20 years, mass spectrometry (MS) has emerged as the most powerful tool for large-scale identification and characterization of proteins. Bottom-up proteomics, the most common MS-based proteomics approach, has always been challenging in terms of data management, processing, analysis and visualization, with modern instruments capable of producing several gigabytes of data out of a single experiment...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28508547/functional-phosphatome-requirement-for-protein-homeostasis-networked-mitochondria-and-sarcomere-structure-in-c-%C3%A2-elegans-muscle
#10
Susann Lehmann, Joseph J Bass, Thomas F Barratt, Mohammed Z Ali, Nathaniel J Szewczyk
BACKGROUND: Skeletal muscle is central to locomotion and metabolic homeostasis. The laboratory worm Caenorhabditis elegans has been developed into a genomic model for assessing the genes and signals that regulate muscle development and protein degradation. Past work has identified a receptor tyrosine kinase signalling network that combinatorially controls autophagy, nerve signal to muscle to oppose proteasome-based degradation, and extracellular matrix-based signals that control calpain and caspase activation...
May 15, 2017: Journal of Cachexia, Sarcopenia and Muscle
https://www.readbyqxmd.com/read/28506684/study-of-preanalytic-and-analytic-variables-for-clinical-next-generation-sequencing-of-circulating-cell-free-nucleic-acid
#11
Meenakshi Mehrotra, Rajesh R Singh, Wei Chen, Richard S P Huang, Alaa A Almohammedsalim, Bedia A Barkoh, Crystal M Simien, Marcos Hernandez, Carmen Behrens, Keyur P Patel, Mark J Routbort, Russell R Broaddus, L Jeffrey Medeiros, Ignacio I Wistuba, Scott Kopetz, Rajyalakshmi Luthra
Detection of mutations in plasma circulating cell-free DNA (cfDNA) by next-generation sequencing (NGS) has opened up new possibilities for monitoring treatment response and disease progression in patients with solid tumors. However, implementation of cfDNA genotyping in diagnostic laboratories requires systematic assessment of preanalytical parameters and analytical performance of NGS platforms. We assessed the effects of peripheral blood collection tube and plasma separation time on cfDNA yield and integrity and performance of the Ion PGM, Proton, and MiSeq NGS platforms...
May 12, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28506246/vipie-web-pipeline-for-parallel-characterization-of-viral-populations-from-multiple-ngs-samples
#12
Jake Lin, Lenka Kramna, Reija Autio, Heikki Hyöty, Matti Nykter, Ondrej Cinek
BACKGROUND: Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols. RESULTS: We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters...
May 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28480143/analysis-of-microsatellites-from-the-transcriptome-of-downy-mildew-pathogens-and-their-application-for-characterization-of-pseudoperonospora-populations
#13
Emma C Wallace, Lina M Quesada-Ocampo
Downy mildew pathogens affect several economically important crops worldwide but, due to their obligate nature, few genetic resources are available for genomic and population analyses. Draft genomes for emergent downy mildew pathogens such as the oomycete Pseudoperonospora cubensis, causal agent of cucurbit downy mildew, have been published and can be used to perform comparative genomic analysis and develop tools such as microsatellites to characterize pathogen population structure. We used bioinformatics to identify 2,738 microsatellites in the P...
2017: PeerJ
https://www.readbyqxmd.com/read/28469393/bioinformatics-education-in-pathology-training-current-scope-and-future-direction
#14
REVIEW
Michael R Clay, Kevin E Fisher
Training anatomic and clinical pathology residents in the principles of bioinformatics is a challenging endeavor. Most residents receive little to no formal exposure to bioinformatics during medical education, and most of the pathology training is spent interpreting histopathology slides using light microscopy or focused on laboratory regulation, management, and interpretation of discrete laboratory data. At a minimum, residents should be familiar with data structure, data pipelines, data manipulation, and data regulations within clinical laboratories...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28462035/whole-genome-sequencing-of-group-a-streptococcus-development-and-evaluation-of-an-automated-pipeline-for-emmgene-typing
#15
Georgia Kapatai, Juliana Coelho, Steven Platt, Victoria J Chalker
Streptococcus pyogenes group A Streptococcus (GAS) is the most common cause of bacterial throat infections, and can cause mild to severe skin and soft tissue infections, including impetigo, erysipelas, necrotizing fasciitis, as well as systemic and fatal infections including septicaemia and meningitis. Estimated annual incidence for invasive group A streptococcal infection (iGAS) in industrialised countries is approximately three per 100,000 per year. Typing is currently used in England and Wales to monitor bacterial strains of S...
2017: PeerJ
https://www.readbyqxmd.com/read/28461555/cell-scientist-to-watch-mitchell-guttman
#16
(no author information available yet)
Mitchell received a bachelor's degree in molecular and computational biology and a master's degree in computational biology and bioinformatics from the University of Pennsylvania. He then joined the laboratory of Eric Lander at the Broad Institute of MIT and Harvard and was awarded his PhD in 2012. The same year he was named in the Forbes '30 under 30: science and healthcare' list of rising stars and received an NIH early independence award. Mitchell subsequently moved to the California Institute of Technology as an Assistant Professor to establish his own laboratory...
May 1, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28460613/novel-information-about-neisseria-meningitides-identification-of-the-most-important-type-ii-toxin-antitoxin-systems
#17
Abbas Maleki, Sobhan Ghafourian, Behzad Badakhsh, Iraj Pakzad, Nourkhoda Sadeghifard
BACKGROUND: Toxin antitoxin systems is the one of the important elements among pathogenic bacteria ‎which have proven roles such as biofilm formation, cell programed death and persister cells formation‎. Neisseria meningitidis due to create of serious diseases in humans must be highlighted. OBJECTIVE: The current study aimed to identify of mazEF and relBE TA systems in N. meningitidis. METHOD: The potential TA loci were searched in database by bioinformatics analysis and then, experimental analysis was performed by PCR assay...
April 27, 2017: Infectious Disorders Drug Targets
https://www.readbyqxmd.com/read/28460352/characterization-of-nist-human-mitochondrial-dna-srm-2392-and-srm-2392-i-standard-reference-materials-by-next-generation-sequencing
#18
Sarah Riman, Kevin M Kiesler, Lisa A Borsuk, Peter M Vallone
Standard Reference Materials SRM 2392 and 2392-I are intended to provide quality control when amplifying and sequencing human mitochondrial genome sequences. The National Institute of Standards and Technology (NIST) offers these SRMs to laboratories performing DNA-based forensic human identification, molecular diagnosis of mitochondrial diseases, mutation detection, evolutionary anthropology, and genetic genealogy. The entire mtGenome (∼16569bp) of SRM 2392 and 2392-I have previously been characterized at NIST by Sanger sequencing...
April 15, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28453672/primerize-2d-automated-primer-design-for-rna-multidimensional-chemical-mapping
#19
Siqi Tian, Rhiju Das
Summary: Rapid RNA synthesis of comprehensive single mutant libraries and targeted multiple mutant libraries is enabling new multidimensional chemical approaches to solve RNA structures. PCR assembly of DNA templates and in vitro transcription allow synthesis and purification of hundreds of RNA mutants in a cost-effective manner, with sharing of primers across constructs allowing significant reductions in expense. However, these protocols require organization of primer locations across numerous 96 well plates and guidance for pipetting, non-trivial tasks for which informatics and visualization tools can prevent costly errors...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453671/wright-fisher-exact-solver-wfes-scalable-analysis-of-population-genetic-models-without-simulation-or-diffusion-theory
#20
Ivan Krukov, Bianca de Sanctis, A P Jason de Koning
Motivation: The simplifying assumptions that are used widely in theoretical population genetics may not always be appropriate for empirical population genetics. General computational approaches that do not require the assumptions of classical theory are therefore quite desirable. One such general approach is provided by the theory of absorbing Markov chains, which can be used to obtain exact results by directly analyzing population genetic Markov models, such as the classic bi-allelic Wright-Fisher model...
May 1, 2017: Bioinformatics
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