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https://www.readbyqxmd.com/read/28914640/machine-learning-novel-bioinformatics-approaches-for-combating-antimicrobial-resistance
#1
Nenad Macesic, Fernanda Polubriaginof, Nicholas P Tatonetti
PURPOSE OF REVIEW: Antimicrobial resistance (AMR) is a threat to global health and new approaches to combating AMR are needed. Use of machine learning in addressing AMR is in its infancy but has made promising steps. We reviewed the current literature on the use of machine learning for studying bacterial AMR. RECENT FINDINGS: The advent of large-scale data sets provided by next-generation sequencing and electronic health records make applying machine learning to the study and treatment of AMR possible...
September 12, 2017: Current Opinion in Infectious Diseases
https://www.readbyqxmd.com/read/28905878/detecting-splicing-patterns-in-genes-involved-in-hereditary-breast-and-ovarian-cancer
#2
Grégoire Davy, Antoine Rousselin, Nicolas Goardon, Laurent Castéra, Valentin Harter, Angelina Legros, Etienne Muller, Robin Fouillet, Baptiste Brault, Anna S Smirnova, Fréderic Lemoine, Pierre de la Grange, Marine Guillaud-Bataille, Virginie Caux-Moncoutier, Claude Houdayer, Françoise Bonnet, Cécile Blanc-Fournier, Pascaline Gaildrat, Thierry Frebourg, Alexandra Martins, Dominique Vaur, Sophie Krieger
Interpretation of variants of unknown significance (VUS) is a major challenge for laboratories performing molecular diagnosis of hereditary breast and ovarian cancer (HBOC), especially considering that many genes are now known to be involved in this syndrome. One important way these VUS can have a functional impact is through their effects on RNA splicing. Here we present a custom RNA-Seq assay plus bioinformatics and biostatistics pipeline to analyse specifically alternative and abnormal splicing junctions in 11 targeted HBOC genes...
October 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28895579/a-sexually-dimorphic-peptidergic-system-in-the-lower-spinal-cord-controlling-penile-function-in-non-human-primates
#3
T Ito, T Oti, K Takanami, K Satoh, Y Ueda, T Sakamoto, H Sakamoto
STUDY DESIGN: Experimental animal study. OBJECTIVES: Although a population of gastrin-releasing peptide (GRP) neurons in the lumbar spinal cord has an important role in erection and ejaculation in rats, little information exists on this GRP system in primates. To identify the male-specific GRP system in the primate spinal cord, we studied the lumbosacral cord in macaque monkeys as a non-human primate model. SETTING: University laboratory in Japan...
September 12, 2017: Spinal Cord
https://www.readbyqxmd.com/read/28890761/hypothetical-protein-bpsl3393-of-burkholderia-pseudomallei-is-involved-in-ethanolamine-catabolism
#4
Ooi Gim Luan, Hokchai Yam, Razip Samian, Mustafa Fadzil Farid Wajidi, Nor Muhammad Mahadi, Suriani Mohamad, Nazalan Najimudin
Burkholderia pseudomallei is a soil-dwelling bacterium that causes a globally emerging disease called melioidosis. Approximately one third of the in silico annotated genes in its genome are classified as hypothetical genes. This group of genes is difficult to be functionally characterised partly due to the absence of noticeable phenotypes under conventional laboratory settings. A bioinformatic survey of hypothetical genes revealed a gene designated as BPSL3393 that putatively encodes a small protein of 11 kDA with a CoA binding domain...
July 2017: Tropical Life Sciences Research
https://www.readbyqxmd.com/read/28883610/analysis-of-bioactive-amino-acids-from-fish-hydrolysates-with-a-new-bioinformatic-intelligent-system-approach
#5
Mohamed Abd Elaziz, Ahmed Monem Hemdan, AboulElla Hassanien, Diego Oliva, Shengwu Xiong
The current economics of the fish protein industry demand rapid, accurate and expressive prediction algorithms at every step of protein production especially with the challenge of global climate change. This help to predict and analyze functional and nutritional quality then consequently control food allergies in hyper allergic patients. As, it is quite expensive and time-consuming to know these concentrations by the lab experimental tests, especially to conduct large-scale projects. Therefore, this paper introduced a new intelligent algorithm using adaptive neuro-fuzzy inference system based on whale optimization algorithm...
September 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28881996/improved-data-driven-likelihood-factorizations-for-transcript-abundance-estimation
#6
Mohsen Zakeri, Avi Srivastava, Fatemeh Almodaresi, Rob Patro
Motivation: Many methods for transcript-level abundance estimation reduce the computational burden associated with the iterative algorithms they use by adopting an approximate factorization of the likelihood function they optimize. This leads to considerably faster convergence of the optimization procedure, since each round of e.g. the EM algorithm, can execute much more quickly. However, these approximate factorizations of the likelihood function simplify calculations at the expense of discarding certain information that can be useful for accurate transcript abundance estimation...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28878141/intestinal-and-circulating-micrornas-in-coeliac-disease
#7
REVIEW
Cristina Felli, Antonella Baldassarre, Andrea Masotti
MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression at the post-transcriptional level and play a key role in the pathogenesis of autoimmune and gastrointestinal diseases. Previous studies have revealed that miRNAs are dysregulated in intestinal biopsies of patients affected by coeliac disease (CD). Combined bioinformatics analyses of miRNA expression profiles and mRNA target genes as classified by Gene Ontology, are powerful tools to investigate the functional role of miRNAs in coeliac disease...
September 6, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28874442/use-of-next-generation-sequencing-to-detect-ldlr-gene-copy-number-variation-in-familial-hypercholesterolemia
#8
Michael A Iacocca, Jian Wang, Jacqueline S Dron, John F Robinson, Adam D McIntyre, Henian Cao, Robert A Hegele
Familial hypercholesterolemia (FH) is a heritable condition of severely elevated LDL cholesterol, caused predominantly by autosomal codominant mutations in the LDL receptor gene (LDLR). In providing a molecular diagnosis for FH, the current procedure often includes targeted next-generation sequencing (NGS) panels for the detection of small-scale DNA variants, followed by multiplex ligation-dependent probe amplification (MLPA) in LDLR for the detection of whole-exon copy number variants (CNVs). The latter is essential as ~10% of FH cases are attributed to CNVs in LDLR; accounting for them decreases false negative findings...
September 5, 2017: Journal of Lipid Research
https://www.readbyqxmd.com/read/28867564/different-histories-of-two-highly-variable-ltr-retrotransposons-in-sunflower-species
#9
Flavia Mascagni, Andrea Cavallini, Tommaso Giordani, Lucia Natali
In the Helianthus genus, very large intra- and interspecific variability related to two specific retrotransposons of Helianthus annuus (Helicopia and SURE) exists. When comparing these two sequences to sunflower sequence databases recently produced by our lab, the Helicopia family was shown to belong to the Maximus/SIRE lineage of the Sirevirus genus of the Copia superfamily, whereas the SURE element (whose superfamily was not even previously identified) was classified as a Gypsy element of the Ogre/Tat lineage of the Metavirus genus...
August 31, 2017: Gene
https://www.readbyqxmd.com/read/28861524/deep-sequencing-of-rna-from-blood-and-oral-swab-samples-reveals-the-presence-of-nucleic-acid-from-a-number-of-pathogens-in-patients-with-acute-ebola-virus-disease-and-is-consistent-with-bacterial-translocation-across-the-gut
#10
Miles W Carroll, Sam Haldenby, Natasha Y Rickett, Bernadett Pályi, Isabel Garcia-Dorival, Xuan Liu, Gary Barker, Joseph Akoi Bore, Fara Raymond Koundouno, E Diane Williamson, Thomas R Laws, Romy Kerber, Daouda Sissoko, Nóra Magyar, Antonino Di Caro, Mirella Biava, Tom E Fletcher, Armand Sprecher, Lisa F P Ng, Laurent Rénia, N'faly Magassouba, Stephan Günther, Roman Wölfel, Kilian Stoecker, David A Matthews, Julian A Hiscox
In this study, samples from the 2013-2016 West African Ebola virus outbreak from patients in Guinea with Ebola virus disease (EVD) were analyzed to discover and classify what other pathogens were present. Throat swabs were taken from deceased EVD patients, and peripheral blood samples were analyzed that had been taken from patients when they presented at the treatment center with acute illness. High-throughput RNA sequencing (RNA-seq) and bioinformatics were used to identify the potential microorganisms. This approach confirmed Ebola virus (EBOV) in all samples from patients diagnosed as acute positive for the virus by quantitative reverse transcription-PCR in deployed field laboratories...
July 2017: MSphere
https://www.readbyqxmd.com/read/28859346/data-science-priorities-for-a-university-hospital-based-institute-of-infectious-diseases-a-viewpoint
#11
Alain-Jacques Valleron
Automation of laboratory tests, bioinformatic analysis of biological sequences, and professional data management are used routinely in a modern university hospital-based infectious diseases institute. This dates back to at least the 1980s. However, the scientific methods of this 21st century are changing with the increased power and speed of computers, with the "big data" revolution having already happened in genomics and environment, and eventually arriving in medical informatics. The research will be increasingly "data driven," and the powerful machine learning methods whose efficiency is demonstrated in daily life will also revolutionize medical research...
August 15, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28859321/course-based-undergraduate-research-experiences-in-molecular-biosciences-patterns-trends-and-faculty-support
#12
Jack T H Wang
Inquiry-driven learning, research internships and course-based undergraduate research experiences all represent mechanisms through which educators can engage undergraduate students in scientific research. In life sciences education, the benefits of undergraduate research have been thoroughly evaluated, but limitations in infrastructure and training can prevent widespread uptake of these practices. It is not clear how faculty members can integrate complex laboratory techniques and equipment into their unique context, while finding the time and resources to implement undergraduate research according to best practice guidelines...
August 15, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28855395/rare-autosomal-trisomies-revealed-by-maternal-plasma-dna-sequencing-suggest-increased-risk-of-feto-placental-disease
#13
Mark D Pertile, Meredith Halks-Miller, Nicola Flowers, Catalin Barbacioru, Sarah L Kinnings, Darcy Vavrek, William K Seltzer, Diana W Bianchi
Whole-genome sequencing (WGS) of maternal plasma cell-free DNA (cfDNA) can potentially evaluate all 24 chromosomes to identify abnormalities of the placenta, fetus, or pregnant woman. Current bioinformatics algorithms typically only report on chromosomes 21, 18, 13, X, and Y; sequencing results from other chromosomes may be masked. We hypothesized that by systematically analyzing WGS data from all chromosomes, we could identify rare autosomal trisomies (RATs) to improve understanding of feto-placental biology...
August 30, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28854630/does-the-promoter-constitute-a-barrier-in-the-horizontal-transposon-transfer-process-insight-from-bari-transposons
#14
Antonio Palazzo, Ruggiero Caizzi, Luigi Viggiano, René Massimiliano Marsano
The contribution of the transposons' promoter in the horizontal transfer process is quite overlooked in the scientific literature. To shed light on this aspect we have mimicked the horizontal transfer process in laboratory and assayed in a wide range of hosts (fly, human, yeast and bacteria) the promoter activity of the 5' terminal sequences in Bari1 and Bari3, two Drosophila transposons belonging to the Tc1-mariner superfamily. These sequences are able to drive the transcription of a reporter gene even in distantly related organisms at least at the episomal level...
June 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28854616/bio-docklets-virtualization-containers-for-single-step-execution-of-ngs-pipelines
#15
Baekdoo Kim, Thahmina Ali, Carlos Lijeron, Enis Afgan, Konstantinos Krampis
Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis...
August 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28843296/research-techniques-made-simple-bioinformatics-for-genome-scale-biology
#16
Amy C Foulkes, David S Watson, Christopher E M Griffiths, Richard B Warren, Wolfgang Huber, Michael R Barnes
High-throughput biology presents unique opportunities and challenges for dermatological research. Drawing on a small handful of exemplary studies, we review some of the major lessons of these new technologies. We caution against several common errors and introduce helpful statistical concepts that may be unfamiliar to researchers without experience in bioinformatics. We recommend specific software tools that can aid dermatologists at varying levels of computational literacy, including platforms with command line and graphical user interfaces...
September 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28838317/applying-next-generation-sequencing-with-microdroplet-pcr-to-determine-the-disease-causing-mutations-in-retinal-dystrophies
#17
Xinjing Wang, Wadih M Zein, Leera D'Souza, Chimere Roberson, Keith Wetherby, Hong He, Angela Villarta, Amy Turriff, Kory R Johnson, Yang C Fann
BACKGROUND: Inherited Retinal dystrophy (IRD) is a broad group of inherited retinal disorders with heterogeneous genotypes and phenotypes. Next generation sequencing (NGS) methods have been broadly applied for analyzing patients with IRD. Here we report a novel approach to enrich the target gene panel by microdroplet PCR. METHODS: This assay involved a primer library which targeted 3071 amplicons from 2078 exons comprised of 184 genes involved in retinal function and/or retinal development...
August 24, 2017: BMC Ophthalmology
https://www.readbyqxmd.com/read/28837856/secure-and-robust-cloud-computing-for-high-throughput-forensic-microsatellite-sequence-analysis-and-databasing
#18
Sarah F Bailey, Melissa K Scheible, Christopher Williams, Deborah S B S Silva, Marina Hoggan, Christopher Eichman, Seth A Faith
Next-generation Sequencing (NGS) is a rapidly evolving technology with demonstrated benefits for forensic genetic applications, and the strategies to analyze and manage the massive NGS datasets are currently in development. Here, the computing, data storage, connectivity, and security resources of the Cloud were evaluated as a model for forensic laboratory systems that produce NGS data. A complete front-to-end Cloud system was developed to upload, process, and interpret raw NGS data using a web browser dashboard...
August 8, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28836827/analyzing-the-lncrna-mirna-and-mrna-regulatory-network-in-prostate-cancer-with-bioinformatics-software
#19
Jin-Hua He, Ze-Ping Han, Mao-Xian Zou, Li Wang, Yu Bing Lv, Jia Bin Zhou, Ming-Rong Cao, Yu-Guang Li
Information processing tools and bioinformatics software have significantly advanced researchers' ability to process and analyze biological data. Molecular data from human and model organism genomes help researchers identify topics for study, which, in turn, improves predictive accuracy, facilitates the identification of relevant genes, and simplifies the validation of laboratory data. The objective of this study was to explore the regulatory network constituted by long noncoding RNA (lncRNA), miRNA, and mRNA in prostate cancer (PCa)...
August 24, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28830434/rational-confederation-of-genes-and-diseases-ngs-interpretation-via-genecards-malacards-and-varelect
#20
Noa Rappaport, Simon Fishilevich, Ron Nudel, Michal Twik, Frida Belinky, Inbar Plaschkes, Tsippi Iny Stein, Dana Cohen, Danit Oz-Levi, Marilyn Safran, Doron Lancet
BACKGROUND: A key challenge in the realm of human disease research is next generation sequencing (NGS) interpretation, whereby identified filtered variant-harboring genes are associated with a patient's disease phenotypes. This necessitates bioinformatics tools linked to comprehensive knowledgebases. The GeneCards suite databases, which include GeneCards (human genes), MalaCards (human diseases) and PathCards (human pathways) together with additional tools, are presented with the focus on MalaCards utility for NGS interpretation as well as for large scale bioinformatic analyses...
August 18, 2017: Biomedical Engineering Online
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