Advanced Molecular Detection Clips Content (Published on 11/15/2018)
Wanted: Big, Hairy Audacious Goals
(blog post) Brennan P. NLM Musings from the Mezzanine, Nov 13, 2018.
Hospitals Build Case for Pathogen Sequencing to Track Resistance, Monitor Outbreaks
Heger M. GenomeWeb, Nov 15, 2018.
First Universal Flu Vaccine to Enter Phase 3 Trial
Taylor AP. The Scientist, Nov 12, 2018.
Task force spotlights US tick-borne disease as cases set records
Schnirring L. CIDRAP, Nov 14, 2018.
A pivotal day in worlds response to Ebola nears: the launch of a clinical trial
Branswell H. STAT, Nov 12, 2018.
Improved mosquito genome points to population-control strategies
Celniker SE. Nature, Nov 14, 2018.
Do gut bacteria make a second home in our brains?
Servik K. Science, Nov 9,. 2018.
Finding a sensible approach to sensitive data.
et al. Scientific data 2018 Nov 180253
CONCEPTS / COMMENTS
Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.
Meisel Jacquelyn S et al. Microbiome 2018 Nov (1) 197
Familiar barriers still unresolved-a perspective on the Zika virus outbreak research response.
Koopmans Marion et al. The Lancet. Infectious diseases 2018 Nov
Translating microbiome futures.
Taroncher-Oldenburg Gaspar et al. Nature biotechnology 2018 Nov (11) 1037-1042
METHODS / TOOLS
panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data.
Treepong Panisa et al. Bioinformatics (Oxford, England) 2018 Nov (22) 3795-3800
Motif scraper: a cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files.
Roberson Elisha D O et al. Bioinformatics (Oxford, England) 2018 Nov (22) 3926-3928
PAIPline: pathogen identification in metagenomic and clinical next generation sequencing samples.
Andrusch Andreas et al. Bioinformatics (Oxford, England) 2018 Sep (17) i715-i721
Distributed retrieval engine for the development of cloud-deployed biological databases
Bouzaglo D, et al. BioData Mining, Nov 12, 2018.
Putting benchmarks in their rightful place: The heart of computational biology.
Peters Bjoern et al. PLoS computational biology 2018 Nov (11) e1006494
EVOLUTION / ECOLOGY / POPULATIONS
First Paleogenetic Evidence of Probable Syphilis and Treponematoses Cases in the Brazilian Colonial Period.
Guedes Lucélia et al. BioMed research international 2018 8304129
Translocation of a Stray Cat Infected with Rabies from North Carolina to a Terrestrial Rabies-Free County in Ohio, 2017.
Singh Amber J et al. MMWR. Morbidity and mortality weekly report 2018 Oct (42) 1174-1177
Whole genome sequencing of Trypanosoma cruzi field isolates reveals extensive genomic variability and complex aneuploidy patterns within TcII DTU.
Reis-Cunha João Luís et al. BMC genomics 2018 Nov (1) 816
Improved reference genome of Aedes aegypti informs arbovirus vector control
Matthews BJ, et al. Nature, Nov 14, 2018.
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
Phenotypic and Genotypic Characterization of Carbapenem-resistant Enterobacteriaceae: Data From a Longitudinal Large-scale CRE Study in China (2012-2016).
Wang Qi et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Nov (suppl_2) S196-S205
Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital.
Manara Serena et al. Genome medicine 2018 Nov (1) 82
The genetic diversity of multi and extensively drug resistant Mycobacterium tuberculosis in the capital of Iran revealed by whole genome sequencing.
Vaziri Farzam et al. Journal of clinical microbiology 2018 Nov
The phylogenomics of evolving virus virulence.
Geoghegan Jemma L et al. Nature reviews. Genetics 2018 Oct
Mutations in Plasmodium falciparum actin-binding protein coronin confer reduced artemisinin susceptibility.
Demas Allison R et al. Proceedings of the National Academy of Sciences of the United States of America 2018 Nov
DETECTION / DIAGNOSIS
A highly multiplexed broad pathogen detection assay for infectious disease diagnostics.
Koehler Jeffrey W et al. PLoS neglected tropical diseases 2018 Nov (11) e0006889
Microbiological Diagnostic Performance of Metagenomic Next-generation Sequencing When Applied to Clinical Practice.
Miao Qing et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Nov (suppl_2) S231-S240
Amplification-free, sequence-specific 16S rRNA detection at 1 aM.
Koo Bonhye et al. Lab on a chip 2018 07 (15) 2291-2299
Transmission of Mycobacterium tuberculosis From Patients Who Are Nucleic Acid Amplification Test Negative.
Xie Yingda L et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018 Nov (11) 1653-1659
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) proteomic profiling of cerebrospinal fluid in the diagnosis of enteroviral meningitis: a proof-of-principle study.
Torres Ignacio et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2018 Dec (12) 2331-2339
Increasing proportions of HIV-1 non-B subtypes and of NNRTI resistance between 2013 and 2016 in Germany: Results from the national molecular surveillance of new HIV-diagnoses.
Hauser Andrea et al. PloS one 2018 (11) e0206234
Bayesian Phylogeography and Pathogenic Characterization of Smallpox Based on HA, ATI, and CrmB Genes.
Adam Dillon C et al. Molecular biology and evolution 2018 Nov (11) 2607-2617
Development of Molecular Diagnosis Using Multiplex Real-Time PCR and T4 Phage Internal Control to Simultaneously Detect Cryptosporidium parvum, Giardia lamblia, and Cyclospora cayetanensis from Human Stool Samples.
Shin Ji-Hun et al. The Korean journal of parasitology 2018 Oct (5) 419-427
Simultaneous Quantification of Plasmodium Antigens and Host Factor CRP in Asymptomatic Individuals with Confirmed Malaria Using a Novel Multiplex Immunoassay.
Jang Ihn Kyung et al. Journal of clinical microbiology 2018 Nov
Multiplex real-time PCR for diagnosing malaria in a non-endemic setting: a prospective comparison to conventional methods.
Nijhuis R H T et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2018 Dec (12) 2323-2329
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
Creating a web-based electronic tool to aid tuberculosis (TB) cluster investigation: data integration in TB surveillance activities in the United Kingdom, 2013 to 2016.
Davidson Jennifer A et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2018 Nov (44)
Whole Genome Sequencing for Determining the Source of Mycobacterium bovis Infections in Livestock Herds and Wildlife in New Zealand.
Price-Carter Marian et al. Frontiers in veterinary science 2018 272
Echovirus type 6 transmission clusters and the role of environmental surveillance in early warning, the Netherlands, 2007 to 2016.
Monge Susana et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2018 Nov (45)
Characterisation of HIV-1 transmission clusters and drug-resistant mutations in Denmark, 2004 to 2016.
Petersen Andreas et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2018 Nov (44)
ANTIMICROBIALS / VACCINES / INTERVENTIONS
Influenza H5/H7 Virus Vaccination in Poultry and Reduction of Zoonotic Infections, Guangdong Province, China, 2017-18.
Wu Jie et al. Emerging infectious diseases 2019 Jan (1)
An Open-Labeled Study on Fecal Microbiota Transfer in Irritable Bowel Syndrome Patients Reveals Improvement in Abdominal Pain Associated with the Relative Abundance of Akkermansia Muciniphila.
Cruz-Aguliar Rebeca M et al. Digestion 2018 Nov 1-12
Genetic Predisposition to Infectious Disease.
Klebanov Nikolai et al. Cureus 2018 Aug (8) e3210
Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression
Schmiedel BJ, et al. Cell, Nov 15, 2018.
Prevalence of inherited blood disorders and associations with malaria and anemia in Malawian children.
McGann Patrick T et al. Blood advances 2018 Nov (21) 3035-3044
Human bacterial repertoire of the urinary tract: a potential paradigm shift.
Morand Aurélie et al. Journal of clinical microbiology 2018 Nov
Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer.
Shah Manasi S et al. PloS one 2018 (11) e0207002
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