BOL: Related items

NCBI to assist in Virus Hunting Data Science Hackathon

BioStar — Thu, 15 Nov 2018 12:55:01 -0600

NCBI Hackathon are pleased to announce the second installment of the SoCal Bioinformatics Hackathon. From January 9-11, 2019, the NCBI will help run a bioinformatics hackathon in Southern California hosted by the Computational Sciences Research Center at San Diego State University!

NCBI Hackathon specifically looking for folks who have experience in computational virus hunting or adjacent fields to identify known, taxonomically-definable and novel viruses from a few hundred thousand metagenomic datasets that we’ll put on cloud infrastructure. This event is for researchers, including students and postdocs, who are already engaged in the use of bioinformatics data or in the development of pipelines for virological analyses from high-throughput experiments. If this describes you, please apply! The event is open to anyone selected for the hackathon and willing to travel to SDSU (see below).

https://ncbiinsights.ncbi.nlm.nih.gov/2018/11/09/ncbi-sdsu-virus-hunting-data-science-hackathon-january-2019/

Langya Virus Update !

Neel — Fri, 12 Aug 2022 05:31:10 -0500

https://www.ncbi.nlm.nih.gov/nuccore/OM101125,OM101126,OM101127,OM101128,OM101129,OM101130?

Zoonotic Henipavirus

https://pubmed.ncbi.nlm.nih.gov/35921459/

https://www.ncbi.nlm.nih.gov/nuccore/OM069646,,OM069567,OM069568,OM069569,OM069570,OM069571,OM069572,OM069573,OM069574,OM069575,OM069576,OM069577,OM069578,OM069579,OM069580,OM069581,OM069582,OM069583,OM069584,OM069585,OM069586,OM069587,OM069588,OM069589,OM069590,OM069591,OM069592,OM069593,OM069594,OM069595,OM069596,OM069597,OM069598,OM069599,OM069600,OM069601,OM069602,OM069603,OM069604,OM069605,OM069606,OM069607,OM069608,OM069609,OM069610,OM069611,OM069612,OM069613,OM069614,OM069615,OM069616,OM069617,OM069618,OM069619,OM069620,OM069621,OM069622,OM069623,OM069624,OM069625,OM069626,OM069627,OM069628,OM069629,OM069630,OM069631,OM069632,OM069633,OM069634,OM069635,OM069636,OM069637,OM069638,OM069639,OM069640,OM069641,OM069642,OM069643,OM069644,OM069645,OM069646

UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment

BioStar — Mon, 05 Aug 2024 23:01:29 -0500

UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment

Using state of the art tools, easily extended for other viruses
Tool and database updates for critical components via Conda
Built using modern design patterns with Conda and Snakemake
Extensible and easy to customize
Submission Ready Genomes
Customizable reporting with comprehensive visualization

https://ikim-essen.github.io/uncovar/

Github https://github.com/IKIM-Essen/uncovar

Address of the bookmark: https://ikim-essen.github.io/uncovar/

Coronavirus Resources !

Neel — Wed, 25 Mar 2020 17:11:33 -0500

2019nCoVR features comprehensive integration of genomic and proteomic sequences as well as their metadata information from the GISAID, NCBI, NMDC and CNCB/NGDC. It also incorporates a wide range of relevant information including scientific literatures, news, and popular articles for science dissemination, and provides visualization functionalities for genome variation analysis results based on all collected 2019-nCoV strains.

Annotation

https://bigd.big.ac.cn/ncov/variation/annotation

Genome wharehouse

https://bigd.big.ac.cn/gwh/browse/index

Released Genome

https://bigd.big.ac.cn/ncov/release_genome

Download data

ftp://download.big.ac.cn/Genome/Viruses/Coronaviridae/

Raw data

https://bigd.big.ac.cn/gsa/browse/run/?tag=Coronaviridae

Address of the bookmark: https://bigd.big.ac.cn/ncov/about

Calling variants in non-diploid systems

Neel — Sat, 26 Jun 2021 15:37:49 -0500

The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been accomplished on human mitochondrial DNA although the same approaches will work equally good on viral and bacterial genomes (Rebolledo-Jaramillo et al. 2014, Li et al. 2015).

Address of the bookmark: https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html

What is Healthcare Informatics?

Wed, 12 Mar 2014 14:49:54 -0500

Incorporating information technologies and information management, this work describes evolving areas of efficiency in the healthcare industry due to healthcare informatics enhancements. Beginning with an overview of how information management can enhance organizational efficiency the book delves into how informatics can impact productivity for healthcare providers and reduce costs. It stresses the incorporation of available information technologies along with appropriate management tactics to ensure the most effective informatics outcomes that can drive efficiencies. Areas that are addressed include project management in healthcare, knowledge management, decision support systems, business intelligence, Six Sigma, and advanced analytics such as data mining.

WuXi has acquired NextCODE Health

Pranjali Yadav — Mon, 19 Jan 2015 08:17:35 -0600

Shanghai, China-headquartered pharmatech company WuXi (NYSE: WX) has acquired NextCODE Health, a genomic analysis and bioinformatics company based in the USA.

The acquisition was made for $65 million in cash, and WuXi plans to merge its genome center with NextCODE Health to form a new company, WuXi NextCODE Genomics. The business will be headquartered in Shanghai and have operations in Cambridge, Massachusetts, and Reykjavik, Iceland.

With the huge unmet medical needs in diseases with a genetic component and the rapid advances in genomics and bioinformatics, now is the right time for WuXi to make a strategic investment in this field, and NextCODE is the right partner. This new venture of WuXi NextCODE Genomics will create important new genomic and bioinformatic products and services to help make personalized treatment and medicine a reality. It will also enable doctors to provide better treatments to patients.

Early Genome Screening: The New Health Horoscope!

LEGE — Thu, 02 Jan 2025 19:44:36 -0600

In an era where precision medicine is reshaping healthcare, genome screening is emerging as the modern equivalent of a health horoscope. It offers insights into our biological "stars," unraveling predispositions to various conditions and empowering individuals with knowledge to navigate their health journeys proactively. But how reliable is this "horoscope," and how does it impact our lives?

Understanding Genome Screening

Genome screening involves analyzing an individual's DNA to identify genetic variations that may influence health and disease susceptibility. This can range from simple single-gene tests to comprehensive whole-genome sequencing. By peering into our genetic blueprint, we can uncover risks for conditions like cancer, diabetes, cardiovascular diseases, and even rare genetic disorders.

The process is straightforward: a saliva or blood sample is collected, and advanced sequencing technologies decipher the genetic code. The results provide a personalized health map, guiding lifestyle modifications, preventive measures, or medical interventions.

A Shift from Reactive to Proactive Healthcare

Traditional healthcare often focuses on treating diseases after they manifest. Genome screening flips this model on its head, enabling a shift toward prevention and early intervention. For instance:

Cancer Risk Management: Individuals with BRCA1 or BRCA2 gene mutations can opt for enhanced screening programs or preventive surgeries to mitigate their risk of breast and ovarian cancers.
Cardiovascular Health: Genetic predispositions to conditions like familial hypercholesterolemia can prompt early cholesterol monitoring and lifestyle adjustments.
Rare Diseases: Identifying carriers of genetic disorders can aid in family planning and reduce the incidence of inherited conditions.

The Ethical and Practical Concerns

While genome screening offers incredible promise, it is not without challenges:

Accuracy and Interpretation: Genetic predisposition does not guarantee disease. Misinterpretation of results can lead to unnecessary anxiety or unwarranted medical interventions.
Privacy and Data Security: Genetic data is highly sensitive. Ensuring robust data protection measures is crucial to prevent misuse.
Accessibility and Equity: High costs and limited availability may restrict access to genome screening, exacerbating health disparities.

Balancing Science and Pseudoscience

The comparison of genome screening to horoscopes isn’t entirely unfounded. Both offer predictive insights, but the scientific foundation of genome screening distinguishes it from astrology. Unlike the alignment of celestial bodies, genetic predictions are based on rigorous data and evidence. However, the probabilistic nature of genetic predispositions underscores the importance of interpreting results in conjunction with clinical and lifestyle factors.

The Road Ahead

As genome screening becomes more affordable and integrated into routine healthcare, its potential to transform lives is immense. Policymakers, healthcare providers, and genetic counselors must collaborate to ensure ethical implementation, public awareness, and equitable access.

Imagine a future where your genetic "horoscope" is a trusted guide, not just a prediction. Early genome screening could help chart a healthier path for generations, making it a cornerstone of personalized medicine. After all, our genes might just hold the key to unlocking a future of better health and well-being.

Genomic Medicine - Bruce Korf (2014)

Tue, 24 Jun 2014 07:58:44 -0500

May 21, 2014 - Current Topics in Genome Analysis 2014 A lecture series covering contemporary areas in genomics and bioinformatics. More: http://www.genome.gov/COURSE2014

The Sheppard Lab

Fri, 09 Aug 2024 02:48:34 -0500

Ineos Oxford Institute of Antimicrobial Research – Department of Biology – University of Oxford

Our research centres on the use of genetics/genomics and phenotypic studies to address complex questions in the ecology, epidemiology and evolution of microbes. Our most recent interest focuses upon comparative genome analysis to describe the core and flexible genome of pathogenic bacteria (Campylobacter, Acinetobacter, Escherichia coli, Helicobacter, Staphylococcus and Streptococcus suis) and how this is related to population genetic structuring, the maintenance of species, and the evolution of host/niche adaptation and virulence.

More at https://sheppardlab.com/research/