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Items tagged with: bioinformatics
I wanted to share with you a new thing I'm working on: https://biohandbook.me/
It's a resource for practical best practices and tips to use in bioinformatic analyses. The idea is to work together to define standards and workflows and write them down. I love the open science, FAIR data and FAIR code philosophy but there are not many easy-to-use and direct resources around to actually tell you how to do things in the bioinformatics world.
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#bioinformatics #handbook #OpenScience
The Handbook
The Handbook # Welcome to Hedmad’s Handbook of Nice and Practical Tips! 🎉 This handbook aims to: Collect useful and practical day-to-day tips on how to conduct bioinformatics analyses; Set standards for data formats, workflows, project structure and …biohandbook.me
So many good points in this piece by
@PhilippBayer
My highlight in this screenshot (#science delivery & success is a TEAM effort!), but if you're vaguely involved in #academia +/- #bioinformatics, do have a read and think how it all may apply to you. #academicchatter @academicchatter
https://genomic.social/@PhilippBayer/110644840476993836
A new blog-post: the two cultures of bioinformatics, and how academia selects against one https://philippbayer.github.io/blerg/posts/2023_07_02_the_two_cultures/
Hello everyone!
I’m an associate prof at Virginia Tech studying viral diversity. Lately my group has been focusing on giant viruses, but we are also interested in other protist viruses, and the role of viral endogenization in host genome evolution.
#GiantViruses #ViralDiversity #TreeOfLife #Protists #Microbiology #Bioinformatics #Evolution #Virology #Genomics
Recently we have been examining the strange and complex genes encoded in giant virus genomes!
https://doi.org/10.1093/femsre/fuad053
Studying some phage genes with scattered, partial alignments in varying degrees (40~+90%) of ID against closely related cousins (~93% ANI).
I'm thinking intragenic insertion/shuffling - but what kind of signals could I look for here? Common scars? Models to reference? #phage #bioinformatics #genomics
https://www.biorxiv.org/content/10.1101/2023.06.03.543588v1 #bioinformatics #HumanGenome #genomics
miniBUSCO: a faster and more accurate reimplementation of BUSCO
Motivation Assembly completeness evaluation of genome assembly is a critical assessment of the accuracy and reliability of genomic data. An incomplete assembly can lead to errors in gene predictions, annotation, and other downstream analyses.bioRxiv
Accounting for 16S rRNA copy number prediction uncertainty and its implications in bacterial diversity analyses
https://www.nature.com/articles/s43705-023-00266-0
#microbiology #bioinformatics #microbiome
Accounting for 16S rRNA copy number prediction uncertainty and its implications in bacterial diversity analyses - ISME Communications
ISME Communications - Accounting for 16S rRNA copy number prediction uncertainty and its implications in bacterial diversity analysesNature
https://doi.org/10.1038/s43705-023-00259-z
#microbiology #bioinformatics
Distribution and diversity of ‘Tectomicrobia’, a deep-branching uncultivated bacterial lineage harboring rich producers of bioactive metabolites - ISME Communications
ISME Communications - Distribution and diversity of ‘Tectomicrobia’, a deep-branching uncultivated bacterial lineage harboring rich producers of bioactive metabolitesNature
Master or PhD positions
University of Ottawa
Master and PhD in #Canada fully funded positions in #bioinformatics
See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-ottawa-27778-master-or-phd-positions/?feed_id=46627
#ScienceJobs #hiring #research #bioinformatics #machine learning
Ottawa #Canada #PhDStudent #ResearchAssistant
https://jobrxiv.org/job/university-of-ottawa-27778-master-or-phd-positions/?feed_id=46627
Master or PhD positions
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!jobRxiv
The best practice for microbiome analysis using R
Abstract. With the gradual maturity of sequencing technology, many microbiome studies have published, driving the emergence and advance of related analysis toolWen, Tao (Oxford University Press)
https://www.nature.com/articles/d41586-023-01300-w
#genomics #bioinformatics
Every base everywhere all at once: pangenomics comes of age
Multi-genome assemblies called pangenomes can capture genetic diversity in a species, but researchers are still working out how best to build and explore them.Eisenstein, Michael
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011032
#genomics #bioinformatics
JASPER: A fast genome polishing tool that improves accuracy of genome assemblies
Advances in long-read sequencing technologies have dramatically improved the contiguity and completeness of genome assemblies.journals.plos.org
A field-wide assessment of differential expression profiling by high-throughput sequencing reveals widespread bias
A large-scale examination of differential RNA expression study datasets submitted to the NCBI GEO repository from 2008-2020 reveals widespread bias, as assessed by the distribution of p values and estimated proportions of true null hypotheses.doi.org
An overview of bioinformatics courses delivered at the academic level in Italy: Reflections and recommendations from BITS
In Italian universities, bioinformatics courses are increasingly being incorporated into different study paths.journals.plos.org
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05144-z
#bioinformatics #pathogens #viruses
Pathogen detection in RNA-seq data with Pathonoia - BMC Bioinformatics
Background Bacterial and viral infections may cause or exacerbate various human diseases and to detect microbes in tissue, one method of choice is RNA sequencing.BioMed Central
https://www.biorxiv.org/content/10.1101/2023.02.18.529053v1
#phylogeny #phylogenomics #bioinformatics #BigData #visualization #vizbi #myxozoan @dee_unil
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Matreex: compact and interactive visualisation of large gene families provides evidence for loss of intraflagellar transport in a myxozoan
Studying gene family evolution strongly benefits from insightful visualisations. However, the ever-growing number of sequenced genomes is leading to increasingly larger gene families, which challenges existing gene tree visualisations.bioRxiv
High-resolution metagenomic reconstruction of the freshwater spring bloom - Microbiome
Background The phytoplankton spring bloom in freshwater habitats is a complex, recurring, and dynamic ecological spectacle that unfolds at multiple biological scales.BioMed Central
@NCBI
nt and nr (I certainly have!)
From https://youtu.be/2FW1dk5YQ3I?t=484 and https://youtu.be/KLBE0AuH-Sk?t=692 (cued to the right spots in the video)
#Bioinformatics #Genomics
NCBI Minute: Using BLAST Well
Presented October 3, 2018. In this webinar, the NCBI BLAST team lead will show you how to be more effective with NCBI’s standalone BLAST applications. You wi...YouTube
https://apply.interfolio.com/118539
RT 😀
What other genomics/evolution classics do people always keep around?
#genomics #bioinformatics #evolution #microbiology
