#pangenome — Public Fediverse posts

Cochetel & Cantu publish a new MBE Review on plant pangenomes, outlining major paradigms from gene-based catalogs to haplotype-resolved graphs, core and variable compartments, and how graph-based frameworks enable analyses that are difficult with single linear references.

🔗 https://doi.org/10.1093/molbev/msag087

#evobio #molbio #pangenome

Researchers decoded the #pangenome of 33 oat lines, revealing their full #geneticdiversity to support breeding of more resilient, high-yield #crops in the face of #climatechange: http://go.tum.de/651300

📷iStock/ Evgeniy Andreev

From Kozhikode to Dubai, Malayali geneticist Dr Nasna Nassir is making history — leading the Arab Pangenome Project that fills a critical gap in global medical research and opens new doors for personalised healthcare. https://english.mathrubhumi.com/news/kerala/malayali-scientist-develops-first-arab-pangenome-bridging-global-genetic-data-gap-sq7ecgsa?utm_source=dlvr.it&utm_medium=mastodon #Arab #Pangenome #Genomics #Genetics #Malayali

"We propose that at least part of the #pangenome can be understood as a set of #genes with relationships that govern their likely cohabitants, analogous to an ecosystem’s set of interacting organisms. Our findings indicate that intragenomic gene fitness effects may be key drivers of #prokaryotic #evolution, influencing the repeated emergence of complex gene–gene relationships across the pangenome."

https://www.pnas.org/doi/10.1073/pnas.2304934120

Some really great talks and discussions today on advances in virus-livestock omics at the #Turing institute, who kindly supported the event. Talks include those by Ge Wu and Marie Di Placido (pictures) from the #Pirbright Institute.

Great to have input from the #BBSRC and #SFTC #Harttree Centre too.

Looking forward to new adventures in this area...

#livestock #virus #genomics #antibody #genome #mutation #pangenome #omics #transcriptomics #spatialtranscriptomics #fmdv​

Last chance to register for our meeting "Advancing virus-livestock omics" on Thurs 28th Sept at the Alan Turing Institute.

Registration closes end of Mon 25th.

See https://www.turing.ac.uk/events/advancing-virus-livestock-omics

Register here: https://t.ly/wYA7d

Schedule below

Zoom stream possible for those from further afield

#livestock #virus #genomics #antibody #genome #mutation #pangenome #omics #transcriptomics #spatialtranscriptomics #fmdv

The future release of #delly2 will contain a 'Pan-genome based SV caller' https://github.com/dellytools/delly/commit/00bdb661f6524623a4da275c0beb4331d8f7d4a3#diff-7e4c9a6f514d8ac9f231bdc1ce58ddae1fa9bdbfb05f7055fc401d71d2039ee0R46 #sv #structuralvariant #pangenome #bioinformatics

Been working on a #pangenome tutorial comparing alignments with #minimap2 (left) and #seqseqpan (right) and adding genome features, including species-specific sequences, sequence similarity, TEs, and ATAC-seq (data from Heliconius butterflies). https://stevenvb12.github.io/

Been working on a #pangenome tutorial comparing alignments with #minimap2 (left) and #seqseqpan (right) and adding genome features, including species-specific sequences, sequence similarity, TEs, and ATAC-seq (data from Heliconius butterflies). https://stevenvb12.github.io/

The Genetics Of Temperature Adaptation: How Does Life Thrive In Extreme Conditions? https://astrobiology.com/2023/03/the-genetics-of-temperature-adaptation-how-does-life-thrive-in-extreme-conditions.html

The #methanogen core & #pangenome: conservation and variability across biology’s growth temperature extremes https://academic.oup.com/dnaresearch/article/30/1/dsac048/6862058

"#Methanogens can thrive across a range of temperature extremes, from -2.5 to 122 °C, making them ideal candidates to study temperature adaptation... Thermotolerant organisms had smaller genomes and a higher fraction of core genome."

Looking forward to presenting a poster at the leading #Cannabis Science Event, The #EmeraldConference, 1-3 March: “Exploring the full spectrum of genetic variation in Cannabis with Pantograph”. A #pangenome browser for better trait predictions 🧬👉 https://bit.ly/3kp1NkY


#Pantograph #visualization

I am late but here is my #introduction
I am a #genomics scientist at #IRD, French National Research institute for #sustainable development.
I use #bioinformatics, #NGS, #graph genome and #pangenome to understand the impact of #anthropization on #plant evolution... I have also some touch on #insect and #algae #genome, #antibiotic resistance, #vizualisation and so on.
I am also working for #openscience
And I am found of #rpg #ttrpg