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Next up, Jonathan Mudge presents Producing reference gene annotation for the human pangenome. #GenomeInformatics24

Next up, Caitlin Collins presenting "Molecular clocks in the accessory genome?: Investigating rates of gene gain, loss, and selection". #GenomeInformatics24

V interesting thread on using LoganSearch to find fusions

62.7% of total system energy is spent on data movement during processing. We want to lower energy costs by moving computation close to memory by moving compute to DRAM.

It is clear that Roland Faure knows the cardinal rule of presenting on sequencing algorithms, you never talk about the reverse complement. #genomeinformatics24 Very cool work on reducing sequencing using sketches that are sequences and can be fed into other assembly algorithms

Many thanks to Zamin Iqbal Pall Melsted and Nicky Mulder for a great meeting Wellcome Connecting Science Learning and Training. We met old friends, learned a lot, and made new connections for future research directions.

Prof Kristie Dotson giving the The Royal Institute of Philosophy Cardiff University annual lecture 2024 on epistemic frailty and the need for philosophical artists - hosted by our own A. N. 🌈 🍂 - exciting, confounding, inspiring 🔥

csvtk users, if you use `filter2/mutate2/mutate3` a lot like me, please update it to v0.31.1. I've fixed the slow speed since v0.27.0 (Aug 2023)😅. Conda-forge and Bioconda are not synced now. please download the binaries from GitHub. github.com/shenwei356/csv…

Massive away win for the little fella.

My kid came home from school yesterday and told me his class is supposed to dress up as Elvis for morning assembly. I told him I think he means elves. He disagreed. I can’t wait to hear how his day went when ‘The King’ returns home.

Update: He just got home and he doesn’t want to talk about it.

BREAKING: Donald Trump has ordered a communications blackout at America's federal health agencies, per WaPo. The CDC, FDA, HHS and NIH have all been told to pause external communications, including publishing scientific reports, updating websites or issuing health advisories.

Thrilled that our work on this problem with Karel Břinda, Zamin Iqbal, and others is out in Nature Methods today! We used phylogenetic compression (described in the thread) to compress every microbe ever sequenced onto a flash drive so that it can be searched with a laptop!

A decade ago, we had thousands of bacterial genomes. Now, we have millions. How to scale computational methods? Our paper in Nature Methods answers this: use evolutionary history to guide compression and search. …From terabytes to tens of GBs… w/@Baym Zamin Iqbal et al. 🧵1/

The number of sequenced microbes is growing exponentially, but computational power grows at a slower rate. The result? BLAST – the "Google of biology" – can search only a fraction of sequenced microbes, and that fraction is shrinking exponentially over time. 2/

🚨 Just out in Science: 2/3 of bacterial gene families have a preferred position on the chromosome—and natural selection put them there! science.org/doi/10.1126/sc… Heinrich-Heine-Universität Düsseldorf CEPLAS

Tomorrow at the Systems Virology Journal Club, Tamanash Bhattacharya will present his beautiful work with Harmit S. Malik on optimizing temperature-dependent trade-off between protein production and processing in alphaviruses through stop codon selectivity pubmed.ncbi.nlm.nih.gov/40249804/

Carl Sagan was really ahead of his time. Absolutely prescient quote from one of his final interviews.

Most people don’t get that “Harvard” isn’t one thing, it’s three: a fictional college, a shorthand for elitism, and a real school with smart, dedicated people The administration thinks they are attacking the first, justifying it with the second, and it’s the third who get hurt

Very glad to see this preprint by Heng Li and @meyersonlab confirming our finding of artifactual fold-back INV in long reads (Fig S1 in our Nature Methods paper presenting #SAVANA, which filters such artifacts to improve SV calling, hence their relevance nature.com/articles/s4159…