If you missed my presentation at #BOSC2024, I just put up a version on YouTube

Paper at: https://doi.org/10.1371/journal.pcbi.1011920

https://youtu.be/yCgvvVQJE9I

@themaklin @EricPelletier @Pashadag

This is now published at PLOS CB!
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011920

Streaming in one hour

https://www.youtube.com/live/ydv9djKM7Oo

Nice N&V Forum by @JakobWirbel, Ami Bhatt, Alexander Probst discussing how this study and the related Rodríguez del Río et al. provide insight into the vast structural and functional diversity of previously unknown microbial protein families

https://www.nature.com/articles/d41586-024-00077-w

@LBNLBioSci @apcamargo @BorkLab @luispedro @alvarordr

@thomieh we will look everywhere using the GMGCv1 dataset

https://www.nature.com/articles/s41586-021-04233-4

New experiment: I will work on a project (starting question: what antibiotic resistance genes co-occur in genomes/metagenomes and does it matter?) completely in the open

Everyone is welcome!

First stream is on Monday/Tuesday (depending on your timezone)

https://youtu.be/0aX6b9z5uNo

A new preprint from the lab of @luispedro in collaboration with our group, making use of our SPIRE database of global microbiome data to identify 965 million non-redundant small open reading frames (<100 amino acids) https://www.biorxiv.org/content/10.1101/2023.12.27.573469v1?med=mas

New video: "The GMGC as a window into the global microbiome" on YouTube
https://youtu.be/L7YWtYVoI8U

We biology geeks may sound elitist when we use scientific names instead of common names, but we're really just trying to avoid this:

powerful datavis can be simple and non-graphical.

here's a project of mine from a good while ago: "autocomplete" for passwords, based on all passwords extracted from the "collection leaks".

https://passwords.yetzt.me/

metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies https://doi.org/10.1186/s13059-022-02810-y #microbiology #bioinformatics

Hi, I guess this is my #introduction? I'm a Bioinformatics student interested in machine learning, genomics, and in vivo gene therapy. When I'm not doing science, I'm usually obsessing over your dog, being a coffee snob, running my beer club, or I'm at the hockey rink.

Now, I promise I'm good at computer science, but my skills seem to be limited to science and I am not understanding how on EARTH to log onto this platform directly from the app 😂

A variety of thought-provoking findings and hypotheses, but a bottom line well-known to most PIs: the productivity of our labs is primarily dependent on our trainees.

Cherish and support them.

https://www.science.org/doi/10.1126/sciadv.abq7056?utm_campaign=SciAdv&utm_source=Twitter&utm_medium=ownedSocial

Inspecting further, we saw many proteins show very poor correlation with their cognate mRNA but instead a strong correlation with another transcript, which are usually but not always their known protein-protein interaction partners.

@siderophores you can do First Author, Second Author,..., Your Name,..., Second to Last Author, Last Author

metaMIC manuscript by Senying Lai et al. out at GenomeBiology!

Can we identify missassembled contigs? Can we fix them?

Not always, but often yes

Looking at read mappings and sequence features, we can identify situations where the assemblers got it wrong

Missassembled contigs are relatively rare, but binning corrected contigs leads to a 10-20% in the number of high-quality bins obtained

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02810-y

So now that I'm satisfied that I might be on #Mastodon #FediVerse for a while, here is my #introduction. I am computational biologist interested in protein function prediction, microbial #genome #evolution. Since #biology is now a #BigData #science, I am also looking into various #DataScience aspects of biological #data especially data #bias and #imbalance, and how these biases affect our understanding of #life.

#NewPaper — how does #HGT affect #microbiome dynamics and stability?

Using models + experiments we show that mobile resistance genes generally increase microbiome stability. But effects can differ markedly for donors and recipients of mobile genes and also depends on how species interact — sometimes causing entirely opposing effects on the stability of different species

#AMR #Plasmid

@PLOSBiology

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001847

@iddux the system used to allow me to change the deadlines and I would try to do so, but no longer

PSA: If I, as an academic editor for PLOS Comp Bio, invite you as a reviewer, be aware that the deadline is set by the system at 10 days

Feel free to treat it as 20 days or 30 days

It is very rare that this would be the bottleneck

A higher rate of review acceptances at 20 days would probably result in faster overall Peer review than everyone who currently accepts strictly abiding by the 10 days