Source code with comments is public now, should be easy to understand. It's still in dev, e.g., no heuristics now.

Wavefront alignment algorithm (WFA) in Golang
github.com/shenwei356/wfa

#MVIF Q&A right now with Serena Manara
celiodias
Zhenrun Jerry Zhang
Lu Wu

The polls are OPEN – don’t forget to vote for your favorite one!

Indexing All Life's Known Biological Sequences biorxiv.org/content/10.110… metagraph.ethz.ch/search

A vulnerability in #Rstats has been discovered nvd.nist.gov/vuln/detail/CV…

Completely missed that a new version of bwa 0.7.18 was released last week (now supports ARM and that compiler issue that's been there for a while). First release in >6 years. github.com/lh3/bwa/releas…

What I’m reading this week in genome assembly, synthetic biology, genAI/LLMs in bioinformatics, microbial genomics, biosecurity, etc, … 🧬🖥️🧵

Our own Yiqian presenting at Microbiome Virtual International Forum!

youtube.com/watch?v=gpcT1_…

A nice review of long-read genome assemblers and its associated #bioinformatics terms

sciencedirect.com/science/articl…

Ten quick tips for avoiding pitfalls in multi-omics data integration analyses journals.plos.org/ploscompbiol/a…

Ok, this is pretty crazy.

SQL has been the lingua franca of database querying since the dawn of time.

But for the first time in over three decades (!), ISO just published a NEW database query language called GQL -- the Graph Query Language!

Non-antibiotic pharmaceuticals are toxic against Escherichia coli with no evolution of cross-resistance to antibiotics

by Rebecca J Hall, McNally lab group, Dr. Laura Carter, Jessica Blair, Michael Bottery Ann Snaith, Sarah Element, et al. in npj Antimicrobials and Resistance

nature.com/articles/s4425…

Alright everybody, what will undoubtedly forever be the lab's strangest discovery is now out in Nature. It's a protein that evolved to self-assemble into a Sierpinski fractal. nature.com/articles/s4158… 1/n

Foldseek got published in 2024 in Volume 42 of Nature Biotechnology. Here is the timeline of FS releases:
Source code: 2021/07
Webserver: 2022/01
Preprint: 2022/02
Journal: 2023/05
Print: 2024/02

Bye Bye ChatGPT

Nvidia just launched Chat with RTX and it's free for everyone.

Here are the details (+ how to download):

Google Colab wizard Pablo Arantes - @pabloarantes.bsky.social and I are thrilled to share a new colab notebook for running the subsampled AlphaFold2 approach for predicting protein conformational ensembles detailed in nature.com/articles/s4146…

Here's a link to the notebook:

colab.research.google.com/github/GMdSilv…

what's the best bioinformatics book that you've read? for me: oreilly.com/library/view/b… by Vince Buffalo

I am proud to announce that I have been awarded an MarieSkłodowskaCurie grant. I extend a special thanks to Ramiro Logares and the ICM-CSIC for their invaluable mentoring throughout this process.

Amazing week for the lab! big congrats Sandra Garces Pastor Sandra Garcés Pastor for the Junior Leader fellowship #laCaixaFoundation Becas Fundación "la Caixa" , Mattia Greco Mattia Greco for the Beatriu de Pinos Recerca i Universitats & celiodias for the MarieSkłodowskaCurie 🥳👏🙌

New review paper with celiodias and César de la Fuente

We explore how mining small peptides from (meta)genomes is different from mining full-sized enzymes and how we need new methods and approaches (AI/ML instead of sequence alignment)

doi.org/10.1002/pmic.2…

A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer

by Marija Dmitrijeva | on vacation 🇲🇽, Luis Pedro Coelho🌻🇮🇱 et al. in NatureEcoEvo

nature.com/articles/s4155…