New paper in collaboration with the @asantoslopez.bsky.social lab!

www.biorxiv.org/content/10.1...

Quarterly updates from the Lab!

This June, the focus is on Alexandre Areias Castro, who is working on metabolic modeling of the microbiome with the aim of giving us a new view on microbial composition, focused of "functional roles" instead of taxonomy

bigdatabiology.substack.com/p/bdb-lab-up...

argnorm Normalize antibiotic resistance genes (ARGs) results by using the ARO ontology (developed by CARD).

New version of argNorm! Will be available frombioconda & funcscan in the next few days

We fixed how NCBI genes were being handled. It is a fundamentally more principled way and should fix a few corner cases (particularly if data has been run through hARMonization)

pypi.org/project/argn...

MSCA Postdoctoral Fellowships 2025 MSCA Postdoctoral Fellowships enhance the creative and innovative potential of researchers holding a PhD and who wish to acquire new skills through advanced training, international, interdisciplinary ...

Anyone from Europe wants to spend 2 years in sunny Queensland working on the global microbiome?

Get in touch (even if all you have right now is a vague idea, just email early)! We also have a lot of friends in Europe for the return phase.

marie-sklodowska-curie-actions.ec.europa.eu/calls/msca-p...

An tutorial by our own Alexandre on metabolic modeling

areias03.github.io/blog/intro-t...

If you have used argNorm and ran into any issues or tried it and found it didn't really solve your problem, please reach out!

We are very interested in helping users

ArgNorm 0.8.0 released!

More information including English language names for outputs and a bugfix for handling abricate+resfinder outputs

argnorm.readthedocs.io/en/latest/wh...

PhD Position in AI in Microbiology - VIB About the labThe lab of Jeroen Raes (VIB, KU Leuven) is home to a vibrant, dynamic and international group of researchers in the field of gut microbial ecology and its clinical applications. In additi...

🚨PhD position in AI in Microbiology!

We’re looking for a PhD researcher passionate about developing automated systems for microbiological research.

🌍 More info & apply:
jobs.vib.be/j/109363/phd...
@vibmicrobes.bsky.social @vibai.bsky.social

BDB-Lab March 2025 Updates Extremely open science

Updates from the group (newsletter, sent 4x/year)

Focusing on #ExtremelyOpenScience this quarter

bigdatabiology.substack.com/p/bdb-lab-ma...

We really strongly recommend that you use `SemiBin2` unless you have old scripts that you are trying to adapt (in which case, running `SemiBin1` will still work, but this won't be available in the next release)!

SemiBin v2.2.0 released!

This includes a lot of minor fixes rather than any big new features

Generally speaking, SemiBin v2.2.0 is more robust, will fail in fewer corner cases and will give you better error messages when it does.

semibin.readthedocs.io/en/latest/wh...

YouTube video by BigDataBiology-Lab How to install SemiBin using pixi (including GPU support)

How to install SemiBin using pixi (including GPU support)

Pixi is conda modernized and makes everything easier

youtu.be/kqp8qV4S8dk

We are a supportive environment for everyone to thrive and produce excellence, impactful science!

Get in touch!

www.big-data-biology.org/manual/

Discovery of antimicrobial peptides in the global microbiome with machine learning A machine-learning-based approach predicts nearly one million new antibiotics from the global microbiome, with 79 out of 100 tested peptides being active in vitro and several showing efficacy comparab...

Or perhaps you are excited about the potential of small proteins to solve truly global problems?

www.cell.com/cell/fulltex...

SPIRE: a Searchable, Planetary-scale mIcrobiome REsource Abstract. Meta’omic data on microbial diversity and function accrue exponentially in public repositories, but derived information is often siloed according

Or work with an international team on expanding our view of the global microbiome, expanding SPIRE?

academic.oup.com/nar/article/...

A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments - Nature Communications Here, the authors present SemiBin, a siamese deep neural network framework that incorporates information from reference genomes, able to extract better metagenome-assembled genomes (MAGs) in seve...

Want to work at the intersection of modern AI and biology? Perhaps develop the next SemiBin?

www.nature.com/articles/s41...

We are looking for PhD students!

Fully funded studentships available to work on a range of topics, from small proteins to developing computational tools to study the global microbiome

ArgNorm version 0.7.0 released!

A lot of improvements, including an update to CARD v4, support for AMRFinderPlus 4, an updated manual curation for many genes

argnorm.readthedocs.io/en/latest/wh...

Urinary Microbiome of Reproductive-Age Asymptomatic European Women Baterial diversity in healthy female urinary tract

Check out @biorxivpreprint.bsky.social on healthy urinary microbiome from BacTdrugs - Luísa Peixe lab led by Svetlana U. Perović

NGLess tutorial: assembling metagenomes (FRANÇAIS) English version: https://youtu.be/EIkmZ8kN6j0Portuguese version: https://youtu.be/6PQ1YFEXpfcGerman version: https://youtu.be/iJ8ffOC-9_gFrench version: http...

Français
https://buff.ly/4a8lrYx

NGLess tutorial: assembling metagenomes (PORTUGUÊS) English version: https://youtu.be/EIkmZ8kN6j0Portuguese version: https://youtu.be/6PQ1YFEXpfcGerman version: https://youtu.be/iJ8ffOC-9_gFrench version: http...

Português

https://buff.ly/3WfPw2n

Assembling metagenomes using NGLess (ENGLISH) English version: https://youtu.be/EIkmZ8kN6j0Portuguese version: https://youtu.be/6PQ1YFEXpfcGerman version: https://youtu.be/iJ8ffOC-9_gFrench version: http...

NGLess tutorial (in 4 languages)

English:

Assembling multiple metagenomes using NGLess Luis Pedro Coelho shows how to use NGLess to process multiple metagenomesPrevious tutorial (single sample): https://youtu.be/EIkmZ8kN6j0Github link: https://...

Assembling multiple metagenomes using NGLess

BigDataBiology-Lab This is Luis Pedro Coelho's lab (BDB-Lab) We post tutorials on our tools, highlights of our work, and other content To get in touch: luispedro@big-data-biology.org

Our YouTube channel has videos on our work including tutorials on our tools and we are happy to do them on request as well (if you have a question that we think others would like to see answered as well)

Like & subscribe to keep up to date

mvif winners

Congratulation to the #MVIF #34 winners!!!

💐 Vedanth Ramji (@bigdatabiology.bsky.social)
💐 Kurtis Budden

Besides the fame, there's a $200 prize to the prize winners, so make sure to vote and to submit an abstract for next time!

How to retrieve amino acid versions of GMGC unigenes for subcatalogs #science #tutorial #microbiomeLuis Pedro Coelho answers a subscriber question about how to get amino acid versions of the GMGCv1 subcatalogshttps://github.co...

How to obtain amino acid versions of GMGCv1 subcalogs

"A global survey of eco-evolutionary pressures acting on horizontal gene transfer" by
Marija Dmitrijeva et al.
https://buff.ly/3DDBBgj

The antimicrobial peptides (AMPs) of the global microbiome!

From 72 diffferent habitats (the best current sampling of the global microbiome) we obtained almost 1 million candidate AMPs

https://buff.ly/404s9Ky

Our paper on nurturing a #PositiveResearchCulture within your #research #team published by @wellcometrust.bsky.social gives useful tips for your lab. As well as making you a good team leader, nurturing culture pays off in building your science: 1/11

wellcomeopenresearch.org/articles/9-3...

BDB-Lab January 2025 Updates Wishing you a happy new year from warm & sunny Queensland

News from our lab for the past quarter, focusing on new lab members!

bigdatabiology.substack.com/p/bdb-lab-ja...