Lightnews — Scholar-powered news

bigdatabiology.bsky.social @bigdatabiology.bsky.social · 14d

September 2025 updates!

A focus on Anna's preprint, but several other updates too, including Faith Adegoke joining us to work on AMR and several other preprints

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

BDB-Lab September 2025 Updates

Dogs and other microbiomes

bigdatabiology.substack.com

1 2

Reposted

Anna Cusco @annacusco.bsky.social · 15d

Finally, the results of my postdoc at the
@bigdatabiology.bsky.social lab in Shanghai see the light! The work includes my three favorite things research-wise: 🦠 microbiome, 🧬 long-reads, and 🐶 dogs.

See our new preprint:
www.biorxiv.org/content/10.1...

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort

Pet dogs are considered part of the family, and understanding their gut microbiomes can provide insights into both animal and household health. Most comprehensive studies, however, relied on short-rea...

www.biorxiv.org

3 10 20

Reposted

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 20d

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort https://www.biorxiv.org/content/10.1101/2025.09.17.676595v1

5 6

Reposted

Luis Pedro Coelho @luispedrocoelho.bsky.social · 20d

Full thread will come later, but @annacusco.bsky.social's preprint on the dog pet gut microbiome is out!

Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases

doi.org/10.1101/2025...

14 32

Reposted

Alvaro San Millan @sanmillan.bsky.social · Aug 13

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

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

15 25

bigdatabiology.bsky.social @bigdatabiology.bsky.social · Jun 25

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...

1 1

bigdatabiology.bsky.social @bigdatabiology.bsky.social · Jun 24

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...

argnorm

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

pypi.org

1 2

bigdatabiology.bsky.social @bigdatabiology.bsky.social · May 15

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...

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 ...

marie-sklodowska-curie-actions.ec.europa.eu

1 1

bigdatabiology.bsky.social @bigdatabiology.bsky.social · Apr 19

An tutorial by our own Alexandre on metabolic modeling

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

A (not so) short introduction to Metabolic Modelling – Alexandre Areias Castro

A practical introduction to concepts, methods and tools that will initiate you in systems biology.

areias03.github.io

3

bigdatabiology.bsky.social @bigdatabiology.bsky.social · Apr 14

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

bigdatabiology.bsky.social @bigdatabiology.bsky.social · Apr 13

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...

What's New - argNorm: Normalize ARG annotations to ARO

argnorm.readthedocs.io

1 4 1

Reposted

Raes Lab @raeslab.org · Apr 8

🚨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

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...

jobs.vib.be

11 10

bigdatabiology.bsky.social @bigdatabiology.bsky.social · Mar 25

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

Focusing on #ExtremelyOpenScience this quarter

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

BDB-Lab March 2025 Updates

Extremely open science

bigdatabiology.substack.com

1

bigdatabiology.bsky.social @bigdatabiology.bsky.social · Mar 21

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)!

bigdatabiology.bsky.social @bigdatabiology.bsky.social · Mar 21

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...

What's New - SemiBin

semibin.readthedocs.io

1 2 4

bigdatabiology.bsky.social @bigdatabiology.bsky.social · Mar 18

How to install SemiBin using pixi (including GPU support)

Pixi is conda modernized and makes everything easier

youtu.be/kqp8qV4S8dk

How to install SemiBin using pixi (including GPU support)

YouTube video by BigDataBiology-Lab

youtu.be

1

bigdatabiology.bsky.social @bigdatabiology.bsky.social · Mar 17

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

Get in touch!

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

Lab Manual and Policies

Manual Big Data Biology Lab

www.big-data-biology.org

bigdatabiology.bsky.social @bigdatabiology.bsky.social · Mar 17

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

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

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...

www.cell.com

1

bigdatabiology.bsky.social @bigdatabiology.bsky.social · Mar 17

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

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

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

academic.oup.com

1

bigdatabiology.bsky.social @bigdatabiology.bsky.social · Mar 17

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

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

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...

www.nature.com

1

bigdatabiology.bsky.social @bigdatabiology.bsky.social · Mar 17

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

1 13 4

bigdatabiology.bsky.social @bigdatabiology.bsky.social · Mar 8

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...

What's New - argNorm: Normalize ARG annotations to ARO

argnorm.readthedocs.io