@bigdatabiology.bsky.social
Pinned
BDB-Lab March 2025 Updates
Extremely open science
bigdatabiology.substack.com
Updates from the group (newsletter, sent 4x/year)
Focusing on #ExtremelyOpenScience this quarter
bigdatabiology.substack.com/p/bdb-lab-ma...
Focusing on #ExtremelyOpenScience this quarter
bigdatabiology.substack.com/p/bdb-lab-ma...
Reposted
I would like to thank all co-authors: Yiqian Duan, Fernando Gil, Alexei Chklovski, Nithya Kruthi, Shaojun Pan, Sofia Forslund, Susanne Lau, Ulrike Löber, Xing-Ming Zhao, and especially @luispedrocoelho.bsky.social
And of course, all the dog owners and the main characters of this story 🐶
And of course, all the dog owners and the main characters of this story 🐶
September 23, 2025 at 10:42 AM
I would like to thank all co-authors: Yiqian Duan, Fernando Gil, Alexei Chklovski, Nithya Kruthi, Shaojun Pan, Sofia Forslund, Susanne Lau, Ulrike Löber, Xing-Ming Zhao, and especially @luispedrocoelho.bsky.social
And of course, all the dog owners and the main characters of this story 🐶
And of course, all the dog owners and the main characters of this story 🐶
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...
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
September 24, 2025 at 4:55 AM
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...
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...
Reposted
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...
@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
September 23, 2025 at 11:24 AM
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...
@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...
Reposted
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
September 18, 2025 at 6:17 AM
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
Reposted
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...
Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases
doi.org/10.1101/2025...
September 18, 2025 at 12:01 PM
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...
Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases
doi.org/10.1101/2025...
Reposted
August 13, 2025 at 6:39 AM
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...
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...
June 25, 2025 at 3:14 AM
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...
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...
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...
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
June 24, 2025 at 7:24 AM
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...
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...
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...
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
May 15, 2025 at 2:22 AM
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...
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...
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...
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
April 13, 2025 at 11:44 AM
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...
More information including English language names for outputs and a bugfix for handling abricate+resfinder outputs
argnorm.readthedocs.io/en/latest/wh...
Reposted
🚨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
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
April 8, 2025 at 7:44 AM
🚨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
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
Updates from the group (newsletter, sent 4x/year)
Focusing on #ExtremelyOpenScience this quarter
bigdatabiology.substack.com/p/bdb-lab-ma...
Focusing on #ExtremelyOpenScience this quarter
bigdatabiology.substack.com/p/bdb-lab-ma...
BDB-Lab March 2025 Updates
Extremely open science
bigdatabiology.substack.com
March 25, 2025 at 10:19 PM
Updates from the group (newsletter, sent 4x/year)
Focusing on #ExtremelyOpenScience this quarter
bigdatabiology.substack.com/p/bdb-lab-ma...
Focusing on #ExtremelyOpenScience this quarter
bigdatabiology.substack.com/p/bdb-lab-ma...
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...
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
March 21, 2025 at 4:29 AM
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...
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...
How to install SemiBin using pixi (including GPU support)
Pixi is conda modernized and makes everything easier
youtu.be/kqp8qV4S8dk
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
March 18, 2025 at 4:38 AM
How to install SemiBin using pixi (including GPU support)
Pixi is conda modernized and makes everything easier
youtu.be/kqp8qV4S8dk
Pixi is conda modernized and makes everything easier
youtu.be/kqp8qV4S8dk
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
Fully funded studentships available to work on a range of topics, from small proteins to developing computational tools to study the global microbiome
March 17, 2025 at 6:30 AM
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
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...
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
March 8, 2025 at 5:16 AM
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...
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...
Check out @biorxivpreprint.bsky.social on healthy urinary microbiome from BacTdrugs - Luísa Peixe lab led by Svetlana U. Perović
Urinary Microbiome of Reproductive-Age Asymptomatic European Women
Baterial diversity in healthy female urinary tract
buff.ly
February 4, 2025 at 3:35 AM
Check out @biorxivpreprint.bsky.social on healthy urinary microbiome from BacTdrugs - Luísa Peixe lab led by Svetlana U. Perović
NGLess tutorial (in 4 languages)
English:
English:
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...
buff.ly
January 28, 2025 at 9:04 AM
NGLess tutorial (in 4 languages)
English:
English:
Assembling multiple metagenomes using NGLess
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://...
buff.ly
January 28, 2025 at 7:35 AM
Assembling multiple metagenomes using NGLess
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
Like & subscribe to keep up to date
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
buff.ly
January 28, 2025 at 3:35 AM
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
Like & subscribe to keep up to date
Reposted
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!
💐 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!
January 21, 2025 at 4:14 PM
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!
💐 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 obtain amino acid versions of GMGCv1 subcalogs
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...
buff.ly
January 21, 2025 at 9:04 AM
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
Marija Dmitrijeva et al.
https://buff.ly/3DDBBgj
January 21, 2025 at 7:35 AM
"A global survey of eco-evolutionary pressures acting on horizontal gene transfer" by
Marija Dmitrijeva et al.
https://buff.ly/3DDBBgj
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
From 72 diffferent habitats (the best current sampling of the global microbiome) we obtained almost 1 million candidate AMPs
https://buff.ly/404s9Ky
January 21, 2025 at 3:35 AM
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
From 72 diffferent habitats (the best current sampling of the global microbiome) we obtained almost 1 million candidate AMPs
https://buff.ly/404s9Ky