@bigdatabiology.bsky.social
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pinned post!
Updates from the group (newsletter, sent 4x/year) Focusing on
#ExtremelyOpenScience
this quarter
bigdatabiology.substack.com/p/bdb-lab-ma...
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BDB-Lab March 2025 Updates
Extremely open science
https://bigdatabiology.substack.com/p/bdb-lab-march-2025-updates
8 months ago
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reposted by
Anna Cusco
about 2 months ago
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 🐶
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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...
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BDB-Lab September 2025 Updates
Dogs and other microbiomes
https://bigdatabiology.substack.com/p/bdb-lab-september-2025-updates
about 2 months ago
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reposted by
Anna Cusco
about 2 months ago
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...
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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...
https://www.biorxiv.org/content/10.1101/2025.09.17.676595v1
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reposted by
bioRxiv Microbiology
about 2 months ago
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
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reposted by
Luis Pedro Coelho
about 2 months ago
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...
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reposted by
Alvaro San Millan
3 months ago
New paper in collaboration with the
@asantoslopez.bsky.social
lab!
www.biorxiv.org/content/10.1...
add a skeleton here at some point
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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...
5 months ago
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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...
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argnorm
Normalize antibiotic resistance genes (ARGs) results by using the ARO ontology (developed by CARD).
https://pypi.org/project/argnorm/
5 months ago
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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...
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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 ...
https://marie-sklodowska-curie-actions.ec.europa.eu/calls/msca-postdoctoral-fellowships-2025
6 months ago
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An tutorial by our own Alexandre on metabolic modeling
areias03.github.io/blog/intro-t...
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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.
https://areias03.github.io/blog/intro-to-metabolic-modelling/
7 months ago
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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...
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What's New - argNorm: Normalize ARG annotations to ARO
https://argnorm.readthedocs.io/en/latest/whatsnew/#version-080-released-on-12-april-2025
7 months ago
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reposted by
Raes Lab
7 months ago
🚨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
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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...
https://jobs.vib.be/j/109363/phd-position-in-ai-in-microbiology
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Updates from the group (newsletter, sent 4x/year) Focusing on
#ExtremelyOpenScience
this quarter
bigdatabiology.substack.com/p/bdb-lab-ma...
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BDB-Lab March 2025 Updates
Extremely open science
https://bigdatabiology.substack.com/p/bdb-lab-march-2025-updates
8 months ago
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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...
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What's New - SemiBin
https://semibin.readthedocs.io/en/latest/whatsnew/#version-220
8 months ago
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How to install SemiBin using pixi (including GPU support) Pixi is conda modernized and makes everything easier
youtu.be/kqp8qV4S8dk
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How to install SemiBin using pixi (including GPU support)
YouTube video by BigDataBiology-Lab
https://youtu.be/kqp8qV4S8dk
8 months ago
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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
8 months ago
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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...
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What's New - argNorm: Normalize ARG annotations to ARO
https://argnorm.readthedocs.io/en/latest/whatsnew/#version-070-5-march-2025
8 months ago
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Check out
@biorxivpreprint.bsky.social
on healthy urinary microbiome from BacTdrugs - Luísa Peixe lab led by Svetlana U. Perović
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Urinary Microbiome of Reproductive-Age Asymptomatic European Women
Baterial diversity in healthy female urinary tract
https://buff.ly/425d3Xx
9 months ago
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NGLess tutorial (in 4 languages) English:
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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...
https://buff.ly/4j7L53D
10 months ago
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Assembling multiple metagenomes using NGLess
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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://...
https://buff.ly/4jdtozQ
10 months ago
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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
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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:
[email protected]
https://buff.ly/4fSs4PC
10 months ago
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reposted by
Microbiome Virtual International Forum
10 months ago
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!
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How to obtain amino acid versions of GMGCv1 subcalogs
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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...
https://buff.ly/429H5JY
10 months ago
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"A global survey of eco-evolutionary pressures acting on horizontal gene transfer" by Marija Dmitrijeva et al.
https://buff.ly/3DDBBgj
10 months ago
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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
10 months ago
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reposted by
Adrian Liston
10 months ago
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...
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https://wellcomeopenresearch.org/articles/9-341/v1/f3
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News from our lab for the past quarter, focusing on new lab members!
bigdatabiology.substack.com/p/bdb-lab-ja...
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BDB-Lab January 2025 Updates
Wishing you a happy new year from warm & sunny Queensland
https://bigdatabiology.substack.com/p/bdb-lab-january-2025-updates
10 months ago
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A catalogue of small proteins from the global microbiome! As part of our ongoing efforts to understand small proteins in prokaryotes, we catalogued almost 1 billion sequences
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A catalogue of small proteins from the global microbiome
Small open reading frames (smORFs) shorter than 100 codons are widespread and perform essential roles in microorganisms, where they encode proteins active in several cell functions, including signal…
https://buff.ly/3PfYyIK
10 months ago
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Check out Vedanth's video to learn more about what argNorm is
https://buff.ly/3ZWwY8y
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argNorm Tutorial
#science #bioinformatics #tutorial #pythonVedanth Ramji, a student researcher at the Big Data Biology Lab, presents how to use argNorm on various ARG annotat...
https://buff.ly/4gZoggJ
10 months ago
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SemiBin2 Tutorial
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SemiBin2 Tutorial
#science #tutorialLuis Pedro Coelho present a tutorial on SemiBin2Tutorial datahttps://github.com/BigDataBiology/SemiBin_tutorial/SemiBin2: https://youtu.be/...
https://buff.ly/3ZVGc52
10 months ago
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Yiqian presenting at MicrobiomeVIF earlier in 2024
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YiQian Duan - A catalogue of small proteins from the global microbiome | S03 MVIF28
Title of the presentation: A catalogue of small proteins from the global microbiomeSpeaker: YiQian Duan More info on this event: https://www.microbiome-vif.o...
https://buff.ly/49XFBUQ
10 months ago
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Review paper with Celio Dias Junior and De La Fuente Upenn 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)
https://buff.ly/3ONEr4w
11 months ago
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In June,
@luispedrocoelho.bsky.social
found found 863,498 molecules that can potentially kill infectious microbes and become the source of antibiotics. And they're all from the natural world!
https://buff.ly/3D8ZoV5
11 months ago
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Check out our
#extremelyopenscience
episodes for the year as we wrap up 2024!!
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Extremely Open Science 2024 (Season 2)
More information: https://www.big-data-biology.org/extremely-open-science/ Main repository: https://github.com/BigDataBiology/sardyne
https://buff.ly/41UHVKb
11 months ago
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For more information on long-term sustainability of software in bioinformatics that
@luispedrocoelho.bsky.social
presented at BOSC2024, read more in the
@plos.org
journals.plos.org/ploscompbiol...
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For long-term sustainable software in bioinformatics
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011920
11 months ago
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If you are interested in Sustainable Research Software. Luis recorded his presentation from BOSC2024. Have a watch!
https://buff.ly/3ZKhKVo
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Sustainable Research Software
#science #presentationLuis Pedro Coelho does a re-recording of his #BOSC2024 presentation on sustaiable software in bioinformatics.This talk was given at the...
https://buff.ly/3ZtkAwj
11 months ago
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Revisiting when argNorm became part of nf-core/funcscan! Great work from Vedanth to get this integrated
11 months ago
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Back in August, A/P
@luispedrocoelho.bsky.social
, presented at ISME's conference in South Africa. Luis spoke about microbes and the microbiome to local school children of Cape Town. To find out more about CMR's exciting research, reach out.
11 months ago
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Have you seen the GMSC manuscript published in
@naturecomms.bsky.social
(open access)? We constructed a small protein catalog from the global microbiome
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A catalog of small proteins from the global microbiome - Nature Communications
Here, the authors built a non-redundant catalogue of nearly 1 billion putative small proteins from the global microbiome as a publicly-available resource, and highlight how some highly prevalent and…
https://buff.ly/4gtgZpf
11 months ago
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Check out our Youtube channel where we post tutorials on our tools, highlights of our work, and other content.
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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:
[email protected]
https://buff.ly/4gsu81N
11 months ago
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Every 3 months, we send out an update email. Subscribe on Substack to get the updates (we really only send 4 emails per year). This was our September update:
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BDB-Lab September Updates
Small proteins still have a lot to tell us
https://buff.ly/3ZGRX0e
11 months ago
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Check out this review featuring A/Prof Luis Pedro Coelho, which highlights recent advancements and current challenges in the field of orthology-based research.
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https://buff.ly/41p1OsT
11 months ago
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CMR Director Prof Gene Tyson sat down with journalist Elissa Lawrence to discuss one of his favourite topics: the human microbiome. Read more about Prof Tyson’s career as a microbial ecologist and his hopes for the future of microbiome science.
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Gut instinct: why microbiome health is the new frontier of medicine
https://buff.ly/4fa6iqz
11 months ago
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Latest Big Data Biology Lab Updates
t.co/akVYnWAuka
11 months ago
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Vedanth Ramji will speak in a few minutes at mVIF on argNorm Still time to register!
cassyni.com/s/mvif-34
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Cassyni | Science starts with a seminar
Seamlessly organise, run and publish academic research seminars. Get started in minutes.
https://cassyni.com/s/mvif-34?utm_campaign=MVIF.34+starts+in+16+hours%2C+with+Prof.+Sean+Gibbons%21+%F0%9F%8C%9F&utm_medium=email&utm_source=newsletter
12 months ago
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reposted by
Bork Group at EMBL Heidelberg
12 months ago
In "Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota", @inanna-nalytica.bsky.social showed that a supposed T2D #microbiome signature is actually driven by drug treatment with metformin (2015)
www.nature.com/artic...
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Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
Nature - There is growing evidence from metagenome-wide association studies that several common human disorders, such as type 2 diabetes mellitus (T2D), are associated with intestinal dysbiosis, an...
https://www.nature.com/articles/nature15766
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reposted by
Svetlana Ugarcina Perovic
about 1 year ago
Hey
#AMR
people, the argNorm preprint is now available on
#QUT
ePrints:
eprints.qut.edu.au/252448
We* designed a tool for normalizing ARG annotations across currently popular tools & dbs. *@svetlanaup.bsky.social Vedanth Ramji Hui Chong Yiqian Duan Finlay Maguire
@luispedrocoelho.bsky.social
1/6
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reposted by
Microbiome Virtual International Forum
12 months ago
It's Wednesday! ...and
#MVIF
34 program is out! 🤩 ⭐️MicroTalks: 🇹🇼 Ha T. Doan 🇦🇺 Vedanth Ramji ⭐️ Keynote: 🇺🇸 Sean Gibbons
@gibbological.bsky.social
⭐️Selected talks: 🇯🇵 Yuya Kiguchi 🇦🇺 Kurtis Budden 🇨🇭 Amit Halkhoree (#Roche) Registration:
cassyni.com/s/mvif-34
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reposted by
Vivek Mutalik
12 months ago
www.nature.com/articles/s41...
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A river of resistant genes uncovered by metagenomics - Nature Reviews Microbiology
This Genome Watch discusses the use of metagenomic sequencing to investigate resistome dynamics in river ecosystems and their associations with the mobilome and microbiome, underscoring the role of ri...
https://www.nature.com/articles/s41579-024-01127-w
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reposted by
Vaughn Cooper
12 months ago
🚨Travel awards for Early Career Researchers to attend ASM Microbe🧫 1. Awarded through ASM Branches 2. $1650 per award, 3 per branch 3. Apps open now! 4. Named for Peggy Cotter, ASM past president & advocate 5. A proud accomplishment when I was COMS Chair 6. Apply / share!
asm.org/Travel-Award...
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Peggy Cotter Travel Award
ASM is a nonprofit professional society that publishes scientific journals and advances microbiology through advocacy, global health and diversity in STEM programs.
https://asm.org/Travel-Award/Peggy-Cotter-Travel-Awards-Early-Career-Branch-Mem?_zs=e7xpl&_zl=9W5A3
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