FGeneBERT: function-driven pre-trained gene language model for metagenomics academic.oup.com/bib/article/... 🧬🖥️🧪 github.com/jane-pyc/Ope...
November 10, 2025 at 3:00 PM
FGeneBERT: function-driven pre-trained gene language model for metagenomics academic.oup.com/bib/article/... 🧬🖥️🧪 github.com/jane-pyc/Ope...
💬 “It’s operationally very lightweight, you can use it in-field for taxonomic classification on a standard laptop, or undertake larger, complex analysis using HPC.”
💻🧬 Scientists at Earlham Institute introduce MARTi, a new tool for real-time #nanopore #metagenomics.
@genomeresearch.bsky.social
💻🧬 Scientists at Earlham Institute introduce MARTi, a new tool for real-time #nanopore #metagenomics.
@genomeresearch.bsky.social
New software tool MARTi fast-tracks identification and response to microbial threats.
An open-source software tool that powers real-time analysis and visualisation of metagenomic data
buff.ly
October 28, 2025 at 9:02 AM
💬 “It’s operationally very lightweight, you can use it in-field for taxonomic classification on a standard laptop, or undertake larger, complex analysis using HPC.”
💻🧬 Scientists at Earlham Institute introduce MARTi, a new tool for real-time #nanopore #metagenomics.
@genomeresearch.bsky.social
💻🧬 Scientists at Earlham Institute introduce MARTi, a new tool for real-time #nanopore #metagenomics.
@genomeresearch.bsky.social
🧬 New insights into the diversity of #CRISPR–Cas systems!
#Metagenomic analyses uncovered 4,112 Cas12 proteins and 6 novel subtypes.
🤖 #AI-based Cas12fam annotates 18 domains.
🌿 Cas12 subtypes show habitat-specific enrichment.
🔗 doi.org/10.1002/imo2...
#microbiome #metagenomics #bioinformatics
#Metagenomic analyses uncovered 4,112 Cas12 proteins and 6 novel subtypes.
🤖 #AI-based Cas12fam annotates 18 domains.
🌿 Cas12 subtypes show habitat-specific enrichment.
🔗 doi.org/10.1002/imo2...
#microbiome #metagenomics #bioinformatics
Metagenomic mining reveals novel Cas12 subtypes and their evolutionary diversification
We identified 4112 Cas12 Proteins and 6 new Cas12 subtypes, revealed their significant diversity in N-terminal regions, repeat sequences, and sequences motifs. We developed an AI-driven algorithm, Ca...
onlinelibrary.wiley.com
October 21, 2025 at 2:25 PM
🧬 New insights into the diversity of #CRISPR–Cas systems!
#Metagenomic analyses uncovered 4,112 Cas12 proteins and 6 novel subtypes.
🤖 #AI-based Cas12fam annotates 18 domains.
🌿 Cas12 subtypes show habitat-specific enrichment.
🔗 doi.org/10.1002/imo2...
#microbiome #metagenomics #bioinformatics
#Metagenomic analyses uncovered 4,112 Cas12 proteins and 6 novel subtypes.
🤖 #AI-based Cas12fam annotates 18 domains.
🌿 Cas12 subtypes show habitat-specific enrichment.
🔗 doi.org/10.1002/imo2...
#microbiome #metagenomics #bioinformatics
🌊🧬🦠 Our new study on seawater microbes from the Great Barrier Reef! 🪸🐠🌊
🔗 microbiomejournal.biomedcentral.com/articles/10....
👇 Key findings in threads below 👇
#CoralReef #Microbiome #MarineScience #GreatBarrierReef #Metagenomics #Monitoring
🔗 microbiomejournal.biomedcentral.com/articles/10....
👇 Key findings in threads below 👇
#CoralReef #Microbiome #MarineScience #GreatBarrierReef #Metagenomics #Monitoring
Gene content of seawater microbes is a strong predictor of water chemistry across the Great Barrier Reef - Microbiome
Background Seawater microbes (bacteria and archaea) play essential roles in coral reefs by facilitating nutrient cycling, energy transfer, and overall reef ecosystem functioning. However, environmenta...
microbiomejournal.biomedcentral.com
January 17, 2025 at 12:29 AM
🌊🧬🦠 Our new study on seawater microbes from the Great Barrier Reef! 🪸🐠🌊
🔗 microbiomejournal.biomedcentral.com/articles/10....
👇 Key findings in threads below 👇
#CoralReef #Microbiome #MarineScience #GreatBarrierReef #Metagenomics #Monitoring
🔗 microbiomejournal.biomedcentral.com/articles/10....
👇 Key findings in threads below 👇
#CoralReef #Microbiome #MarineScience #GreatBarrierReef #Metagenomics #Monitoring
Our student @bergfeldt.bsky.social is currently defending her PhD thesis on metagenomics 🧬🦠 of ancient human populations, with Carles Lalueza-Fox from @ibe-barcelona.bsky.social as opponent.
Good luck, Nora!
Good luck, Nora!
March 21, 2025 at 9:35 AM
Our student @bergfeldt.bsky.social is currently defending her PhD thesis on metagenomics 🧬🦠 of ancient human populations, with Carles Lalueza-Fox from @ibe-barcelona.bsky.social as opponent.
Good luck, Nora!
Good luck, Nora!
📰 A recent article, supported by our project, was published in Pensoft Publishers' (@pensoft.net) Metabarcoding and Metagenomics journal.
🧬 The study evaluates the TRLs of molecular tools for #monitoring like #eDNA and DNA #metabarcoding.
👀 Full article:
mbmg.pensoft.net/article/1308...
🧬 The study evaluates the TRLs of molecular tools for #monitoring like #eDNA and DNA #metabarcoding.
👀 Full article:
mbmg.pensoft.net/article/1308...
September 19, 2025 at 10:37 AM
📰 A recent article, supported by our project, was published in Pensoft Publishers' (@pensoft.net) Metabarcoding and Metagenomics journal.
🧬 The study evaluates the TRLs of molecular tools for #monitoring like #eDNA and DNA #metabarcoding.
👀 Full article:
mbmg.pensoft.net/article/1308...
🧬 The study evaluates the TRLs of molecular tools for #monitoring like #eDNA and DNA #metabarcoding.
👀 Full article:
mbmg.pensoft.net/article/1308...
Whole genome metagenomics is better than the standard of care in detecting the causal bugs of CNS infections 🧪 🧬
Metagenomics hits the clinic to diagnose CNS infections
Whole genome metagenomics is better than the standard of care in detecting the causal bugs of CNS infections
buff.ly
November 26, 2024 at 4:00 PM
Whole genome metagenomics is better than the standard of care in detecting the causal bugs of CNS infections 🧪 🧬
The official application route is now open for this PhD on belowground trophic networks using molecular dietary analysis, metagenomics and ecoacoustics! 🥳🔊🕸️🧬
www.ncl.ac.uk/postgraduate...
www.ncl.ac.uk/postgraduate...
January 11, 2024 at 2:06 PM
The official application route is now open for this PhD on belowground trophic networks using molecular dietary analysis, metagenomics and ecoacoustics! 🥳🔊🕸️🧬
www.ncl.ac.uk/postgraduate...
www.ncl.ac.uk/postgraduate...
Quick intro! I’m a microbiologist at Cornell studying freshwater microbes using metagenomics 🦠🧬💻. I code in R and Julia, and teaching workshops in the Carpentries. Otherwise you’ll find me DIY renovating with my boyfriend🏳️🌈🛠️🏡, snuggling with my 🐶 , or running/biking/swimming/skiing/anything
September 7, 2023 at 5:45 PM
Quick intro! I’m a microbiologist at Cornell studying freshwater microbes using metagenomics 🦠🧬💻. I code in R and Julia, and teaching workshops in the Carpentries. Otherwise you’ll find me DIY renovating with my boyfriend🏳️🌈🛠️🏡, snuggling with my 🐶 , or running/biking/swimming/skiing/anything
Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes. #Long-read #Sequencing #Metagenomics #SoilMicrobiome #Genomics #Bioinformatics @biorxivpreprint.bsky.social 🧪🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 24, 2025 at 9:15 AM
Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes. #Long-read #Sequencing #Metagenomics #SoilMicrobiome #Genomics #Bioinformatics @biorxivpreprint.bsky.social 🧪🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
The RAT is out! 🐀 Our new Read Annotation Tool integrates taxonomic signals from MAGs, contigs, and reads from #metagenomics 🧬 into one microbial community profile with great sensitivity and precision. Read the article at www.nature.com/articles/s41.... 🧵 (1/5)
Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes - Nature Communications
Metagenomic taxonomic profiling usually relies either on reads or assembled contigs/MAGs. Here, authors present RAT, a tool that integrates taxonomic signals from reads, contigs, and MAGs into one pro...
www.nature.com
May 13, 2024 at 10:12 AM
The RAT is out! 🐀 Our new Read Annotation Tool integrates taxonomic signals from MAGs, contigs, and reads from #metagenomics 🧬 into one microbial community profile with great sensitivity and precision. Read the article at www.nature.com/articles/s41.... 🧵 (1/5)
🚀 The Shotgun Metagenomics course with @epasolli.bsky.social & @paolomanghi is officially underway!🧬✨
Over the next 4 days, participants will learn the theory & hands-on practice of cutting-edge bioinformatics tools for metagenomics🦠, including tools for visualising their results.💻📊
Over the next 4 days, participants will learn the theory & hands-on practice of cutting-edge bioinformatics tools for metagenomics🦠, including tools for visualising their results.💻📊
December 10, 2024 at 1:52 PM
🚀 The Shotgun Metagenomics course with @epasolli.bsky.social & @paolomanghi is officially underway!🧬✨
Over the next 4 days, participants will learn the theory & hands-on practice of cutting-edge bioinformatics tools for metagenomics🦠, including tools for visualising their results.💻📊
Over the next 4 days, participants will learn the theory & hands-on practice of cutting-edge bioinformatics tools for metagenomics🦠, including tools for visualising their results.💻📊
mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies https://academic.oup.com/bioinformatics/article/41/2/btaf037/7978911 🧬🖥️🧪 https://github.com/EBI-Metagenomics/mettannotator
February 21, 2025 at 7:30 PM
mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies https://academic.oup.com/bioinformatics/article/41/2/btaf037/7978911 🧬🖥️🧪 https://github.com/EBI-Metagenomics/mettannotator
What I’m reading this week, mostly in the world of single-cell omics, metagenomics / microbial genomics, genome assembly, generative AI in bioinformatics, … 🧬🖥️🧵
February 2, 2024 at 3:30 PM
What I’m reading this week, mostly in the world of single-cell omics, metagenomics / microbial genomics, genome assembly, generative AI in bioinformatics, … 🧬🖥️🧵
EMBO course - Microbial metagenomics: 360 approach
When I added Heidelberg to my vision board at the start of 2025, I was really not convinced that this dream can come true 🥹🤩
I cannot keep only for myself, how great (and intense!) the course was 👩🏻🔬💻🧬 thank you!
@embo.org @events.embl.org
When I added Heidelberg to my vision board at the start of 2025, I was really not convinced that this dream can come true 🥹🤩
I cannot keep only for myself, how great (and intense!) the course was 👩🏻🔬💻🧬 thank you!
@embo.org @events.embl.org
April 14, 2025 at 7:24 PM
EMBO course - Microbial metagenomics: 360 approach
When I added Heidelberg to my vision board at the start of 2025, I was really not convinced that this dream can come true 🥹🤩
I cannot keep only for myself, how great (and intense!) the course was 👩🏻🔬💻🧬 thank you!
@embo.org @events.embl.org
When I added Heidelberg to my vision board at the start of 2025, I was really not convinced that this dream can come true 🥹🤩
I cannot keep only for myself, how great (and intense!) the course was 👩🏻🔬💻🧬 thank you!
@embo.org @events.embl.org
🧬 What’s in your washing machine? Prof. Katie Laird & Dr. Caroline Cayrou from DMU reveal the #AMR risks of laundering healthcare uniforms at home.
youtu.be/GTREfKiM6r8
Their video story (our first!) explains why they chose Novogene for their sequencing.
#genomics #laundry #metagenomics
youtu.be/GTREfKiM6r8
Their video story (our first!) explains why they chose Novogene for their sequencing.
#genomics #laundry #metagenomics
Customer Story: Domestic Laundry and the Rise of AMR | Novogene x De Montfort University
YouTube video by Novogene
youtu.be
June 5, 2025 at 10:29 AM
🧬 What’s in your washing machine? Prof. Katie Laird & Dr. Caroline Cayrou from DMU reveal the #AMR risks of laundering healthcare uniforms at home.
youtu.be/GTREfKiM6r8
Their video story (our first!) explains why they chose Novogene for their sequencing.
#genomics #laundry #metagenomics
youtu.be/GTREfKiM6r8
Their video story (our first!) explains why they chose Novogene for their sequencing.
#genomics #laundry #metagenomics
ganon2: up-to-date and scalable metagenomics analysis. #Metagenomics #Genomics #Bioinformatics 🧬 🖥️ @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 11, 2024 at 7:05 PM
ganon2: up-to-date and scalable metagenomics analysis. #Metagenomics #Genomics #Bioinformatics 🧬 🖥️ @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
At #GenomeScience this week? Catch up with the Earlham Institute team presenting talks on:
🦠 #Metagenomics, #microbiomes, and #longread sequencing
🌾 Wheat pan genomics
🧬 Benchmarking long-read #scRNA-Seq Approaches
📚 A new short-read #RNAlibrary preparation kit
www.genomescience.org.uk/speakers/
🦠 #Metagenomics, #microbiomes, and #longread sequencing
🌾 Wheat pan genomics
🧬 Benchmarking long-read #scRNA-Seq Approaches
📚 A new short-read #RNAlibrary preparation kit
www.genomescience.org.uk/speakers/
July 9, 2025 at 11:20 AM
At #GenomeScience this week? Catch up with the Earlham Institute team presenting talks on:
🦠 #Metagenomics, #microbiomes, and #longread sequencing
🌾 Wheat pan genomics
🧬 Benchmarking long-read #scRNA-Seq Approaches
📚 A new short-read #RNAlibrary preparation kit
www.genomescience.org.uk/speakers/
🦠 #Metagenomics, #microbiomes, and #longread sequencing
🌾 Wheat pan genomics
🧬 Benchmarking long-read #scRNA-Seq Approaches
📚 A new short-read #RNAlibrary preparation kit
www.genomescience.org.uk/speakers/
From tracking SARS-CoV-2 in wastewater to discovering hidden marine RNA viruses, CLAE unlocks read-level viral variant detection and fixes short-read misassemblies.
⚡ Portable, field-ready
🧬 A game-changer for epidemiology & environmental surveillance.
#RNAvirus #metagenomics
⚡ Portable, field-ready
🧬 A game-changer for epidemiology & environmental surveillance.
#RNAvirus #metagenomics
September 12, 2025 at 3:34 PM
From tracking SARS-CoV-2 in wastewater to discovering hidden marine RNA viruses, CLAE unlocks read-level viral variant detection and fixes short-read misassemblies.
⚡ Portable, field-ready
🧬 A game-changer for epidemiology & environmental surveillance.
#RNAvirus #metagenomics
⚡ Portable, field-ready
🧬 A game-changer for epidemiology & environmental surveillance.
#RNAvirus #metagenomics
How does living in space change the life around you?
Salido et al report one of the neatest things I've read all month. Sampling bacteria in the international space station, they show how that environment is an extreme subset of bacterial diversity.
🧪
🧬 💻
#metagenomics
www.cell.com/cell/fulltex...
Salido et al report one of the neatest things I've read all month. Sampling bacteria in the international space station, they show how that environment is an extreme subset of bacterial diversity.
🧪
🧬 💻
#metagenomics
www.cell.com/cell/fulltex...
The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns
With long-term space travel and extraterrestrial habitation becoming feasible, understanding
how space environmental exposures, microbial communities, and molecular profiles differ
from Earth is cruci...
www.cell.com
February 28, 2025 at 1:50 PM
How does living in space change the life around you?
Salido et al report one of the neatest things I've read all month. Sampling bacteria in the international space station, they show how that environment is an extreme subset of bacterial diversity.
🧪
🧬 💻
#metagenomics
www.cell.com/cell/fulltex...
Salido et al report one of the neatest things I've read all month. Sampling bacteria in the international space station, they show how that environment is an extreme subset of bacterial diversity.
🧪
🧬 💻
#metagenomics
www.cell.com/cell/fulltex...
🧬Insightful metagenomics talk from Jeferyd Yepes García (University of Fribourg) on MAGFlow (@nextflow.io pipeline MAGs analysis) & BIgMAG (an interactive dashboard to visualize & communicate results). Together, MAGFlow/BIgMAG makes analysis easier, reproducible, and collaborative
October 23, 2025 at 2:17 PM
🧬Insightful metagenomics talk from Jeferyd Yepes García (University of Fribourg) on MAGFlow (@nextflow.io pipeline MAGs analysis) & BIgMAG (an interactive dashboard to visualize & communicate results). Together, MAGFlow/BIgMAG makes analysis easier, reproducible, and collaborative
I’m thrilled to announce that I will be participating as a trainer on behalf of Wenzel Lab in the upcoming workshop “Microbial Metagenomics: 360° Approach”! 🧬🔬
If you are interested in metagenomics, make sure to apply: www.embl.org/about/info/c...
#EMBLEvents #EMBO #openhardware #microfluidics
If you are interested in metagenomics, make sure to apply: www.embl.org/about/info/c...
#EMBLEvents #EMBO #openhardware #microfluidics
December 15, 2024 at 12:20 AM
I’m thrilled to announce that I will be participating as a trainer on behalf of Wenzel Lab in the upcoming workshop “Microbial Metagenomics: 360° Approach”! 🧬🔬
If you are interested in metagenomics, make sure to apply: www.embl.org/about/info/c...
#EMBLEvents #EMBO #openhardware #microfluidics
If you are interested in metagenomics, make sure to apply: www.embl.org/about/info/c...
#EMBLEvents #EMBO #openhardware #microfluidics
Happy to share that our new paper is out! 🧬 We used metagenomics to study the microbial communities in an 8,000-year sedimentary sequence from Lake Cadagno.
Check it out here: www.frontiersin.org/journals/mic...
#microbiology #genomics #microbiology #sediments #DNA #sequencing
Check it out here: www.frontiersin.org/journals/mic...
#microbiology #genomics #microbiology #sediments #DNA #sequencing
Frontiers | Persistent functional and taxonomic groups dominate an 8,000-year sedimentary sequence from Lake Cadagno, Switzerland
www.frontiersin.org
February 15, 2025 at 9:58 PM
Happy to share that our new paper is out! 🧬 We used metagenomics to study the microbial communities in an 8,000-year sedimentary sequence from Lake Cadagno.
Check it out here: www.frontiersin.org/journals/mic...
#microbiology #genomics #microbiology #sediments #DNA #sequencing
Check it out here: www.frontiersin.org/journals/mic...
#microbiology #genomics #microbiology #sediments #DNA #sequencing
Presenting my first PhD research next week at ASAS-CSAS 2025 in Florida!
🧬 Steer microbiome + linseed oil + Vitamin B12.
Been a ride through the dark arts of metagenomics.
📅 July 8, 3:15 PM | Diplomat Ballroom 5
#Microbiome #AnimalScience #SDState #LivestockScience #PhDLife #ASASCSAS2025
🧬 Steer microbiome + linseed oil + Vitamin B12.
Been a ride through the dark arts of metagenomics.
📅 July 8, 3:15 PM | Diplomat Ballroom 5
#Microbiome #AnimalScience #SDState #LivestockScience #PhDLife #ASASCSAS2025
July 1, 2025 at 1:21 PM
Presenting my first PhD research next week at ASAS-CSAS 2025 in Florida!
🧬 Steer microbiome + linseed oil + Vitamin B12.
Been a ride through the dark arts of metagenomics.
📅 July 8, 3:15 PM | Diplomat Ballroom 5
#Microbiome #AnimalScience #SDState #LivestockScience #PhDLife #ASASCSAS2025
🧬 Steer microbiome + linseed oil + Vitamin B12.
Been a ride through the dark arts of metagenomics.
📅 July 8, 3:15 PM | Diplomat Ballroom 5
#Microbiome #AnimalScience #SDState #LivestockScience #PhDLife #ASASCSAS2025