Andreas Sjödin
@druvus.bsky.social
Microbial genomics and forensics, Metagenomics, Francisella, Long-read seq, AI
Reposted by Andreas Sjödin
Excited to share our new call for papers at @asm.org's MRA journal. Do you have a database, software, or web-based tool that would be a great resource for the micro community? Consider submitting it to MRA! journals.asm.org/journal/mra/...
Microbial Databases, Software Tools, and Web Services
Publish your microbial database or software tool in MRA to gain recognition, citations, and community trust.
journals.asm.org
July 23, 2025 at 3:38 PM
Excited to share our new call for papers at @asm.org's MRA journal. Do you have a database, software, or web-based tool that would be a great resource for the micro community? Consider submitting it to MRA! journals.asm.org/journal/mra/...
Our latest paper in Scientific Reports: First detection of #Sindbis #virus in wild birds in Nigeria! Screened 504 birds, found SINV RNA in African Thrushes, sequenced genome linking to Algeria, Spain & Kenya. Calls for enhanced surveillance & One Health 🦜🦟 doi.org/10.1038/s415...
First detection of Sindbis virus in wild birds in Nigeria - Scientific Reports
Scientific Reports - First detection of Sindbis virus in wild birds in Nigeria
doi.org
July 10, 2025 at 1:40 PM
Our latest paper in Scientific Reports: First detection of #Sindbis #virus in wild birds in Nigeria! Screened 504 birds, found SINV RNA in African Thrushes, sequenced genome linking to Algeria, Spain & Kenya. Calls for enhanced surveillance & One Health 🦜🦟 doi.org/10.1038/s415...
Back a London Calling 10 years after my first #NanoporeConf
May 21, 2025 at 3:34 PM
Back a London Calling 10 years after my first #NanoporeConf
Reposted by Andreas Sjödin
Not a single marine species among the 50! most studied bacteria. Gobsmacking.
Ten species comprise half of the bacteriology literature, leaving most species unstudied www.biorxiv.org/content/10.1...
Ten species comprise half of the bacteriology literature, leaving most species unstudied www.biorxiv.org/content/10.1...
www.biorxiv.org
January 6, 2025 at 9:30 AM
Not a single marine species among the 50! most studied bacteria. Gobsmacking.
Ten species comprise half of the bacteriology literature, leaving most species unstudied www.biorxiv.org/content/10.1...
Ten species comprise half of the bacteriology literature, leaving most species unstudied www.biorxiv.org/content/10.1...
Does anyone have updated benchmarks for #Dorado basecalling on different GPUs, including Apple Silicon? #Nanopore #Sequencing
December 26, 2024 at 10:38 AM
Does anyone have updated benchmarks for #Dorado basecalling on different GPUs, including Apple Silicon? #Nanopore #Sequencing
Reposted by Andreas Sjödin
Kun-peng: claims; as fast/faster than Kraken2 with the accuracy comparable to sylph! Very cool.
The design here reinforces a strong feeling I've had for a few years - moving forward in bioinfo. system-friendly & ext. memory algorithms will come to prevail. (& rust!)
www.biorxiv.org/content/10.1...
The design here reinforces a strong feeling I've had for a few years - moving forward in bioinfo. system-friendly & ext. memory algorithms will come to prevail. (& rust!)
www.biorxiv.org/content/10.1...
Kun-peng: an ultra-memory-efficient, fast, and accurate pan-domain taxonomic classifier for all
Comprehensive metagenomic sequence classification of diverse environmental samples faces significant computing memory challenges due to exponentially expanding genome databases. Here, we present Kun-p...
www.biorxiv.org
December 22, 2024 at 3:42 PM
Kun-peng: claims; as fast/faster than Kraken2 with the accuracy comparable to sylph! Very cool.
The design here reinforces a strong feeling I've had for a few years - moving forward in bioinfo. system-friendly & ext. memory algorithms will come to prevail. (& rust!)
www.biorxiv.org/content/10.1...
The design here reinforces a strong feeling I've had for a few years - moving forward in bioinfo. system-friendly & ext. memory algorithms will come to prevail. (& rust!)
www.biorxiv.org/content/10.1...
December 12, 2024 at 1:54 PM
Reposted by Andreas Sjödin
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...
Sign up for next year's CBRNe Protection Symposium! A perfect opportunity to learn more about the latest in CBRNe protection research, showcase your own research. We also welcome abstract submissions for oral or poster presentation. More information here: ow.ly/g2kv50Ui2Hx
Via @FOIresearch on X
Via @FOIresearch on X
15th CBRNe Protection Symposium and the Exhibition of CBRNe protection equipment – Welcome to The 15th CBRNe September 30 – October 2, 2025 in Malmö, Sweden
ow.ly
December 6, 2024 at 10:09 AM
Sign up for next year's CBRNe Protection Symposium! A perfect opportunity to learn more about the latest in CBRNe protection research, showcase your own research. We also welcome abstract submissions for oral or poster presentation. More information here: ow.ly/g2kv50Ui2Hx
Via @FOIresearch on X
Via @FOIresearch on X
Working on designing a new hybridisation capture panel for a virus family. Previously used CATCH to select optimal set of probes but now looking for alt tools setting tiling coverage to 2 or 3 intead of complete coverage. Any recommendation of tools or code that can do it? #bioinformatics
December 6, 2024 at 9:56 AM
Working on designing a new hybridisation capture panel for a virus family. Previously used CATCH to select optimal set of probes but now looking for alt tools setting tiling coverage to 2 or 3 intead of complete coverage. Any recommendation of tools or code that can do it? #bioinformatics
Reposted by Andreas Sjödin
MMseqs2 Release 16 Highlights: GPU-accelerated search📄, ORF or new 6-frame translated search modes, contig taxonomy always keeps the longest ORF, bug fixes (reduced memory and higher sensitivity) and relicensed as MIT
📄 biorxiv.org/content/10.1...
💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶
📄 biorxiv.org/content/10.1...
💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶
November 27, 2024 at 9:08 AM
MMseqs2 Release 16 Highlights: GPU-accelerated search📄, ORF or new 6-frame translated search modes, contig taxonomy always keeps the longest ORF, bug fixes (reduced memory and higher sensitivity) and relicensed as MIT
📄 biorxiv.org/content/10.1...
💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶
📄 biorxiv.org/content/10.1...
💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶
Reposted by Andreas Sjödin
Please share! Applications due Dec 15th for a starting date in Sep 2025.
Fully Funded PhD Opportunity in Evolutionary Biology at the U of Rhode Island. Join us to explore the origin and early evolution of eukaryotes using cutting-edge comparative (meta)genomics and molecular evolution approaches. Applications are due December 15th. Contact me ASAP at laura.eme@uri.edu
November 26, 2024 at 5:48 PM
Please share! Applications due Dec 15th for a starting date in Sep 2025.
Reposted by Andreas Sjödin
Latest data from AllTheBacteria described in our updated preprint. All illumina WGS bacterial+archaeal sequence data to Aug 2024 consistently assembled, QC, and now AMR profiling. That's 2.4 million genomes. Gene annotations almost done , coming next. Please use!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
AllTheBacteria - all bacterial genomes assembled, available and searchable
The bacterial sequence data publicly available at the global DNA archives is a vast source of information on the evolution of bacteria and their mobile elements. However, most of it is either unassemb...
www.biorxiv.org
November 15, 2024 at 6:59 PM
Latest data from AllTheBacteria described in our updated preprint. All illumina WGS bacterial+archaeal sequence data to Aug 2024 consistently assembled, QC, and now AMR profiling. That's 2.4 million genomes. Gene annotations almost done , coming next. Please use!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Andreas Sjödin
We're looking for Reviewing Editors, over at Microbiology Resource Announcements (MRA) - call in the link below.
It's an ideal position for early-career researchers looking for a steady editing role.
#microbiology #editing #publishing #scipub #genomics #sequencing
journals.asm.org/mra/open-cal...
It's an ideal position for early-career researchers looking for a steady editing role.
#microbiology #editing #publishing #scipub #genomics #sequencing
journals.asm.org/mra/open-cal...
Microbiology Resource Announcements Open Call for Reviewing Editors
Microbiology Resource Announcements is looking for microbiologists with expertise in genome sequencing to join our Board of Reviewing Editors.
journals.asm.org
November 15, 2024 at 8:54 AM
We're looking for Reviewing Editors, over at Microbiology Resource Announcements (MRA) - call in the link below.
It's an ideal position for early-career researchers looking for a steady editing role.
#microbiology #editing #publishing #scipub #genomics #sequencing
journals.asm.org/mra/open-cal...
It's an ideal position for early-career researchers looking for a steady editing role.
#microbiology #editing #publishing #scipub #genomics #sequencing
journals.asm.org/mra/open-cal...
Spending my afternoon installing Ubuntu on my old MacBook Pro 2012. Hopefully it will be a good complement to my M3 MacBook
November 4, 2024 at 3:37 PM
Spending my afternoon installing Ubuntu on my old MacBook Pro 2012. Hopefully it will be a good complement to my M3 MacBook
Reposted by Andreas Sjödin
Modern microbiology: Embracing complexity through integration across scales
A review from @merenbey.bsky.social and Jill Banfield
www.cell.com/cell/abstrac...
A review from @merenbey.bsky.social and Jill Banfield
www.cell.com/cell/abstrac...
Modern microbiology: Embracing complexity through integration across scales
This review explores the history of microbiology and contemplates the future of this
evolving discipline as microbiologists embrace rapidly emerging technologies to explore
systems of great complexity...
www.cell.com
September 19, 2024 at 3:15 PM
Modern microbiology: Embracing complexity through integration across scales
A review from @merenbey.bsky.social and Jill Banfield
www.cell.com/cell/abstrac...
A review from @merenbey.bsky.social and Jill Banfield
www.cell.com/cell/abstrac...
Reposted by Andreas Sjödin
I'm going to be advertising a PhD studentship (open to international students) working on long read pangenome / assembly algorithms in bacteria. Would suit someone with maths/compsci background. Aptitude and interest more important than experience. Do please spread the word. Advert to follow
October 22, 2024 at 5:56 PM
I'm going to be advertising a PhD studentship (open to international students) working on long read pangenome / assembly algorithms in bacteria. Would suit someone with maths/compsci background. Aptitude and interest more important than experience. Do please spread the word. Advert to follow
Reposted by Andreas Sjödin
Great three-part blog post by James Fellows Yates about adding software to bioconda: ubinfie.github.io/2024/08/16/a...
Adding bioinformatic software to Bioconda - a reference guide
In this first part of a three part guide, this post aims to provide an (opinionated) guide to adding a tool or package to Bioconda.
ubinfie.github.io
September 11, 2024 at 8:05 PM
Great three-part blog post by James Fellows Yates about adding software to bioconda: ubinfie.github.io/2024/08/16/a...
Reposted by Andreas Sjödin
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
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
October 10, 2024 at 7:56 AM
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
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
Reposted by Andreas Sjödin
I created a genomics+bioinformatics starter pack. If I left you off, *please* reply and I'll add you! go.bsky.app/B5YYBfq
Genomics+Bioinformatics Starter Pack 🧬🖥️
Join the conversation
go.bsky.app
October 22, 2024 at 12:34 PM
I created a genomics+bioinformatics starter pack. If I left you off, *please* reply and I'll add you! go.bsky.app/B5YYBfq
Reposted by Andreas Sjödin
Last chance to fill in our survey! Have your say while you can :) Thanks for all those of you that already have!
Want to have your say about BEAST2 future developments?
Fill in our BEAST2 user and developer survey :)
forms.gle/mTWvaXHZAA12...
Fill in our BEAST2 user and developer survey :)
forms.gle/mTWvaXHZAA12...
BEAST 2 user and developer experience and future development survey
This survey aims to gather feedback from the BEAST2 user and developer community to inform the development of future versions of BEAST. Your insights will help us prioritise features, address pain poi...
forms.gle
October 21, 2024 at 3:46 AM
Last chance to fill in our survey! Have your say while you can :) Thanks for all those of you that already have!
Delighted to see our work on simplifying real-time analysis of nanopore reads, even without bioinformatics skills, being published! #Nanopore #Bioinformatics #plotly
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Nanometa live: a user-friendly application for real-time metagenomic data analysis and pathogen identification
AbstractSummary. Nanometa Live presents a user-friendly interface designed for real-time metagenomic data analysis and pathogen identification utilizing Oxford
academic.oup.com
February 26, 2024 at 11:47 AM
Delighted to see our work on simplifying real-time analysis of nanopore reads, even without bioinformatics skills, being published! #Nanopore #Bioinformatics #plotly
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Lets start the scientific evaluation of different Semla buns
February 13, 2024 at 4:56 PM
Lets start the scientific evaluation of different Semla buns
Reposted by Andreas Sjödin
A metagenomic alpha-diversity index for microbial functional biodiversity academic.oup.com/femsec/artic... #jcampubs
February 12, 2024 at 2:12 PM
A metagenomic alpha-diversity index for microbial functional biodiversity academic.oup.com/femsec/artic... #jcampubs
Reposted by Andreas Sjödin
Md. Hasin Abrar and I recently posted a pre-print "PLA-complexity of k-mer multisets" We explore a measure of a k-mer multiset complexity, first suggested by Boffa et al, which we call the PLA-complexity.
doi.org/10.1101/2024...
(1/n)
doi.org/10.1101/2024...
(1/n)
PLA-complexity of k-mer multisets
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
doi.org
February 13, 2024 at 7:47 AM
Md. Hasin Abrar and I recently posted a pre-print "PLA-complexity of k-mer multisets" We explore a measure of a k-mer multiset complexity, first suggested by Boffa et al, which we call the PLA-complexity.
doi.org/10.1101/2024...
(1/n)
doi.org/10.1101/2024...
(1/n)