Samuel Lampa
@smllmp.bsky.social
Clinical Microbiology #Bioinformatics @ Karolinska Hospital | PhD alum http://pharmb.io | Author of scipipe.org | Looking to get more into genomic algorithms & systems understanding of microbes+hosts, TEs etc
Married to Emebet. Dad. Sinner saved by grace.
Married to Emebet. Dad. Sinner saved by grace.
With #RAMmageddon upon us I think we really need to start working smarter, not just pouring more hardware at problems.
That's one reason I believe platforms like Modular's MAX will only grow in importance, by enabling more innovation in the AI stack. www.modular.com/max
That's one reason I believe platforms like Modular's MAX will only grow in importance, by enabling more innovation in the AI stack. www.modular.com/max
MAX: A high-performance inference framework for AI
MAX provides powerful libraries and tools to develop, optimize and deploy AI on GPUs fast. Get incredible performance, hardware portability, and complete control over every layer of the stack.
www.modular.com
February 18, 2026 at 10:17 AM
With #RAMmageddon upon us I think we really need to start working smarter, not just pouring more hardware at problems.
That's one reason I believe platforms like Modular's MAX will only grow in importance, by enabling more innovation in the AI stack. www.modular.com/max
That's one reason I believe platforms like Modular's MAX will only grow in importance, by enabling more innovation in the AI stack. www.modular.com/max
Reposted by Samuel Lampa
Super happy that the AllTheBacteria hypothetical proteins are now in AFDB - hopefully we can start to understand the function of some of them at least 😁
The AlphaFold Database, jointly developed with Google DeepMind, now contains datasets from specialist communities.
This includes rich datasets for microbes, viruses & parasites associated with tropical diseases.
Explore the new datasets in the AlphaFold Database.
www.ebi.ac.uk/about/news/u...
This includes rich datasets for microbes, viruses & parasites associated with tropical diseases.
Explore the new datasets in the AlphaFold Database.
www.ebi.ac.uk/about/news/u...
AlphaFold Database welcomes community datasets
Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities
www.ebi.ac.uk
February 18, 2026 at 4:46 AM
Super happy that the AllTheBacteria hypothetical proteins are now in AFDB - hopefully we can start to understand the function of some of them at least 😁
Reposted by Samuel Lampa
🚨📢📄 Article in press in Genome Biology doi.org/10.1186/s130...
We introduce panREPET, a reference-free pipeline to detect shared transposable element (TE) insertions across pangenomes and retrace their evolutionary dynamics #TEsky 🧵👇
We introduce panREPET, a reference-free pipeline to detect shared transposable element (TE) insertions across pangenomes and retrace their evolutionary dynamics #TEsky 🧵👇
A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species - Genome Biology
Background The role of transposable elements (TEs) in host adaptation has gained interest in recent years. Individuals of the same species undergo independent TE insertions, providing genetic variabil...
doi.org
February 16, 2026 at 8:38 AM
🚨📢📄 Article in press in Genome Biology doi.org/10.1186/s130...
We introduce panREPET, a reference-free pipeline to detect shared transposable element (TE) insertions across pangenomes and retrace their evolutionary dynamics #TEsky 🧵👇
We introduce panREPET, a reference-free pipeline to detect shared transposable element (TE) insertions across pangenomes and retrace their evolutionary dynamics #TEsky 🧵👇
Reposted by Samuel Lampa
From #OUP 's #Briefings in Bioinformatics journal | Pathways, outputs and impact of #NIH -supported #bioinformatics & #genomics graduate trainees in #Africa | #Education #OpenScience #H3ABionet #H3Africa 🧬 🖥️ 🧪 🔓
⬇️
academic.oup.com/bib/article/...
⬇️
academic.oup.com/bib/article/...
Pathways, outputs and impact of NIH-supported bioinformatics and genomics graduate trainees in Africa
Abstract. Global biomedical and health research is increasingly relying on genomic and computational approaches, largely driven by the increasing volumes o
academic.oup.com
February 13, 2026 at 5:02 PM
From #OUP 's #Briefings in Bioinformatics journal | Pathways, outputs and impact of #NIH -supported #bioinformatics & #genomics graduate trainees in #Africa | #Education #OpenScience #H3ABionet #H3Africa 🧬 🖥️ 🧪 🔓
⬇️
academic.oup.com/bib/article/...
⬇️
academic.oup.com/bib/article/...
Reposted by Samuel Lampa
A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods
This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.
www.nature.com
February 9, 2026 at 3:16 PM
A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)
Reposted by Samuel Lampa
Community service:
Updated the oxford-bioinformatics template repo because apparently the template changed again, and it's still the top google hit, and figuring out the right parameters remains messy, and they are still inconsistent.
github.com/RagnarGrootK...
Updated the oxford-bioinformatics template repo because apparently the template changed again, and it's still the top google hit, and figuring out the right parameters remains messy, and they are still inconsistent.
github.com/RagnarGrootK...
GitHub - RagnarGrootKoerkamp/oxford-bioinformatics-template: Improved version of the Oxford Bioinformatics paper template
Improved version of the Oxford Bioinformatics paper template - RagnarGrootKoerkamp/oxford-bioinformatics-template
github.com
February 4, 2026 at 4:23 PM
Community service:
Updated the oxford-bioinformatics template repo because apparently the template changed again, and it's still the top google hit, and figuring out the right parameters remains messy, and they are still inconsistent.
github.com/RagnarGrootK...
Updated the oxford-bioinformatics template repo because apparently the template changed again, and it's still the top google hit, and figuring out the right parameters remains messy, and they are still inconsistent.
github.com/RagnarGrootK...
Reposted by Samuel Lampa
“Suicides rise following commencement of Daylight Saving Time, compared to the return to Standard Time.”
February 4, 2026 at 9:24 PM
“Suicides rise following commencement of Daylight Saving Time, compared to the return to Standard Time.”
Reposted by Samuel Lampa
We're recruiting 1-2 Group Leaders in Data Science and AI for Molecular & Health Data!
Candidates with strong background in ML/AI/data science and interest in applying analytical methods to large-scale molecular and health data are particularly encouraged to apply:
🔗 jobs.helsinki.fi/job/Helsinki...
Candidates with strong background in ML/AI/data science and interest in applying analytical methods to large-scale molecular and health data are particularly encouraged to apply:
🔗 jobs.helsinki.fi/job/Helsinki...
February 5, 2026 at 8:19 AM
We're recruiting 1-2 Group Leaders in Data Science and AI for Molecular & Health Data!
Candidates with strong background in ML/AI/data science and interest in applying analytical methods to large-scale molecular and health data are particularly encouraged to apply:
🔗 jobs.helsinki.fi/job/Helsinki...
Candidates with strong background in ML/AI/data science and interest in applying analytical methods to large-scale molecular and health data are particularly encouraged to apply:
🔗 jobs.helsinki.fi/job/Helsinki...
Reposted by Samuel Lampa
🚨 The final version is out: how transposons help keep our hearts beating ❤️
Proud of this one with @1995dana.bsky.social, huge thanks to @trono-lab.bsky.social.
Give it a read! #TEsky
Proud of this one with @1995dana.bsky.social, huge thanks to @trono-lab.bsky.social.
Give it a read! #TEsky
It is finally out! If you are interested in TE-derived CREs, and newly described, but evolutionary old KZFP-TE mechanistic modalities, read it at www.cell.com/cell-reports....
Thankful to everyone who took part in this work, namely @orpsf.bsky.social and other @trono-lab.bsky.social members. 🫀🧬✨
Thankful to everyone who took part in this work, namely @orpsf.bsky.social and other @trono-lab.bsky.social members. 🫀🧬✨
Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity
Milovanović et al. uncover a mechanism by which KZFPs restrict the activity of transposon-derived
cis-regulatory elements to safeguard cardiomyocyte functionality. This work extends
the classical TE-K...
www.cell.com
January 30, 2026 at 7:34 PM
🚨 The final version is out: how transposons help keep our hearts beating ❤️
Proud of this one with @1995dana.bsky.social, huge thanks to @trono-lab.bsky.social.
Give it a read! #TEsky
Proud of this one with @1995dana.bsky.social, huge thanks to @trono-lab.bsky.social.
Give it a read! #TEsky
Reposted by Samuel Lampa
AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates 🥨 www.biorxiv.org/content/10.6... 🧬💻🧪 github.com/marbl/anianns
January 29, 2026 at 3:00 PM
AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates 🥨 www.biorxiv.org/content/10.6... 🧬💻🧪 github.com/marbl/anianns
Reposted by Samuel Lampa
1. The thing about science that these jokers don't understand is that science cannot be vibe-coded.
Whatever its flaws, the point with vibe coding is that you're trying to quickly make something that sorta works, where you can immediately sorta see if it sorta works and then sorta use it.
Whatever its flaws, the point with vibe coding is that you're trying to quickly make something that sorta works, where you can immediately sorta see if it sorta works and then sorta use it.
“The idea is to put ChatGPT front and center inside software that scientists use to write up their work in much the same way that chatbots are now embedded into popular programming editors.
It’s vibe coding, but for science.”
It’s vibe coding, but for science.”
OpenAI’s latest product lets you vibe code science
Prism is a ChatGPT-powered text editor that automates much of the work involved in writing scientific papers.
www.technologyreview.com
January 27, 2026 at 10:09 PM
1. The thing about science that these jokers don't understand is that science cannot be vibe-coded.
Whatever its flaws, the point with vibe coding is that you're trying to quickly make something that sorta works, where you can immediately sorta see if it sorta works and then sorta use it.
Whatever its flaws, the point with vibe coding is that you're trying to quickly make something that sorta works, where you can immediately sorta see if it sorta works and then sorta use it.
Reposted by Samuel Lampa
Using gen AI means sacrificing accuracy for convenience. Its purpose is to cut corners. If that’s how you roll, science has no need for you.
We’re getting so many journal submissions from people who think ‘it kinda works’ is the standard to aim for.
1. The thing about science that these jokers don't understand is that science cannot be vibe-coded.
Whatever its flaws, the point with vibe coding is that you're trying to quickly make something that sorta works, where you can immediately sorta see if it sorta works and then sorta use it.
Whatever its flaws, the point with vibe coding is that you're trying to quickly make something that sorta works, where you can immediately sorta see if it sorta works and then sorta use it.
January 28, 2026 at 6:50 AM
Using gen AI means sacrificing accuracy for convenience. Its purpose is to cut corners. If that’s how you roll, science has no need for you.
Reposted by Samuel Lampa
⏰ Closing soon! The Webber group is looking for a Research Scientist to use high throughput transposon mutagenesis to help understand mechanisms of action, host susceptibility and resistance to antimicrobials.
💷 £37,500 to £45,350
🗓️ Apply by 28 January 2026
➡️ buff.ly/8iXH22u
💷 £37,500 to £45,350
🗓️ Apply by 28 January 2026
➡️ buff.ly/8iXH22u
January 26, 2026 at 9:01 AM
⏰ Closing soon! The Webber group is looking for a Research Scientist to use high throughput transposon mutagenesis to help understand mechanisms of action, host susceptibility and resistance to antimicrobials.
💷 £37,500 to £45,350
🗓️ Apply by 28 January 2026
➡️ buff.ly/8iXH22u
💷 £37,500 to £45,350
🗓️ Apply by 28 January 2026
➡️ buff.ly/8iXH22u
Reposted by Samuel Lampa
I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻
Please repost
Apply here: www.wur.nl/en/vacancy/p...
Please repost
Apply here: www.wur.nl/en/vacancy/p...
January 5, 2026 at 10:45 PM
I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻
Please repost
Apply here: www.wur.nl/en/vacancy/p...
Please repost
Apply here: www.wur.nl/en/vacancy/p...
Reposted by Samuel Lampa
A holocentric pangenome links karyotype evolution to meiotic recombination https://www.biorxiv.org/content/10.64898/2026.01.17.700048v1
January 21, 2026 at 5:32 AM
A holocentric pangenome links karyotype evolution to meiotic recombination https://www.biorxiv.org/content/10.64898/2026.01.17.700048v1
Reposted by Samuel Lampa
In case useful @iandunt.bsky.social , @soniaz.bsky.social has just shown me how to turn off the AI summary in google search! Just add -noai. Just did a simple test comparing you and @dorianlynskey.bsky.social
January 19, 2026 at 6:14 PM
In case useful @iandunt.bsky.social , @soniaz.bsky.social has just shown me how to turn off the AI summary in google search! Just add -noai. Just did a simple test comparing you and @dorianlynskey.bsky.social
Reposted by Samuel Lampa
I can’t help thinking how Barbara McClintock would have responded to papers like this. I mean, beyond, I TOLD YOU!
Many thanks to the folks who responded to my #TEsky query about transposable elements. Wow, what an amazing field that’s become.
Many thanks to the folks who responded to my #TEsky query about transposable elements. Wow, what an amazing field that’s become.
This one comes to mind, though specific to mammals: link.springer.com/article/10.1...
Molecular effects of transposable element sequences in mammalian cells - Genome Biology
Transposable elements (TEs) are often epigenetically repressed in eukaryotic cells, but still affect the molecular state of the cell in certain contexts. A flurry of recent studies have elucidated new...
link.springer.com
January 19, 2026 at 1:38 PM
I can’t help thinking how Barbara McClintock would have responded to papers like this. I mean, beyond, I TOLD YOU!
Many thanks to the folks who responded to my #TEsky query about transposable elements. Wow, what an amazing field that’s become.
Many thanks to the folks who responded to my #TEsky query about transposable elements. Wow, what an amazing field that’s become.
Reposted by Samuel Lampa
For those of us interested in software development, data structure design etc in science, this is a must-read. A taste of what is happening in communities letting AI agents go wild writing code, creating PRs, writing documentation : spoiler - humans get addicted, lose perspective, slop everywhere.
Weekend thoughts on Gas Town, Beads, slop AI browsers, and AI-generated PRs flooding overwhelmed maintainers. I don't think we're ready for our new powers we're wielding. lucumr.pocoo.org/2026/1/18/ag...
Agent Psychosis: Are We Going Insane?
What’s going on with the AI builder community right now?
lucumr.pocoo.org
January 19, 2026 at 7:40 AM
For those of us interested in software development, data structure design etc in science, this is a must-read. A taste of what is happening in communities letting AI agents go wild writing code, creating PRs, writing documentation : spoiler - humans get addicted, lose perspective, slop everywhere.
Reposted by Samuel Lampa
vibe coding is the new doom scrolling?
Weekend thoughts on Gas Town, Beads, slop AI browsers, and AI-generated PRs flooding overwhelmed maintainers. I don't think we're ready for our new powers we're wielding. lucumr.pocoo.org/2026/1/18/ag...
Agent Psychosis: Are We Going Insane?
What’s going on with the AI builder community right now?
lucumr.pocoo.org
January 19, 2026 at 12:51 AM
vibe coding is the new doom scrolling?
Reposted by Samuel Lampa
Giving this a bump. I’ve had lots of friendly likes and follows, thanks— but no citations!
Pls drop a reference into the cup to support a poor historian who’s trying to get the science right!
#TEsky
Pls drop a reference into the cup to support a poor historian who’s trying to get the science right!
#TEsky
Hey, good folks of #TEsky—
Looking for good recent review, suitable for undergrads, of the fnxns of transposable elements in the genome, for class session on the nonlinear, highly regulated, 4D nucleome. Suggestions welcome!
(I'm the author of the "other book" on Barbara McClintock)
TIA!
Looking for good recent review, suitable for undergrads, of the fnxns of transposable elements in the genome, for class session on the nonlinear, highly regulated, 4D nucleome. Suggestions welcome!
(I'm the author of the "other book" on Barbara McClintock)
TIA!
The Tangled Field: Barbara McClintock's Search for the Patterns of Genetic Control
Buy The Tangled Field: Barbara McClintock's Search for the Patterns of Genetic Control on Amazon.com ✓ FREE SHIPPING on qualified orders
www.amazon.com
January 18, 2026 at 1:57 PM
Giving this a bump. I’ve had lots of friendly likes and follows, thanks— but no citations!
Pls drop a reference into the cup to support a poor historian who’s trying to get the science right!
#TEsky
Pls drop a reference into the cup to support a poor historian who’s trying to get the science right!
#TEsky
Reposted by Samuel Lampa
🆕 Vacancy! We are looking for a Research Scientist to join an exciting multipartner consortium in the END2AMR project to help develop novel antimicrobials using high throughput transposon mutagenesis.
💷 £37,500 to £45,350
🗓️ Apply by 28 January 2026
➡️ buff.ly/8iXH22u
💷 £37,500 to £45,350
🗓️ Apply by 28 January 2026
➡️ buff.ly/8iXH22u
January 16, 2026 at 2:00 PM
🆕 Vacancy! We are looking for a Research Scientist to join an exciting multipartner consortium in the END2AMR project to help develop novel antimicrobials using high throughput transposon mutagenesis.
💷 £37,500 to £45,350
🗓️ Apply by 28 January 2026
➡️ buff.ly/8iXH22u
💷 £37,500 to £45,350
🗓️ Apply by 28 January 2026
➡️ buff.ly/8iXH22u
Reposted by Samuel Lampa
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!
HLi Lab - Vacancies
Openings
hlilab.github.io
January 14, 2026 at 3:44 PM
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!
Reposted by Samuel Lampa
💡ESCMID Study Groups are a major way we support innovation & research in CM/ID. We encourage our members to participate and join a Study Group. It's a great way to support your career development and build your network! 🌍
Learn more: https://ow.ly/TCR450XNzeY
#IDSky #clinmicro
Learn more: https://ow.ly/TCR450XNzeY
#IDSky #clinmicro
January 12, 2026 at 10:20 AM
💡ESCMID Study Groups are a major way we support innovation & research in CM/ID. We encourage our members to participate and join a Study Group. It's a great way to support your career development and build your network! 🌍
Learn more: https://ow.ly/TCR450XNzeY
#IDSky #clinmicro
Learn more: https://ow.ly/TCR450XNzeY
#IDSky #clinmicro
Reposted by Samuel Lampa
"Cann's Principles of Molecular Virology 7th Edition revised extensively by Ed Rybicki, is an easily accessible introduction to modern virology, presenting principles in a clear and concise manner."
**Selected for Doody’s Core Titles® 2024 in Microbiology**
www.sciencedirect.com/book/9780128...
**Selected for Doody’s Core Titles® 2024 in Microbiology**
www.sciencedirect.com/book/9780128...
Cann's Principles of Molecular Virology
**Selected for Doody’s Core Titles® 2024 in Microbiology**Cann's Principles of Molecular Virology, Seventh Edition provides an easily access...
www.sciencedirect.com
December 12, 2024 at 2:13 PM
"Cann's Principles of Molecular Virology 7th Edition revised extensively by Ed Rybicki, is an easily accessible introduction to modern virology, presenting principles in a clear and concise manner."
**Selected for Doody’s Core Titles® 2024 in Microbiology**
www.sciencedirect.com/book/9780128...
**Selected for Doody’s Core Titles® 2024 in Microbiology**
www.sciencedirect.com/book/9780128...