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.
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...
Reposted by Samuel Lampa
Now published in gigascience: academic.oup.com/gigascience/.... Key messages: SVs are highly enriched in low-complexity/tandem-repeat regions and are harder to call. They behave differently from transposon insertions. Always stratify if you study SVs.
January 6, 2026 at 10:55 PM
Now published in gigascience: academic.oup.com/gigascience/.... Key messages: SVs are highly enriched in low-complexity/tandem-repeat regions and are harder to call. They behave differently from transposon insertions. Always stratify if you study SVs.
Reposted by Samuel Lampa
Sequencing Instrumrnt Outlook 2026
My observations & predictions on sequencing instrument companies
🧬🖥️
omicsomics.blogspot.com/2026/01/sequ...
My observations & predictions on sequencing instrument companies
🧬🖥️
omicsomics.blogspot.com/2026/01/sequ...
Sequencing Instrument Outlook 2026
A computational biologist's personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery
omicsomics.blogspot.com
January 5, 2026 at 3:23 AM
Sequencing Instrumrnt Outlook 2026
My observations & predictions on sequencing instrument companies
🧬🖥️
omicsomics.blogspot.com/2026/01/sequ...
My observations & predictions on sequencing instrument companies
🧬🖥️
omicsomics.blogspot.com/2026/01/sequ...
Reposted by Samuel Lampa
Linux is good now. The author had enough of Windows and Microsoft shenanigans. I'm brave enough to say it: Linux is good now, and if you want to feel like you actually own your PC, make 2026 the year of Linux on (your) desktop
www.pcgamer.com/software/lin...
www.pcgamer.com/software/lin...
I'm brave enough to say it: Linux is good now, and if you want to feel like you actually own your PC, make 2026 the year of Linux on (your) desktop
Now if you don't mind I'm going to delete the root folder and see what happens.
www.pcgamer.com
January 2, 2026 at 11:19 AM
Linux is good now. The author had enough of Windows and Microsoft shenanigans. I'm brave enough to say it: Linux is good now, and if you want to feel like you actually own your PC, make 2026 the year of Linux on (your) desktop
www.pcgamer.com/software/lin...
www.pcgamer.com/software/lin...
Reposted by Samuel Lampa
I ❤️ Diversity-Generating Retroelements! DGRs are abundant in prokaryotes and have been domesticated to create protein diversity via reverse transcription. This new structural study reveals a unique way of priming RT via precise positioning of the RNA around the enzyme.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
RNA control of reverse transcription in a diversity-generating retroelement - Nature
This study presents cryogenic electron microscopy structural analysis of a diversity-generating retroelement (DGR) reverse transcription system from Bordetella bacteriophage, with results indicating t...
www.nature.com
January 8, 2025 at 8:10 PM
I ❤️ Diversity-Generating Retroelements! DGRs are abundant in prokaryotes and have been domesticated to create protein diversity via reverse transcription. This new structural study reveals a unique way of priming RT via precise positioning of the RNA around the enzyme.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Samuel Lampa
Systematic comparative benchmarking of computational methods for the detection of transposable elements in long-read sequencing data www.biorxiv.org/content/10.1... 🧬🖥️🧪
October 2, 2025 at 3:55 PM
Systematic comparative benchmarking of computational methods for the detection of transposable elements in long-read sequencing data www.biorxiv.org/content/10.1... 🧬🖥️🧪
A very good composer I've never heard of 😳 - much in line with Händel and also the Swedish Johann Helmich Roman - with very festive and delightful music: William Boyce
www.youtube.com/watch?v=TXSQ...
www.youtube.com/watch?v=TXSQ...
I. Allegro
YouTube video by Aradia Ensemble - Topic
www.youtube.com
December 29, 2025 at 2:33 PM
A very good composer I've never heard of 😳 - much in line with Händel and also the Swedish Johann Helmich Roman - with very festive and delightful music: William Boyce
www.youtube.com/watch?v=TXSQ...
www.youtube.com/watch?v=TXSQ...
Reposted by Samuel Lampa
Hey folks, am looking for examples of circularised/full plasmid sequences from "unusual " bacterial species, sequenced since 2020 (as independent validation for a plasmid identification tool that was trained on refseq2020+plsdb). Any tips? #microsky
December 22, 2025 at 11:03 PM
Hey folks, am looking for examples of circularised/full plasmid sequences from "unusual " bacterial species, sequenced since 2020 (as independent validation for a plasmid identification tool that was trained on refseq2020+plsdb). Any tips? #microsky
Reposted by Samuel Lampa
Our preprint on predicting drug resistance in bacteria is now out in @plosbiology.org. We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. Work from @yanyingyu.bsky.social with @nwheeler443.bsky.social.
Biased sampling driven by bacterial population structure confounds machine learning prediction of antimicrobial resistance
Machine learning methods have emerged as promising tools to predict antimicrobial resistance (AMR) and uncover resistance determinants from genomic data. This study shows that sampling biases driven b...
journals.plos.org
December 17, 2025 at 2:55 PM
Our preprint on predicting drug resistance in bacteria is now out in @plosbiology.org. We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. Work from @yanyingyu.bsky.social with @nwheeler443.bsky.social.
Molecular effects of transposable element sequences in mammalian cells #TESky
(Wen, MC.C., Welch, J.D. Genome Biol 26, 403 (2025)).
Interesting review of new-found functions of TEs in mammalian genomes, especially over the last three years.
doi.org/10.1186/s130... #TEWorldwide
(Wen, MC.C., Welch, J.D. Genome Biol 26, 403 (2025)).
Interesting review of new-found functions of TEs in mammalian genomes, especially over the last three years.
doi.org/10.1186/s130... #TEWorldwide
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...
doi.org
November 28, 2025 at 8:05 AM
Molecular effects of transposable element sequences in mammalian cells #TESky
(Wen, MC.C., Welch, J.D. Genome Biol 26, 403 (2025)).
Interesting review of new-found functions of TEs in mammalian genomes, especially over the last three years.
doi.org/10.1186/s130... #TEWorldwide
(Wen, MC.C., Welch, J.D. Genome Biol 26, 403 (2025)).
Interesting review of new-found functions of TEs in mammalian genomes, especially over the last three years.
doi.org/10.1186/s130... #TEWorldwide
Reposted by Samuel Lampa
Thrilled to share our new review in Current Opinion in Genetics & Development on TE driven innovation in gene regulation🤘. I am honored to be part of this with two major TE aficionados @cedricfeschotte.bsky.social and @trono-lab.bsky.social
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
November 15, 2025 at 5:23 PM
Thrilled to share our new review in Current Opinion in Genetics & Development on TE driven innovation in gene regulation🤘. I am honored to be part of this with two major TE aficionados @cedricfeschotte.bsky.social and @trono-lab.bsky.social
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
Reposted by Samuel Lampa
#TEsky TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution doi.org/10.1093/nar/...
TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution
Abstract. Transposable elements (TEs) are repetitive DNA sequences typically silenced in normal tissues. Their dysregulation in cancer can significantly im
doi.org
November 27, 2025 at 1:45 PM
#TEsky TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution doi.org/10.1093/nar/...
Reposted by Samuel Lampa
Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2
GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing
A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim
github.com
November 25, 2025 at 2:13 PM
Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2
I might be biased (as they mention scipipe.org), but a recommended related paper:
www.nature.com/articles/s41... #sciworkflows
www.nature.com/articles/s41... #sciworkflows
November 13, 2025 at 8:45 PM
I might be biased (as they mention scipipe.org), but a recommended related paper:
www.nature.com/articles/s41... #sciworkflows
www.nature.com/articles/s41... #sciworkflows
Reposted by Samuel Lampa
The last episode of the three part debate is out today! Check it out on the platform of your choice
🤩 Don't forget to give us stars and reviews to help spread the podcast to new listeners!
🤩 Don't forget to give us stars and reviews to help spread the podcast to new listeners!
🍏 We just finished a three part debate on @nextflow.io! Please don't hate me for volunteering on the cons side of the debate! Subscribe to #microbinfie on the podcast app of your choice or go here m.soundcloud.com/microbinfie/...
146 - NextFlow debate 1
Play 146 - NextFlow debate 1 by Micro Binfie Podcast on desktop and mobile. Play over 320 million tracks for free on SoundCloud.
m.soundcloud.com
November 13, 2025 at 5:17 PM
The last episode of the three part debate is out today! Check it out on the platform of your choice
🤩 Don't forget to give us stars and reviews to help spread the podcast to new listeners!
🤩 Don't forget to give us stars and reviews to help spread the podcast to new listeners!
⚠️Important bugfix release, 0.5.1 of SciCommander (tool to track shell commands in a reproducible way), fixing the scanning of output files and audit files in subdirectories!
github.com/samuell/scic...
github.com/samuell/scic...
Release 0.5.1: Fix handling of outputs in sub-folders · samuell/scicommander
This is a bugfix release that fixes #21 and makes sure that output paths in subfolders of the main directory are correctly handled.
Thanks to @GuilloteauQ for reporting it!
Changes
Fixes #21
Adds ...
github.com
November 13, 2025 at 6:20 PM
⚠️Important bugfix release, 0.5.1 of SciCommander (tool to track shell commands in a reproducible way), fixing the scanning of output files and audit files in subdirectories!
github.com/samuell/scic...
github.com/samuell/scic...
Reposted by Samuel Lampa
Metagenomics colleagues!
I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.
Please help and share!
I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.
Please help and share!
November 11, 2025 at 8:21 PM
Metagenomics colleagues!
I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.
Please help and share!
I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.
Please help and share!