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.
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!
Reposted by Samuel Lampa
📢 Just released 0.5.0 of SciCommander, a tool to automatically track provenance information about shell commands, into HTML reports with the full provenance graph for every output. This version brings much improved usability and better looks.
github.com/samuell/scic...
#provenance #bioinformatics
github.com/samuell/scic...
#provenance #bioinformatics
November 6, 2025 at 8:27 PM
📢 Just released 0.5.0 of SciCommander, a tool to automatically track provenance information about shell commands, into HTML reports with the full provenance graph for every output. This version brings much improved usability and better looks.
github.com/samuell/scic...
#provenance #bioinformatics
github.com/samuell/scic...
#provenance #bioinformatics
Reposted by Samuel Lampa
1/ Everyone’s chasing AI.
But in bioinformatics, solid foundations still win.
Here’s why mastering the basics matters more than ever. 🧵
But in bioinformatics, solid foundations still win.
Here’s why mastering the basics matters more than ever. 🧵
November 9, 2025 at 2:45 PM
1/ Everyone’s chasing AI.
But in bioinformatics, solid foundations still win.
Here’s why mastering the basics matters more than ever. 🧵
But in bioinformatics, solid foundations still win.
Here’s why mastering the basics matters more than ever. 🧵
This has been a fantastic course, very well done @valentinapeona.bsky.social and @ritarebollo.bsky.social ! 🙌
Looking forward to continue diving into the field 😊
Looking forward to continue diving into the field 😊
This week we're running the Transposable Elements course with @valentinapeona.bsky.social and @ritarebollo.bsky.social
www.physalia-courses.org/courses-work...
#TE25 #Bioinformatics #Genomics
www.physalia-courses.org/courses-work...
#TE25 #Bioinformatics #Genomics
November 7, 2025 at 3:50 PM
This has been a fantastic course, very well done @valentinapeona.bsky.social and @ritarebollo.bsky.social ! 🙌
Looking forward to continue diving into the field 😊
Looking forward to continue diving into the field 😊
Reposted by Samuel Lampa
This week we're running the Transposable Elements course with @valentinapeona.bsky.social and @ritarebollo.bsky.social
www.physalia-courses.org/courses-work...
#TE25 #Bioinformatics #Genomics
www.physalia-courses.org/courses-work...
#TE25 #Bioinformatics #Genomics
November 4, 2025 at 3:04 PM
This week we're running the Transposable Elements course with @valentinapeona.bsky.social and @ritarebollo.bsky.social
www.physalia-courses.org/courses-work...
#TE25 #Bioinformatics #Genomics
www.physalia-courses.org/courses-work...
#TE25 #Bioinformatics #Genomics
📢 Just released 0.5.0 of SciCommander, a tool to automatically track provenance information about shell commands, into HTML reports with the full provenance graph for every output. This version brings much improved usability and better looks.
github.com/samuell/scic...
#provenance #bioinformatics
github.com/samuell/scic...
#provenance #bioinformatics
November 6, 2025 at 8:27 PM
📢 Just released 0.5.0 of SciCommander, a tool to automatically track provenance information about shell commands, into HTML reports with the full provenance graph for every output. This version brings much improved usability and better looks.
github.com/samuell/scic...
#provenance #bioinformatics
github.com/samuell/scic...
#provenance #bioinformatics
Reposted by Samuel Lampa
At @embo.org #EMBOMobileGenome and want to connect with other TE researchers and follow the latest goings on?
Use #TEworldwide and #TEsky in your posts to be featured in the TEworldwide feed, which you can also find here:
bsky.app/profile/did:...
Use #TEworldwide and #TEsky in your posts to be featured in the TEworldwide feed, which you can also find here:
bsky.app/profile/did:...
November 5, 2025 at 5:14 AM
At @embo.org #EMBOMobileGenome and want to connect with other TE researchers and follow the latest goings on?
Use #TEworldwide and #TEsky in your posts to be featured in the TEworldwide feed, which you can also find here:
bsky.app/profile/did:...
Use #TEworldwide and #TEsky in your posts to be featured in the TEworldwide feed, which you can also find here:
bsky.app/profile/did:...
November 6, 2025 at 11:12 AM
Reposted by Samuel Lampa
Time to kick off #EMBOMobileGenome for 2025! A great selection of speakers and posters on the agenda!
#TEWorldwide #TESky
#TEWorldwide #TESky
November 4, 2025 at 12:32 PM
Time to kick off #EMBOMobileGenome for 2025! A great selection of speakers and posters on the agenda!
#TEWorldwide #TESky
#TEWorldwide #TESky
Reposted by Samuel Lampa
@tobybarilbio.bsky.social and I are very excited to release MycoMobilome! A very extensive effort to discover, QC and annotate TEs across the fungal kingdom.
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
October 29, 2025 at 4:32 PM
@tobybarilbio.bsky.social and I are very excited to release MycoMobilome! A very extensive effort to discover, QC and annotate TEs across the fungal kingdom.
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
Reposted by Samuel Lampa
A horrific mass murder is unfolding in Sudan, where no one can see it. The RSF are murdering civilians in El Fasher, having finally defeated the Sudanese army forces holding out in the city. The BBC has managed to speak to some who escaped
www.youtube.com/watch?v=i7fC...
www.youtube.com/watch?v=i7fC...
Sudanese survivors of el-Fasher siege tell the BBC about RSF brutality | BBC News
YouTube video by BBC News
www.youtube.com
November 1, 2025 at 7:14 AM
A horrific mass murder is unfolding in Sudan, where no one can see it. The RSF are murdering civilians in El Fasher, having finally defeated the Sudanese army forces holding out in the city. The BBC has managed to speak to some who escaped
www.youtube.com/watch?v=i7fC...
www.youtube.com/watch?v=i7fC...
Reposted by Samuel Lampa
Make sure to register ASAP!
bsky.app/profile/jlst...
bsky.app/profile/jlst...
Come join the Workshop on Phylogenomics in Cesky Krumlov, Czechia, from January 25 through February 7, 2026!
Applications close November 15!
#phylogenetics #evolution #genomics #ai
evomics.org/apply-worksh...
Applications close November 15!
#phylogenetics #evolution #genomics #ai
evomics.org/apply-worksh...
Apply: Workshop on Phylogenomics 2026 - Evolution and Genomics
Application for the 2026 Workshop on Phylogenomics Use this form to apply for the 2026 Workshop on Phylogenomics being held in Cesky Krumlov, Czechia from 25th January through 7th February, ...
evomics.org
October 30, 2025 at 6:50 PM
Make sure to register ASAP!
bsky.app/profile/jlst...
bsky.app/profile/jlst...
Reposted by Samuel Lampa
Used EMBL-EBI data resources to find, analyse, or archive your data? 🧬
Now’s your turn: tell us how you’ve used them + why they matter.
It takes 15 mins and helps keep these services open and free for all.
👉 tinyurl.com/bdf73zpp
Closes 16 July
#opendata #FAIRdata
Now’s your turn: tell us how you’ve used them + why they matter.
It takes 15 mins and helps keep these services open and free for all.
👉 tinyurl.com/bdf73zpp
Closes 16 July
#opendata #FAIRdata
June 17, 2025 at 8:00 PM
Used EMBL-EBI data resources to find, analyse, or archive your data? 🧬
Now’s your turn: tell us how you’ve used them + why they matter.
It takes 15 mins and helps keep these services open and free for all.
👉 tinyurl.com/bdf73zpp
Closes 16 July
#opendata #FAIRdata
Now’s your turn: tell us how you’ve used them + why they matter.
It takes 15 mins and helps keep these services open and free for all.
👉 tinyurl.com/bdf73zpp
Closes 16 July
#opendata #FAIRdata
The @scikit-learn.org docs are such a nice overview of the common types of learning in classical machine learning! A great visual overview and guide for newcomers.
scikit-learn.org
scikit-learn.org
October 25, 2025 at 10:32 PM
The @scikit-learn.org docs are such a nice overview of the common types of learning in classical machine learning! A great visual overview and guide for newcomers.
scikit-learn.org
scikit-learn.org
I did all of those!
October 25, 2025 at 7:38 PM
I did all of those!
Reposted by Samuel Lampa
Version 3 of the Snakemake rolling paper is now pulbished on @f1000publishing.bsky.social: f1000research.com/articles/10-...
We have updated the presented features and the design patterns.
#sciworkflows #reproducibility
We have updated the presented features and the design patterns.
#sciworkflows #reproducibility
F1000Research Article: Sustainable data analysis with Snakemake.
Read the latest article version by Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Peter C. van Dyken, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Forster, Filipe G. Vi...
f1000research.com
September 23, 2025 at 10:18 AM
Version 3 of the Snakemake rolling paper is now pulbished on @f1000publishing.bsky.social: f1000research.com/articles/10-...
We have updated the presented features and the design patterns.
#sciworkflows #reproducibility
We have updated the presented features and the design patterns.
#sciworkflows #reproducibility
Always nice when someone has not only cited you, but also actually read your paper 😊 Hat tip to the authors! 👍
doi.org/10.1016/j.co... #sciworkflows
doi.org/10.1016/j.co... #sciworkflows
October 24, 2025 at 10:10 PM
Always nice when someone has not only cited you, but also actually read your paper 😊 Hat tip to the authors! 👍
doi.org/10.1016/j.co... #sciworkflows
doi.org/10.1016/j.co... #sciworkflows
Reposted by Samuel Lampa
The next five videos from our #IMMEM XIV poster presentations are available now on our YouTube channel and cover topics like #microbiome, transmission and more. #IDSky
https://youtube.com/playlist?list=PLBG53xT7PX7v-C3XcKHnKeVP1NxsrLqBU&si=tpFqDe_obR6LZLtx
https://youtube.com/playlist?list=PLBG53xT7PX7v-C3XcKHnKeVP1NxsrLqBU&si=tpFqDe_obR6LZLtx
IMMEM XIV Poster presentations
Explore the different post presentations that were recorded as part of the 14th edition of the International Meeting on Microbial Epidemiological Markers (IM...
youtube.com
October 22, 2025 at 12:50 PM
The next five videos from our #IMMEM XIV poster presentations are available now on our YouTube channel and cover topics like #microbiome, transmission and more. #IDSky
https://youtube.com/playlist?list=PLBG53xT7PX7v-C3XcKHnKeVP1NxsrLqBU&si=tpFqDe_obR6LZLtx
https://youtube.com/playlist?list=PLBG53xT7PX7v-C3XcKHnKeVP1NxsrLqBU&si=tpFqDe_obR6LZLtx