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Reposted by Samuel Lampa

SciLifeLab @scilifelab.se · 16h

We’re launching a major #recruitment call for staff scientists in #ComputationalBiology, #DataScience, and #AI to strengthen Sweden’s life science research. 🧪🖥️

Positions are based at SciLifeLab sites across Sweden’s leading universities.

Learn more and apply ↓
www.scilifelab.se/news/scilife...

SciLifeLab launches major recruitment call for staff scientists in computational biology, data science and AI

Computational methods and artificial intelligence on large-scale molecular data are transforming the study of biological systems and processes, ranging from molecular structures and cellular processes...

www.scilifelab.se

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Samuel Lampa @smllmp.bsky.social · 22h

Exciting, congrats!

Reposted by Samuel Lampa

Ben Langmead @benlangmead.bsky.social · 1d

I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.

Burrows-Wheeler Indexing - YouTube

Videos on : (a) the Burrows-Wheeler Transform (BWT), (b) the FM Index, which uses the BWT to construct a full-text index, (c) Wheeler graphs, (d) r-index, an...

www.youtube.com

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Reposted by Samuel Lampa

Rob Patro @robp.bsky.social · 2d

It absolutely warms my heart when I click on a pre-print that includes a bunch of top methods folks from industry and I see (1) open-source software (with a good license; MIT in this case) that is (2) written in Rust. Bravo @pacbio.bsky.social!

Moar Rust plz!

github.com/PacificBiosc...

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Samuel Lampa @smllmp.bsky.social · 2d

Note: You can "upload" your own files to it, by clicking the cog wheel.

Samuel Lampa @smllmp.bsky.social · 2d

"Pro tip": If you are in a restricted environment & need quick access to a linux terminal running locally in the browser for some #bioinformatics messing around - check the sandbox.bio terminal playground. Made a bitly link for for convenience: bit.ly/bioterminal

Screenshot of the sandbox.bio playground for running a linux environment in the browser

Samuel Lampa @smllmp.bsky.social · 2d

"Pro tip": If you are in a restricted environment & need quick access to a linux terminal running locally in the browser for some #bioinformatics messing around - check the sandbox.bio terminal playground. Made a bitly link for for convenience: bit.ly/bioterminal

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Reposted by Samuel Lampa

EMBL-EBI @ebi.embl.org · 8d

There are millions of openly available microbial genomes, but searching them can be slow.

Until now 🥁

Introducing LexicMap, a new alignment tool that lets scientists search these data in minutes, helping track antibiotic resistance, trace outbreaks, and more.

www.ebi.ac.uk/about/news/r...
🦠

How to rapidly search the world’s microbial DNA

By making the world’s microbial DNA easier to explore, LexicMap helps researchers track outbreaks, study antibiotic resistance, and understand microbial diversity.

www.ebi.ac.uk

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Reposted by Samuel Lampa

Sarah Alexander @sarah1alexander.bsky.social · 13d

please read this thread - even if you don;t get time to read the paper!!!!! just the best - great work, really really great.

Zamin Iqbal @zaminiqbal.bsky.social · 13d

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

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Reposted by Samuel Lampa

Zamin Iqbal @zaminiqbal.bsky.social · 13d

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

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Samuel Lampa @smllmp.bsky.social · 12d

Super fascinating! Congrats Zam!

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Reposted by Samuel Lampa

Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 12d

🖥️🧬🧪 Publication Alert!

I’m very excited to share our latest paper: “NovumRNA: Accurate prediction of non-canonical #tumor #antigens from RNA #sequencing data”

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Samuel Lampa @smllmp.bsky.social · 12d

Very interesting!

EMBL-EBI @ebi.embl.org · 12d

Antimicrobial resistance (AMR) causes over a million deaths each year, and is rising.

Scientists analysed 40,000 bacterial plasmids across 100 years and six continents, to reveal that a few plasmids evolved after antibiotic use to drive most multi-drug resistance.

www.ebi.ac.uk/about/news/r...
🧬💻

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Reposted by Samuel Lampa

BF Francis Ouellette @bffo.bsky.social · 15d

From @plos.org #Computational #Biology | Ten simple rules for building and maintaining sustainable high-performance computing infrastructure for research in resource-limited settings | #Africa #HPC #PLOSCBTSR 🖥️ 🧪 🔓
⬇️
journals.plos.org/ploscompbiol...

Ten simple rules for building and maintaining sustainable high-performance computing infrastructure for research in resource-limited settings

journals.plos.org

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Reposted by Samuel Lampa

Physalia-courses@Online @physaliacourses.bsky.social · 16d

Only 1 seat left @oskolkov.bsky.social

Physalia-courses@Online @physaliacourses.bsky.social · Sep 2

We would like to inform you that only four seats are left for the in-person course, “Machine Learning for Multi-Omics Integration,” with @oskolkov.bsky.social taking place on 15–17 December at the University of Barcelona @irbio-ub.bsky.social

www.physalia-courses.org/courses-work...

Machine Learning for Multi-Omics Integration

15-17 December 2025 Dept. Evolutionary Biology, Ecology & Environmental Sciences Faculty of Biology, University of Barcelona Institut de Recerca de la Biodiversitat (IRBio) Av. Diagonal, 643, Les ...

www.physalia-courses.org

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Reposted by Samuel Lampa

Migle Gabrielaite @mgabrielaite.bsky.social · 16d

I can't believe that only now I found out about BakRep by @oschwengers.bsky.social. There you can search and interactively explore all the genomes from AllTheBacteria that includes >2.4 million genomes assembled by @zaminiqbal.bsky.social group.

BakRep

bakrep.computational.bio

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Reposted by Samuel Lampa

ESCMID @escmid.bsky.social · 16d

We wrapped up #IMMEM XIV over the weekend and it was a fantastic success with over 250 participants from 35 countries. A big thank you to the organisers and specifically @esgem-sg.bsky.social our study group on epidemiological markers! The content will be available on ESCMID media soon. #clinmicro

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Reposted by Samuel Lampa

Ebenn @efosternyarko.bsky.social · 18d

Honoured + super grateful to give an oral talk on efforts by #PulseNETAfrica to enhance capacity of public health labs across Africa for cholera mgt + a poster describing investigation of a neonatal kleb pneumoniae ST39 outbreak in a rural hospital in the Gambia at #IMMEM XIV in beautiful Porto 🇵🇹

ESCMID @escmid.bsky.social · 19d

We are on to day 3 of the #IMMEM conference in Porto after some great talks and the first poster session featuring the research that's being done by our community! Today we'll be covering environmental surveillance for #ID and #AMR and how best to share pathogen data. #IDsky #clinmicro

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Samuel Lampa @smllmp.bsky.social · 18d

ReporTree looked/looks amazing, and seems like it might just solve all our interactive visualization needs for outbreak investigations etc!
github.com/insapathogen...

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Reposted by Samuel Lampa

Migle Gabrielaite @mgabrielaite.bsky.social · 20d

Matthijs S. Berends continues #IMMEMXIV bioinformatics session with the presentation of AMRgen that combines genotype and phenotype data and interpretation. It definitely should save hours of manual labor (at least for bacteria with known resistance mechanisms).

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Reposted by Samuel Lampa

Nick Loman @pathogenomenick.bsky.social · 19d

Terrific new feature presented by @theo.io on @pathoplexus.org called SeqSets for generating DOIs for sequence subsets used in publications, that can then be tracked for impact via CrossRef that will allow data generators to track impact! #IMMEMXiV

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Reposted by Samuel Lampa

Kat Holt @katholt.bsky.social · May 22

Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight)
interpretamr.github.io/AMRrules

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Samuel Lampa @smllmp.bsky.social · 19d

😅

Samuel Lampa @smllmp.bsky.social · 19d

Interesting, didn't know about CLIMB! Btw, I like that one can get 500TB of FastSSD storage ;)
www.climb.ac.uk/training/

CLIMB-BIG-DATA | Cloud Infrastructure for GenomicsPricing – CLIMB | Cloud Infrastructure for Microbial Bioinformatics

www.climb.ac.uk

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Reposted by Samuel Lampa

ESCMID @escmid.bsky.social · 19d

We are on to day 3 of the #IMMEM conference in Porto after some great talks and the first poster session featuring the research that's being done by our community! Today we'll be covering environmental surveillance for #ID and #AMR and how best to share pathogen data. #IDsky #clinmicro

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Reposted by Samuel Lampa

Louise Roer @louiseroer.bsky.social · 20d

✨Célia Souque just showcased the outcomes of the 12th Microbial Bioinformatics Hackathon at IMMEM XIV.

She brilliantly presented the first sneak-peek of PORT – Plasmid Outbreak Reporting Tool! 🧬
Looking forward to continuing this collaboration with PORT!

#IMMEM #Hackathon #Plasmids #ESGEM #ESGMAP

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