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Reposted by Samuel Lampa

Ben Langmead @benlangmead.bsky.social · 1d

New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....

Illustration of Burrows-Wheeler Transform and many auxiliary structures from the input string how$now$brown$cow$#

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Reposted by Samuel Lampa

Akanksha Thawani, PhD @akankshathawani.bsky.social · Aug 19

Extremely excited to share that I’m joining Columbia University @columbiauniversity.bsky.social as an Assistant Professor!

We will explore how the mobile genome works—how transposons shape us, our DNA and how they can be harnessed to build useful technologies. #NewPI #RNAsky #TEsky

thawanilab.org

The Thawani Lab at Columbia University

The Thawani Lab at Columbia University describing their research on mobile genome, cryo-electron microscopy and genome engineering

thawanilab.org

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Reposted by Samuel Lampa

Vivek Mutalik @vivekmutalik.bsky.social · 12h

This was one of the best meetings I attended in a very long time. So proud to see my team presenting their unpublished work on diverse aspects of characterizing receptors & crispri of 100’s of phages, building sophisticated predictive models & systematic lineage tracking of phage-host coevolution!

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Reposted by Samuel Lampa

Rob Patro @robp.bsky.social · 5d

Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬

Rob Patro @robp.bsky.social · 7d

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....

If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

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Reposted by Samuel Lampa

James Briscoe @jamesbriscoe.bsky.social · 5d

The @crick.ac.uk is recruiting Early Career Group Leaders

- Lab set-up, research costs, salaries for up to 5 researchers
- Support for up to 12 years
- Access to our core facilities
- Competitive salary
- Fantastic colleagues
- All areas of biology

Deadline 27 Nov

www.crick.ac.uk/careers-stud...

Early career group leaders

We appoint researchers from across biology and biomedicine to set up their first groups at the Crick.

www.crick.ac.uk

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Reposted by Samuel Lampa

Ewan Birney @ewanbirney.bsky.social · 6d

Some thoughts on the blossoming of genomic medicine stimulated by the excellent @ga4gh.org meeting in lovely Uppsala Sweden. www.linkedin.com/pulse/though...

Thoughts from Uppsala - Genomic Medicine blossoming

I have had a wonderful three days in Uppsala Sweden, at the Global Alliance for Genomics and Health plenary hosted locally by the generous SciLifeLab . It was a meeting of course focused on the standa...

www.linkedin.com

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Reposted by Samuel Lampa

John Lees @bacpop.org · 16d

Now published, our tool to run (almost) all biological models interactively in your web browser

Paper: academic.oup.com/bioinformati...
Website: biomodels.bacpop.org
Code: github.com/bacpop/SBMLt...

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Reposted by Samuel Lampa

SciLifeLab @scilifelab.se · 7d

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 · 7d

Exciting, congrats!

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Reposted by Samuel Lampa

Ben Langmead @benlangmead.bsky.social · 8d

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 · 9d

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 · 9d

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

Samuel Lampa @smllmp.bsky.social · 9d

"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 · 9d

"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 · 15d

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 · 19d

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 · 19d

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 · 19d

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 · 19d

Super fascinating! Congrats Zam!

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Reposted by Samuel Lampa

Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 19d

🖥️🧬🧪 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 · 19d

Very interesting!

EMBL-EBI @ebi.embl.org · 19d

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 · 22d

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 · 23d

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 · 23d

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 · 23d

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 · 25d

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 · 26d

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 · 25d

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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