Samuel Lampa

Our Metabuli taxonomic classifier is now available as an app compatible with Windows, Linux, and macOS. It features an interactive visualization developed by @sunjaelee.bsky.social, along with improvements to Metabuli by @jbeom.bsky.social.
📄 academic.oup.com/bioinformati...

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

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/....

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

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

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 So proud to see my team presenting their unpublished work on diverse aspects of characterizing receptors & crispri of 100’s of phages, building sophisticated predictive models & systematic lineage tracking of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!

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! 🖥️🧬

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

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...

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...

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

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...

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...

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...

Exciting, congrats!

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...

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.

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...

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

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

"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

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.

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...
🦠

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

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

Super fascinating! Congrats Zam!

🖥️🧬🧪 Publication Alert!

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

Very interesting!

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

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...

Only 1 seat left @oskolkov.bsky.social

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.

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

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 🇵🇹

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

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).

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

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

😅