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

🖥️🧬🧪 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!

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

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

✨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

Come see my poster at IMMEM Poster 151. 🔬 QualiBact – provides robust, data-driven QC thresholds for 304 bacterial species, built from >2.4M assemblies (AllTheBacteria + RefSeq). ⚙️ SpecCheck – an open-source command-line tool that applies these standards […] [Original post on mstdn.science]

The most anticipated session at #IMMEMXIV is, of course, about bioinformatics. It starts with presentation of the hackathon that took place prior to the conference. All the code is on GitHub (link in the pictures).

Registered too late for a poster for @escmid.bsky.social #IMMEMXIV but happy to discuss SciCommander with anyone interested 😊 See: livesys.se/posts/rewrit... Captures provenance of ad-hoc commands while skipping already computed steps - "The benefits of a pipeline tool without the pipeline tool".

A nice illustration of the usefulness of our tool #MSTclust for handling bacterial population structures by @sylvainbrisse.bsky.social during #IMMEMXIV in Porto 🇵🇹 gitlab.pasteur.fr/GIPhy/MSTclust

The second day of #immemxiv in Porto starts with GTDB taxonomy by Maria Chuvochina. NCBI often lacks species assignments and, from my personal experience, can be incorrect often than expected. Also, ~2% of all species are fuzzy/hard to discriminate by ANI.

Having a blast at the #IMMEMXIV @escmid.bsky.social conference on microbial typing in Porto, Portugal. So much to learn as a newcomer in the field and so many knowledgeable people in the same place! #microsky

...and the poster Is up!! #IMMEMXIV

Excited to kick off #IMMEMXIV in Porto, Portugal with the first session focusing on #plasmid typing for surveillance! A fantastic session thanks to our 5 great speakers and now we are going into the first debate session on strain typing in high-income vs low-resource settings. #IDSky #clinmicro

Bioinformaticians / computational biologists take note - know where you should take your OS tool chain from and do not introduce backdoors.

🗓 Pathoplexus turns ONE! 🎂🎉 In the past year we’ve grown from 4 pathogens to a truly global, community-driven platform for transparent, equitable & impactful pathogen sequence sharing. 📰 Read the full update: pathoplexus.org/news/2025-08... 1/10

I sincerely appreciate the opportunity to visit @ebi.embl.org (thanks to the @embl.org Sabbatical fellowship). The guidance and support I received from Zam (@zaminiqbal.bsky.social), John (@bacpop.org) and other colleagues have been immensely valuable! You changed my career！❤️

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

New preprint from my lab! We describe how transposable elements are activated in Parkinson’s disease, which is linked to an interferon response. We believe this study significantly advances our understanding of transposons and their role in human brains. www.biorxiv.org/content/10.1...

How cells lock down “jumping genes”: Researchers from IMBA and IMP identify the first protein interactions that trigger PIWI–piRNA–mediated transposon silencing, using AlphaFold predictions, genetics, biochemistry and cell biology. Read more: www.viennabiocenter.org/about/news/t...

Microsoft Word to begin saving people's documents in the cloud *by default* Reminder that LibreOffice is free and a good drop-in replacement for Microsoft Office software: www.libreoffice.org www.theverge.com/news/767522/...

From asfiston.bsky.social & colleagues in @plos.org #Computational #Biology | Why and how to set up a Bioinformatics Learning Lab (BILL) | #Bioinformatics #Education #OpenScience #OpenEducationalResources 🧬 🖥️ 🧪🔓CC/ @ppalagi.bsky.social ⬇️ journals.plos.org/ploscompbiol...

Interested in 16S analysis of bacterial samples w @nanoporetech.com ? New: v0.4.0 of the TRANA pipeline (previously known as GMS_16S), by Frans Wallin w contributions fr Ryan James Kennedy, Sofia Stamouli, Katharina Dannenberg, Olivia Andersson: github.com/genomic-medi... github.com/genomic-medi...

Keep and eye 👁️ (and an ear! 👂) out for a new Binfie podcast all about Pathoplexus 1 year in!

I can't believe the biggest bottleneck in my lab right now is scrounging to afford more storage for processing data, not sequencing costs, technique or analysis difficulty.

Finally printed and submitted my thesis :) You may call me Dr. now 🎓 curiouscoding.nl/thesis.pdf

New paper from our lab! We found that LINE-1 transposons contribute to early human brain development. Funded by @asapresearch.parkinsonsroadmap.org www.cell.com/cell-genomic...

We did it! We caught Starship #transposons moving between #fungal species in the lab, including between species separated by ~100my. We think Starships are a mediator of HGT in fungi, akin to conjugative elements in bacteria. Check out the preprint. www.biorxiv.org/content/10.1...

Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁 Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5

We are excited to officially welcome a new group leader at the MPI-IE in #Freiburg. 🎉 Dr Juliane Glaser 🥳 – she studies epigenetic mechanisms of embryonic development, with a focus on transposable elements. 👉 Interview: www.ie-freiburg.mpg.de/6043545/2025... Welcome, @julianeg.bsky.social!

We wrote a review on Transposable Elements (TEs) and almost all aspects of TE silencing and their roles in biological processes & disease. www.nature.com/articles/s41...

The 25th iteration of the excellent Conference for Algorithms in Bioinformatics (WABI) starts tomorrow at UMD @umdscience.bsky.social at the Brendan Iribe Center. You can find details at the website wabiconf.github.io/2025/. We'll use the tag #WABI25 for the meeting!

🧬🖥️ We are thrilled to be hosting the 25th International Conference on Algorithms for Bioinformatics (WABI 2025) next week at UMD! Look at this amazing lineup of proceedings papers: drops.dagstuhl.de/entities/vol...

tgv is becoming so good. Next release gonna be epic. On a side note, I stopped using AI all together a month ago (except occasionally turning on tabbing for boilerplate). I'm so much happier. Coding is much more flowy and I'm learning a ton. Vim motion boosts productivity way more than any AI.

I'm certainly a #julialang evangalist, but I've toned it down a bit - a lot of scientists don't have the time or inclination to go against the grain. Then again, when someone makes it this easy... #tidytuesday #rstats nrennie.rbind.io/blog/introdu...

I’ve got something exciting to share. After years of working with labs around the world, I’m starting something new! I’ve seen how many labs want to do more with genomics, but the path forward isn’t always clear. The process is complex, and without the right guidance, it’s easy to get stuck.

Because, as I learned early on in academic research, unfortunately, great ideas exist in relative obscurity all too often. Sometimes, they are rediscovered at a time where they catch on, other times not.

GRN inference algorithms often build on prior knowledge of e.g. TF binding. Build up-to-date priors with our new tool SPONGE, now out in Bioinformatics: academic.oup.com/bioinformati...

Identifying reproducible biomarkers for microbiome association studies requires sample sizes of thousands www.sciencedirect.com/science/arti...

🧬💻 We're hiring a #Bioinformatics #Developer @emblebi.bsky.social! Join the @ensembl.bsky.social Variation team building open-source tools to support global research & clinical genomics. Collaborative team; real impact. 👉 Apply: embl.wd103.myworkdayjobs.com/en-US/EMBL/j... ⏰ Deadline: 10 August

I am starting a computational lab at LIOS, Riga, Latvia, and going to recruit a few people. Please DM if you are interested in a postdoc or PhD position in my Metabolic Research Group within the TARGETWISE project. I can highly recommend Riga, it is a beautiful city with very good living conditions.