Create accountLogin

Recent searches

No recent searches

Search options

Only available when logged in.
med-mastodon.com is one of the many independent Mastodon servers you can use to participate in the fediverse.
Medical community on Mastodon

Administered by:

Server stats:

414
active users

med-mastodon.com: AboutProfiles directoryPrivacy policy

Mastodon: AboutGet the appKeyboard shortcutsView source codev4.3.8

#bioinformatics

19 posts19 participants2 posts today
Public
nf-core

🧑🏾‍💻 Need help with anything #nfcore #nextflow (#bioinformatics) pipelines, whether running or developing?

⏰ Today's EMEA friendly weekly helpdesk is at 10:00 CEST (Berlin time) on the nf-core gather.town! nf-co.re/join#gather-town

📅 Note that we also have other regular helpdesks for different TZs!

- 🌏 Asia-Pacific: Wednesdays @ 15:00 NZDT
- 🌎 Americas: Tuesdays @ 14:00 ET

Join the nf-core slack for more details and reminders!

nf-co.reJoin nf-coreRead about the different ways you can get involved with nf-core
Public
Center for Health Data Science

🟣Health Data Science Day 2025🟣

🎤SPEAKER REVEAL: Richard Röttger
Prof. of Bioinformatics at SDU & head of the Computational Biology Group, Richard develops ML methods to decode complex biomedical data—from omics to patient records—to drive discovery and precision medicine.

🗓️ 6 Nov 2025
📍 Panum, University of Copenhagen
👥 Open to all in Health Data Science
🌍 heads.ku.dk/calendar/2025/even

#healthdatascience#bioinformatics#machinelearning
Public
Jane

Harvard researcher Dr. Kseniia Petrova wrote an Op-Ed in the NYT this week about her experience in ICE detention, where she has been living in 1 room with 100 other women for 3 months, and what it means for her research, and our research community more broadly: nytimes.com/2025/05/13/opinion

Background on Kseniia's journey to the United States and her jailing by ICE in February: nytimes.com/2025/04/11/science

In rat testis a complex structure of the spermatozoa tails nest in a central spiral. NoRI’s findings about the testes may one day help us treat testicular cancer.
Kseniia Petrova, a Harvard scientist, in 2021. She has been in a Louisiana prison since Feb. 16.
“Any problem I have with data, she has a solution,” a colleague said. A photograph taken from her desk at Harvard showing a cheerful hand-drawn note that says "hello, Kseniia!" decorated with a heart and lots of tiny colorful flowers
A rat small intestine
#BostonMA#Biology#STEM
Public
Marc Robinson-Rechavi

Postdoc job opportunity! We're looking for early career researcher in evolutionary genomics to study the relation between intra-specific gene expression variability, polymorphism, and macro-evolutionary rates. We have all of the data in 3 fishes and amphioxus, just waiting for your expertise and enthusiasm!
tinyurl.com/3aewk286
#EvoDevo #MolecularEvolution #bioinformatics #PopulationGenomics #RNAseq #PostDoc

tinyurl.comOpportunités de carrière : Postdoctoral position in evolutionary genomics (22280)
Public
David Mankins

#ai #llm #bioinformatics

Surprise! AI might be useful for science after all.

A bioinformaticist friend writes:

Well, looks like I've been replaced by AI.

Here is a paper from Aviv Regev's group that uses multi agent models (LLMs that talk to each other) to basically do one of the pipelines that my group was responsible for at ReadCoor.

One task that I am happy to see that they included was building probe panels, which are sets of (usually) genes that can be used to see what is going on inside a sample. Five years ago, this was a very onerous task that included loads of manual literature search and curation. I can't imagine doing it now without at least starting with a Deep Research or similar LLM query. (I was the manager so my role in this was to repeatedly say "Wow. That looks awful. Thanks for doing that.")

There is stuff around the AI that is I think is pure hype, but this is the kind of practical, important task that most humans hate and that AI is really great at.

Pretty neat stuff!
*It did take them 30 more people to build the AI than we had to build the pipeline. But that'll go down.
**I should add that our panels were really great. During AGBT 2020, people who came to our booth were gathered around the screens showing our panels. Seeing the genes they cared about included really gave people an understanding of the potential for in situ sequencing.

biorxiv.org/content/10.1101/20

bioRxiv · SpatialAgent: An Autonomous AI Agent for Spatial BiologyAdvances in AI are transforming scientific discovery, yet spatial biology, a field that deciphers the molecular organization within tissues, remains constrained by labor-intensive workflows. Here, we present SpatialAgent, a fully autonomous AI agent dedicated for spatial-biology research. SpatialAgent integrates large language models with dynamic tool execution and adaptive reasoning. SpatialAgent spans the entire research pipeline, from experimental design to multimodal data analysis and hypothesis generation. Tested on multiple datasets comprising two million cells from human brain, heart, and a mouse colon colitis model, SpatialAgent performance surpassed the best computational methods, matched or outperformed human scientists across key tasks, and scaled across tissues and species. By combining autonomy with human collaboration, SpatialAgent establishes a new paradigm for AI-driven discovery in spatial biology ### Competing Interest Statement The authors have declared no competing interest.
Public
Lskatz ☑

🚨 Teaching bioinformatics? Or learning it solo?
Check out my free & open Fundamentals of Bioinformatics course materials: lectures, slides, and exercises — no coding background required.
🔬🧬👩‍💻

📚 github.com/lskatz/fundamentals
⭐️ Star it, share it, and level up!

Contribute to lskatz/fundamentals-of-bioinformatics development by creating an account on GitHub.
GitHubGitHub - lskatz/fundamentals-of-bioinformaticsContribute to lskatz/fundamentals-of-bioinformatics development by creating an account on GitHub.
#bioinformatics#opensource#STEMeducation
Public
naturepoker

For people with hmmalign experience. When running post-alignment trim (i.e. clipkit/trimal), how do you handle insertion gap added by hmmalign?

AFAIK many trimmers don't count '.' as AA gap character - and manually adjusting '.' to recognized gap character can significantly alter results

First thing to notice here is that hmmalign uses both lower case and upper case residues, and it uses two different characters for gaps. This is beacause there are two different kinds of columns: 'match' columns in which residues are assigned to match states and gaps are treated as deletions relative to consensus, and insert columns where residues are assigned to insert states and gaps in other sequences are just padding for the alignment to accommodate those insertions.
#bioinformatics#alignment
Public
naturepoker

Whoa iqtree is finally up to version 3. It's setup in a separate github repo so if you rely on automated setup scripts (like I do) you'll have to make minor changes.

Time to run some tests to see if recent results remain consistent.

github.com/iqtree/iqtree3

IQ-TREE version 3: software for phylogenetics. Contribute to iqtree/iqtree3 development by creating an account on GitHub.
GitHubGitHub - iqtree/iqtree3: IQ-TREE version 3: software for phylogeneticsIQ-TREE version 3: software for phylogenetics. Contribute to iqtree/iqtree3 development by creating an account on GitHub.
#microbiology#bioinformatics
ExploreLive feeds
About