Does your paper really suck? Oded Rechavi, at QED Science, believes that if your paper is not in the top 1% of their QED score then it "sucks". But what is this QED score and what is its purpose? If a paper is not in the 1% does it really suck? My thoughts here: www.sina.bio/posts/does-y...

Hi everyone, I am looking for a new industry role in computational biology! Check out my portfolio of genomics, statistics, ML, and biophysics work at gennadygorin.github.io, and reach out if you have any suggestions or open roles!

"We therefore argue that publication systems should optimize separately for the dissemination of data and results versus the conveying of novel ideas, and the former should be machine-readable." - This is such a good point. Machine readability is a goal too often viewed as just an addon to >

sina b@sina.bio · 6mo ago

If you work in AI for Science, take a moment to familiarize yourself with a common failure mode: paranormal citations (or paracites). Our paper describes them.

1/ LLMs are great at text extraction, but sometimes they hallucinate. A simple way to catch hallucinations is to check if the extracted text actually exists in the source. Turns out this is harder than it sounds. (new paper with Aaron Streets) www.biorxiv.org/content/10.6...

Interesting article on LLM text extraction and the connection of that problem to (computational biology) sequence alignment. www.biorxiv.org/content/10.6... by @sina.bio and Aaron Streets.

"publication systems [should] distinguish between dissemination of results & communication of ideas, and optimize them separately. Results should be in explicit, machine-readable form, while narrative text serves as an interpretive layer for human readers" www.biorxiv.org/content/10.6...

If you work in AI for Science, take a moment to familiarize yourself with a common failure mode: paranormal citations (or paracites). Our paper describes them.

Lior Pachter@lpachter.bsky.social · 6mo ago

AI hallucinations in science manuscripts are a nuisance. Paranormal citations, or paracites, will be a nightmare. www.biorxiv.org/content/10.6... (w/ @sina.bio & @lauraluebbert.com).

AI hallucinations in science manuscripts are a nuisance. Paranormal citations, or paracites, will be a nightmare. www.biorxiv.org/content/10.6... (w/ @sina.bio & @lauraluebbert.com).

Peer review is often opaque and confusing. @elife.bsky.social worked to change that. In a new preprint, we show how eLife’s Publish, Review, Curate model makes it possible to evaluate AI-generated reviews (with OpenEval) against human peer review. w/ @lauraluebbert.com and @lpachter.bsky.social

bioRxivpreprint@biorxivpreprint.bsky.social · 6mo ago

Science should be machine-readable https://www.biorxiv.org/content/10.64898/2026.01.30.702911v1

single-cell is a fun field. for instance, one of the heavily curated bixbench scenarios is about interpreting the results of a sc analysis and comparing to ground truth. this ground truth is, of course, based on DE analyses with some truly remarkable p-values for n=5

Andrew White 🐦‍⬛@andrew.diffuse.one · last yr.

Half of an AI scientist is rejecting or accepting hypotheses. FutureHouse and Science Machines just put out ~300 novel hypotheses from ~50 published papers along with ground-truth data. Humans take 4.2 hours to solve these and frontier models get 10-20% correct. This is like SWE-bench for comp bio

"No one is coming out of the sky to give you your grant money. Your citation portfolio won’t survive this market crash. Your credentials mean nothing. Everything is going to change." New for @undark.org undark.org/2025/03/06/o...

How Science Can Adapt to a New Normal

Opinion | In the wake of attacks on the research enterprise, scientists need to focus on protecting its fragile infrastructure.

undark.org

Not really my field but I love the abstract! www.biorxiv.org/content/10.1...

Is Tanimoto a metric?

No. However, here we show how to generate a metric consistent with the Tanimoto similarity. We also explore new properties of this index, and how it relates to other popular alternatives. ### Competi...

biorxiv.org

“blocking retro nasal sensation with a nose clip significantly reduces the subjective and objective neural responses to sucrose taste”

bioRxivpreprint@biorxivpreprint.bsky.social · last yr.

Retro Nasal blockade reduces the Neural Processing of Sucrose in the Human Brain https://www.biorxiv.org/content/10.1101/2025.02.11.637706v1

Amazing to me how useful looking at data in 2D PCA continues to be, even though the approach sounds crazy on paper—"p-dimensional ellipsoid", rantings of a madman. PCA is the cockroach of dimension reduction. I expect it to be present in any advanced galactic civilization.

"One thing is certain: The changes we make ourselves will be healthier than the ones our adversaries demand." New work for @undark.org: undark.org/2025/02/06/o...

The End of Science’s Peacetime

Opinion | Defending the practice of science from its adversaries will require dealing with some uncomfortable truths.

undark.org

🧵 On a Friday night, the NIH twitter account announced the most significant change to research funding in decades. What are indirect costs, how are universities funded and what are the impacts?

Reminder: there is little evidence that brain computation works in the same way as neural networks. Quote from "Understanding Deep Learning by Simon Prince (@simonprinceai.bsky.social)"

why is this desirable? Language models are helpful in parsing unstructured data, but QC reports are already structured...

Seqera@seqera.io · 2y ago

The gold standard in #bioinformatics reporting just got even better! #AI Summaries are now available in @multiqc.info🎉 Find out more: hubs.la/Q033Kjp30

An often overlooked point in genomics: "Molecular omics resources should require sex annotation: a call for action" by @gliomath.bsky.social www.nature.com/articles/s41...

Molecular omics resources should require sex annotation: a call for action - Nature Methods

The most commonly used omics databases are a compilation of results from primarily male-only and sex-agnostic studies. The pervasive use of these databases critically hinders progress toward fully acc...

nature.com

TIL about the watch command in the terminal: it reruns a command at set intervals, and is perfect for monitoring GPU usage or tracking real-time system updates.

In this year's user survey, 89% of respondents said that EMBL-EBI data resources empowered them to undertake work that would otherwise not have been possible 💪 Big thank you to everyone who filled in the survey - we appreciate your input! Explore further findings: www.ebi.ac.uk/about/news/a...

Fuelling discovery together: 2024 user survey learnings

Blog post by Eleni Tzampatzopoulou, EMBL-EBI Impact Manager In summer 2024, EMBL-EBI ran a user survey, inviting our community to let us know how they use the open data resources we jointly manage wit...

ebi.ac.uk

Cool to see our open source syringe pumps being made in the wild ! Original article: www.nature.com/articles/s41...

Principles of open source bioinstrumentation applied to the poseidon syringe pump system - Scientific Reports

Scientific Reports - Principles of open source bioinstrumentation applied to the poseidon syringe pump system

nature.com

Brandon Scott@minesbioimaging.bsky.social · 2y ago

I hear you can't make 10 without first making 1. Thanks @lpachter.bsky.social for open-sourcing a great design.

gonna post up in a cafe and speedrun a new protein diffusion model "from scratch" with Claude live poasting my way thru it, public Git repo last did this in June and it's really at the edge of both of our capabilities

I often make microfluidic emulsions and microparticles for scalable biology experiments, but the other day I was thinking, what if we polymerize the continuous phase of an emulsion? come learn about a delightful little branch of science, polyHIPEs!

I am honestly stoked by the ability to customize one's algorithm on @bsky.app. It's a killer feature (over Twitter) that makes it actually useable for scientific communication. Simply pick the feed you want to follow and boom you get the relevant content.

It’s out!! We subjected soils from 30 different locations across Europe to extreme events and found that soil fungal and bacterial communities showed consistent responses that could be predicted from their origin! With @knightjar.bsky.social and many collaborators! www.nature.com/articles/s41...

Soil microbiomes show consistent and predictable responses to extreme events - Nature

Soils from 30 grasslands across Europe were subjected to 4 contrasting extreme climatic events under drought, flood, freezing and heat conditions, with the results suggesting that soil microbiomes fro...

nature.com

(1/5) Tired of Excel messing up your gene names? Just released gfix, a simple command-line tool that fixes Excel-converted gene names in spreadsheets. No custom file conversions required- just supply your excel file as is! 🛠️ github.com/sbooeshaghi/gfix

GitHub - sbooeshaghi/gfix: Fix Excel-converted gene names in files.

Fix Excel-converted gene names in files. Contribute to sbooeshaghi/gfix development by creating an account on GitHub.

github.com

Car emissions, pollutants, and noise are large drivers of health outcomes and we have the technology to address these issues.

Harold Pimentel@hjp.bsky.social · 2y ago

I think the work we do in genetics and genomics is really fundamental to so many aspects of human disease, etc. However, I often worry that as a society we are not doing enough to combat the obvious health implications of things like driving, our food environment etc.