sina b @sina.bio · 29/06/2026Does 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... 120
Reposted by sina bGennady Gorin @goringennady.bsky.social · 02/03/2026Hi 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!gennadygorin.github.ioGennady Gorin, Ph.D.Senior Scientist applying stochastic models for therapeutic discovery 121
Reposted by sina bRoland Gromes @gromesroland.bsky.social · 20/02/2026"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 > 121
sina b @sina.bio · 11/02/20261/ 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...biorxiv.org 112
Reposted by sina bLior Pachter @lpachter.bsky.social · 11/02/2026Interesting 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.biorxiv.org 081
Reposted by sina bRichard Sever @richardsever.bsky.social · 03/02/2026"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...biorxiv.org 1156
sina b @sina.bio · 03/02/2026If 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. 082
Reposted by sina bLior Pachter @lpachter.bsky.social · 03/02/2026AI 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). 23211
sina b @sina.bio · 03/02/2026Peer 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 2189
Reposted by sina bGennady Gorin @goringennady.bsky.social · 06/03/2025single-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=5 221
Reposted by sina bC. Brandon Ogbunu @cbo.bsky.social · 06/03/2025"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...undark.orgHow Science Can Adapt to a New NormalOpinion | In the wake of attacks on the research enterprise, scientists need to focus on protecting its fragile infrastructure. 516879
Reposted by sina bDavide CIttaro @daweonline.bsky.social · 23/02/2025Not really my field but I love the abstract! www.biorxiv.org/content/10.1...biorxiv.orgIs 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... 021
sina b @sina.bio · 12/02/2025“blocking retro nasal sensation with a nose clip significantly reduces the subjective and objective neural responses to sucrose taste” 000
Reposted by sina bRichard McElreath 🐈⬛ @rmcelreath.bsky.social · 10/02/2025Amazing 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. 38812
Reposted by sina bC. Brandon Ogbunu @cbo.bsky.social · 06/02/2025"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...undark.orgThe End of Science’s PeacetimeOpinion | Defending the practice of science from its adversaries will require dealing with some uncomfortable truths. 613278
sina b @sina.bio · 08/02/2025🧵 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? 130
sina b @sina.bio · 23/01/2025Reminder: 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)" 140
sina b @sina.bio · 23/01/2025why is this desirable? Language models are helpful in parsing unstructured data, but QC reports are already structured... 020
sina b @sina.bio · 17/01/2025An 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...nature.comMolecular omics resources should require sex annotation: a call for action - Nature MethodsThe 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... 141
sina b @sina.bio · 17/12/2024TIL 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. 010
Reposted by sina bEMBL-EBI @ebi.embl.org · 17/12/2024In 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...ebi.ac.ukFuelling discovery together: 2024 user survey learningsBlog 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... 0153
sina b @sina.bio · 13/12/2024Cool to see our open source syringe pumps being made in the wild ! Original article: www.nature.com/articles/s41...nature.comPrinciples of open source bioinstrumentation applied to the poseidon syringe pump system - Scientific ReportsScientific Reports - Principles of open source bioinstrumentation applied to the poseidon syringe pump system 040
Reposted by sina bJase Gehring @skyjase.bsky.social · 08/12/2024gonna 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 041
Reposted by sina bJase Gehring @skyjase.bsky.social · 06/12/2024I 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! 121
sina b @sina.bio · 27/11/2024I 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. 010
Reposted by sina bFranciska de Vries 🟥 @frantecol.bsky.social · 27/11/2024It’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...nature.comSoil microbiomes show consistent and predictable responses to extreme events - NatureSoils 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... 16571164
Reposted by sina bsina b @sina.bio · 27/11/2024(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/gfixgithub.comGitHub - 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. 1143
sina b @sina.bio · 27/11/2024Car emissions, pollutants, and noise are large drivers of health outcomes and we have the technology to address these issues. 030
sina b @sina.bio · 27/11/2024(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/gfixgithub.comGitHub - 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. 1143
sina b @sina.bio · 26/11/2024The dreaded gene name turns date in Excel strikes again (in a published paper!).. this happens because MARCH3 is interpreted as March 3rd by Excel's automatic date formatting. (previously I was bamboozled by SEPT1 (Septin 1)! 000
sina b @sina.bio · 26/11/2024This claim in a published paper gives the same energy as "trending towards significance". "Two additional [cell types] were characterized by gradual expression of genes, such as [gene 1] and [gene 2]" 020
sina b @sina.bio · 26/11/2024TIL about "ChEMBL" a manually curated database of bioactive molecules with drug-like properties from @ebi.embl.org. Each molecule has extensive metadata, like indications and studies. Here is an example for AMINOPHYLLINE, an FDA approved drug for treatment of asthma. 🧪 www.ebi.ac.uk/chembl/explo...ebi.ac.ukCompound: AMINOPHYLLINE (CHEMBL1370561)Report card for Compound AMINOPHYLLINE (CHEMBL1370561). C16H24N10O4, Small molecule, AMINOPHYLLIN, Aminophylline, AMINOPHYLLINE, AMINOPHYLLINE DYE FREE, AMINOPH... 131
Reposted by sina bEMBL-EBI @ebi.embl.org · 26/11/2024Great question! Some of our most frequently used data resources include Europe PMC, @ensembl.bsky.social, and UniProt to name a few. You can find information on the usage of each resource in this independent impact report: www.embl.org/documents/wp...embl.org 131
sina b @sina.bio · 25/11/2024Is there an equivalent term for “retweeting” a post on Bluesky? “Reposting” feels.. inadequate.. 010
sina b @sina.bio · 25/11/2024I visited Hinxton, UK for an incredible conference ( #GenomeInformatics24, thx to @pmelsted.bsky.social, @zaminiqbal.bsky.social, and Nicky Mulder). And I got to see where the magic happens. 040
sina b @sina.bio · 25/11/2024This is an incredible testament to the utility of structured and reusable data. #methodsmatter 020
sina b @sina.bio · 25/11/2024Aspiring bioinfotmaticians take note- Unix (e.g proficiency with the command line) is a crucial skill that saves time and headache. 000
sina b @sina.bio · 24/11/2024344 words you can spell on a calculator www.mathsquad.com/calculatorwo... 000
Reposted by sina bPrakash Lab at Stanford @prakashlab.bsky.social · 23/11/2024Optimist: The cup is half full Pessimist: The cup is half empty. Oceanographer: Let’s strap the cup to a CTD Rosette and plunge it to the depths of the ocean, to see how small it gets. 2242
sina b @sina.bio · 23/11/2024ChatGPT usage in the wild. @ebi.embl.org is using it to describe cell types on their Cell Type Ontologies site. www.ebi.ac.uk/ols4/ontolog... 000
sina b @sina.bio · 22/11/2024I'm giving a talk in 30 min @ucberkeleyofficial.bsky.social on The Human Commons Cell Atlas- a project where we develop code and tools to build cell atlases from publicly available data. All are welcome to attend in person! (no zoom :/) 000
Reposted by sina bLior Pachter @lpachter.bsky.social · 22/11/2024verb: punt; 3rd person present: punts; past tense: punted; past participle: punted; gerund or present participle: punting Old English punt, from Latin ponto, denoting a flat-bottomed ferry boat. "@sina.bio is processing 320 billion single-cell RNA-seq reads while punting" 042
Reposted by sina bTim Triche, Jr.🔰 @timtriche.bsky.social · 14/11/2024Oh wow this is exactly the example Cynthia Wohlberger used. “Jumper and Hasabis really ought to have shared the Nobel with… the PDB” 031
sina b @sina.bio · 21/11/2024Hi, I’m Sina! A bioinformatics PhD @ucberkeleyofficial.bsky.social developing tools for single-cell data 🧬. When I’m not coding in a café ☕️ or biking around the bay area 🚴♂️, I’m planning experiments, staying active, and building things with my hands. Follow for science and life updates! 🌟 2142