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Shubhra Agrawal

@shubhra-a.bsky.social
60 followers 253 following 79 posts

Techno-commercial role @ Elucidata FAIR data enthusiast, interested in bioinformatics and AI Personal account

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Reposted by Shubhra Agrawal
Žiga Avsec @avsecz.bsky.social · 25/06/2025
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
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Nils Gilman @nilsgilman.bsky.social · 17/06/2025
Saying LLMs are worthless/pernicious because they sometimes make mistakes & is causing a general decline in reading skills (true) is like saying Google Maps is worthless/pernicous just because it sometimes gives you bad directions & has caused a general decline in human navigation skills (also true)
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Reuters @reuters.com · 17/06/2025
Eli Lilly nears $1.3 billion deal for gene-editing biotech Verve Therapeutics, FT reports reut.rs/3Zy8t2b
reut.rs
Eli Lilly nears $1.3 billion deal for gene-editing biotech Verve Therapeutics, FT reports
Eli Lilly is in advanced talks to acquire gene editing startup Verve Therapeutics for up to $1.3 billion, the Financial Times reported on Monday, citing people familiar with the matter.
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Shubhra Agrawal @shubhra-a.bsky.social · 16/06/2025
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Shubhra Agrawal @shubhra-a.bsky.social · 21/01/2025
TIL 10/365: blood genotyping is not as straightforward as most of us have been taught. the most surprising part for me was that some people can safely take blood from 1 type but can't donate to the same type. this TIL is inspired by the thread here -> bsky.app/profile/alan...
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Shubhra Agrawal @shubhra-a.bsky.social · 21/01/2025
TIL 9/365: Boehringer Ingelheim has an open science portal opnMe where they pose unsolved challenges in different therapeutics areas and invite participants to share their solutions. Promising ideas get funding support! Check out the list of challenges: www.opnme.com/opn2experts
opnme.com
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Shubhra Agrawal @shubhra-a.bsky.social · 21/01/2025
TIL 8/365: Phone SIM cards have a shelf life 😆 Sounds obvious in retrospect, never considered it as a possible explanation for my near constant network failure. ran around customer care portals for a month before someone suggested i change it 🫠
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Shubhra Agrawal @shubhra-a.bsky.social · 21/01/2025
TIL 7/365: Being a 'woman' is hard i decided to learn the basics of styling and makeup this year. but beyond the active time spent shopping/trying products on, there is so much homework that the average woman does on fabrics,design,skin types,hair types,markets and trends. i feel like a toddler 🧒
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Reposted by Shubhra Agrawal
Mark O. Martin @markowenmartin.bsky.social · 21/01/2025
Here goes—-on with my day!
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Shubhra Agrawal @shubhra-a.bsky.social · 17/01/2025
TIL 6/365: US is now going to control the export of cell sorters and mass spec machines because biological data + AI poses a security risk in the wrong hands. huh. i'm not familiar with wet-lab, unfortunately. it might make large scale NGS harder in the short term but i'm sure there are ways ??
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Reposted by Shubhra Agrawal
Simon P. Couch @simonpcouch.com · 16/01/2025
Meet gander, a chat interface for R data scientists🪿 gander automatically incorporates context from your #rstats environment and surrounding code and can be used with any model supported by ellmer in either RStudio or Positron. Read more: simonpcouch.github.io/gander/
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Shubhra Agrawal @shubhra-a.bsky.social · 17/01/2025
TIL 5/365: My ADHD ass is dysregulated 90% of the time. I just never realised it before because I associate emotional dysregulation with bursts of temper, or extreme mood swings (: apparently, flip-flopping between internal screaming and static-noise-no-thought phases counts too.
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Shubhra Agrawal @shubhra-a.bsky.social · 15/01/2025
TIL 4/365: I am helpless against the Lego shelves 😩 Especially the 3-in-1 kind
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Reposted by Shubhra Agrawal
Mike Feigin 🥯 @mikefeigin.bsky.social · 14/01/2025
Please for the love of Satan, post more jokes!!
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Shubhra Agrawal @shubhra-a.bsky.social · 14/01/2025
TIL 3/365: there is an upper limit to how many people you can directly manage while working on active projects yourself :| i also think I blew wayy past this limit months ago. any sage advice from people who've been there? 😅
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Reposted by Shubhra Agrawal
Shubhra Agrawal @shubhra-a.bsky.social · 12/01/2025
One of my focus areas for 2025 is to 'build publicly' at work. Not a novel concept, but definitely an area of improvement for me. but why stop there? so i'll be starting a TIL (Today, I learned) series on bsky with the aim to share 365 TIL posts this year.
media.tenor.com
a man with his mouth open and the words one after the other behind him
Alt: gif of David from Schitts creek saying "one after the other, consecutively, in a row"
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Reposted by Shubhra Agrawal
Hani Goodarzi @genophoria.bsky.social · 13/01/2025
With 100 millions single cell gene expression measurements, using >1000 drugs across 60 cell line models, Tahoe-100M is larger than all public single-cell transcriptomic data combined. And it is 50x larger than all drug-perturbed single-cell data put together.
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Shubhra Agrawal @shubhra-a.bsky.social · 13/01/2025
TIL 2/365: core facilities in academia have a transparency problem researchers get access to the raw data, and the processed excel file from the core. The in-between details important for drawing any verifiable conclusions? gone. even basics like the target library used for LCMS could be missing 🤷‍♀️
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Shubhra Agrawal @shubhra-a.bsky.social · 12/01/2025
TIL 1/365 lncRNAs might be a lot more important for single cell: cell type annotation than I previously thought (okay, I never thought about it before 🤷‍♀️) most of the current public SC datasets don't even capture lncRNAs consistently. def going to explore this more
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Shubhra Agrawal @shubhra-a.bsky.social · 12/01/2025
One of my focus areas for 2025 is to 'build publicly' at work. Not a novel concept, but definitely an area of improvement for me. but why stop there? so i'll be starting a TIL (Today, I learned) series on bsky with the aim to share 365 TIL posts this year.
media.tenor.com
a man with his mouth open and the words one after the other behind him
Alt: gif of David from Schitts creek saying "one after the other, consecutively, in a row"
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Reposted by Shubhra Agrawal
Ariel Rokem @arokem.org · 10/01/2025
Quarto is great! Another option that elegantly addresses this issue is jupytext: jupytext.readthedocs.io/en/latest/, which creates a version-control friendly twin of your notebook and keeps them in sync as you work.
jupytext.readthedocs.io
Jupytext — Jupytext documentation
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Bo Wang @bowang87.bsky.social · 10/01/2025
How to build a virtual cell is the “Holy Grail” of the biology! A great read from The Atlantic @theatlantic.com ! Also thanks for highlighting our scGPT, the model that started the new wave of foundation models in biology! www.theatlantic.com/technology/a...
theatlantic.com
A Virtual Cell Is a ‘Holy Grail’ of Science. It’s Getting Closer.
Large language models may unlock a new and valuable type of research.
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Kieran Campbell @kieranrcampbell.bsky.social · 10/01/2025
When asked about knockout vs knockdown, Google AI wonderfully bet-hedges on whether you're interested in genetics or boxing
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Richard Sever @richardsever.bsky.social · 07/01/2025
Btw - this is another case where my frequent point that not just IF but also PubMed/PMC are obstacles to innovation applies: if a journal does a novel form of post-hoc change that doesn't fit in PubMed's rigid framework, it's not registered (so is disincentivized)
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Ted Underwood @tedunderwood.com · 05/01/2025
Part of the reason people are glum about AI is that researchers themselves represent the goal as full equivalence for human agency (“AGI”). While I get the theoretical interest, I think what most customers want (and what we’ve really produced so far) is closer to “prosthetics for thinking.”
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Stephen Turner @stephenturner.us · 06/01/2025
Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing pubmed.ncbi.nlm.nih.gov/39755959 🧬🖥️🧪 github.com/Nextflow4Metabolomics/ne…
pubmed.ncbi.nlm.nih.gov
Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing - PubMed
Reproducibility in untargeted metabolomics data processing remains a significant challenge due to software limitations and the complex series of steps required. To address these issues, we developed…
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Reposted by Shubhra Agrawal
Kieran Campbell @kieranrcampbell.bsky.social · 01/01/2025
Hopeful it’s the year use cases that add value and/or improve outcomes actually crystallize. Seem to be stuck between lots of hype on one end and people convinced of 0 utility on the other
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Stats @final-stats.bsky.social · 30/12/2024
This is absolutely amazing news. Currently it takes an average of 10 YEARS for women in the US to be diagnosed with endometriosis. A decade of agony, of horrible painful suffering every month could be eliminated for millions of women.
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Reposted by Shubhra Agrawal
Robert Manchild @robertmanchild.com · 27/12/2024
What’s it called when you can’t get motivated and also can’t relax because I’m that.
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Shubhra Agrawal @shubhra-a.bsky.social · 27/12/2024
Lovely read. Some obscure childhood stories disproportionately inform our current understanding of the world. I'm reminded of a short story I read in high school; it was a scientific record from Mars evaluating the earth as a livable planet. spoiler alert: Earth Failed!
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Reposted by Shubhra Agrawal
Raphael Gottardo @rgottardo.bsky.social · 22/12/2024
Precision Dermatology 2.0: #DataScience + #Immunology + #Genomics + #Clinical Science. Interdisciplinary collaboration at its best at the @CHUV. www.chuv.ch/fr/chuv-home... Paper on @naturecomms.bsky.social www.nature.com/articles/s41...
chuv.ch
Eczéma, psoriasis, lupus et autres maladies inflammatoires de la peau : des signatures génomiques pour améliorer le diagnostic et le traitement
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BrunetLab @brunetlab.bsky.social · 18/12/2024
Thrilled to see this paper out!! 🧪 Spatial transcriptomics of brain aging and 'spatial aging clocks' identify cells that have pro-aging or pro-rejuvenating effects on their neighbors! Huge CONGRATS to Eric Sun and all authors! Fantastic collaboration with @jameszou.bsky.social! rdcu.be/d33uQ 🧵
rdcu.be
Spatial transcriptomic clocks reveal cell proximity effects in brain ageing
Nature - A spatially resolved single-cell transcriptomics map of the mouse brain at different ages reveals signatures of ageing, rejuvenation and disease, including ageing effects associated with T...
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Shubhra Agrawal @shubhra-a.bsky.social · 16/12/2024
burn-out induced fermentation weekend is over, back on the corporate saddle for the week 🫡 Send prayers
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Timothy Stiles @stiles.io · 10/12/2024
I love when people post the tiny little details of their lab work here.
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Shubhra Agrawal @shubhra-a.bsky.social · 11/12/2024
🖥️🧬 folks, when using chatbots, what are some #Bioinformatics coding problems you've had good or bad experiences with? Care to comment?
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Nextflow @nextflow.io · 03/12/2024
Are you looking for job opportunities where your #Nextflow skills are valued? Check the list we've compiled below. 👇 #Jobs #Opportunities
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Ned Batchelder @nedbat.com · 02/12/2024
Got an email, "Thank you for coverage․py." I immediately thought, "they're going to want something, or complain about something." Nope! It was all positive. Ended with "Thanks again for this awesome Python contribution!" If you like what someone has done, tell them!
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Will Macnair @willmacnair.bsky.social · 07/11/2024
I made a starter pack for single cell and spatial people on BlueSky! 🧬🧪🥳 I’m certain it’s very incomplete, so please just let me know if you’d like to be included 😊 go.bsky.app/U57Mar8
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Patrick Chovanec @prchovanec.bsky.social · 24/11/2024
My one constructive criticism on BlueSky, as a community: we need to “like” less and “retweet” more. In the absence of an algorithm, that’s the way we find each other and reward good content.
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Rebecca Taylor @beccaet.bsky.social · 02/12/2024
I'm sure you're aware, but for others who may not be, Public Health Scotland found 0 cases of #CervicalCancer among women who'd received #HPV vaccination: publichealthscotland.scot/news/2024/ja...
publichealthscotland.scot
No cervical cancer cases detected in vaccinated women following HPV immunisation - News - Public Health Scotland
An exciting new study from PHS, in collaboration with the Universities of Strathclyde and Edinburgh, shows that no cervical cancer cases have been detected in women vaccinated at age 12-13 since the H...
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Shubhra Agrawal @shubhra-a.bsky.social · 02/12/2024
having never used twitter, bluesky is really testing my high school precis writing skills
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Shubhra Agrawal @shubhra-a.bsky.social · 02/12/2024
Prediction: Shubhra will likely evolve into a go-to source for bioinformatics insights, peppered with her own brand of humor that keeps followers both informed and entertained. blueskyroast.com/roast/shubhr... A roast? this felt like a love letter ☺️ P.S. yes, i checked the terms. no data storage
blueskyroast.com
Shubhra: The Bioinformatics Whisperer of Bluesky
A blend of tech savvy and quirky humor that keeps followers guessing.
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Shubhra Agrawal @shubhra-a.bsky.social · 29/11/2024
In case you were wondering how my day is going
media.tenor.com
a cartoon of a man with a mustache and a yellow jacket holding his hair in the air
ALT: a cartoon of a man with a mustache and a yellow jacket holding his hair in the air
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Roderick @shfo.bsky.social · 15/10/2023
I'm not sure how many pathological BAM files they have, but BioJulia has a pretty good compilation of test files in different formats: github.com/BioJulia/For...
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Shubhra Agrawal @shubhra-a.bsky.social · 27/11/2024
🩺🖥️ I need to do a deep dive on UK Biobank data, understand the types of data available, practical insights into how data is usually structured/accessed/processed etc. Any pointers with respect to existing resources I could use for this? Or any experts who would be open to hop on as a consultant?
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Lior Pachter @lpachter.bsky.social · 26/11/2024
It's multiple things: www.biorxiv.org/content/10.1...
biorxiv.org
The impact of package selection and versioning on single-cell RNA-seq analysis
Standard single-cell RNA-sequencing analysis (scRNA-seq) workflows consist of converting raw read data into cell-gene count matrices through sequence alignment, followed by analyses including filterin...
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Shubhra Agrawal @shubhra-a.bsky.social · 26/11/2024
Was out for a walk in the neighbourhood tonight and waved to a 2 yr old out with his parents. He ran up, grabbed my finger and was ready to take me home with them 😂 not sure if this is some new and adorable kidnapping ring, or if I looked like an approachable shaggy dog
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ChristopherE @christopher664023.bsky.social · 08/11/2024
In 1890, the X and Y chromosomes were discovered. It was found that the men who were tested had 46 chromosomes, including an X and a Y, while women who were tested also had 46 chromosomes, including 2 X chromosomes. So obviously the conclusion was that the Y chromosome defined masculinity.
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Shubhra Agrawal @shubhra-a.bsky.social · 25/11/2024
How do I get my hands on this? the year-end 'strategy meets' are fast approaching 👀
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Sandra Newman @sannewman.bsky.social · 12/02/2024
Humans share 70% of our DNA with zebrafish. So when you're having difficulty getting anything done, it's usually because a zebrafish is using the DNA.
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