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Babak Alipanahi

@babaka.bsky.social
1.1K followers 323 following 87 posts

computational biology, artificial intelligence and large-scale datasets to improve human health

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Reposted by Babak Alipanahi
Eric Topol @erictopol.bsky.social · 14/06/2026
Discovery of a 14-protein biomarker that predicts lung cancer 5.6 years before it is diagnosed, even in non-smokers, and an anti-inflammatory medicine that prevents its progression. And, challenging dogma, the proteins are not coming from cancerous cells!
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Eric Topol @erictopol.bsky.social · 09/04/2026
A new feature @science.org on the clusters of cells that enhance the spread of cancer, and what can be done to break them up www.science.org/content/arti...
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Adam Auton @adamauton.bsky.social · 09/04/2026
Were you inspired by our paper on the genetics of GLP-1 drug response? www.nature.com/articles/s41... Want to make impactful discoveries with the world's best genetic dataset? We're hiring! StatGen: tinyurl.com/ys4mvhej Risk Prediction: tinyurl.com/psamt294 Data Products: tinyurl.com/2ff7eavb
nature.com
Genetic predictors of GLP1 receptor agonist weight loss and side effects - Nature
Identification of genetic variants associated with the efficacy and side effects of GLP1 medications could underpin development of precision medicine approaches in the treatment of obesity.
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Babak Alipanahi @babaka.bsky.social · 08/04/2026
Fantastic results from 23andMe team led by amazing @adamauton.bsky.social on the efficacy of GLP-1 drug response.
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Adam Auton @adamauton.bsky.social · 08/04/2026
Delighted to share our latest research from the 23andMe Research Team, just published in @nature.com ! We looked at data from >27,000 participants to uncover how human genetics influences weight loss efficacy and side effects of GLP-1 medications like semaglutide. A short thread 🧵👇
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Nature @nature.com · 30/03/2026
A national screening programme increased the number of people diagnosed with early-stage lung cancer in England over half a decade go.nature.com/4veTAjw
go.nature.com
Huge lung-cancer screening campaign boosts early diagnosis
A programme that offers scans to smokers between the ages of 55 and 74 detects a large number of early-stage lung tumours.
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Babak Alipanahi @babaka.bsky.social · 30/03/2026
"[Some], model in hand, go around looking around for problems to solve. Some of them have realized that DNA sequencing is super-efficient and is generating reams of data, so they’ve latched onto this." "This is not how good science gets done. You don’t start with a tool and then look for problems."
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JHU Computer Science @jhucompsci.bsky.social · 26/03/2026
Congratulations to 3rd-year undergrad Steven Tan (first author!!), @benlangmead.bsky.social, @mohsenzakeri.bsky.social, & @sinamajidian.bsky.social on their Best Paper Award at @acm-bcb.bsky.social 2025! 🏆
cs.jhu.edu
Langmead Lab team recognized with Best Paper Award at ACM-BCB 2025
The winning paper presents a software tool for quickly and accurately identifying which species’ DNA are present in a sample.
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Manuel Irimia @mirimiam.bsky.social · 02/03/2026
🚨🧬🚨 We're looking for a specialized Research Assistant to spearhead a project aimed at exploring new RNA therapeutics in diabetes and other metabolic disorders. Junior or Senior, we're hoping to recruit a highly motivated and self-driven scientist interested in both basic and applied science. 🦄
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Eric Topol @erictopol.bsky.social · 20/02/2026
142,000 participants! The largest randomized trial of a multi-cancer early detection (MCED) test failed its primary endpoint genomeweb.com/cancer/grail... Had the enrollment been risk-based instead of age 50, it would likely have been very positive.
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Katharine Hayhoe @katharinehayhoe.com · 13/02/2026
Bluesky is the new science Twitter, new study by @whysharksmatter.bsky.social and Julia Wester concludes! "Results show that for every reported professional benefit that scientists once gained from Twitter, scientists can now gain that benefit more effectively on Bluesky than on Twitter."
academic.oup.com
Scientists no Longer Find Twitter Professionally Useful, and have Switched to Bluesky
Synopsis. Social media has become widely used by the scientific community for a variety of professional uses, including networking and public outreach. For
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All You Need is Lungs @allyouneedislungs.bsky.social · 11/02/2026
There’s growing agreement in the research that non-smoking #lungcancer is increasing and that our approaches to understanding and early detection haven’t kept pace. This Trends in Cancer piece brings a lot of that thinking together in one place. #LCSM 🔗 www.cell.com/trends/cance...
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Eric Topol @erictopol.bsky.social · 08/02/2026
Is it time for a new standard of care when it comes to mammograms in the era of AI? erictopol.substack.com/p/why-all-ma...
erictopol.substack.com
Why All Mammograms Should Incorporate A.I.
A very impressive body of evidence has accumulated
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Lior Pachter @lpachter.bsky.social · 03/02/2026
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).
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Adam Phillippy @aphillippy.bsky.social · 02/02/2026
Time for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]
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Babak Alipanahi @babaka.bsky.social · 27/01/2026
A good, enjoyable paper on AUROC vs AUPRC under class imbalance. In a nutshell, AUPRC's superiority is a myth. AUROC with bootstrapping all the way! arxiv.org/abs/2401.06091
arxiv.org
A Closer Look at AUROC and AUPRC under Class Imbalance
In machine learning (ML), a widespread claim is that the area under the precision-recall curve (AUPRC) is a superior metric for model comparison to the area under the receiver operating characteristic...
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Stein Aerts @steinaerts.bsky.social · 15/01/2026
TF-MINDI is out! A new method to learn cis-regulatory codes through rich embeddings of TF binding sites. TF-MINDI decomposes motif neighbourhoods, and works downstream of any sequence-to-function deep learning model. We deeply study the enhancer code in human neural development, check out the thread
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Eric Topol @erictopol.bsky.social · 07/01/2026
Vaccines, the most impressive public health intervention in medical history, and where we could be headed if there was not efforts to negate truth, facts, and evidence A great, open-access, review and perspective by @scientificdiscovery.dev
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Heng Li @lh3lh3.bsky.social · 06/01/2026
Now published in Algorithms for Molecular Biology: link.springer.com/article/10.1.... Key message: a tiny CNN model with 7k parameters can capture main splice signals across vertebrates+insect and halves the minimap2 & miniprot junction error rate. I always use this new feature now.
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Heng Li @lh3lh3.bsky.social · 06/01/2026
Now published in gigascience: academic.oup.com/gigascience/.... Key messages: SVs are highly enriched in low-complexity/tandem-repeat regions and are harder to call. They behave differently from transposon insertions. Always stratify if you study SVs.
academic.oup.com
Validate User
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David A Knowles @davidaknowles.bsky.social · 06/01/2026
Excited to see this out www.nature.com/articles/s41...! Nonparametric kernel-based tests for spatially variable isoform usage in spatial transcriptomics. So many interesting examples in the CNS and cancer, we're only scratching the surface!
nature.com
Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM - Nature Biotechnology
Differential isoform usage is identified with high statistical power from spatial transcriptomics data.
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Nature @nature.com · 15/12/2025
Nature research paper: Uncovering the role of LINE-1 in the evolution of lung adenocarcinoma go.nature.com/4oUHIPb
go.nature.com
Uncovering the role of LINE-1 in the evolution of lung adenocarcinoma - Nature
Lung adenocarcinomas bearing the ID2 mutational signature display increased LINE-1 retrotransposon activity, which contributes to their fast evolutionary dynamics and aggressive phenotype.
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exai bio @exai.bio · 12/12/2025
That’s a wrap on #SABCS25! Thank you to Dr. Lee Schwartzberg for presenting data demonstrating our platform’s ability to detect early stage breast cancer with high accuracy. #AI #RNA #earlydetection Learn more here: www.exai.bio/publications...
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Eric Topol @erictopol.bsky.social · 12/12/2025
Important new, large (N>28,000 women) randomized clinical trial of breast cancer screening: age-based vs risk-based by polygenic risk score, genomics "opportunity to modernize screening" jamanetwork.com/journals/jam...
jamanetwork.com
Risk-Based vs Annual Breast Cancer Screening
This randomized clinical trial examines whether risk-based screening is a safe and effective alternative to annual mammography for detecting breast cancer in women 40 years and older.
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Albert Vilella, PhD. @albertvilella.bsky.social · 08/12/2025
Even though the highest-profile names in today’s corporate Cambridge are in biotech and software, the influx of defense startups hearkens back to an earlier era — which, in 1922, saw the birth of Raytheon, now synonymous with the old guard of defense contractors. www.thecrimson.com/article/2025...
thecrimson.com
As Cambridge Faces a Life Sciences Downturn, Startups Turn to a New Industry: Warfare | News | The Harvard Crimson
As biotech firms shed jobs and life sciences funding dries up, policymakers have started to see defense technology as a way to buttress the Massachusetts economy. Industry experts say Cambridge may be...
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Shematologist, MD @shematologist.medsky.social · 06/12/2025
SCIENCE SAVES LIVES. Overall pediatric cancer survival rate increased from 63% in mid 1970s to 87%‼️between 2015 & 2021. And this isn’t due to supplements, eating better or avoiding red food dye. It’s due to science & industry working together to develop & approve therapies!
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Damir Baranasic @da-bar.bsky.social · 03/12/2025
JASPAR 2026 is out 🎉 The new release massively expands the TF motif collections and adds a dedicated DeepLearning collection of motifs learned from deep learning models. Database: jaspar.elixir.no Paper (NAR): doi.org/10.1093/nar/... 🧵1/2
jaspar.elixir.no
JASPAR: An open-access database of transcription factor binding profiles
JASPAR is the largest open-access database of curated and non-redundant transcription factor (TF) binding profiles from six different taxonomic groups.
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Heng Li @lh3lh3.bsky.social · 03/12/2025
579 high-quality human genomes from @humanpangenome.bsky.social, Arab Pangenome and individual papers (CHM13, CN1, KSA001, I002C, YAO and KOREF1). Sequences available in the AGC format (3.7GB) and FM-index in the ropebwt3 format (20.3GB). For details, see github.com/lh3/human-asm
github.com
GitHub - lh3/human-asm: A collection of high-quality human genomes
A collection of high-quality human genomes. Contribute to lh3/human-asm development by creating an account on GitHub.
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Babak Alipanahi @babaka.bsky.social · 02/12/2025
A nice paper on distilling AI-based splicing models into much simpler additive models: "[...] the distilled models achieve this without modeling RNA structure or feature interactions, indicating that [AI]-based splicing models recognize exons primarily through simple additive sequence features."
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Albert Vilella, PhD. @albertvilella.bsky.social · 19/11/2025
Abbott Laboratories is nearing a potential acquisition of Exact Sciences Corp, in what would be its largest deal in nearly a decade, people familiar with the matter said. www.bloomberg.com/news/article...
bloomberg.com
Abbott Nears Deal for Cancer Test Maker Exact Sciences
Abbott Laboratories is nearing a potential acquisition of medical-testing company Exact Sciences Corp., in what would be its largest deal in nearly a decade, people familiar with the matter said.
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Harmit Singh Malik @harmitmalik.bsky.social · 12/11/2025
Are you an early-stage graduate student (2nd or 3rd year) or early-stage postdoc based in the US or Canada, working primarily in Drosophila? Would you like to help improve the experience of all trainees working in Drosophila research? If so, read on. (Please repost to reach a broad audience.)
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loic-yengo.bsky.social @loic-yengo.bsky.social · 12/11/2025
First time on Bsky and first big announcement! I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature. Our manuscript is here: www.nature.com/articles/s41....
nature.com
Estimation and mapping of the missing heritability of human phenotypes - Nature
WGS data were used from 347,630 individuals with European ancestry in the UK Biobank to obtain high-precision estimates of coding and non-coding rare variant heritability for 34 co...
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exai bio @exai.bio · 07/11/2025
Yesterday our co-founder and CSO @babak-a.bsky.social presented at the Biotech-Pharma Statistics Workshop (BBSW) about the powerful combination of AI and cell-free RNA to detect early-stage lung cancer in the blood.
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The New York Times @nytimes.com · 07/11/2025
This version of the Persian dish tahchin incorporates common Thanksgiving ingredients. It is deeply savory and buttery, like stuffing, and some may say even better because it has a whole lot more texture coming from the crispy rice that everyone will be fighting over.
nyti.ms
Caramelized Onion, Cranberry and Rosemary Tahchin  Recipe
Tahchin is a Persian rice dish in which the rice is mixed with yogurt, oil, egg yolks and saffron and baked until a golden crust forms at the bottom (Persians refer to this as the tahdig) The rice on the inside becomes buttery and almost cake-like and is often layered with chicken and barberries, a tart dried fruit that has a beautiful crimson color This version incorporates common Thanksgiving ingredients like rosemary, sweet-tart cranberries and buttery onions to make a striking dish that feels more like a main than a side
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Steven Yu @stevenyuyy.bsky.social · 04/11/2025
Introducing Molview - the ipython/jupyter widget version of nano-protein-viewer🔍:
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Dr. Genevieve Eastabrook, MD FRCSC (she/her) @placentadoc.bsky.social · 31/10/2025
Neurodevelopmental Outcomes of 3-Year-Old Children Exposed to Maternal Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in Utero I hate to say “I told you so…” but nevertheless: I told you so.
journals.lww.com
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Adam Auton @adamauton.bsky.social · 28/10/2025
Delighted to see our method, PRSformer, at #NeurIPS2025! PRSformer is AI model for population-scale disease-risk prediction from individual genomes. It lays the groundwork for phenome-wide risk prediction. www.biorxiv.org/content/10.1...
biorxiv.org
PRSformer: Disease Prediction from Million-Scale Individual Genotypes
Predicting disease risk from DNA presents an unprecedented emerging challenge as biobanks approach population scale sizes (N>106 individuals) with ultra-high-dimensional features (L>105 genotypes). Cu...
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Babak Alipanahi @babaka.bsky.social · 22/10/2025
Simultaneously comical and tragic.
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 21/10/2025
Are you a PhD student interested in ML and biology or health? Come do an internship with me, @avapamini.bsky.social, Alex Lu, @lcrawford.bsky.social, or Kristen Severson at MSRNE! Applications are due Dec 1: make sure you include a research statement! jobs.careers.microsoft.com/global/en/jo...
jobs.careers.microsoft.com
Search Jobs | Microsoft Careers
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Albert Vilella, PhD. @albertvilella.bsky.social · 21/10/2025
What do you do if you are part of the tech-bro uber-rich cabal? Try and become immortal! There are now about a dozen biotech companies in the loosely defined space of "Longevity"
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NPR @npr.org · 16/10/2025
Consumer Reports expressed concern about high levels of lead in some two dozen protein powders, but only with repeated high exposure. Here's what to know before you make your next grocery run.
n.pr
A study found lead in popular protein powders. Here's why you shouldn't panic
Consumer Reports expressed concern about high levels of lead in some two dozen protein powders, but only with repeated high exposure. Here's what to know before you make your next grocery run.
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Andrea Love, PhD | Biomedical Scientist @drandrealove.bsky.social · 24/09/2025
The strongest predictor of autism is genetics. Data: • If one identical twin has ASD, the other has a 90–99% chance. • Compare that to 31–67% chance for fraternal twins. • Non-twin siblings have ~20% likelihood of ASD, 7-fold higher than general population. 1/
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Babak Alipanahi @babaka.bsky.social · 24/09/2025
Wow...what? Apple does protein folding now? As the name implies, it is a "simple" and general-purpose transformer-based method, which relies on a non-domain-specific flow-matching objective rather than domain knowledge.
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Babak Alipanahi @babaka.bsky.social · 22/09/2025
Such an amazing method and such a good study! Have to read it more carefully, but shows huge potential. Combining evolutionary and population genomics + language model is a great idea.
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Jonathan Wosen @jonathanwosen.bsky.social · 20/08/2025
I'm a science journalist for @statnews.com looking to talk with folks who applied to biomedical Ph.D. programs and had offers rescinded earlier this year. What have you been up to since then? You can reach me at jonathan.wosen@statnews.com or via Signal (username jwosen.27). #journorequest
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 04/08/2025
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉 www.nature.com/articles/s41... We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures! 🧵
Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.
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Babak Alipanahi @babaka.bsky.social · 04/08/2025
This is a pretty stark reminder that every methods paper needs proper baselines: "We compared five foundation and two deep learning models against deliberately simple baselines for predicting transcriptome changes after single or double perturbations. None outperformed the baselines."
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Babak Alipanahi @babaka.bsky.social · 01/08/2025
RNA for the win! The once-overlooked black sheep of the macromolecules is slowly yet surely claiming its rightful place and prominence.
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Institute of Molecular Genetics @imgprague.bsky.social · 01/08/2025
🧬 Happy RNA Day! 🎉 A tiny molecule with a massive impact #RNA! From translating genetic code to fighting diseases through mRNA vaccines, RNA is currently at the heart of innovation in science and medicine.
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Babak Alipanahi @babaka.bsky.social · 29/07/2025
Didn't know Ben Blencowe has a part-time appointment at Crick! Should be a productive collaboration!
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