Babak Alipanahi
@babak-a.bsky.social
Chief Scientist at @exai.bio — I use computational biology, machine learning and large-scale datasets to improve human health
Reposted by Babak Alipanahi
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.)
(Please repost to reach a broad audience.)
November 12, 2025 at 4:49 AM
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.)
(Please repost to reach a broad audience.)
Reposted by Babak Alipanahi
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....
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....
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...
www.nature.com
November 12, 2025 at 5:57 PM
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....
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....
Reposted by Babak Alipanahi
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.
November 7, 2025 at 5:04 PM
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.
Reposted by Babak Alipanahi
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.
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
nyti.ms
November 7, 2025 at 4:15 PM
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.
Reposted by Babak Alipanahi
Introducing Molview - the ipython/jupyter widget version of nano-protein-viewer🔍:
November 4, 2025 at 2:00 AM
Introducing Molview - the ipython/jupyter widget version of nano-protein-viewer🔍:
Reposted by Babak Alipanahi
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.
I hate to say “I told you so…” but nevertheless: I told you so.
journals.lww.com
October 31, 2025 at 2:52 AM
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.
I hate to say “I told you so…” but nevertheless: I told you so.
Reposted by Babak Alipanahi
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
October 28, 2025 at 10:23 PM
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...
www.biorxiv.org/content/10.1...
Simultaneously comical and tragic.
October 22, 2025 at 6:56 PM
Simultaneously comical and tragic.
Reposted by Babak Alipanahi
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...
Applications are due Dec 1: make sure you include a research statement!
jobs.careers.microsoft.com/global/en/jo...
Search Jobs | Microsoft Careers
jobs.careers.microsoft.com
October 21, 2025 at 7:32 PM
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...
Applications are due Dec 1: make sure you include a research statement!
jobs.careers.microsoft.com/global/en/jo...
Reposted by Babak Alipanahi
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"
October 21, 2025 at 1:53 PM
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"
Reposted by Babak Alipanahi
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.
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.
n.pr
October 16, 2025 at 5:32 PM
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.
Reposted by Babak Alipanahi
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/
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/
September 24, 2025 at 8:16 PM
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/
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/
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.
SimpleFold: Folding Proteins is Simpler than You Think [new]
Folding Proteins is Simpler than You Think
...by using a flow-matching objective and general-purpose transformers, achieving competitive results without complex domain-specific components.
Folding Proteins is Simpler than You Think
...by using a flow-matching objective and general-purpose transformers, achieving competitive results without complex domain-specific components.
September 24, 2025 at 3:36 PM
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.
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.
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 6:51 PM
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.
Reposted by Babak Alipanahi
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
August 20, 2025 at 7:43 PM
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
Reposted by Babak Alipanahi
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!
🧵
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!
🧵
August 4, 2025 at 1:52 PM
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!
🧵
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!
🧵
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."
An analysis shows that current deep learning models do not beat linear baselines in predicting gene perturbation effects, thus emphasizing the importance of further method development and evaluation. @const-ae.bsky.social @wkhuber.bsky.social @s-anders.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines - Nature Methods
The analysis presented in this Brief Communication shows that, despite their complexity, current deep learning models do not outperform linear baselines in predicting gene perturbation effects, thus e...
www.nature.com
August 4, 2025 at 6:55 PM
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."
RNA for the win! The once-overlooked black sheep of the macromolecules is slowly yet surely claiming its rightful place and prominence.
🧬 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.
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.
August 1, 2025 at 7:52 PM
RNA for the win! The once-overlooked black sheep of the macromolecules is slowly yet surely claiming its rightful place and prominence.
Reposted by Babak Alipanahi
🧬 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.
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.
August 1, 2025 at 12:44 PM
🧬 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.
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.
Didn't know Ben Blencowe has a part-time appointment at Crick! Should be a productive collaboration!
Meet Jernej Ule (@ulelab.bsky.social) and Ben Blencowe, who set up the Brain RNA Regulatory Networks satellite lab here at the Crick.
We spoke to Ben and Jernej about their research into RNA auto-gated vectors and their potential applications in gene therapy.
www.crick.ac.uk/news/2025-07...
We spoke to Ben and Jernej about their research into RNA auto-gated vectors and their potential applications in gene therapy.
www.crick.ac.uk/news/2025-07...
Introducing... Jernej Ule and Ben Blencowe
We spoke to Jernej Ule and Ben Blencowe, who recently set up the Brain RNA Regulatory Networks satellite lab here at the Crick.
www.crick.ac.uk
July 29, 2025 at 6:43 PM
Didn't know Ben Blencowe has a part-time appointment at Crick! Should be a productive collaboration!
Reposted by Babak Alipanahi
Predicting the translation efficiency of messenger RNA in mammalian cells go.nature.com/4mgXR0C
Predicting the translation efficiency of messenger RNA in mammalian cells - Nature Biotechnology
A deep convolutional neural network model predicts the influence of the full-length mRNA sequence on translation efficiency.
go.nature.com
July 25, 2025 at 3:37 PM
Predicting the translation efficiency of messenger RNA in mammalian cells go.nature.com/4mgXR0C
@atulbutte.bsky.social's last paper. He will be dearly missed.
Auto-MedCalc: Automated Biomarkers Discovery and Risk Score Generation with AI Agents [new]
Uses AI agents to automate biomarker discovery and risk score generation from multi-source biomedical data for improved diagnosis.
Uses AI agents to automate biomarker discovery and risk score generation from multi-source biomedical data for improved diagnosis.
July 16, 2025 at 9:25 PM
@atulbutte.bsky.social's last paper. He will be dearly missed.
Reposted by Babak Alipanahi
How did the pandemic start?
I have avoided publicly commenting on this for 5 years. Here's my take as someone who has no stake at all in the game.
gidmk.substack.com/p/pandemic-r...
I have avoided publicly commenting on this for 5 years. Here's my take as someone who has no stake at all in the game.
gidmk.substack.com/p/pandemic-r...
Pandemic Revisionism, Part One: COVID-19 Origins
Because people keep getting this very wrong.
gidmk.substack.com
July 7, 2025 at 9:46 PM
How did the pandemic start?
I have avoided publicly commenting on this for 5 years. Here's my take as someone who has no stake at all in the game.
gidmk.substack.com/p/pandemic-r...
I have avoided publicly commenting on this for 5 years. Here's my take as someone who has no stake at all in the game.
gidmk.substack.com/p/pandemic-r...
Reposted by Babak Alipanahi
Summary Table of the massive defunding of biomedical research in the United States
www.nytimes.com/interactive/...
www.nytimes.com/interactive/...
July 6, 2025 at 3:13 PM
Summary Table of the massive defunding of biomedical research in the United States
www.nytimes.com/interactive/...
www.nytimes.com/interactive/...
Amgen’s MariTide (GLP‑1 agonist + GIP antagonist), a once‑monthly injection, is demonstrating strong efficacy. The mean percentage change in body weight from baseline to week 52 ranged from −12.3% to −16.2%. Impressive results!
www.nejm.org/doi/full/10....
www.nejm.org/doi/full/10....
Once-Monthly Maridebart Cafraglutide for the Treatment of Obesity — A Phase 2 Trial | NEJM
Maridebart cafraglutide (known as MariTide) is a long-acting peptide–antibody conjugate
that combines glucagon-like peptide-1 receptor agonism and glucose-dependent insulinotropic
polypeptide recep...
www.nejm.org
June 27, 2025 at 9:00 PM
Amgen’s MariTide (GLP‑1 agonist + GIP antagonist), a once‑monthly injection, is demonstrating strong efficacy. The mean percentage change in body weight from baseline to week 52 ranged from −12.3% to −16.2%. Impressive results!
www.nejm.org/doi/full/10....
www.nejm.org/doi/full/10....