Alireza Karbalayghareh
@karbalayghareh.bsky.social
Senior Research Scientist at CZ Biohub New York, AI/ML Platform. Building causal AI models of immune cells.
Reposted by Alireza Karbalayghareh
Exciting symposium on AI and Biology at EMBO | EMBL in Heidelberg on 10-13 March 2026!
Excellent lineup of invited speakers across various scales of biology!
Deadline for abstract submission is coming up — Dec 2.
🔗 www.embl.org/about/info/c...
#EESAIBio @EMBLEvents
Excellent lineup of invited speakers across various scales of biology!
Deadline for abstract submission is coming up — Dec 2.
🔗 www.embl.org/about/info/c...
#EESAIBio @EMBLEvents
November 7, 2025 at 12:16 AM
Exciting symposium on AI and Biology at EMBO | EMBL in Heidelberg on 10-13 March 2026!
Excellent lineup of invited speakers across various scales of biology!
Deadline for abstract submission is coming up — Dec 2.
🔗 www.embl.org/about/info/c...
#EESAIBio @EMBLEvents
Excellent lineup of invited speakers across various scales of biology!
Deadline for abstract submission is coming up — Dec 2.
🔗 www.embl.org/about/info/c...
#EESAIBio @EMBLEvents
Our review of the current AI modeling approaches for predicting the regulatory genome, what we do best, which tasks we struggle most, and where we should be heading to address those challenges:
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Predicting the regulatory genome - Nature Reviews Genetics
In this Comment, the authors overview the latest deep learning models for predicting regulatory function from genomic sequence and highlight key topics going forward, including the trade-off between s...
www.nature.com
September 21, 2025 at 1:09 PM
Our review of the current AI modeling approaches for predicting the regulatory genome, what we do best, which tasks we struggle most, and where we should be heading to address those challenges:
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Alireza Karbalayghareh
Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
September 18, 2025 at 4:14 PM
Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
Reposted by Alireza Karbalayghareh
@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease.
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
August 19, 2025 at 12:29 AM
@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease.
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
Reposted by Alireza Karbalayghareh
One thing that really bothers me with the new "virtual cell" terminology is that it is currently largely focused on a very narrow definition of models that can predict effects of trans perturbations (gene dosage, drugs etc) on gene expression. 1/
June 28, 2025 at 10:38 AM
One thing that really bothers me with the new "virtual cell" terminology is that it is currently largely focused on a very narrow definition of models that can predict effects of trans perturbations (gene dosage, drugs etc) on gene expression. 1/
Reposted by Alireza Karbalayghareh
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
June 25, 2025 at 2:29 PM
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
Great opportunity!
@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/
June 20, 2025 at 7:30 PM
Great opportunity!
Reposted by Alireza Karbalayghareh
The premier conference on Machine Learning for Computational Biology is Sep 9-10 at the NY Genome Center in NYC!
Submission deadline is June 1 for 2-page abstracts and 8-page papers (eligible for proceedings track).
Registration is now open! (Link below)
Please retweet!
Submission deadline is June 1 for 2-page abstracts and 8-page papers (eligible for proceedings track).
Registration is now open! (Link below)
Please retweet!
May 16, 2025 at 11:26 AM
The premier conference on Machine Learning for Computational Biology is Sep 9-10 at the NY Genome Center in NYC!
Submission deadline is June 1 for 2-page abstracts and 8-page papers (eligible for proceedings track).
Registration is now open! (Link below)
Please retweet!
Submission deadline is June 1 for 2-page abstracts and 8-page papers (eligible for proceedings track).
Registration is now open! (Link below)
Please retweet!
Reposted by Alireza Karbalayghareh
Free in-person registration is open for #MLCB2025! Sept 10-11 at @nygenome.org and online at youtube.com/@mlcbconf. Paper/abstract deadline is June 1, more deets including our fantastic invited speaker lineup at mlcb.org! Please RP.
Machine Learning in Computational Biology
Youtube channel for the Machine Learning in Computational Biology conference: https://mlcb.github.io/
youtube.com
May 15, 2025 at 12:24 AM
Free in-person registration is open for #MLCB2025! Sept 10-11 at @nygenome.org and online at youtube.com/@mlcbconf. Paper/abstract deadline is June 1, more deets including our fantastic invited speaker lineup at mlcb.org! Please RP.
Reposted by Alireza Karbalayghareh
The short talk and scholarship deadlines for the @keystonesymposia.bsky.social AI in Molecular Biology meeting in September are coming up fast, May 20th. Looking forward to seeing the submissions! www.keystonesymposia.org/conferences/...
May 11, 2025 at 9:29 PM
The short talk and scholarship deadlines for the @keystonesymposia.bsky.social AI in Molecular Biology meeting in September are coming up fast, May 20th. Looking forward to seeing the submissions! www.keystonesymposia.org/conferences/...
Great work!
Our latest work now online in Cell:
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
April 18, 2025 at 12:42 AM
Great work!
Very cool work!
Disease diagnostics using machine learning of B cell and T cell receptor sequences
www.science.org/doi/10.1126/...
TL;DR: BCRs ARE ALL YOU NEED!
(Well actually .... keep reading) 1/
www.science.org/doi/10.1126/...
TL;DR: BCRs ARE ALL YOU NEED!
(Well actually .... keep reading) 1/
Disease diagnostics using machine learning of B cell and T cell receptor sequences
Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system’s own record of antigen ...
www.science.org
February 22, 2025 at 10:44 PM
Very cool work!
Reposted by Alireza Karbalayghareh
My heart goes out to all of the people at the NIH and CDC who were fired recently. These people weren't fired for being bad at their job or a waste of resources -- they were fired because they were easy to fire by outsiders trying to meet a quota. They worked years/decades.. for this?
February 16, 2025 at 1:31 PM
My heart goes out to all of the people at the NIH and CDC who were fired recently. These people weren't fired for being bad at their job or a waste of resources -- they were fired because they were easy to fire by outsiders trying to meet a quota. They worked years/decades.. for this?
Reposted by Alireza Karbalayghareh
It’s been buried in all the news today, but every scientist in the US should pay attention to this:
Mike Lauer went out on a limb for us all, sending out a memo saying institutes should start awarding grants. And it looks like Trump/Musk fired him for that. 🧪
Mike Lauer went out on a limb for us all, sending out a memo saying institutes should start awarding grants. And it looks like Trump/Musk fired him for that. 🧪
NEW: In a further sign of turmoil at the NIH, Mike Lauer, who oversees the agency's $39 billion extramural budget that goes to research outside the NIH, has resigned effective tomorrow.
This comes after top NIH official Larry Tabak abruptly retired yesterday.
This comes after top NIH official Larry Tabak abruptly retired yesterday.
February 14, 2025 at 9:40 PM
It’s been buried in all the news today, but every scientist in the US should pay attention to this:
Mike Lauer went out on a limb for us all, sending out a memo saying institutes should start awarding grants. And it looks like Trump/Musk fired him for that. 🧪
Mike Lauer went out on a limb for us all, sending out a memo saying institutes should start awarding grants. And it looks like Trump/Musk fired him for that. 🧪
Reposted by Alireza Karbalayghareh
98% of NIH grants that should have gone out this month, didn't. Despite court orders 'unfreezing' the funds, they are frozen. Biomedical research will grind to a halt. Clinical trials will end. All for no reason: the total impact on the US budget is miniscule
February 12, 2025 at 3:19 PM
98% of NIH grants that should have gone out this month, didn't. Despite court orders 'unfreezing' the funds, they are frozen. Biomedical research will grind to a halt. Clinical trials will end. All for no reason: the total impact on the US budget is miniscule
Reposted by Alireza Karbalayghareh
[SAVE THE DATE] MLCB 2025 is happening Sept 10-11 at the NY Genome Center in NYC!
Attend the premier conference at the intersection of ML & Bio, share your research and make lasting connections!
Submission deadline: June 1
More details: mlcb.github.io
Help spread the word—please RT! #MLCB2025
Attend the premier conference at the intersection of ML & Bio, share your research and make lasting connections!
Submission deadline: June 1
More details: mlcb.github.io
Help spread the word—please RT! #MLCB2025
February 5, 2025 at 2:50 AM
[SAVE THE DATE] MLCB 2025 is happening Sept 10-11 at the NY Genome Center in NYC!
Attend the premier conference at the intersection of ML & Bio, share your research and make lasting connections!
Submission deadline: June 1
More details: mlcb.github.io
Help spread the word—please RT! #MLCB2025
Attend the premier conference at the intersection of ML & Bio, share your research and make lasting connections!
Submission deadline: June 1
More details: mlcb.github.io
Help spread the word—please RT! #MLCB2025
Reposted by Alireza Karbalayghareh
#MLCB2025 will be Sept 10-11 at @nygenome.org in NYC! Paper deadline June 1st & in-person registration will open in May. Please sign up for our mailing list groups.google.com/g/mlcb/ for future announcements. More details at mlcb.github.io. Please RP!
January 27, 2025 at 6:40 PM
#MLCB2025 will be Sept 10-11 at @nygenome.org in NYC! Paper deadline June 1st & in-person registration will open in May. Please sign up for our mailing list groups.google.com/g/mlcb/ for future announcements. More details at mlcb.github.io. Please RP!
Reposted by Alireza Karbalayghareh
Our ChromBPNet preprint out!
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
December 25, 2024 at 11:48 PM
Our ChromBPNet preprint out!
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
Great positions! Go work with Peter, he is excellent!
I'm hiring:
1. Research associate (wet-lab w/ phd) to generate mpra perturbation data
2. ML postdoc to build multimodal generative AI for DNA (eg diffusion and LLMs)
3. Bioinformatician (any level) to process and harmonize functional genomics data to train foundation models
DM me if interested!
1. Research associate (wet-lab w/ phd) to generate mpra perturbation data
2. ML postdoc to build multimodal generative AI for DNA (eg diffusion and LLMs)
3. Bioinformatician (any level) to process and harmonize functional genomics data to train foundation models
DM me if interested!
December 23, 2024 at 8:28 PM
Great positions! Go work with Peter, he is excellent!
Reposted by Alireza Karbalayghareh
1/ 🎄 What’s the best gift under the tree for a computational biologist? 🎁 A new experimental assay that refines our view of gene regulation: ACCESS-ATAC! This creative idea from Richard Sherwood was developed collaboratively between his lab and mine. #Genomics
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 23, 2024 at 3:18 PM
1/ 🎄 What’s the best gift under the tree for a computational biologist? 🎁 A new experimental assay that refines our view of gene regulation: ACCESS-ATAC! This creative idea from Richard Sherwood was developed collaboratively between his lab and mine. #Genomics
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Alireza Karbalayghareh
Proud of this work spearheaded by the phenomenal @jlfan.bsky.social and @mingxz.bsky.social in collaboration w/ Ben Izar! The past 3 years we've worked hard to unravel how #CNVs shape #tumor phenotypic plasticity seen in #singlecell #RNAseq data ➡️ #Echidna 🦔
December 18, 2024 at 2:08 PM
Proud of this work spearheaded by the phenomenal @jlfan.bsky.social and @mingxz.bsky.social in collaboration w/ Ben Izar! The past 3 years we've worked hard to unravel how #CNVs shape #tumor phenotypic plasticity seen in #singlecell #RNAseq data ➡️ #Echidna 🦔
Reposted by Alireza Karbalayghareh
🎆4 years in the making! Thrilled to share the 1st spatial single cell aging clock ⏰ www.nature.com/articles/s41...
We use #AI + spatial transcriptomics to discover what makes some cells age faster/slower in the brain 🧠
Led by Eric Sun and awesome collaboration w/ @brunetlab.bsky.social🧵
We use #AI + spatial transcriptomics to discover what makes some cells age faster/slower in the brain 🧠
Led by Eric Sun and awesome collaboration w/ @brunetlab.bsky.social🧵
December 18, 2024 at 10:19 PM
🎆4 years in the making! Thrilled to share the 1st spatial single cell aging clock ⏰ www.nature.com/articles/s41...
We use #AI + spatial transcriptomics to discover what makes some cells age faster/slower in the brain 🧠
Led by Eric Sun and awesome collaboration w/ @brunetlab.bsky.social🧵
We use #AI + spatial transcriptomics to discover what makes some cells age faster/slower in the brain 🧠
Led by Eric Sun and awesome collaboration w/ @brunetlab.bsky.social🧵
Reposted by Alireza Karbalayghareh
🚨 We’re hiring! 🚨
The Simons Center for Quantitative Biology at Cold Spring Harbor Laboratory is looking for a Research Technician to join our team.
If you’re passionate about genomics, AI, and experimental science, we want to hear from you.
Help us spread the word!
jobrxiv.org/job/cold-spr...
The Simons Center for Quantitative Biology at Cold Spring Harbor Laboratory is looking for a Research Technician to join our team.
If you’re passionate about genomics, AI, and experimental science, we want to hear from you.
Help us spread the word!
jobrxiv.org/job/cold-spr...
Research Technician - Cold Spring Harbor Laboratory
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!
jobrxiv.org
December 17, 2024 at 1:44 AM
🚨 We’re hiring! 🚨
The Simons Center for Quantitative Biology at Cold Spring Harbor Laboratory is looking for a Research Technician to join our team.
If you’re passionate about genomics, AI, and experimental science, we want to hear from you.
Help us spread the word!
jobrxiv.org/job/cold-spr...
The Simons Center for Quantitative Biology at Cold Spring Harbor Laboratory is looking for a Research Technician to join our team.
If you’re passionate about genomics, AI, and experimental science, we want to hear from you.
Help us spread the word!
jobrxiv.org/job/cold-spr...