Tal Korem
@tkorem.bsky.social
Microbiome, metagenomics, ML, and reproductive health. All views are mine. So are all your base
Pinned
Tal Korem
@tkorem.bsky.social
· Aug 7
Korem Lab - Microbiome Systems Biology @ Columbia | New York, USA
We apply systems biology approaches to decipher the metabolic interactions between the microbiome and its human host in diverse clinical settings, aiming towards personalized microbiome-based therapeu...
www.koremlab.science
We are hiring a postdoc - come work with us (www.koremlab.science) at the intersection of #microbiome, data science, and women's health!
Message or email me if interested. 🖥️ 🧬
Message or email me if interested. 🖥️ 🧬
Reposted by Tal Korem
"This could take down Democrats, too."
I know. And I frankly wouldn't give even an itty bitty damn if it implicated every Democratic man in Congress, every Democratic hopeful for 2028 and every Democrat who has even thought about running for office.
Down with the sex predators, wherever they are.
I know. And I frankly wouldn't give even an itty bitty damn if it implicated every Democratic man in Congress, every Democratic hopeful for 2028 and every Democrat who has even thought about running for office.
Down with the sex predators, wherever they are.
November 13, 2025 at 1:15 AM
"This could take down Democrats, too."
I know. And I frankly wouldn't give even an itty bitty damn if it implicated every Democratic man in Congress, every Democratic hopeful for 2028 and every Democrat who has even thought about running for office.
Down with the sex predators, wherever they are.
I know. And I frankly wouldn't give even an itty bitty damn if it implicated every Democratic man in Congress, every Democratic hopeful for 2028 and every Democrat who has even thought about running for office.
Down with the sex predators, wherever they are.
Among the Schumer victimhood and his "opposition to the deal", this post really stuck with me. He was aware & grinning
Senate Democrats are meeting behind closed doors to discuss the emerging deal. “Stay tuned,” Schumer tells us with a grin.
November 12, 2025 at 2:40 PM
Among the Schumer victimhood and his "opposition to the deal", this post really stuck with me. He was aware & grinning
Reposted by Tal Korem
White paper: github.com/aqlaboratory...
GitHub Repo: github.com/aqlaboratory...
Huggingface: huggingface.co/OpenFold/Ope...
Testimonials: openfold.ghost.io/openfold3-co...
GitHub Repo: github.com/aqlaboratory...
Huggingface: huggingface.co/OpenFold/Ope...
Testimonials: openfold.ghost.io/openfold3-co...
github.com
October 28, 2025 at 6:30 PM
White paper: github.com/aqlaboratory...
GitHub Repo: github.com/aqlaboratory...
Huggingface: huggingface.co/OpenFold/Ope...
Testimonials: openfold.ghost.io/openfold3-co...
GitHub Repo: github.com/aqlaboratory...
Huggingface: huggingface.co/OpenFold/Ope...
Testimonials: openfold.ghost.io/openfold3-co...
Reposted by Tal Korem
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
October 28, 2025 at 6:30 PM
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
Reposted by Tal Korem
Just to be super clear, if you’re phoning in your peer review to ai you should quit your job so someone else who actually likes science can have it.
October 16, 2025 at 11:37 PM
Just to be super clear, if you’re phoning in your peer review to ai you should quit your job so someone else who actually likes science can have it.
I never knew I needed this thread
The only visually overwhelming flag that is also a 10/10 state flag
Happy Friday to the Maryland State flag
August 16, 2025 at 2:48 AM
I never knew I needed this thread
We are hiring a postdoc - come work with us (www.koremlab.science) at the intersection of #microbiome, data science, and women's health!
Message or email me if interested. 🖥️ 🧬
Message or email me if interested. 🖥️ 🧬
Korem Lab - Microbiome Systems Biology @ Columbia | New York, USA
We apply systems biology approaches to decipher the metabolic interactions between the microbiome and its human host in diverse clinical settings, aiming towards personalized microbiome-based therapeu...
www.koremlab.science
August 7, 2025 at 1:41 PM
We are hiring a postdoc - come work with us (www.koremlab.science) at the intersection of #microbiome, data science, and women's health!
Message or email me if interested. 🖥️ 🧬
Message or email me if interested. 🖥️ 🧬
Reposted by Tal Korem
I am seeking a postdoc for my group at UCLA. We work at the intersection of population genetics x microbiome (garud.eeb.ucla.edu). If interested, please message me!
Garud Lab
garud.eeb.ucla.edu
July 22, 2025 at 5:51 PM
I am seeking a postdoc for my group at UCLA. We work at the intersection of population genetics x microbiome (garud.eeb.ucla.edu). If interested, please message me!
Reposted by Tal Korem
Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io
Guidelines for preventing and reporting contamination in low-biomass microbiome studies
Nature Microbiology - In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize...
rdcu.be
June 21, 2025 at 7:59 PM
Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io
Reposted by Tal Korem
Reposted by Tal Korem
Not getting much attention, except in a recent NYTimes story, is a provision to increase the tax on university endowments and those of other nonprofits.
May 22, 2025 at 10:22 AM
Not getting much attention, except in a recent NYTimes story, is a provision to increase the tax on university endowments and those of other nonprofits.
Reposted by Tal Korem
New paper in Genome Biology!
genomebiology.biomedcentral.com/articles/10....
We introduce scale models, a generalization of normalizations that explciitly account for uncertainty in biological system scale (e.g., microbial load).
genomebiology.biomedcentral.com/articles/10....
We introduce scale models, a generalization of normalizations that explciitly account for uncertainty in biological system scale (e.g., microbial load).
Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization - Genome Biology
Statistical normalizations are used in differential analyses to address sample-to-sample variation in sequencing depth. Yet normalizations make strong, implicit assumptions about the scale of biologic...
genomebiology.biomedcentral.com
May 22, 2025 at 4:43 PM
New paper in Genome Biology!
genomebiology.biomedcentral.com/articles/10....
We introduce scale models, a generalization of normalizations that explciitly account for uncertainty in biological system scale (e.g., microbial load).
genomebiology.biomedcentral.com/articles/10....
We introduce scale models, a generalization of normalizations that explciitly account for uncertainty in biological system scale (e.g., microbial load).
Reposted by Tal Korem
as a resident of syracuse, ny, a rust belt town that used to be an economic epicenter for the nation: syracuse university is our largest local employer now and if it goes under, so does my town, which has the largest concentration of child poverty in the nation.
There is a false dichotomy drawn between "the ivory tower" and "the real world," and I'm here to report that in a post-industrial society, your real-world economy absolutely hinges on the university.
University towns are factory towns. Universities drive economic activity, not the other way around.
University towns are factory towns. Universities drive economic activity, not the other way around.
A must read
May 18, 2025 at 2:16 PM
as a resident of syracuse, ny, a rust belt town that used to be an economic epicenter for the nation: syracuse university is our largest local employer now and if it goes under, so does my town, which has the largest concentration of child poverty in the nation.
Reposted by Tal Korem
"I'm still in shock. I know that there have been political issues around Harvard in recent weeks, but antibiotic resistance isn't one of them." My conversation with Harvard microbiologist @baym.lol, one of many researchers there who just lost millions in fed. grants. www.wbur.org/news/2025/05...
Antibiotic research at Harvard lab threatened by federal funding cuts
Microbiologist Michael Baym studies antibiotic resistance at Harvard Medical School. He lost millions in federal funding this week.
www.wbur.org
May 16, 2025 at 10:59 PM
"I'm still in shock. I know that there have been political issues around Harvard in recent weeks, but antibiotic resistance isn't one of them." My conversation with Harvard microbiologist @baym.lol, one of many researchers there who just lost millions in fed. grants. www.wbur.org/news/2025/05...
Reposted by Tal Korem
Our paper explaining why Gihawi et al. failed to prove an error in the normalization used by the 2020 cancer #microbiome analysis now out as a Matters Arising in @asm.org #mSystems (w/ @george-austin.bsky.social) 🖥️ 🧬
Thread explaining the key points below.
journals.asm.org/doi/10.1128/...
Thread explaining the key points below.
journals.asm.org/doi/10.1128/...
May 2, 2025 at 1:59 PM
Our paper explaining why Gihawi et al. failed to prove an error in the normalization used by the 2020 cancer #microbiome analysis now out as a Matters Arising in @asm.org #mSystems (w/ @george-austin.bsky.social) 🖥️ 🧬
Thread explaining the key points below.
journals.asm.org/doi/10.1128/...
Thread explaining the key points below.
journals.asm.org/doi/10.1128/...
Our paper explaining why Gihawi et al. failed to prove an error in the normalization used by the 2020 cancer #microbiome analysis now out as a Matters Arising in @asm.org #mSystems (w/ @george-austin.bsky.social) 🖥️ 🧬
Thread explaining the key points below.
journals.asm.org/doi/10.1128/...
Thread explaining the key points below.
journals.asm.org/doi/10.1128/...
May 2, 2025 at 1:59 PM
Our paper explaining why Gihawi et al. failed to prove an error in the normalization used by the 2020 cancer #microbiome analysis now out as a Matters Arising in @asm.org #mSystems (w/ @george-austin.bsky.social) 🖥️ 🧬
Thread explaining the key points below.
journals.asm.org/doi/10.1128/...
Thread explaining the key points below.
journals.asm.org/doi/10.1128/...
Reposted by Tal Korem
Come and work with me!
The Nature Micro team is expanding and we're looking for someone to champion microbial ecology, plant micro & related areas for the journal
Knowledge of microbial ecology/plant micro is desirable but we're open to applications from all microbiologists
Link below 👇
The Nature Micro team is expanding and we're looking for someone to champion microbial ecology, plant micro & related areas for the journal
Knowledge of microbial ecology/plant micro is desirable but we're open to applications from all microbiologists
Link below 👇
📢We are #hiring a full time editor to handle areas including microbial ecology & plant microbiology🦠🌱
This position will work closely with @naturecomms.bsky.social
#microsky #microbiomesky #ecologysky 🧪
Available in NYC, Madrid, or other US offices
Read more & apply here: shorturl.at/yvdYJ
This position will work closely with @naturecomms.bsky.social
#microsky #microbiomesky #ecologysky 🧪
Available in NYC, Madrid, or other US offices
Read more & apply here: shorturl.at/yvdYJ
Associate or Senior Editor (Nature Microbiology), Nature Communications
Title: Associate or Senior Editor (Nature Microbiology), Nature Communications Organisation: Nature Portfolio Locations: New York, Philadelphia, Washington DC, Jersey City or Madrid – hybrid working m...
springernature.wd3.myworkdayjobs.com
April 11, 2025 at 4:14 PM
Come and work with me!
The Nature Micro team is expanding and we're looking for someone to champion microbial ecology, plant micro & related areas for the journal
Knowledge of microbial ecology/plant micro is desirable but we're open to applications from all microbiologists
Link below 👇
The Nature Micro team is expanding and we're looking for someone to champion microbial ecology, plant micro & related areas for the journal
Knowledge of microbial ecology/plant micro is desirable but we're open to applications from all microbiologists
Link below 👇
Reposted by Tal Korem
OUT NOW: Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models
@tkorem.bsky.social & co
#microsky #microbiomesky 🧪
www.nature.com/articles/s41...
@tkorem.bsky.social & co
#microsky #microbiomesky 🧪
www.nature.com/articles/s41...
Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models - Nature Microbiology
DEBIAS-M corrects technical variability in microbiome data in a manner both interpretable and suitable for machine learning. In extensive benchmarks, DEBIAS-M facilitates robust analyses that generali...
www.nature.com
March 27, 2025 at 4:34 PM
OUT NOW: Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models
@tkorem.bsky.social & co
#microsky #microbiomesky 🧪
www.nature.com/articles/s41...
@tkorem.bsky.social & co
#microsky #microbiomesky 🧪
www.nature.com/articles/s41...
Happy to share DEBIAS-M, our new method for domain adaptation and bias correction in #microbiome data.🧬🖥️
Microbiome data is very variable, with substantial study- and batch-effects. DEBIAS-M corrects these, enabling robust and generalizable analyses.
A quick thread:
www.nature.com/articles/s41...
Microbiome data is very variable, with substantial study- and batch-effects. DEBIAS-M corrects these, enabling robust and generalizable analyses.
A quick thread:
www.nature.com/articles/s41...
Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models - Nature Microbiology
DEBIAS-M corrects technical variability in microbiome data in a manner both interpretable and suitable for machine learning. In extensive benchmarks, DEBIAS-M facilitates robust analyses that generali...
www.nature.com
March 27, 2025 at 4:01 PM
Happy to share DEBIAS-M, our new method for domain adaptation and bias correction in #microbiome data.🧬🖥️
Microbiome data is very variable, with substantial study- and batch-effects. DEBIAS-M corrects these, enabling robust and generalizable analyses.
A quick thread:
www.nature.com/articles/s41...
Microbiome data is very variable, with substantial study- and batch-effects. DEBIAS-M corrects these, enabling robust and generalizable analyses.
A quick thread:
www.nature.com/articles/s41...
Reposted by Tal Korem
Just let me try and cure cancer for fucks sake.
March 11, 2025 at 3:49 PM
Just let me try and cure cancer for fucks sake.
Reposted by Tal Korem
Whomst among ass profs is not tired of Unprecedented Times? I want a precedent of faculty position straight from PhD and uninterrupted federal science funding for a 50 year career pls.
Oh great… the same new PIs who were hit by a global pandemic just as they started are now trying to renew their grants and get tenure when the funding agencies are actively being destroyed. But sure.... that COVID tenure clock extension reeaaallly made a difference....
January 23, 2025 at 4:32 PM
Whomst among ass profs is not tired of Unprecedented Times? I want a precedent of faculty position straight from PhD and uninterrupted federal science funding for a 50 year career pls.
Reposted by Tal Korem
GET is finally published!
- Paper: t.ly/iQct_ (new validations, dry and wet)
- Model: t.ly/4jnUI (new tutorial on PBMC 10x Multiome data, and yes you can even fine-tune it on a Macbook)
- Analysis package: t.ly/OqLAL
- Demo: t.ly/rbFQB
- Docker: t.ly/86n_i
- Paper: t.ly/iQct_ (new validations, dry and wet)
- Model: t.ly/4jnUI (new tutorial on PBMC 10x Multiome data, and yes you can even fine-tune it on a Macbook)
- Analysis package: t.ly/OqLAL
- Demo: t.ly/rbFQB
- Docker: t.ly/86n_i
A foundation model of transcription across human cell types - Nature
A foundation model learns transcriptional regulatory syntax from chromatin accessibility and sequence data across a range of cell types to predict gene expression and transcription factor interactions...
t.ly
January 8, 2025 at 4:16 PM
GET is finally published!
- Paper: t.ly/iQct_ (new validations, dry and wet)
- Model: t.ly/4jnUI (new tutorial on PBMC 10x Multiome data, and yes you can even fine-tune it on a Macbook)
- Analysis package: t.ly/OqLAL
- Demo: t.ly/rbFQB
- Docker: t.ly/86n_i
- Paper: t.ly/iQct_ (new validations, dry and wet)
- Model: t.ly/4jnUI (new tutorial on PBMC 10x Multiome data, and yes you can even fine-tune it on a Macbook)
- Analysis package: t.ly/OqLAL
- Demo: t.ly/rbFQB
- Docker: t.ly/86n_i
Now out "in print": we review domain adaptation methods, along with gaps and considerations for datasets of "biological scale" (many features, few samples, etc.). A fun CIFAR-funded collaboration with @meganakpeters.bsky.social 🧬 🖥️
www.science.org/doi/full/10....
www.science.org/doi/full/10....
Domain adaptation in small-scale and heterogeneous biological datasets
Research using biological data can benefit from domain adaptation modeling approaches, but it also carries distinct challenges.
www.science.org
December 22, 2024 at 9:19 PM
Now out "in print": we review domain adaptation methods, along with gaps and considerations for datasets of "biological scale" (many features, few samples, etc.). A fun CIFAR-funded collaboration with @meganakpeters.bsky.social 🧬 🖥️
www.science.org/doi/full/10....
www.science.org/doi/full/10....
Reposted by Tal Korem
• Author accepted manuscripts (peer reviewed articles) must be made available in Pubmed Central WITHOUT EMBARGO upon the official date of publication.
• Policy effective date is Dec 31, 2025 (no end date).
• Policy effective date is Dec 31, 2025 (no end date).
December 18, 2024 at 2:58 AM
• Author accepted manuscripts (peer reviewed articles) must be made available in Pubmed Central WITHOUT EMBARGO upon the official date of publication.
• Policy effective date is Dec 31, 2025 (no end date).
• Policy effective date is Dec 31, 2025 (no end date).
Probably an unpopular opinion, but I’ve seen it advertised recently so a warning: I believe that junior group leader positions are typically a bad career move.
December 4, 2024 at 4:39 PM
Probably an unpopular opinion, but I’ve seen it advertised recently so a warning: I believe that junior group leader positions are typically a bad career move.