Tami Lieberman
@contaminatedsci.bsky.social
Associate Professor, MIT
Still thinking about the 10^9 mutations generated in your microbiome today.
Website: http://lieberman.science
Still thinking about the 10^9 mutations generated in your microbiome today.
Website: http://lieberman.science
Pinned
Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...
Reposted by Tami Lieberman
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
www.embl.org
January 16, 2026 at 6:33 PM
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
Reposted by Tami Lieberman
Peer Review is broken because a generation of Editors were trained that peer review is sacrosanct. Thus we have Editors who are clerks, sending and re-sending manuscripts to reviewers until they are happy. That's not the job. Be an Editor, not a clerk. Use your skill and judgement. Make decisions.
January 14, 2026 at 7:59 PM
Peer Review is broken because a generation of Editors were trained that peer review is sacrosanct. Thus we have Editors who are clerks, sending and re-sending manuscripts to reviewers until they are happy. That's not the job. Be an Editor, not a clerk. Use your skill and judgement. Make decisions.
Reposted by Tami Lieberman
We extracted (parts of) 12 books in experiments with 4 frontier-lab, production LLMs.
We prompted the LLMs with a short prefix of a book and asked them to complete the rest. For Harry Potter and the Sorcerer’s Stone, we extracted 95.8% of the book from jailbroken Claude 3.7 Sonnet.
We prompted the LLMs with a short prefix of a book and asked them to complete the rest. For Harry Potter and the Sorcerer’s Stone, we extracted 95.8% of the book from jailbroken Claude 3.7 Sonnet.
January 7, 2026 at 8:31 PM
We extracted (parts of) 12 books in experiments with 4 frontier-lab, production LLMs.
We prompted the LLMs with a short prefix of a book and asked them to complete the rest. For Harry Potter and the Sorcerer’s Stone, we extracted 95.8% of the book from jailbroken Claude 3.7 Sonnet.
We prompted the LLMs with a short prefix of a book and asked them to complete the rest. For Harry Potter and the Sorcerer’s Stone, we extracted 95.8% of the book from jailbroken Claude 3.7 Sonnet.
Reposted by Tami Lieberman
What are the main sources of gene expression noise in bacteria, and why do slower growing bacteria exhibit more expression noise? TLDR: we found growth-rate fluctuations are a key driver of gene expression noise that increase as average growth rate decreases.
www.biorxiv.org/content/10.6...
1/n
www.biorxiv.org/content/10.6...
1/n
www.biorxiv.org
January 13, 2026 at 12:47 PM
What are the main sources of gene expression noise in bacteria, and why do slower growing bacteria exhibit more expression noise? TLDR: we found growth-rate fluctuations are a key driver of gene expression noise that increase as average growth rate decreases.
www.biorxiv.org/content/10.6...
1/n
www.biorxiv.org/content/10.6...
1/n
Reposted by Tami Lieberman
A novel membrane-spanning one-component system controls β-glucan utilization in marine Bacteroidota https://www.biorxiv.org/content/10.64898/2026.01.10.698779v1
January 12, 2026 at 4:16 AM
A novel membrane-spanning one-component system controls β-glucan utilization in marine Bacteroidota https://www.biorxiv.org/content/10.64898/2026.01.10.698779v1
Reposted by Tami Lieberman
Sequential evolution of antidote and toxin links genetic incompatibility with immune responses https://www.biorxiv.org/content/10.64898/2026.01.07.698274v1
January 9, 2026 at 2:31 AM
Sequential evolution of antidote and toxin links genetic incompatibility with immune responses https://www.biorxiv.org/content/10.64898/2026.01.07.698274v1
On my way to two *awesome* back-to-back conferences:
First, GRC on Microbiome Editing in Pomona, CA
www.grc.org/microbiome-e...
Then, Keystone Conference on Human Microbiomes in Banff (co-organizing)
www.keystonesymposia.org/conferences/...
First, GRC on Microbiome Editing in Pomona, CA
www.grc.org/microbiome-e...
Then, Keystone Conference on Human Microbiomes in Banff (co-organizing)
www.keystonesymposia.org/conferences/...
2026 Microbiome Editing Conference GRC
The 2026 Gordon Research Conference on Microbiome Editing will be held in Pomona, California. Apply today to reserve your spot.
www.grc.org
January 11, 2026 at 7:26 PM
On my way to two *awesome* back-to-back conferences:
First, GRC on Microbiome Editing in Pomona, CA
www.grc.org/microbiome-e...
Then, Keystone Conference on Human Microbiomes in Banff (co-organizing)
www.keystonesymposia.org/conferences/...
First, GRC on Microbiome Editing in Pomona, CA
www.grc.org/microbiome-e...
Then, Keystone Conference on Human Microbiomes in Banff (co-organizing)
www.keystonesymposia.org/conferences/...
Reposted by Tami Lieberman
🚨Call for papers🚨
Microbial Evolution: Impacts on Human Health
in the society journal Evolution, Medicine, and Public Health
Guest Editors: Bob Woods, Silvie Huijben & Camilo Barbosa
EIC: me
This will be great, please submit and share!
academic.oup.com/emph/pages/m...
Microbial Evolution: Impacts on Human Health
in the society journal Evolution, Medicine, and Public Health
Guest Editors: Bob Woods, Silvie Huijben & Camilo Barbosa
EIC: me
This will be great, please submit and share!
academic.oup.com/emph/pages/m...
January 9, 2026 at 4:49 PM
🚨Call for papers🚨
Microbial Evolution: Impacts on Human Health
in the society journal Evolution, Medicine, and Public Health
Guest Editors: Bob Woods, Silvie Huijben & Camilo Barbosa
EIC: me
This will be great, please submit and share!
academic.oup.com/emph/pages/m...
Microbial Evolution: Impacts on Human Health
in the society journal Evolution, Medicine, and Public Health
Guest Editors: Bob Woods, Silvie Huijben & Camilo Barbosa
EIC: me
This will be great, please submit and share!
academic.oup.com/emph/pages/m...
Reposted by Tami Lieberman
What a breakthrough! Such a puzzle for 30 years, this is real progress!
I wonder how general this mechanism of repression is for other systems where highly-selective expression is needed.
www.biorxiv.org/content/10.6...
I wonder how general this mechanism of repression is for other systems where highly-selective expression is needed.
www.biorxiv.org/content/10.6...
The transcription of a single olfactory receptor per neuron is enforced by epigenetic silencing of their enhancers
The ability to discriminate thousands of odors in our environment requires each olfactory neuron to express a single olfactory receptor from hundreds of available genes. The biochemical mechanism enfo...
www.biorxiv.org
January 7, 2026 at 7:46 PM
What a breakthrough! Such a puzzle for 30 years, this is real progress!
I wonder how general this mechanism of repression is for other systems where highly-selective expression is needed.
www.biorxiv.org/content/10.6...
I wonder how general this mechanism of repression is for other systems where highly-selective expression is needed.
www.biorxiv.org/content/10.6...
Reposted by Tami Lieberman
Happy that our work on the evolution of Yellowstone cyanobacteria is now published in @elife.bsky.social: doi.org/10.7554/eLif...! Did a lot of work in revision—many thanks to the anonymous reviewers for great suggestions! Also see the eLife digest for a summary: elifesciences.org/digests/9084...
Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population
Analysis of hundreds of single-cell genomes from Yellowstone National Park shows bacterial species are less cohesive than previously thought.
doi.org
December 31, 2025 at 9:15 PM
Happy that our work on the evolution of Yellowstone cyanobacteria is now published in @elife.bsky.social: doi.org/10.7554/eLif...! Did a lot of work in revision—many thanks to the anonymous reviewers for great suggestions! Also see the eLife digest for a summary: elifesciences.org/digests/9084...
Reposted by Tami Lieberman
New paper up - inspired by the periodic table of the elements, we attempted to organize bacterial diversity in genome-inferred trait space academic.oup.com/ismej/advanc...
Constructing a “periodic table” of bacteria to map diversity in trait space
Abstract. Despite an ever-expanding number of bacterial taxa being discovered, many of these taxa remain uncharacterized with unknown traits and environmen
academic.oup.com
January 6, 2026 at 7:31 PM
New paper up - inspired by the periodic table of the elements, we attempted to organize bacterial diversity in genome-inferred trait space academic.oup.com/ismej/advanc...
Reposted by Tami Lieberman
I'm excited to share that our preprint is now available on bioRxiv! Our study challenges the widespread use of molecular genetic diversity as a predictor adaptive potential, with important implications for how genetic data is used to inform conservation decisions.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Nucleotide diversity is a poor predictor of short-term adaptive potential
A capacity to adapt is essential for a population to avoid extinction in a changing world and is recognised as a global conservation priority. Adaptation requires additive (heritable) genetic variatio...
www.biorxiv.org
January 6, 2026 at 8:26 AM
I'm excited to share that our preprint is now available on bioRxiv! Our study challenges the widespread use of molecular genetic diversity as a predictor adaptive potential, with important implications for how genetic data is used to inform conservation decisions.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Tami Lieberman
New preprint from my lab (with Arya Kaul, @fernpizza.bsky.social, and @brinda.eu), in which we explore new genes hitchhiking on the beneficial deletion that fused them together, and find them in the LTEE, M. Tb/bovis, and across the bacterial tree of life
Novel genes arise from genomic deletions across the bacterial tree of life https://www.biorxiv.org/content/10.64898/2026.01.05.697752v1
January 6, 2026 at 4:12 PM
New preprint from my lab (with Arya Kaul, @fernpizza.bsky.social, and @brinda.eu), in which we explore new genes hitchhiking on the beneficial deletion that fused them together, and find them in the LTEE, M. Tb/bovis, and across the bacterial tree of life
Reposted by Tami Lieberman
🚨My department is hiring a full-time Assistant Teaching Professor to teach undergrad Genetics & Genomics, upper-level Genomics, and an inquiry-based Computational Genomics course where students can do authentic research. 🧬💻
I’m on the search committee. DM me if you’re interested. Please share! 🙏
I’m on the search committee. DM me if you’re interested. Please share! 🙏
Assistant Teaching Professor, Biology
About the Opportunity About the Opportunity: We invite applications from qualified candidates for a full-time Non-Tenure-Track (NTT) Assistant Teaching Professor faculty position within the Department...
northeastern.wd1.myworkdayjobs.com
January 6, 2026 at 2:11 AM
🚨My department is hiring a full-time Assistant Teaching Professor to teach undergrad Genetics & Genomics, upper-level Genomics, and an inquiry-based Computational Genomics course where students can do authentic research. 🧬💻
I’m on the search committee. DM me if you’re interested. Please share! 🙏
I’m on the search committee. DM me if you’re interested. Please share! 🙏
Reposted by Tami Lieberman
I'm just delighted to announce our new preprint on genome-scale perturb-seq in CD4+ T cells. We learned both general lessons about the power of perturb-seq, and specific lessons about T cell biology.
Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025
Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits
Gene regulatory networks encode the fundamental logic of cellular functions, but systematic network mapping remains challenging, especially in cell states relevant to human biology and disease. Here, ...
tinyurl.com
January 5, 2026 at 7:27 PM
I'm just delighted to announce our new preprint on genome-scale perturb-seq in CD4+ T cells. We learned both general lessons about the power of perturb-seq, and specific lessons about T cell biology.
Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
Proud to announce SimPhyNI, a new tool for bacterial GWAS with higher precision and scalability than existing tools. Try it out and let us know what you think!!
High Precision Binary Trait Association on Phylogenetic Trees https://www.biorxiv.org/content/10.64898/2025.12.24.696407v1
January 5, 2026 at 2:55 PM
Proud to announce SimPhyNI, a new tool for bacterial GWAS with higher precision and scalability than existing tools. Try it out and let us know what you think!!
Reposted by Tami Lieberman
Haller, Ralph & Messer present SLiM 5, a major extension of the SLiM simulation framework for simulating multiple chromosomes, enabling a heightened level of realism for full-genome simulations.
🔗 doi.org/10.1093/molbev/msaf313
#evobio #molbio #compbio
🔗 doi.org/10.1093/molbev/msaf313
#evobio #molbio #compbio
January 5, 2026 at 8:53 AM
Haller, Ralph & Messer present SLiM 5, a major extension of the SLiM simulation framework for simulating multiple chromosomes, enabling a heightened level of realism for full-genome simulations.
🔗 doi.org/10.1093/molbev/msaf313
#evobio #molbio #compbio
🔗 doi.org/10.1093/molbev/msaf313
#evobio #molbio #compbio
Reposted by Tami Lieberman
Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm
Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology
Long-read sequence assemblies from metagenomes contain frequent errors.
go.nature.com
January 2, 2026 at 4:39 PM
Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm
Peer review would be much improved if editors read papers in full before sending out for review. They could then provide very basic high level feedback (e.g. reorganize the text for readability [in X way], provide p-values for every claim), saving reviewer time for more meaningful feedback.
December 30, 2025 at 8:28 PM
Peer review would be much improved if editors read papers in full before sending out for review. They could then provide very basic high level feedback (e.g. reorganize the text for readability [in X way], provide p-values for every claim), saving reviewer time for more meaningful feedback.
Reposted by Tami Lieberman
Blog post: Just quit
Quitting projects in science is hard, but we should be doing a lot more of it.
open.substack.com/pub/arjunraj...
Quitting projects in science is hard, but we should be doing a lot more of it.
open.substack.com/pub/arjunraj...
Just quit
Quitting projects in science is hard, but we should be doing a lot more of it.
open.substack.com
December 30, 2025 at 3:02 PM
Blog post: Just quit
Quitting projects in science is hard, but we should be doing a lot more of it.
open.substack.com/pub/arjunraj...
Quitting projects in science is hard, but we should be doing a lot more of it.
open.substack.com/pub/arjunraj...
Reposted by Tami Lieberman
Did you know that my office has a student loan assistance unit?
Recently we achieved $91,264 in forgiveness for a public service worker and helped a librarian struggling with private loans save $50,010.
You don't have to navigate student debt alone - my office is here to help.
Recently we achieved $91,264 in forgiveness for a public service worker and helped a librarian struggling with private loans save $50,010.
You don't have to navigate student debt alone - my office is here to help.
December 29, 2025 at 5:44 PM
Did you know that my office has a student loan assistance unit?
Recently we achieved $91,264 in forgiveness for a public service worker and helped a librarian struggling with private loans save $50,010.
You don't have to navigate student debt alone - my office is here to help.
Recently we achieved $91,264 in forgiveness for a public service worker and helped a librarian struggling with private loans save $50,010.
You don't have to navigate student debt alone - my office is here to help.
Reposted by Tami Lieberman
I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests.
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Know when to co-fold'em
This is the official web page for the James Fraser Lab at UCSF.
fraserlab.com
December 29, 2025 at 10:25 PM
I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests.
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Reposted by Tami Lieberman
A free, open-access library of high-quality organism illustrations for science communication
A free, open-access library of high-quality organism illustrations for science communication
We create vector graphics of model organisms and emerging biological research organisms to enhance our publications. We’re sharing these editable graphics under a CC0 license for other scientists to...
doi.org
December 29, 2025 at 6:03 PM
A free, open-access library of high-quality organism illustrations for science communication
Reposted by Tami Lieberman
[1/3] Is your favorite bacterial isolate hiding a surprise lytic virus with a VERY different lifestyle? Finally I can proudly say that our paper on persistent phages is out in Nature Microbiology. rdcu.be/eWJEp. Well done @peterdoug.bsky.social
Persistent virulent phages exist across bacterial isolates
Nature Microbiology - The long-term existence of diverse virulent phages within cultures of Escherichia coli and others challenges the virulent–temperate dichotomy and points to non-canonical...
rdcu.be
December 29, 2025 at 2:00 PM
[1/3] Is your favorite bacterial isolate hiding a surprise lytic virus with a VERY different lifestyle? Finally I can proudly say that our paper on persistent phages is out in Nature Microbiology. rdcu.be/eWJEp. Well done @peterdoug.bsky.social
Reposted by Tami Lieberman
High Precision Binary Trait Association on Phylogenetic Trees https://www.biorxiv.org/content/10.64898/2025.12.24.696407v1
December 26, 2025 at 1:16 AM
High Precision Binary Trait Association on Phylogenetic Trees https://www.biorxiv.org/content/10.64898/2025.12.24.696407v1