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
Amazing, depressing article about RFK Jr by Michael Scherer in The Atlantic. This graf at the end stayed with me. Our national policy is now based on the difference between 17 and 21 outcomes out of populations of 22000. As usual, hard to know if it is stupidity or dishonesty.
November 24, 2025 at 2:20 PM
Amazing, depressing article about RFK Jr by Michael Scherer in The Atlantic. This graf at the end stayed with me. Our national policy is now based on the difference between 17 and 21 outcomes out of populations of 22000. As usual, hard to know if it is stupidity or dishonesty.
Reposted by Tami Lieberman
Just about one more week to apply for our tenure-track opening in IMES at MIT! Come start your group in an outstanding community at MIT at the interface of medicine and engineering: faculty-searches.mit.edu/imes-search/
MIT Faculty Searches MIT INSTITUTE FOR MEDICAL ENGINEERING AND SCIENCE FACULTY SEARCH
faculty-searches.mit.edu
November 24, 2025 at 12:35 AM
Just about one more week to apply for our tenure-track opening in IMES at MIT! Come start your group in an outstanding community at MIT at the interface of medicine and engineering: faculty-searches.mit.edu/imes-search/
Reposted by Tami Lieberman
#microsky #phagesky #phage
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Chromosomal Curing Drives an Arms Race Between Bacterial Transformation and Prophage
Abstract. Transformation occurs when bacteria import exogenous DNA via the competence machinery and integrate it into their genome through homologous recom
academic.oup.com
November 23, 2025 at 4:39 PM
#microsky #phagesky #phage
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Reposted by Tami Lieberman
It only took us several decades and dozens Nature/Nature Genetics papers but we finally got to the conclusion that plant and animal breeders (and Lewontin) arrived at from the start: twin studies suck!
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
The missing heritability question is now (mostly) answered
Not with a bang but with a whimper
theinfinitesimal.substack.com
November 21, 2025 at 11:40 PM
It only took us several decades and dozens Nature/Nature Genetics papers but we finally got to the conclusion that plant and animal breeders (and Lewontin) arrived at from the start: twin studies suck!
Another great post from Sasha demonstrating what will ring true to many of us-- our environments include our siblings, making it unlikely that siblings have identical environments.
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
The missing heritability question is now (mostly) answered
Not with a bang but with a whimper
theinfinitesimal.substack.com
November 21, 2025 at 10:55 PM
Another great post from Sasha demonstrating what will ring true to many of us-- our environments include our siblings, making it unlikely that siblings have identical environments.
Reposted by Tami Lieberman
So there you have it, twin study estimates were greatly inflated, and molecular data sets the record straight. I walk through possible counter-arguments, but ultimately the uncomfortable truth is that genes contribute to traits much less than we always thought.
November 21, 2025 at 10:34 PM
So there you have it, twin study estimates were greatly inflated, and molecular data sets the record straight. I walk through possible counter-arguments, but ultimately the uncomfortable truth is that genes contribute to traits much less than we always thought.
Reposted by Tami Lieberman
I literally could not stop myself from inappropriately laughing out loud for real
November 21, 2025 at 12:24 AM
I literally could not stop myself from inappropriately laughing out loud for real
Reposted by Tami Lieberman
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Tami Lieberman
This work highlights how interactions between MGEs can produce unique effects where both benefit from their nested existence. Furthermore, we have extended TnpB’s mechanism that sheds light on why TnpB is so successful.
November 20, 2025 at 10:12 PM
This work highlights how interactions between MGEs can produce unique effects where both benefit from their nested existence. Furthermore, we have extended TnpB’s mechanism that sheds light on why TnpB is so successful.
Reposted by Tami Lieberman
So we did a similar experiment with conjugative plasmids and found that IS605 provides offensive and defensive benefits to conjugative plasmids, acting like a primitive anti-self defense mechanism to spread plasmids between cells.
November 20, 2025 at 10:12 PM
So we did a similar experiment with conjugative plasmids and found that IS605 provides offensive and defensive benefits to conjugative plasmids, acting like a primitive anti-self defense mechanism to spread plasmids between cells.
Reposted by Tami Lieberman
But in the context of plasmids this results in a newly inserted IS605 to reprogram TnpB to target, and destroy, all IS- plasmids within the cell. With no competition only IS+ plasmids will replicate, biasing their inheritance.
November 20, 2025 at 10:12 PM
But in the context of plasmids this results in a newly inserted IS605 to reprogram TnpB to target, and destroy, all IS- plasmids within the cell. With no competition only IS+ plasmids will replicate, biasing their inheritance.
Reposted by Tami Lieberman
Now that’s a lede.
Story by @taracopp.bsky.social and @michelleboorstein.bsky.social.
Read here: www.washingtonpost.com/national-sec...
Story by @taracopp.bsky.social and @michelleboorstein.bsky.social.
Read here: www.washingtonpost.com/national-sec...
November 20, 2025 at 6:39 PM
Now that’s a lede.
Story by @taracopp.bsky.social and @michelleboorstein.bsky.social.
Read here: www.washingtonpost.com/national-sec...
Story by @taracopp.bsky.social and @michelleboorstein.bsky.social.
Read here: www.washingtonpost.com/national-sec...
Reposted by Tami Lieberman
The President of the United States just called for Democratic members of Congress to be executed. "HANG THEM", he posted.
If you're a person of influence in this country and you haven't picked a side, maybe now would be the time to pick a fucking side.
If you're a person of influence in this country and you haven't picked a side, maybe now would be the time to pick a fucking side.
November 20, 2025 at 4:15 PM
The President of the United States just called for Democratic members of Congress to be executed. "HANG THEM", he posted.
If you're a person of influence in this country and you haven't picked a side, maybe now would be the time to pick a fucking side.
If you're a person of influence in this country and you haven't picked a side, maybe now would be the time to pick a fucking side.
Reposted by Tami Lieberman
Reposted by Tami Lieberman
Early-bird ends Nov 20 (11:59pm MST)! Register for the Human Microbiome Keystone Symposium to save $250 & get free access to the Microbiome Metabolism & Metabolites meeting.
@contaminatedsci.bsky.social
📝 keysym.us/KSMicrobiome26
🎥 youtu.be/MMb_ammY6i4
#KSMicrobiome26 #microbiome #humanmicrobiome
@contaminatedsci.bsky.social
📝 keysym.us/KSMicrobiome26
🎥 youtu.be/MMb_ammY6i4
#KSMicrobiome26 #microbiome #humanmicrobiome
Human Microbiome Meeting Promo
YouTube video by KeystoneSymposia
youtu.be
November 19, 2025 at 9:47 PM
Early-bird ends Nov 20 (11:59pm MST)! Register for the Human Microbiome Keystone Symposium to save $250 & get free access to the Microbiome Metabolism & Metabolites meeting.
@contaminatedsci.bsky.social
📝 keysym.us/KSMicrobiome26
🎥 youtu.be/MMb_ammY6i4
#KSMicrobiome26 #microbiome #humanmicrobiome
@contaminatedsci.bsky.social
📝 keysym.us/KSMicrobiome26
🎥 youtu.be/MMb_ammY6i4
#KSMicrobiome26 #microbiome #humanmicrobiome
Reposted by Tami Lieberman
This seems important. Current AI models can't read graphs. They "see" what they expect to see, even if the data shows something else.
Introducing bluffbench, a new tool to evaluate how well LLMs actually see data plots.
When we trick LLMs with secret #RStats transformations, they can miss the visual contradiction.
bluffbench helps us measure this "blind spot" in AI coding agents. Learn more: posit.co/blog/introdu...
When we trick LLMs with secret #RStats transformations, they can miss the visual contradiction.
bluffbench helps us measure this "blind spot" in AI coding agents. Learn more: posit.co/blog/introdu...
When plotting, LLMs see what they expect to see - Posit
Data science agents need to accurately read plots even when the content contradicts their expectations. Our testing shows today's LLMs still struggle here.
posit.co
November 19, 2025 at 4:58 PM
This seems important. Current AI models can't read graphs. They "see" what they expect to see, even if the data shows something else.
Reposted by Tami Lieberman
Don't miss out on our free virtual symposium (Dec. 12th) focused on microbial metabolites and their effects on the host.
Sponsors: @amiposts.bsky.social, Pendulum, & Liv (@zymoresearch.bsky.social)
Registrants will receive free memberships to Applied Microbiology International.
Details below 👇
Sponsors: @amiposts.bsky.social, Pendulum, & Liv (@zymoresearch.bsky.social)
Registrants will receive free memberships to Applied Microbiology International.
Details below 👇
Join @isbscience.org on December 12 for a Virtual Microbiome Symposium highlighting new discoveries about how gut-derived metabolites affect neural, immune, and endocrine systems. Open to microbiome-curious researchers and practitioners everywhere. isbscience.org/events/2025-...
2025 ISB Virtual Microbiome Symposium - Institute for Systems Biology (ISB)
The gut’s microbial ecosystem produces diverse metabolites that actively shape neural, immune, and endocrine function. Join leading researchers on December 12 as they share new discoveries into these ...
isbscience.org
November 18, 2025 at 11:25 PM
Don't miss out on our free virtual symposium (Dec. 12th) focused on microbial metabolites and their effects on the host.
Sponsors: @amiposts.bsky.social, Pendulum, & Liv (@zymoresearch.bsky.social)
Registrants will receive free memberships to Applied Microbiology International.
Details below 👇
Sponsors: @amiposts.bsky.social, Pendulum, & Liv (@zymoresearch.bsky.social)
Registrants will receive free memberships to Applied Microbiology International.
Details below 👇
Reposted by Tami Lieberman
Thrilled to see this finally announced - and glad to see good things still happening to good people!
Congratulations to Pardis, Christian, and the rest of the Sentinel team! 👏🥳
www.macfound.org/press/press-...
Congratulations to Pardis, Christian, and the rest of the Sentinel team! 👏🥳
www.macfound.org/press/press-...
Sentinel Awarded $100 Million to Prevent Pandemics
www.macfound.org
November 18, 2025 at 10:17 PM
Thrilled to see this finally announced - and glad to see good things still happening to good people!
Congratulations to Pardis, Christian, and the rest of the Sentinel team! 👏🥳
www.macfound.org/press/press-...
Congratulations to Pardis, Christian, and the rest of the Sentinel team! 👏🥳
www.macfound.org/press/press-...
Reposted by Tami Lieberman
people are actually very susceptible to just-so stories about human origins because listening to bullshit helped us survive on the savanna
fake evo-psych has cooked a lot of people's brains
November 18, 2025 at 1:48 AM
people are actually very susceptible to just-so stories about human origins because listening to bullshit helped us survive on the savanna
Reposted by Tami Lieberman
Introducing Foli-seq in @natbiotech.nature.com today. Foli-seq can be used to measure gut-derived RNA from fecal matter (signals of immune, secretory & epithelial cells). We used this to map gut inflammation, drug response, and host-microbe interactions. 💩🧬💊🦠
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut - Nature Biotechnology
Profiling host RNA shed in feces reveals disease states in the gut.
www.nature.com
November 17, 2025 at 8:55 PM
Introducing Foli-seq in @natbiotech.nature.com today. Foli-seq can be used to measure gut-derived RNA from fecal matter (signals of immune, secretory & epithelial cells). We used this to map gut inflammation, drug response, and host-microbe interactions. 💩🧬💊🦠
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Tami Lieberman
Quantitative modelling of multi-signal quorum sensing in Pseudomonas aeruginosa reveals that its las and rhl signalling systems engage in reciprocal, non-linear and synergistic interactions rather than a simple hierarchy.
Quantitative modeling of multi-signal quorum-sensing maps environment to bacterial regulatory responses
Bacterial quorum sensing is often assumed to follow a strict hierarchy, limiting understanding of how multiple signals interact. This study finds that Pseudomonas aeruginosa uses a reciprocal, coopera...
journals.plos.org
November 17, 2025 at 3:46 PM
Quantitative modelling of multi-signal quorum sensing in Pseudomonas aeruginosa reveals that its las and rhl signalling systems engage in reciprocal, non-linear and synergistic interactions rather than a simple hierarchy.
Reposted by Tami Lieberman
I had been elated to attend a scientific talk from a legend. It was fucking weird to see him objectifying these women. No mention of their scientific contributions, only their role as romantic interests. He even joked about how they knew not to work late nights in the lab because he might show up. 🤮
November 8, 2025 at 5:18 PM
I had been elated to attend a scientific talk from a legend. It was fucking weird to see him objectifying these women. No mention of their scientific contributions, only their role as romantic interests. He even joked about how they knew not to work late nights in the lab because he might show up. 🤮
Reposted by Tami Lieberman
📢 Our Dept. of Systems Biology at Columbia University has an open tenure-track Assistant Professor position in the broad area of quantitative biology. Come join our awesome department in NYC! Please circulate.
apply.interfolio.com/177622
Suggested deadline: 12/15/2025.
@columbiasysbio.bsky.social
apply.interfolio.com/177622
Suggested deadline: 12/15/2025.
@columbiasysbio.bsky.social
November 15, 2025 at 4:02 AM
📢 Our Dept. of Systems Biology at Columbia University has an open tenure-track Assistant Professor position in the broad area of quantitative biology. Come join our awesome department in NYC! Please circulate.
apply.interfolio.com/177622
Suggested deadline: 12/15/2025.
@columbiasysbio.bsky.social
apply.interfolio.com/177622
Suggested deadline: 12/15/2025.
@columbiasysbio.bsky.social
Reposted by Tami Lieberman
Very cool print demonstrating how variation in at TonB-dependent transporter repertoires shapes the ability of Bacteroides and Phocaeicola species to utilize fructooligosaccharides (FOS) of different chain lengths
Niche partitioning by resource size in the gut microbiome https://www.biorxiv.org/content/10.1101/2025.11.13.688124v1
November 16, 2025 at 1:48 AM
Very cool print demonstrating how variation in at TonB-dependent transporter repertoires shapes the ability of Bacteroides and Phocaeicola species to utilize fructooligosaccharides (FOS) of different chain lengths
Reposted by Tami Lieberman
Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases
Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...
www.science.org
November 13, 2025 at 8:53 PM
Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...