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...
Registration here ai4id.eventbrite.com
Excited for the 'AI4ID Symposium: Bridging Infection and Artificial Intelligence' on January 28th at the Broad Institute.
The symposium will unite infectious disease researchers, clinicians, and AI experts to discuss how AI can help address the most pressing challenges in infectious diseases.
The symposium will unite infectious disease researchers, clinicians, and AI experts to discuss how AI can help address the most pressing challenges in infectious diseases.
November 10, 2025 at 6:43 PM
Registration here ai4id.eventbrite.com
Excited for the 'AI4ID Symposium: Bridging Infection and Artificial Intelligence' on January 28th at the Broad Institute.
The symposium will unite infectious disease researchers, clinicians, and AI experts to discuss how AI can help address the most pressing challenges in infectious diseases.
The symposium will unite infectious disease researchers, clinicians, and AI experts to discuss how AI can help address the most pressing challenges in infectious diseases.
November 10, 2025 at 5:34 PM
Excited for the 'AI4ID Symposium: Bridging Infection and Artificial Intelligence' on January 28th at the Broad Institute.
The symposium will unite infectious disease researchers, clinicians, and AI experts to discuss how AI can help address the most pressing challenges in infectious diseases.
The symposium will unite infectious disease researchers, clinicians, and AI experts to discuss how AI can help address the most pressing challenges in infectious diseases.
Reposted by Tami Lieberman
The Next Gen Pregnancy Initiative is now accepting applications. Up to $500,000 over 4 years to support bold research into pregnancy duration, fetal growth, and pregnancy complications. Deadline: Dec 4, 2025.
Apply now buff.ly/rNhJKMW #bwfrepro
Apply now buff.ly/rNhJKMW #bwfrepro
Next Gen Pregnancy Initiative - Burroughs Wellcome Fund
by
buff.ly
October 7, 2025 at 9:33 AM
The Next Gen Pregnancy Initiative is now accepting applications. Up to $500,000 over 4 years to support bold research into pregnancy duration, fetal growth, and pregnancy complications. Deadline: Dec 4, 2025.
Apply now buff.ly/rNhJKMW #bwfrepro
Apply now buff.ly/rNhJKMW #bwfrepro
Reposted by Tami Lieberman
Open position at the Swiss Institute of Bioinformatics:
We are looking for a Director of the Center of Pathogen Bioinformatics
apply.refline.ch/499599/0346/...
I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and
We are looking for a Director of the Center of Pathogen Bioinformatics
apply.refline.ch/499599/0346/...
I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and
Director, Center for Pathogen Bioinformatics
The Centre for Pathogen Bioinformatics (CPB) is a unit of SIB which offers expertise and services in pathogen bioinformatics, computational molecular epidemiology and related multi-site project manage...
apply.refline.ch
October 25, 2025 at 1:03 PM
Open position at the Swiss Institute of Bioinformatics:
We are looking for a Director of the Center of Pathogen Bioinformatics
apply.refline.ch/499599/0346/...
I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and
We are looking for a Director of the Center of Pathogen Bioinformatics
apply.refline.ch/499599/0346/...
I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and
Only 48% of US high schools offer calculus.
This seems like a huge problem and an easy place where high schools embracing online courses (+/- AI) could easily benefit students.
This seems like a huge problem and an easy place where high schools embracing online courses (+/- AI) could easily benefit students.
November 6, 2025 at 5:27 PM
Only 48% of US high schools offer calculus.
This seems like a huge problem and an easy place where high schools embracing online courses (+/- AI) could easily benefit students.
This seems like a huge problem and an easy place where high schools embracing online courses (+/- AI) could easily benefit students.
Reposted by Tami Lieberman
Excited to share our newest manuscript on antigen discovery and vaccine design for tuberculosis lead by Owen Leddy (everyone hiring new faculty in a few years, remember this name!)
www.science.org/doi/10.1126/... #TBsky
www.science.org/doi/10.1126/... #TBsky
Immunopeptidomics can inform the design of mRNA vaccines for the delivery of Mycobacterium tuberculosis MHC class II antigens
MHC class II immunopeptidomics in human phagocytes infected with Mycobacterium tuberculosis enables vaccine immunogen design and optimization.
www.science.org
November 5, 2025 at 9:57 PM
Excited to share our newest manuscript on antigen discovery and vaccine design for tuberculosis lead by Owen Leddy (everyone hiring new faculty in a few years, remember this name!)
www.science.org/doi/10.1126/... #TBsky
www.science.org/doi/10.1126/... #TBsky
If you're looking for a faculty position at the intersection of ecology and computing (both broadly defined), please apply to this joint search between the CEE Department and the College of Computing at MIT: cee.mit.edu/people/share...
Faculty Position in the Department of Civil and Environmental Engineering and the Schwarzman College of Computing - cee.mit.edu
The Department of Civil and Environmental Engineering (CEE), together with the Schwarzman College of Computing (SCC) at the Massachusetts Institute of Technology (MIT) in Cambridge MA, seeks candidate...
cee.mit.edu
November 5, 2025 at 7:27 PM
If you're looking for a faculty position at the intersection of ecology and computing (both broadly defined), please apply to this joint search between the CEE Department and the College of Computing at MIT: cee.mit.edu/people/share...
Want to make some new conceptual graphics.
Tried to give Powerpoint's AI 'copilot' a spin. Asked it to make me a slide with 100 circle shape objects randomly distributed. Was excited when it made me a pptx to download...
except this is what it came up with.
Why can't we have nice things?
Tried to give Powerpoint's AI 'copilot' a spin. Asked it to make me a slide with 100 circle shape objects randomly distributed. Was excited when it made me a pptx to download...
except this is what it came up with.
Why can't we have nice things?
November 4, 2025 at 9:01 PM
Want to make some new conceptual graphics.
Tried to give Powerpoint's AI 'copilot' a spin. Asked it to make me a slide with 100 circle shape objects randomly distributed. Was excited when it made me a pptx to download...
except this is what it came up with.
Why can't we have nice things?
Tried to give Powerpoint's AI 'copilot' a spin. Asked it to make me a slide with 100 circle shape objects randomly distributed. Was excited when it made me a pptx to download...
except this is what it came up with.
Why can't we have nice things?
Reposted by Tami Lieberman
New study of 800K+ genomes from gnomAD reveals most “pathogenic” variants in healthy people aren’t truly disease-tolerant. They are explained by annotation errors, mosaicism, or compensatory variants. 🧬
A big step for precision medicine!
www.nature.com/articles/s41...
A big step for precision medicine!
www.nature.com/articles/s41...
Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database - Nature Communications
Here the authors provide an explanation for 95% of examined predicted loss of function variants found in disease-associated haploinsufficient genes in the Genome Aggregation Database (gnomAD),…
www.nature.com
November 4, 2025 at 3:06 PM
New study of 800K+ genomes from gnomAD reveals most “pathogenic” variants in healthy people aren’t truly disease-tolerant. They are explained by annotation errors, mosaicism, or compensatory variants. 🧬
A big step for precision medicine!
www.nature.com/articles/s41...
A big step for precision medicine!
www.nature.com/articles/s41...
Reposted by Tami Lieberman
Academics in Assyria in the 7th c BC complain that admin is preventing them from doing research and teaching
November 3, 2025 at 10:04 AM
Academics in Assyria in the 7th c BC complain that admin is preventing them from doing research and teaching
Reposted by Tami Lieberman
New online! Microbial genomics for antimicrobial resistance ecology and action
Microbial genomics for antimicrobial resistance ecology and action
Nature Reviews Genetics, Published online: 03 November 2025; doi:10.1038/s41576-025-00909-zMicrobial genomics can improve our understanding of antimicrobial resistance dynamics across ecosystems. In this Comment, Kathryn Holt emphasizes the interconnectedness of human, animal and environmental health and calls for greater integration of microbial genomic data through robust analytical frameworks to unravel the complexity of antimicrobial resistance dynamics.
www.nature.com
November 3, 2025 at 1:07 PM
New online! Microbial genomics for antimicrobial resistance ecology and action
Reposted by Tami Lieberman
When ChatGPT was asked to rate 40,000 résumés, it ranked the older male candidates as better quality than the younger female applicants.
Age and gender distortion in online media and large language models - Nature
Stereotypes of age-related gender bias are socially distorted, as evidenced by the age gap in the representations of women and men across various media and algorithms, despite no systematic age differ...
www.nature.com
November 2, 2025 at 9:47 PM
When ChatGPT was asked to rate 40,000 résumés, it ranked the older male candidates as better quality than the younger female applicants.
Reposted by Tami Lieberman
We are racing to find antibiotics with AI, but what if we're ignoring the obvious? 🤔
This paper proves basic science is still here. No AI, Just one gene deletion revealed an intermediate 10-100x more potent against MRSA than the final drug.
pubs.acs.org/doi/10.1021/...
@challis-group.bsky.social
This paper proves basic science is still here. No AI, Just one gene deletion revealed an intermediate 10-100x more potent against MRSA than the final drug.
pubs.acs.org/doi/10.1021/...
@challis-group.bsky.social
Discovery of Late Intermediates in Methylenomycin Biosynthesis Active against Drug-Resistant Gram-Positive Bacterial Pathogens
The methylenomycins are highly functionalized cyclopentanone antibiotics produced by Streptomyces coelicolor A3(2). A biosynthetic pathway to the methylenomycins has been proposed based on sequence an...
pubs.acs.org
November 2, 2025 at 1:26 PM
We are racing to find antibiotics with AI, but what if we're ignoring the obvious? 🤔
This paper proves basic science is still here. No AI, Just one gene deletion revealed an intermediate 10-100x more potent against MRSA than the final drug.
pubs.acs.org/doi/10.1021/...
@challis-group.bsky.social
This paper proves basic science is still here. No AI, Just one gene deletion revealed an intermediate 10-100x more potent against MRSA than the final drug.
pubs.acs.org/doi/10.1021/...
@challis-group.bsky.social
Reposted by Tami Lieberman
Remember the single most important think you can do is bring a friend to vote!
Chris Cullen put together this great graph.
Chris Cullen put together this great graph.
November 1, 2025 at 12:21 PM
Remember the single most important think you can do is bring a friend to vote!
Chris Cullen put together this great graph.
Chris Cullen put together this great graph.
Reposted by Tami Lieberman
New preprint out! 📣🚨
We found that loss-of-function mutations in the carbapenem entry porin OprD of Pseudomonas aeruginosa do more than confer #AntibioticResistance: they reshape the bacterial membrane and interaction with the host, enhancing epithelial colonization capacity 🦠
#Microsky
We found that loss-of-function mutations in the carbapenem entry porin OprD of Pseudomonas aeruginosa do more than confer #AntibioticResistance: they reshape the bacterial membrane and interaction with the host, enhancing epithelial colonization capacity 🦠
#Microsky
Carbapenem-resistance oprD mutations reshape Pseudomonas aeruginosa host-pathogen interactions during infection https://www.biorxiv.org/content/10.1101/2025.10.24.684370v1
October 25, 2025 at 12:29 PM
New preprint out! 📣🚨
We found that loss-of-function mutations in the carbapenem entry porin OprD of Pseudomonas aeruginosa do more than confer #AntibioticResistance: they reshape the bacterial membrane and interaction with the host, enhancing epithelial colonization capacity 🦠
#Microsky
We found that loss-of-function mutations in the carbapenem entry porin OprD of Pseudomonas aeruginosa do more than confer #AntibioticResistance: they reshape the bacterial membrane and interaction with the host, enhancing epithelial colonization capacity 🦠
#Microsky
Reposted by Tami Lieberman
*NEW PAPER*
How much of a threat are within-organism conflicts, really?
In Biology & Philosophy, @martijnschenkel.bsky.social, Manus Patten, and I present a mathematical framework to measure evolutionary individuality in the face of internal conflicts. link.springer.com/article/10.1...
How much of a threat are within-organism conflicts, really?
In Biology & Philosophy, @martijnschenkel.bsky.social, Manus Patten, and I present a mathematical framework to measure evolutionary individuality in the face of internal conflicts. link.springer.com/article/10.1...
October 31, 2025 at 1:24 PM
*NEW PAPER*
How much of a threat are within-organism conflicts, really?
In Biology & Philosophy, @martijnschenkel.bsky.social, Manus Patten, and I present a mathematical framework to measure evolutionary individuality in the face of internal conflicts. link.springer.com/article/10.1...
How much of a threat are within-organism conflicts, really?
In Biology & Philosophy, @martijnschenkel.bsky.social, Manus Patten, and I present a mathematical framework to measure evolutionary individuality in the face of internal conflicts. link.springer.com/article/10.1...
Reposted by Tami Lieberman
The Kim Lab (sskimlab.org) at UC Irvine is recruiting motivated grad students interested in uncovering how transcriptional regulators direct cell fates. We accept students through the CMB (cmb.uci.edu) and MCSB (ccbs.uci.edu/education/mcsb/) PhD programs. Please share with prospective grad students!
Kim Lab at UC Irvine
Visit the post for more.
sskimlab.org
October 30, 2025 at 3:37 PM
The Kim Lab (sskimlab.org) at UC Irvine is recruiting motivated grad students interested in uncovering how transcriptional regulators direct cell fates. We accept students through the CMB (cmb.uci.edu) and MCSB (ccbs.uci.edu/education/mcsb/) PhD programs. Please share with prospective grad students!
Followers who live in Cambridge MA--
Please vote in the city council election. After the citywide repeal of single family zoning this past year (!), the NIMBYs are expected to turn out.
You can vote early at any of the 3 locations through Friday, or in person on Tuesday.
Please vote in the city council election. After the citywide repeal of single family zoning this past year (!), the NIMBYs are expected to turn out.
You can vote early at any of the 3 locations through Friday, or in person on Tuesday.
October 29, 2025 at 11:56 AM
Followers who live in Cambridge MA--
Please vote in the city council election. After the citywide repeal of single family zoning this past year (!), the NIMBYs are expected to turn out.
You can vote early at any of the 3 locations through Friday, or in person on Tuesday.
Please vote in the city council election. After the citywide repeal of single family zoning this past year (!), the NIMBYs are expected to turn out.
You can vote early at any of the 3 locations through Friday, or in person on Tuesday.
Reposted by Tami Lieberman
Analysis of essential genes in Clostridioides difficile by CRISPRi and Tn-seq | Journal of Bacteriology journals.asm.org/doi/10.1128/...
Analysis of essential genes in Clostridioides difficile by CRISPRi and Tn-seq | Journal of Bacteriology
Clostridioides difficile is an opportunistic pathogen for which better antibiotics are sorely needed. Most
antibiotics target pathways that are essential for viability. Here, we use saturation
transpo...
journals.asm.org
October 29, 2025 at 9:14 AM
Analysis of essential genes in Clostridioides difficile by CRISPRi and Tn-seq | Journal of Bacteriology journals.asm.org/doi/10.1128/...
I've been using chatgpt to improve my understanding of mammalian physiology and metabolic regulation, and I must admit its very useful.
October 28, 2025 at 4:51 PM
I've been using chatgpt to improve my understanding of mammalian physiology and metabolic regulation, and I must admit its very useful.
Reposted by Tami Lieberman
Our new preprint, led by Martin (@mfenk.bsky.social), is online. We address the microbiome’s role as a source and incubator of acute infections by combining prospective collection of native samples with population-wide, culture-based sequencing. Please check out Martin’s wonderful thread. ⬇️🧵🎉
Is the human microbiome a source for hospital-associated infections (HAI) and are any genetic changes associated with HAI? In our new preprint, we longitudinally reconstruct the evolutionary processes within the human microbiome leading up to HAI: doi.org/10.1101/2025...
Colonization, translocation, and evolution of opportunistic pathogens during hospital-associated infections
Many commensal bacteria that peacefully reside in the human microbiome are also able to cause acute opportunistic infections. Emerging evidence suggests that within-host evolution contributes to infec...
doi.org
October 27, 2025 at 11:14 AM
Our new preprint, led by Martin (@mfenk.bsky.social), is online. We address the microbiome’s role as a source and incubator of acute infections by combining prospective collection of native samples with population-wide, culture-based sequencing. Please check out Martin’s wonderful thread. ⬇️🧵🎉
Reposted by Tami Lieberman
During an 𝘌𝘯𝘵𝘦𝘳𝘰𝘣𝘢𝘤𝘵𝘦𝘳 𝘩𝘰𝘳𝘮𝘢𝘦𝘤𝘩𝘦𝘪 infection, we observe a short-lived, non-synonymous mutation in the fimbriae regulator gene 𝘧𝘪𝘮𝘡 [F126L] that is first observed in the gut, before being associated with HAI but subsequently swiftly replaced by repeated body-wide sweeps of independent genotypes.
October 27, 2025 at 9:25 AM
During an 𝘌𝘯𝘵𝘦𝘳𝘰𝘣𝘢𝘤𝘵𝘦𝘳 𝘩𝘰𝘳𝘮𝘢𝘦𝘤𝘩𝘦𝘪 infection, we observe a short-lived, non-synonymous mutation in the fimbriae regulator gene 𝘧𝘪𝘮𝘡 [F126L] that is first observed in the gut, before being associated with HAI but subsequently swiftly replaced by repeated body-wide sweeps of independent genotypes.
Reposted by Tami Lieberman
But were those pathogens acquired within the hospital or outside? Inferring the time to the most common recent ancestor reveals, that some lineages arose from a recent bottleneck during the hospital stay, while others have been colonizing the patient already before hospitalization.
October 27, 2025 at 9:25 AM
But were those pathogens acquired within the hospital or outside? Inferring the time to the most common recent ancestor reveals, that some lineages arose from a recent bottleneck during the hospital stay, while others have been colonizing the patient already before hospitalization.
Reposted by Tami Lieberman
Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it:
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
October 23, 2025 at 8:16 PM
Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it:
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...