Sign in

Tami Lieberman

@contaminatedsci.bsky.social
5.2K followers 854 following 1.1K posts

Associate Professor, MIT Still thinking about the 10^9 mutations generated in your microbiome today. Website: lieberman.science

PostsRepliesMedia
Reposted by Tami Lieberman
Sean Gibbons 🦠💩 @gibbological.bsky.social · 10h
Congrats to @mmmicrobiomelab.bsky.social and the @globalmicrobiome.bsky.social for their well-deserved inclusion in the TIME 100 Most Influential Rising Stars! 🤩 Amazing scientists and wonderful humans. 🦠⚕️🌍 time.com/collection/t...
time.com
Mathilde Poyet and Mathieu Groussin Is on the 2026 TIME100 Next
Find out why Mathilde Poyet and Mathieu Groussin is on this year’s list
182
Reposted by Tami Lieberman
Emma Strubell @strubell.bsky.social · 6h
CMU Miami will be built from the ground up as a politically conservative institution, a response to the lack of "viewpoint diversity" (representation of conservative viewpoints) in higher ed that the ("center") right has been complaining about for years.
153
Reposted by Tami Lieberman
Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
Our latest, spearheaded by the truly indefatigable @emderrick.bsky.social in which we search for selective sweeps in nature and genetic targets of selection within a species in the context of a diverse background community @isme-microbes.bsky.social doi.org/10.1093/isme... 🧵 1/n
doi.org
Validate User
43822
Reposted by Tami Lieberman
noam @prywes.bsky.social · 27/09/2026
This is such a great piece of work about an amazing evolutionary story, every part of this is incredible. Congrats @rudycadenabioevo.bsky.social @evanowack.bsky.social Among other surprises, oxygen scavenging instead of photorespiration is not something I was expecting!
093
Reposted by Tami Lieberman
Ezequiel Galpern @eag91.bsky.social · 25/09/2026
🧬 What do deep-learning models for proteins actually learn? Our new review looks at how model predictions relate to fitness, folding stability and function. With @cwjpugh.bsky.social, Mafalda Dias & @jonnyfrazer.bsky.social 🔗 chemrxiv.org/doi/full/10....
chemrxiv.org
From sequences and structures to fitness, folding and function: challenges in the age of AI | ChemRxiv
Deep-learning models have transformed our ability to predict the phenotypic effects of sequence perturbations. Protein language models (pLMs) score the evolutionary propensity of any amino-acid substi...
177
Reposted by Tami Lieberman
Maria Rebolleda-Gomez @mrebolleda.bsky.social · 24/09/2026
Come work with us!
014
Reposted by Tami Lieberman
Maitreya Dunham @maitreya.bsky.social · 24/09/2026
Exciting news: @uwgenome.bsky.social will be hiring for two tenure-track faculty positions this year, one open rank and one assistant professor. Both are “Genome Sciences” interpreted broadly so we welcome applicants working in a variety of fields and methods. Ad will be out shortly.
110498
Reposted by Tami Lieberman
Cell - a Cell Press journal @cp-cell.bsky.social · 23/09/2026
Now online! Direct cell-to-cell transmission of retrotransposons
dlvr.it
Direct cell-to-cell transmission of retrotransposons
Retrotransposons can infect neighboring cells using a mechanism that relies on a small fusogen-like protein rather than on the envelope protein that is typically required for infection.
28037
Reposted by Tami Lieberman
Ben de Bivort @debivort.bsky.social · 22/09/2026
Hello friends, the Harvard Life Science departments have banded together to hire a new colleague working at the intersection of Life Sciences and AI. Could be primarily an experimentalist, or could be primarily a compute/theorist. academicpositions.harvard.edu/postings/16773
academicpositions.harvard.edu
Tenure-Track Professor in Life Science and AI
The Life Sciences Departments in Harvard Faculty of Arts and Sciences seek to recruit a tenure-track professor whose research is at the interface of AI and life sciences, from methodological developme...
34051
Reposted by Tami Lieberman
Anthropic @anthropic.extwitter.link · 23/09/2026
Claude has discovered a previously unknown enzyme system hidden in the DNA of bacteriophages. Beside the enzyme’s gene sits a long array of repeating DNA—a structure that looks somewhat similar to CRISPR. We don’t yet understand what this system does, but only a handful of known systems share it...
anthropic.com
Claude discovers a novel enzyme system with CRISPR-like repeats
Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.
1117
Reposted by Tami Lieberman
Tatta Bio @tattabio.bsky.social · 23/09/2026
In our preprint released last Friday, we show that evolutionary sequence information learned by our genomic language model, gLM2, can be used to design complex, multi-domain enzymes and expand their chemistry beyond their natural repertoire. 🧵 Preprint: www.biorxiv.org/content/10.6...
biorxiv.org
Generative Design of New-to-nature Biosynthetic Assembly Lines with Genomic Language Modeling
Reprogramming biosynthetic assembly lines can extend biosynthesis beyond the chemical space explored by nature. However, this remains difficult because assembly-line function depends on coordinated in...
143
Reposted by Tami Lieberman
Joshua Weitz @joshuasweitz.bsky.social · 01/09/2026
As we show, biphasic decay means that high viral abundances can be maintained through infrequent yet durable persistence rather than continual cycles of rapid virus production and decay... it also means that using viral density alone can lead to over-estimates of viral-induced mortality.
111
Reposted by Tami Lieberman
Martin Pacesa @martinpacesa.bsky.social · 21/09/2026
ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...
4292140
Reposted by Tami Lieberman
David Bikard @dbikard.bsky.social · 21/09/2026
New paper from the lab, out in Nature Microbiology. We ran CRISPRi screens to ask what genes E. coli needs in order to live in a gut and what this can tell us about the gut environment itself. doi.org/10.1038/s41564-026-02471-8
311155
Reposted by Tami Lieberman
Vivek Mutalik @vivekmutalik.bsky.social · 19/09/2026
Some of the smallest 😎 viruses on Earth are all around us. Three or four genes 😍 each, in nearly every environment. We keep finding thousands by sequencing, yet don't know who they infect, can't easily isolate them, or even how the few we have infect a cell. Our new preprint takes this on 🧵👇
Schematics of how single strand RNA and DNA phages infect bacteria with F-pilus
513455
Reposted by Tami Lieberman
Brooke Harrington @ebharrington.bsky.social · 18/09/2026
When I tell you this is one of the most riveting, concise and accurate depictions of the catastrophically defective thought processes behind Effective Altruism and the larger Broligarch Epistemic Universe... Run, don't walk, to read the whole thing (link below), which concludes thus:
Example of the problematic thinking behind Effective Altruism.
7344112
Reposted by Tami Lieberman
Pat Schloss @patschloss.bsky.social · 18/09/2026
Let me get this straight. There's a title. There's a commentary article. There's an abstract. There's a set of bullet point highlights. There's a graphical abstract. AND YOU STILL THINK I NEED YOUR AI AGENT TO SUMMARIZE THE ARTICLE FOR ME?
AI BS from Cell
06921
Reposted by Tami Lieberman
Pedro Beltrao @pedrobeltrao.bsky.social · 18/09/2026
Hive mind science via RL on user sessions. This is a discussion point that will keep coming back. They need to be clearer about what is being used for training.
243
Reposted by Tami Lieberman
Sergey Ovchinnikov @sokrypton.org · 18/09/2026
I do sometimes wonder how much of these improvements are actually coming from us? During my own optimizations with claude in the last year or so, eachtime claude asked if i was willing to share my session transcript, I always said yes.
1193
Reposted by Tami Lieberman
Pedro Beltrao @pedrobeltrao.bsky.social · 18/09/2026
Anthropic has used Claude to optimise structure prediction and design code to improve speed and memory efficiency. 2-3X speed improvements on AF3, 5X on OF3, 5X on BindCraft low memory modes to model large assemblies. All released as open source www.anthropic.com/research/cla...
anthropic.com
How Claude is uplifting biomolecular modeling
Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.
55517
Reposted by Tami Lieberman
Malte Rühlemann @malte.ruehlemann.io · 17/09/2026
Interesting article on how different strains of the same species use different strategies to adapt to the intestinal environment. Additionally: extremely nice visual presentation and lovely color palette!
094
Reposted by Tami Lieberman
Claus Wilke @clauswilke.com · 15/09/2026
The Department of Integrative Biology at UT Austin has two open positions for assistant professors, one in evolutionary biology and one in mechanistic processes. Please share. Apply here: apply.interfolio.com/193270
Two Assistant Professor Positions in Evolutionary Biology and Mechanistic Processes

Description
The Department of Integrative Biology at The University of Texas at Austin seeks to fill two faculty positions in the areas of Evolutionary Biology and Mechanistic Processes, broadly defined. We are looking for candidates who are advancing (1) evolutionary biology or (2) the mechanistic understanding of organismal processes. These positions will be filled at the level of Assistant Professor.


Qualifications
Candidates should be using innovative approaches in evolutionary biology and/or the mechanistic understanding of whole-organism processes. Mechanistic processes include, but are not limited to, behavior, biomechanics, cognition, physiology, and development. The phylogenetic scope of the Evolutionary Biology position may include eukaryotes, prokaryotes, viruses, and the scale may include individual molecules to entire ecosystems and beyond. Candidates for either position may employ experimental, theoretical, or computational frameworks, or a combination thereof. Special consideration will be given to applicants with demonstrated potential for integrating across our target disciplines. 

We seek applicants with a strong record of high-quality research, publications, potential for extramural funding, and a commitment to excellence in teaching and mentorship. A PhD or equivalent is required at the time of appointment, and postdoctoral research experience is strongly recommended.
05483
Reposted by Tami Lieberman
Nature Microbiology @natmicrobiol.nature.com · 16/09/2026
Out Now! Prophage-encoding engineered bacteria enable prophylactic lytic phage therapy for enteric infection in mice #MicroSky
go.nature.com
Prophage-encoding engineered bacteria enable prophylactic lytic phage therapy for enteric infection in mice
Nature Microbiology, Published online: 16 September 2026; doi:10.1038/s41564-026-02484-3An engineered non-pathogenic bacterium produces lytic phages and is protective in mouse models of Salmonella infection.
02816
Reposted by Tami Lieberman
Will Ratcliff @wcratcliff.bsky.social · 15/09/2026
1/17 Submissions are now open for the 2027 Microbial Population Biology GRC! We expect this meeting to be extraordinarily oversubscribed. If you want to come, time is of the essence--apply ASAP! June 27–July 2 • Andover, NH www.grc.org/microbial-po...
310369
Reposted by Tami Lieberman
Michael Baym @baym.lol · 13/09/2026
Ten years ago Tami, Roy, and I released a movie we made of antibiotic resistance evolving in real time. I thought maybe a couple thousand people tops would see it. I couldn't have imagined it would be seen millions of times, and be taught from middle school through the graduate level worldwide
23436127
Reposted by Tami Lieberman
Evgeny Kvon @evgenykvon.bsky.social · 24/08/2026
The newly established Department of Systems Biology (systems.bio.uci.edu) @UCIrvine is hiring a tenure-track Assistant Professor in Systems Biology. Great science, incredible faculty support, and beautiful, sunny SoCal weather! ☀️🌴 Details: recruit.ap.uci.edu/JPF10377. Please share.
recruit.ap.uci.edu
12936
Reposted by Tami Lieberman
Sean Gibbons 🦠💩 @gibbological.bsky.social · 10/09/2026
Hello, NYU! engineering.nyu.edu/news/new-pro...
engineering.nyu.edu
New Professor Sean Gibbons Explores the Hidden World of the Human Microbiome | NYU Tandon School of Engineering
2455
Reposted by Tami Lieberman
Harmit Singh Malik @harmitmalik.bsky.social · 10/09/2026
Reposting this ongoing search (any discipline of biology) for an Assistant to Associate level colleague in the Division of Basic Sciences at Fred Hutch. Great city, great colleagues, great core facilities, great trainees.
16468
Reposted by Tami Lieberman
Benjamin Wolfe @benwolfe.bsky.social · 09/09/2026
One question that we are often asked: are warmer temperatures playing a role in the emergence of this toxic mold in cheese caves? We are working on this! But my inclination is that extreme temperature events could be providing favorable conditions for this mold to establish in cheese caves.
171
Tami Lieberman @contaminatedsci.bsky.social · 08/09/2026
Two announcements regarding AccuSNV, which calls high precision SNVs across microbial genomes: Version 1.1 is now incredibly easy to install, run, and perform downstream analyses with (see image of typical output!). The manuscript was also published this summer in Genome Research! Links next...
15321
Reposted by Tami Lieberman
Paul Rainey @paulbrainey.bsky.social · 07/09/2026
A beautiful piece of detective work by @honour.bsky.social + colleagues revealing the origins of Ralstonia disease of bananas on Martinique. As so often, ICEs (ICERs!) prove to be extraordinary capacitors for evolutionary change. Evolution for evolution's sake 🤔 doi.org/10.1093/gbe/...
doi.org
Interspecies Exchange of Mobile Genetic Elements During a Plant Disease Outbreak
Abstract. Outbreak sequencing provides insight into the origin and evolutionary processes acting on emerging pathogens. Sequencing a historic multihost out
16527
Reposted by Tami Lieberman
Nigel Goldenfeld @nigelgoldenfeld.bsky.social · 06/09/2026
In our work agents develop the ability to trust differentially other agents based on the outcome of their decisions. A complex society and hierarchy can emerge. It is not mandatory. There is a phase diagram based on the interactions between agents. These can be tuned to avoid collectivism!! 🧪⚛️
062
Reposted by Tami Lieberman
Alex Crits-Christoph @acritschristoph.bsky.social · 06/09/2026
Transferable genetic toolsets for nonmodel gut Clostridia enable in vivo reversible control of metabolite production www.nature.com/articles/s41... A nice update to the Jin et al. 2022 paper from Chun-Jun Guo: now with many promoters for gut clostridiales, screened from native metatranscriptomes:
0115
Reposted by Tami Lieberman
Nick Stroustrup @nstroustrup.bsky.social · 05/09/2026
Demographically, acceleration of Pol II degradation looks exactly like aging: it produces a temporal rescaling of the entire survival curve. Rescaled hazard trajectories superimpose, suggesting that Pol II declines can set the rate of aging itself. 17/22
1113
Reposted by Tami Lieberman
Nick Stroustrup @nstroustrup.bsky.social · 05/09/2026
The effect is fairly dramatic in both nematodes and mice. For example: a young adult nematode (equivalent to a teen-ager) contains ~700 million mRNA molecules total. This drops eight-fold by old-age. 3/22
1217
Reposted by Tami Lieberman
John McEnany @johndmcenany.bsky.social · 05/09/2026
Just preprinted my work on rapid evolution in fluctuating environments! When many linked mutations with different environmental tradeoffs compete, I found that mutations with stronger tradeoffs systematically outcompete beneficial “generalist” mutations. Read more here: doi.org/10.64898/202...
doi.org
23010
Reposted by Tami Lieberman
Molecular Biology and Evolution @molbioevol.bsky.social · 04/09/2026
Anker et al. analyzed >123,000 SARS-CoV-2 genomes from the UK's COVID-19 Infection Survey, demonstrating that failing to mask artifactual sites can lead to erroneous downstream conclusions. 🔗 academic.oup.com/mbe/article/... #societyjournal #covid #sarscov2
132
Reposted by Tami Lieberman
Anton Goloborodko @golobor.bsky.social · 03/09/2026
1/ out in @science.org! We found a new asymmetry in large-scale chromosome structure: sister chromatids are shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! A close collaboration w/ @gerlichlab.bsky.social , led by @flaviacorsi.bsky.social www.science.org/doi/10.1126/...
215263
Reposted by Tami Lieberman
anna brogan @apbrogan.bsky.social · 18/08/2026
This is now published! For those interested in microbial mechanotransduction: www.cell.com/current-biol...
cell.com
Microbial GAIN domains undergo autoproteolysis and enable release of diverse cell-surface-associated proteins
Brogan and Rudner report the identification of a microbial autoproteolytic domain that is structurally homologous to the GAIN domain of eukaryotic adhesion GPCRs. Rather than participating in transmem...
13921
Reposted by Tami Lieberman
Roby Bhattacharyya @roby-b.bsky.social · 29/08/2026
Still curious if anyone's had to fight to justify insurance coverage for inpatient admissions when switching early from IV to PO antibiotics... of all the barriers to the early oral switch, this was one I hadn't encountered before, until yesterday #IDSky
1102
Reposted by Tami Lieberman
Alvaro Sanchez @asanchezlab.bsky.social · 21/08/2026
New preprint from the lab: The Latent Simplicity of Microbial Ecological Interactions www.biorxiv.org/content/10.6... We're excited about this one. We find that high-order microbial interactions often obey simple linear laws making microbial communities far more predictable than one might expect
36932
Reposted by Tami Lieberman
Alvaro Sanchez @asanchezlab.bsky.social · 21/08/2026
The most surprising consequence is that presence/absence remained highly predictive of community function even after 10days of population dynamics. Communities moved far from their initial abundances, yet knowing which species were present at the start predicts community biomass at equilibrium!
111
Reposted by Tami Lieberman
Jamie Cate @jhdcate.bsky.social · 27/08/2026
Ribosomes have a strange protein modification in a universally-conserved protein uS11. This modification, isoaspartate, is also conserved in nearly all forms of life. We originally found this modification using cryo-EM, but had no idea how it was formed. 1/ elifesciences.org/articles/60482
elifesciences.org
Structure of the bacterial ribosome at 2 Å resolution
High-resolution maps and models of the bacterial ribosome provide new chemical insights into protein synthesis, and should enable the development of robust tools for cryo-EM structure modeling and ref...
26122
Reposted by Tami Lieberman
STCmicrobeblog @stcmicrobeblog.bsky.social · 27/08/2026
ah, the ocelloid 🧿 already in 2015, Elio was thrilled by it... sure we will study this 👇 with great interest(we also have eyes) #ProtistsOnSky
smallthingsconsidered.blog
The Awe­somest Thing in Bi­ol­ogy
by Elio — So says a blogger by the name of Psi Wavefunction regarding an eye-like structure of some protists called the ocelloid. She wrote this in a now defunct blog eponymously called 'The Ocell…
081
Reposted by Tami Lieberman
Joshua Weitz @joshuasweitz.bsky.social · 25/08/2026
NSF just announced its GRFP solicitation due in October - deadline varies by field: www.nsf.gov/funding/oppo... Now for the bad news... * NSF estimates they will issue 1,500 awards, down from 2,500+ last year. * NSF removed STEM Education and Learning Research as a Major Field.
nsf.gov
NSF Graduate Research Fellowship Program (GRFP)
6139169
Reposted by Tami Lieberman
Hiten Madhani @hitenmadhani.bsky.social · 27/08/2026
Most basic science departments at UCSF are having faculty searches this year. Biochemistry & Biophysics, Microbiology & Immunology, Cellular and Molecular Pharmacology, Physiology and more. We're looking for new and exciting science and nice people. You'll find them all at aprecruit.ucsf.edu
aprecruit.ucsf.edu
Welcome - AP Recruit
University of California, San Francisco Online Faculty Recruitment
311696
Reposted by Tami Lieberman
Erik van Nimwegen @erikvannimwegen.bsky.social · 21/08/2026
Remember this? bsky.app/profile/did:... Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social With help of the reviewers of Nat Biotech it is now updated, extended an officially published here: www.nature.com/articles/s41... 1/n
nature.com
Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature Biotechnology
High-dimensional data are visualized through representation on tree structures.
110446
Reposted by Tami Lieberman
Sebastian Baumgarten @sebbaumgarten.bsky.social · 19/08/2026
The singular job of all known ribosomes: synthesizing protein. Enter the malaria parasite. In our new work, we show that Plasmodium evolved an entire new kind that does just the opposite - inhibit mRNA translation. www.biorxiv.org/content/10.6...
biorxiv.org
18439
Reposted by Tami Lieberman
Molecular Biology and Evolution @molbioevol.bsky.social · 26/08/2026
🎥 Sakalli et al. present Phylo-Movies, a browser-based tool that decomposes topological differences between consecutive phylogenetic trees into interpretable rooted subtree prune-and-regraft moves and animates these transformations. 🔗 academic.oup.com/mbe/article/... #societyjournal #compbio
0177
Reposted by Tami Lieberman
Noah Houpt @noahhoupt.bsky.social · 25/08/2026
Thrilled to see this project officially published in ISMEJ! We showed that filamentous prophages frequently acquired repressor mutations causing hyperactivity which, in turn, drove the evolution of phage resistance with pleiotropic consequences. academic.oup.com/ismej/advanc...
academic.oup.com
Mutations in filamentous bacteriophages spark eco-evolutionary feedbacks in Pseudomonas aeruginosa
Abstract. Microbial populations strongly shape their environment, which can re-route adaptation toward organism-generated fitness optima. However, the cond
14313