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Tami Lieberman

@contaminatedsci.bsky.social
5.2K followers 856 following 1.1K posts

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

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Reposted by Tami Lieberman
Saria McKeithen-Mead, PhD @sciria.bsky.social · 05/10/2026
Pleased to share my first preprint from my postdoc, where I ask what drives mobile DNA movement between bacterial cells in complex communities like the gut microbiome. To answer this, we built a way to capture mobile DNA in the act of moving between cells, using short-read metagenomics. 🧵
doi.org
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Dave Baltrus 🦦 @surtlab.bsky.social · 05/10/2026
In case you hadn’t heard, the lab acquired case is an incredible and sad story The researcher working w/ attenuated strain at BSL2. Strain attenuated by disabling ability to acquire sufficient iron in hosts The researcher unknowingly had rare genetic disorder where their body had >iron levels
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Florent Waltz @florentwaltz.bsky.social · 05/10/2026
Huge congratulations to all three Nobel Laureates, and especially Peter Hegemann! 👏 His seminal work on the green alga Chlamydomonas 🦠 laid the foundation for optogenetics. Thank you for putting Chlamy in the spotlight! ✨ Proof that groundbreaking discoveries don't always come from animal models! 🔬
Chlamydomonas cells
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Brett Baker @archaeal.bsky.social · 02/10/2026
Two Assistant Professor Positions in Evolutionary Biology and Mechanistic Processes - including microbes! faculty.utexas.edu/career/191568
faculty.utexas.edu
Faculty Careers - The University of Texas at Austin
Unleash your intellectual power by joining a world-renowned faculty that is solving the world's most urgent problems. At UT Austin, we provide you the freedom to blaze trails, follow your curiosity, e...
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Prof. Ruth Ley FRS @microbiome.bsky.social · 14/09/2026
It’s more like an assistant professorship actually, without the possibility of tenure. But it’s 6 to 9 years of funding without teaching so great for those who want a pure research opportunity. Add grants on top! 🧫🧪🦠
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Rebecca Sear @rebeccasear.bsky.social · 04/10/2026
Interesting read: anthropology’s problem is that perceptions of the issues it tackles, including race and gender, have changed. Anthropology itself has contributed to this problem by retreating both from “plain English” and public communication
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Don Moynihan @donmoyn.bsky.social · 02/10/2026
Unless Congress reclaims its power, this will just become the new normal. A good first step would be to impeach Vought. www.nytimes.com/2026/10/02/u...
nytimes.com
National Science Foundation Diverted $1.4 Billion in Science Funds Mandated by Congress
The move, affecting about one-fifth of the National Science Foundation’s primary research budget, is the latest sign of how the White House is asserting more control over grants.
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Tami Lieberman @contaminatedsci.bsky.social · 02/10/2026
Thanks for giving it a whirl! AccuSNV was designed for calling variants with extremely high precision as present *or absent* in each strain, even with low coverage -- with phylogenetic construction in mind. I've not found a way to do this super well yet with indels.
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Reposted by Tami Lieberman
Michael Hickerson @hickerlab.bsky.social · 01/10/2026
How much of the tree of life did you eat? Phylodiet scores a meal by phylogenetic diversity: type what you ate and it builds the dated tree of the organisms in it, from ~3,300 edible eukaryotes, back 2 billion years. Last night's dinner, below. 🧵 mjhickerson.github.io/phylodiet/app/phylodiet.html
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Tami Lieberman @contaminatedsci.bsky.social · 01/10/2026
Related: www.nature.com/articles/s41...
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Sean Gibbons 🦠💩 @gibbological.bsky.social · 30/09/2026
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
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Emma Strubell @strubell.bsky.social · 30/09/2026
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.
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Tami Lieberman @contaminatedsci.bsky.social · 30/09/2026
Awesome!!!
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Tami Lieberman @contaminatedsci.bsky.social · 29/09/2026
Reading your syllabus is inspiring, Nick, thanks for sharing
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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
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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!
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Tami Lieberman @contaminatedsci.bsky.social · 25/09/2026
Can you give a good example? I am trying to think about teaching my genomics course in light of Claude code and looking for good examples.
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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...
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Maria Rebolleda-Gomez @mrebolleda.bsky.social · 24/09/2026
Come work with us!
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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.
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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.
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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...
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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.
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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...
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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.
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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...
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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
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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
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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.
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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
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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.
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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.
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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.
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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!
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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.
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Tami Lieberman @contaminatedsci.bsky.social · 16/09/2026
Several folks I know left the editorial board, and presumably stopped submitting there, because of the firing Eisen.
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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.
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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...
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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
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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
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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
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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.
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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.
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Tami Lieberman @contaminatedsci.bsky.social · 08/09/2026
That being said you can get good data (1) you're dealing with a very clonal sample, like from experimental evolution, and (2) you have deep sequencing of the initial clone to mask out problematic sites.
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Tami Lieberman @contaminatedsci.bsky.social · 08/09/2026
Not currently! Its very hard to avoid false positives. I built a snv calling for population sequencing back in 2014, and since then have focused on clones because false positives are hard to avoid (and give more information)
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Tami Lieberman @contaminatedsci.bsky.social · 08/09/2026
Bonus life update who those who read this far -- this publication announcement is a bit delayed because I was on maternity leave this summer, spending time getting to know our first child.
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Tami Lieberman @contaminatedsci.bsky.social · 08/09/2026
We hope this inspires more groups to sequence large (10s-1000s) of microbial isolates -- knowing that you can easily call mutations without laborious filtering and perform evolutionary analyses in the same toolbox.
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Tami Lieberman @contaminatedsci.bsky.social · 08/09/2026
The latest usability updates are the heroic work of @acritschristoph.bsky.social, who joined the work this summer, with great feedback and collaboration from the original authors of the manuscript and members of the lab and a little additional help from Claude Code.
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Tami Lieberman @contaminatedsci.bsky.social · 08/09/2026
AccuSNV has really been a game changer in my lab -- the combination of the CNN filter and usability improvements by Herui and colleagues really made SNV calling a simple step rather than an art to learn for new students. These new updates make it super easy for any microbiologist to get started.
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Tami Lieberman @contaminatedsci.bsky.social · 08/09/2026
Check out the awesome read the docs here: accusnv.readthedocs.io/en/latest/ And the paper here: genome.cshlp.org/content/earl... Github here: github.com/liaoherui/Ac... Downstream analyses can be refined using either command line or notebook options.
accusnv.readthedocs.io
AccuSNV — AccuSNV documentation
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