Tami Lieberman

Last year, we proposed a model of plasmid evolution via fusion and fragmentation (via mge mediated recombination) generating mosaics, by studying historical isolates. Excited to see a MASSIVE paper from @jrpenades.bsky.social , @epcrocha.bsky.social expanding on this
www.biorxiv.org/content/10.6...

The Quickening In a paper titled “THEOREMS FOR A PRICE: Tomorrow’s Semi-Rigorous Mathematics Culture” published in 1993, mathematician Doron Zeilberger wrote: There are writings on the wall that…

Some thoughts on AI based on working on this project: Some thoughts on AI based on working on this project: liorpachter.wordpress.com/2026/02/19/t...

It’s not me, it’s you: Anti-phage nuclease specificity inside a bacterium

Very timely review; thank Alex Hong and @jbdsf.bsky.social for putting this together
journals.plos.org/plospathogen...

Scientists have seen Asgard archaea crawling for the first time. When it comes to the origin of eukaryotes, this is like seeing a feathered dinosaur in the wild. (Video courtesy of Philipp Ralder)

Key findings: Convergence follows preferred, constrained evolutionary paths. The dominant route involves acquiring conjugative IncFIB(Mar)/IncHI1B plasmids with incomplete virulence genes. Iron-scavenging (aerobactin) was the universal trait of convergence — not hypervirulence (Thanks Russo Lab!).

I just did the dumbest thing of my entire career to prove a much more serious point.

I tricked ChatGPT and Google, and made them tell other users I’m a competitive hot-dog-eating world champion

People are using this trick on a massive scale to make AI tell you lies. I’ll explain how I did it

Bacterial metabolic remodeling by convergent evolution unlocks nutrient availability after a host switch Staphylococcus aureus has undergone metabolic remodeling to adapt to the dairy niche.

Insights into how #Staph aureus adapts to the bovine host by unlocking nutrients from the dairy niche. Great work by Amy Pickering, Jamie Gorzynski and others in the group. Bacterial metabolic remodeling by convergent evolution after a host switch.|Science Advances www.science.org/doi/10.1126/...

Sign Epistasis Can be Absent in Multi-peaked Landscapes With Neutral Mutations Abstract. Fitness landscapes provide a rigorous mathematical framework for analyzing evolutionary dynamics, including the study of epistasis, the main obst

Ivankov et al. demonstrate that when neutral mutations are considered, conventional pairwise reciprocal sign epistasis may be entirely absent from a multi-peaked fitness landscape.

🔗 doi.org/10.1093/gbe/evag024

#genome #evolution

AlphaFold Database welcomes community datasets Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities

Delighted to see over 17 million new protein structure predictions from novel proteins in AllTheBacteria are now integrated into the AlphaFold Database at @ebi.embl.org !
Huge work from @gbouras13.bsky.social @oschwengers.bsky.social and friends to generate these.

www.ebi.ac.uk/about/news/u...

Demographic and genetic factors shape the epitope specificity of the human antibody repertoire against viruses - Nature Immunology Patin and colleagues present a mineable Resource database for identifying demographic and genetic factors that impact antiviral antibody repertoires in humans.

🤯
*PhiPseq of 108 health/envt variables + human genetic variation maps antibody repertoire in 1,212 adults.
*Age, sex, birth continent affect specific viral epitopes
*Abs vs variable flu epitopes decrease w/age
*Viral Abs & host genetics affect autoimmune disease risk www.nature.com/articles/s41...

pretty stunning chart

Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmica...

This is a fascinating paper that reveals defined and clear mechanism for a phenomenon that for some seemed unbelievable- the up regulation of genes paralogous to those with specific types of inactivating mutations. This is called transcriptional adaptation 1/ www.science.org/doi/10.1126/...

Systematic discovery of a topical bacterial consortium that targets Staphylococcus aureus to treat atopic dermatitis https://www.biorxiv.org/content/10.64898/2026.02.13.705787v1

Also this one soon after

An AI Agent Published a Hit Piece on Me Summary: An AI agent of unknown ownership autonomously wrote and published a personalized hit piece about me after I rejected its code, attempting to damage my reputation and shame me into acceptin…

AI agent goes nuts on open source maintainer after having its pull request denied. This is a pretty insane story. Open source development as we've been used to for the last few decades is likely over. 1/
theshamblog.com/an-ai-agent-...

Found an additional graphic that gets even more of these quotes together.

I've kept "I hate myself, I hate clover, and I hate bees" pinned above my desk since I first started studying evolutionary biology as an undergraduate. So relatable to get extremely frustrated with your study system.

New preprint from our lab led by fantastic graduate student @titas10.bsky.social, in which we retrace the emergence of antimicrobial function in the mammalian protein lactoferrin.

The moment you’ve all been waiting for…

🦠 SAVE THE DATE! 🦠

BBM2026 will be held from June 22nd - 23rd at Boston University’s George Sherman Union. Our featured speaker this year is Dr. Eric Skaar from Vanderbilt University!

Registration opens soon!

More info at: bostonbacterial.org

#BBM2026

Thrilled to share this study tracking Staph aureus carriage and transmission across the NICU using genomics! Work done w @pjplanet.bsky.social & @ahmedmicrobes.bsky.social and made possible by @centermicrobialmed.bsky.social.

Study co-led by the amazing @qianxuan.bsky.social & Lakshmi Srinivasan!

Our grad-level "Deep Learning" course (MIT's 6.7960) is now freely available online through OpenCourseWare: ocw.mit.edu/courses/6-79...

Lecture videos, psets, and readings are all provided.

Had a lot of fun teaching this with @sarameghanbeery.bsky.social and @jeremybernste.in!

Come on join us! We are searching for the next technical associate to join our lab ~Summer 2026.

This could be a great position for someone who is graduating this spring and is looking for 2 more years of research experience before starting their PhD:
careers.peopleclick.com/careerscp/cl...

Coefficients in logistic regression model based on all pairwise genome comparisons. The response is whether those genomes have at least one called horizontal gene transfer event (based on the cluster-based approach) between them or not. Co-occurrence (based on the hypergeometric approach) is a binary variable indicating whether those genomes significantly co-occur. “Free-living” and “Free-living and particle-attached” indicate whether the genomes being compared are both enriched in samples filtered to enrich for small particles, or those with little or no size filters. The other variables are ordered quantile normalized continuous values. Variables with “diff.” represent the median inter-sample difference in each environmental variable for all samples encoding the two genomes being compared. Coefficient values less than 0 indicate that decreases in those variables are associated with increases in horizontal gene transfer, whereas a positive value represents the opposite. The intercept for this model was −14.35. Error bars represent 95% confidence intervals (1.96 × standard error). All variables were significant (P values <0.05) except for “small particle enriched”.

Co-occurrence is the most important predictor of HGT, followed by phylogenetic distance. Genomes from particle-associated fractions of the water columns tend to share more genes, as do genomes sampled at similar depths, temperatures, salinity, etc. (3/n)

Another Claude project: a static site that pulls in GWAS SNP data from ensemble, multiple public biobanks, open targets, gtex, eqtl catalog, and OMIM.

sashagusev.github.io/gwas_lookup/

Deleted previous post and fixed typo

A paper about QC, precision phylogenetics, AND mutational reversion at scale???

Must read and teach to my class.

Assessing phylogenetic confidence at pandemic scales - Nature A method using subtree pruning and regrafting-based tree assessment (SPRTA), which considers evolutionary relationships between lineages, enhances interpretability of phylogenetic analyses such as tho...

For those interested in phylogenetic uncertainty, we explored the use of SPRTA. The idea is to shift from assessing confidence of clades of taxa, to instead assess whether a lineage evolved from a specific other lineage or not.

www.nature.com/articles/s41...

Awesome, congrats!!!

Data duplication reported in influential Nature paper on gut microbiome-brain axis

pubpeer.com/publications...

Trump has long wanted to weaken the dollar to boost exports. So on one hand it's a success of his policies doing what he intended-- and folks don't want to give him a win. But it's not a win, because it's a bad headline especially if he can't point at higher exports.