Tami Lieberman

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.

The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...

Figure 1 shows they key result

Streptococcus mitis bacteriocins drive contact-dependent lysis of S. pneumoniae facilitating transformation in multispecies environments | mBio Many streptococci are naturally competent, acquiring environmental DNA through transformation. This includes pathogens like Streptococcus pneumoniae and commensals like Streptococcus mitis, which can exchange genetic material through horizontal gene transfer (HGT). For example, S. mitis can acquire pneumococcal capsules, leading to its misidentification in polymicrobial samples such as those obtained from the upper respiratory tract. Understanding the drivers of HGT between these species is therefore critical. Here, we characterize a competence-induced bacteriocin cluster in S. mitis. These bacteriocins lyse pneumococci, promoting DNA release and enhancing gene transfer in dual-species biofilms. Our findings uncover a mechanism by which competence-associated predation promotes interspecies HGT, shaping the evolution and epidemiology of streptococcal populations.

😮👀
Streptococcus mitis bacteriocins drive contact-dependent lysis of S. pneumoniae facilitating transformation in multispecies environments | mBio journals.asm.org/doi/10.1128/...

Bacteria & Constipation Noteworthy — The collaborative work of two bacterial species results in constipation.

Bacteria & Constipation

Noteworthy — The collaborative work of two bacterial species results in constipation.

New AI in genomics fellowship with the sanger institute and Google DeepMind A new research fellowship will explore the application of AI in genomics, funded by Google DeepMind.

Postdoc on AI/biology funded by asanger and DeepMind!

www.sanger.ac.uk/news_item/ne...

Meet three scientists who said no to Epstein The warning signs included a web search, a mother’s doubts, and inklings of a “sexist attitude”

This is a nice contrast to all the awful behavior confirmed through the Epstein files. Proud of @jenlucpiquant.bsky.social & @seanmcarroll.bsky.social for picking up on the sexism & charlatanism right away.

Provocative!

The example button isn't working for me.

TLDR: both studies used experimental evolution comparing single & multiple species in biofilms.

They show strong selection to inhabit diverse biofilm niches that single species can do well w/ few mutations, but multiple species can do better, with only 1-2 muts!
❤️collaborators HL Roder🇩🇰 & Moz Hoque

Collagen binding adhesin restricts Staphylococcus aureus skin infection - Nature Communications Staphylococcus aureus is able to evade host immune responses by expressing surface adhesins, like collagen binding adhesin (Cna). Here, the authors report the role of Cna during S. aureus skin infecti...

Cool new study suggesting that some Staphs use collagen binding to evade immunity on the skin, with a substantial trade-off in terms of bacterial load and disease severity. Congrats to the authors! #microsky

So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).

One of my favorite papers of past few years!

Skin androgens affect virulence of Staphylococcus aureus Nature Microbiology, Published online: 27 February 2026; doi:10.1038/s41564-026-02281-ySex-specific differences in susceptibility to skin infections with Staphylococcus aureus are well described. Testosterone now emerges as a direct modulator of the accessory gene regulator quorum sensing system, increasing S. aureus virulence, which both explains sex-specific differences and informs treatment strategies.

Out Now! Skin androgens affect virulence of Staphylococcus aureus #MicroSky

Indeed. New grants are not getting funded, already funded grants are not getting paid, and non-competitive renewals are being held up.

Focusing on the top line budget, instead of looking at what is really happening on “the ground” is deeply misguided.

🧪 This bacterial strain has been maintained in sterile water since 1994.

Possible carbon sources incl. “phthalic acid - a plastic degradation product likely leached from inoculation tubes“.

Genomic variations accumulated between 1994 and 2022 suggested adaptations to long-term nutrient deprivation

There's still time to apply to the PREP program at the University of Oregon! Deadline is March 2nd, see below for details.

Interbreeding between Neanderthals and modern humans was strongly sex biased Sex biases in admixture and other demographic processes are recurrent features throughout human evolution. For admixture between Neanderthals and anatomically modern humans (AMHs), sex bias has been p...

Many living people carry fragments of Neanderthal DNA, remnants of ancient interbreeding events, with uneven distribution across chromosomes. New work by @sarahtishkoff.bsky.social lab suggests patterns are most consistent with Neanderthal contribution to human populations being highly male biased.🧪

High-throughput analyses of a reconstituted diversity-generating retroelement identify intrinsic and extrinsic determinants of diversification Author summary Our study focuses on Diversity-Generating Retroelements (DGRs), a biological “evolution engine” that microbes and viruses use to rapidly develop new functions within specific genes. DGR...

Published version of our work on diversity-generating retroelements!

We reconstituted a phage DGR in E. coli and deployed high-throughput methods to identify factors influencing the activity of this system. #microsky

journals.plos.org/plosgenetics...

In case you missed it: our review titled "Spatial structure: shaping the ecology and evolution of microbial communities" is out! 🚨

Let me hit you with some highlights on why spatial structure matters. (and why you should care!)

Sharing is appreciated 🙏 🧵👇

doi.org/10.1093/fems...

Screening, sorting, and the feedback cycles that imperil peer review The process of peer review is vital to contemporary science, but is also under enormous strain. This study uses mathematical models to dissect the threats to the long-term viability of peer review, su...

1. Kevin Gross and I have a new paper out today PLOS Biology.

We used economic models based around screening games and the market for unpaid labor to highlight a meltdown cycle threatening peer review.

Now published: our work using phylodynamics from surveillance data to quantify and experimentally validate the fitness impact of antibiotic resistance determinants & how this changes with patterns of antibiotic use: www.nature.com/articles/s41...

Happy 38th birthday to the #LTEE!
#BOTD in 1988.
Keep on evolving!

#science #evolution #microbiology

Virus Evolution: Scaling up efforts to target evolving viruses High-throughput neutralisation tests could lead to a better understanding of the evolution of human influenza.

The final version of record of this study has been published in @elife.bsky.social alongside a nice insight perspective: elifesciences.org/articles/110...

Worth a read and something I was thinking about this morning!

(𝘌. 𝘤𝘰𝘭𝘪, not elephant) chromosome replicationists take note 👇

A set of genetic tools for use in Clostridioides difficile and related species The Clostridia are a phylogenetically diverse group of anaerobic, spore-forming bacteria that include species of medical, veterinary and industrial importance. The last two decades have seen major adv...

New paper alert! A toolbox of genetic tools for use in Clostridia, made available to the community. @microbiologysociety.org @robfagan.bsky.social www.microbiologyresearch.org/content/jour...

Setting higher standards for reports of microbial species in human cancers Nature Cancer - Nagarajan and colleagues overview the current challenges in microbiome analyses from human cancer samples and discuss the optimal practices for improving the standards of reporting...

🎆Very excited to share our perspective piece calling for higher standards in reports on microbial detection in cancers! It was great to put this together with some of the leaders in the field including @stevensalzberg.bsky.social @rafalab.bsky.social Barry Marshall and Eske Willerslev: rdcu.be/e4IaU

Is there recombination with other strains in your system?
Would be happy to chat at length anytime.

This is a very surprising graph. Would be interested to know more about the experiment

4/5) This is the true hidden killer: classic dN/dS tests are very sensitive to positive selection in weakly constrained, fast evolving immune genes. At the same time, the inflation of PN due to likely ongoing balancing selection in the same genes kills the power of MK test to detect excess of DN.

To add one thing: if you have the data to run both classic dN/dS tests and MK tests, choose the latter. dN/dS tests are blind to positive selection in the important, constrained proteome, while MK test will work regardless of constraint, if DFE well estimated.
#evolution #adaptation #popgen