Tami Lieberman

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...

The ERC Starting Grant numbers are out. With a staggering 60% increase in applications and a 15% reduction in funding volume, the success rate drops to an all time low of 5%. That number should be a warning to both future applicants and the @erc.europa.eu. 1/9 erc.europa.eu/news-events/...

Happy World Phage Day to all who celebrate... ... delighted to share new work led by Jacopo Marchi, Chadiga Khalek & joint w/Remy Chait on stable coexistence of phage with migrating bacteria driven by the forces of infection, lysis, and chemotaxis. A 🧵 at the interface between known & unknown.

Here are just a few papers for those who want to explore: Bacterial escape from phage www.science.org/doi/10.1126/... Lysis time variability in plaque expansion journals.plos.org/ploscompbiol... Irregular fronts & phage lysis of motile bacteria www.nature.com/articles/s42...

Over time we learned more (and more to come) about how chemotaxis drives bacteria forward, and how by killing bacteria in the center, the phage leave a zone of relatively high nutrients & chemoattractants. Bacteria migrate to this zone, and yet, it is a (moving) trap.

Tweet from the Minister of Health of Nigeria on the recent travel-associated BVD case. Fantastic work from all countries and institutions involved - phylogeeks will know what the clustering means, but I'll let the relevant authorities report on that.

Bar-Ilan University researchers found that antibiotics can directly alter immune function, even without gut bacteria. In mice, vancomycin changed feeding behavior, disrupted biological clocks, and suppressed immune-related gene expression in the colon. www.nature.com/articles/s41...

Okay this one’s gonna be controversial. In our new preprint, we show that the canonical #Klebsiella pneumoniae 🦠 virulence factors and strain lineage are decoupled from infection severity and patient outcomes. This was a surprise to us #IDSky #KlebClub #MicroSky 🧪 www.medrxiv.org/content/10.6...

We have had a Bose Soundtouch for 7+ years and Bose discontinued our favorite feature -- 6 easy to program preset buttons you could play without your phone or a voice assistant. In case anyone else is going through the same pain -- the STR app completely restored this functionality. st-reborn.de

I hate to do this with real data, but this is a persistent data vis issue in chromosome synteny riparian plots that we Need to get better at. Left, a synteny plot published today. Right, a rearranged version with exactly the same gross arrangement but with reordered chromosomes:

Viruses have parasites too. Our new preprint shows how phages use VIPR to silence parasitic satellites, and how the satellites fight back with its own decoy VIPR RNAs that redirect VIPR to DNA REP elements in the host genome!! www.biorxiv.org/content/10.6...

'Vibe-coded alternatives for Adobe products are surprisingly good' www.xda-developers.com/tried-replac...

A consensual relationship between someone one has mentorship responsibilities over is against MIT policy-- making any of Knouse's statements irrelevant and the damages awarded here ridiculous. I hope justice is found on appeal. I didn't follow the case, but this seems like a legal team failure.

There are two open faculty searches in IMES at MIT (the Institute for Medical Engineering and Sciences)! 1) Computational/ML/AI methods in healthcare, joint with EECS faculty-searches.mit.edu/eecs-imes-se... 2) An open search in biomedicine or bioengineering. faculty-searches.mit.edu/imes-search/

This is like something from a crime novel. Criminals bought lots of the very secure USB-like Ledger devices which are used for password storage, added their own password reading components and then put them back into circulation. They then hacked them all in one go www.ft.com/content/70f6...

1/1 How does a single methyl group activate bacterial defence? In my PhD work with @matthiaswilmanns.bsky.social and @typaslab.bsky.social, we reveal how this tiny DNA modification triggers retron disassembly and toxin activation. Now on bioRxiv: www.biorxiv.org/content/10.6...

LoL-align is out in @natmethods.nature.com! It aligns protein structures without superposition. More sensitive than TM-align and DALI, producing better alignments 5–20× faster. Now available in Foldseek! 📄 www.nature.com/articles/s41... 💾 github.com/steineggerlab/foldseek 🌐 search.foldseek.com

Version 1.3.2 of PearTree released: github.com/artic-networ... Fixes many of the remaining niggling bugs. WebApp updated at peartree.live

Skani (github.com/bluenote-157...) is now v0.4.0! Big performance update: **~2.5x faster** and ~30-40% less RAM for average nucleotide identity (ANI) comparison of genomes. The database format has changed (breaks forward compatibility; watch out!).

Glycosylation is among the most important modifications in biology. We know relatively little about glycobiology, because it is hard to study. This Nat Rev Methods primer describes our best tools for analyzing glycosylation 🔽

5/5 We don’t yet know the mechanism. But the lesson is simple: a fluorescent reporter calibrated in one physiological condition cannot automatically be assumed quantitative in another. Preprint: www.biorxiv.org/content/10.6...

How fast can speciation be? In less than 100 years, certain strains of lab mice have already (partly) lost the ability to hybridize with each others. The molecular mechanism has just been worked out - read below for a genetics detective story ⬇️

Johns Hopkins Biology is hiring a tenure-track Assistant Professor in computational genetics and genomics. Applications due Nov. 8th: apply.interfolio.com/194924 In my experience, this has been an incredibly supportive environment to build a lab. Please feel free to reach out with any questions.

Our paper on detecting (or not) balancing selection is now out, in all its typeset beauty, in the October issue of @molbioevol.bsky.social: academic.oup.com/mbe/article/...

Our new preprint is out! We show that genomically discrete and ecologically cohesive subspecies are a common feature in the global ocean microbiome, and represent a fundamental level at which ecological and evolutionary forces act to shape microbial diversity www.biorxiv.org/content/10.6...

Apply to be my colleague! UW Genome Sciences is hiring two new faculty: one open rank, one assistant. GS is tight-knit, collaborative, and interdisciplinary, with strong PhD students. The search is wide open in terms of research areas (I'm on the search committee). ap.washington.edu/ahr/position...

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. 🧵

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

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! 🔬

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! 🧫🧪🦠

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

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...

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

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...

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

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!

🧬 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....

Come work with us!

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.

Now online! Direct cell-to-cell transmission of retrotransposons

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