iiinova — where your digital self keeps evolving

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...

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Tami Lieberman @contaminatedsci.bsky.social · 06/05/2026

Dr. Indra Gonzalez Ojeda gave a great thesis defense this morning, including some wisdom for starting PhD students, or frankly, anyone.

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Tami Lieberman @contaminatedsci.bsky.social · 22/03/2026

I'm no birder and definitely not a photographer, but if you're anywhere near Delray Beach, I highly recommend visiting The Wakodahatchee Wetlands to see thousands of birds nesting in an extremely dense space and right up to the boardwalk. Sat and watched this anhinga chick feed for quite a while.

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Tami Lieberman @contaminatedsci.bsky.social · 02/02/2026

I asked Gemini to make a slide to add to my opening lecture of "Genomics and Evolution of Infectious Disease" about the Lenski lines to illustrate how bacteria's fast generation time can teach us about evolution generally. The result is funny for many reasons.

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Tami Lieberman @contaminatedsci.bsky.social · 20/01/2026

Thanks! Caught it from from hotel room in Banff thanks to your post

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Tami Lieberman @contaminatedsci.bsky.social · 12/11/2025

Northern lights once again visible from my Cambridge MA rooftop. 🤯

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Tami Lieberman @contaminatedsci.bsky.social · 10/11/2025

Excited for the 'AI4ID Symposium: Bridging Infection and Artificial Intelligence' on January 28th at the Broad Institute. The symposium will unite infectious disease researchers, clinicians, and AI experts to discuss how AI can help address the most pressing challenges in infectious diseases.

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Tami Lieberman @contaminatedsci.bsky.social · 04/11/2025

Want to make some new conceptual graphics. Tried to give Powerpoint's AI 'copilot' a spin. Asked it to make me a slide with 100 circle shape objects randomly distributed. Was excited when it made me a pptx to download... except this is what it came up with. Why can't we have nice things?

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Tami Lieberman @contaminatedsci.bsky.social · 22/09/2025

This phage is almost never a lysogen, simplifying interpretation of viral reads as well. Surprisingly, phage-sensitive C. acnes subphylogroups dominate across the globe. This is true even in samples with high virus-to-microbe ratios.

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Tami Lieberman @contaminatedsci.bsky.social · 22/09/2025

Functional screening for bacterial sensitivity to phage infection using liquid growth culture inhibition scores revealed that despite this apparent weak selective pressure, C. acnes anti-phage defense systems are active, and the primary determinant of phage resistance.

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Tami Lieberman @contaminatedsci.bsky.social · 22/09/2025

Analysis of 3,205 C. acnes genomes reveals a limited, phylogenetically restricted immune repertoire-- under no apparent pressure to diversify. Many genomes lack defense systems, and there is pervasive gene loss deep in the phylogeny— inconsistent with strong phage-driven selection.

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Tami Lieberman @contaminatedsci.bsky.social · 22/09/2025

Join us in Banff for the January 2026 Keystone Microbiome Meeting! We have a great lineup, which will occur in parallel with a special meeting on metabolism in the microbiome. The deadline for both short talks and scholarships is TOMORROW September 23rd!! www.keystonesymposia.org/conferences/...

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Tami Lieberman @contaminatedsci.bsky.social · 23/07/2025

The ancestor of this historical outbreak had a stop codon, that got reverted at least 10 times during the initial outbreak to restore O-antigen synthesis-- suggesting (1) an advantage for O-antigen synthesis during infection and (2) a relatively recent ancestor expressing O-antigen.

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Tami Lieberman @contaminatedsci.bsky.social · 21/07/2025

This is your regular reminder that the BioAnalyzer/TapeStation reports fluorescence units, not # of molecules. Left is bioA trace, and right is fragment size calculated from either read output (blue) or transformation of BioA trace (black). Fig 3 from journals.plos.org/plosone/arti...

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Tami Lieberman @contaminatedsci.bsky.social · 17/07/2025

Abstract deadline for short talks is Sep 23, but abstracts for posters will be accepted until Dec 30.

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Tami Lieberman @contaminatedsci.bsky.social · 06/07/2025

It directly admits that it's built to reflect Elon's voice AND perspectives.

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Tami Lieberman @contaminatedsci.bsky.social · 06/07/2025

Yes it gets even clearer x.com/grok/status/...

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Tami Lieberman @contaminatedsci.bsky.social · 06/07/2025

It's response to my follow up, using the word 'channeling' is pretty damning

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Tami Lieberman @contaminatedsci.bsky.social · 06/07/2025

There is a long reply thread on the original post where Grok goes in and out of first person

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Tami Lieberman @contaminatedsci.bsky.social · 01/05/2025

C. acnes is more stable, with lineages persisting for likely many years, and new colonizations occurring rarely. Strikingly, the lowest intralineage diversity is found on children at the transition to adult-like microbiome, suggesting accelerated colonization of new strains at this time. [8/10]

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Tami Lieberman @contaminatedsci.bsky.social · 01/05/2025

S. epidermidis is really dynamic, with each strain persisting for about 2 years on average. We can see this from both timeseries data and from looking at intralineage mutation accumulation (measured by dMRCA, which is then converted to time -- tMRCA). [7/10]

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Tami Lieberman @contaminatedsci.bsky.social · 01/05/2025

In terms of dynamics, we find very different behavior for each species. In these diagrams, each lineage is represented as the area between two lines, colored by whether it was acquired in early life, late childhood, or adulthood. For more on how we infer these dynamics, read on. [6/10]

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Tami Lieberman @contaminatedsci.bsky.social · 01/05/2025

We revealed commonalities across species, including: -Family members share some, but not all of their lineages. -When lineages are shared, multiple genotypes are typically transmitted, ruling out a single-cell bottleneck. This suggests limited transmission despite ample opportunity. [5/10]

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Tami Lieberman @contaminatedsci.bsky.social · 01/05/2025

We clustered isolates into lineages, which are so close to have originated from on-person diversification of a recent living individual (<100 SNVs across whole genome). As expected, each person has many lineages of both species. [4/10]

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Tami Lieberman @contaminatedsci.bsky.social · 01/05/2025

We studied strain dynamics across children at a K-8 school and their parents. We used culture-based sequencing (~96 colonies/sample!) and metagenomics to study strain dynamics of 2 species. These two species, C. acnes and S. epidermidis, comprise ~80% of adult facial skin microbiomes. [3/10]

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Tami Lieberman @contaminatedsci.bsky.social · 01/05/2025

Strain transmission and stability have been particularly hard to study in the skin microbiome, where a person can harbor many strains of a species (up to 11!). Interestingly, the facial skin is undergoes an oil-driven expansion during adolescence, which might enhance strain migration. [2/10]

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Tami Lieberman @contaminatedsci.bsky.social · 01/05/2025

Do people in the same household share strains when they have the same species? How many cells transmit when a strain is shared? Can strain composition be dynamic when species composition is stable? We answer these and related questions for the facial skin microbiome in our latest paper. 🧵[1/10]

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Tami Lieberman @contaminatedsci.bsky.social · 15/04/2025

If you're a millennial like me, you may also have the below XKCD cartoon burned into your subconscious. It delivers a clear message-- its useless to argue with folks online. I am trying to unwire this part of my brain. Moderates must also our voices, particularly around tough issues.

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Tami Lieberman @contaminatedsci.bsky.social · 04/04/2025

Since last time Trump was President

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Tami Lieberman @contaminatedsci.bsky.social · 27/03/2025

Despite what RFK says, cancer death rates have decreased significantly over the past 15 years. www.cdc.gov/nchs/hus/top... Case rates and death rates are not the same thing. The number of cases can suffer from both under-diagnosis and over-diagnosis.

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Tami Lieberman @contaminatedsci.bsky.social · 24/02/2025

Scrolling through DOGE receipts. What could go wrong with cancelling HHS contracts for Hazardous Abatement?

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Tami Lieberman @contaminatedsci.bsky.social · 11/10/2024

Got a good shot of the Aurora last night from our roof deck in Cambridge MA. Not something I thought I'd ever say.

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Tami Lieberman @contaminatedsci.bsky.social · 30/05/2024

Great day celebrating the graduation of the first two PhD students from the lab, Dr. Jacob Baker and Dr. Veda Khadka. Very proud PI.

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Tami Lieberman @contaminatedsci.bsky.social · 05/02/2024

I like how mine looks when I require a frequency of 2.

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Tami Lieberman @contaminatedsci.bsky.social · 17/12/2023

Still feeling warm and fuzzy from my labs holiday party last weekend. It's been a good year for the Lieberman Lab and more great things are just around the corner.

A gathering of the Lieberman Lab and partners crowded around a table, with folks holding their gains from a white elephant gift swap, including a mug with the PIs face on it with laser eyes.

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Tami Lieberman @contaminatedsci.bsky.social · 12/12/2023

Flying to Santa Barbara on Sunday to spend a week at KITP. This weather forecast is a practical joke just for me, right?

Beautiful weather predicted until Saturday, and then rain every day thereafter.

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Tami Lieberman @contaminatedsci.bsky.social · 29/11/2023

NYTimes leaving out an Oxford Comma is amusing

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Tami Lieberman @contaminatedsci.bsky.social · 25/08/2023

Lovely to see a Cambridge park in the NYTimes. But... Is it me, or does it appear that this carefully planted Miyawaki forest is full of Tree of Heaven (invasive species)? www.nytimes.com/2023/08/24/c...

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