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Ira Zibbu

@coolscootre.bsky.social
115 followers 140 following 85 posts

Evolution enthusiast/ Computer Nerd/ Molecular wizard-in-training. PhD student watching 80,000 generations of bacterial evolution @ Barrick Lab, Michigan State University. Enjoyer of all things post-modern and in the zeitgeist.

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Reposted by Ira Zibbu
Simons Foundation @simonsfoundation.org · 22h
We're committing $23M over 5 years to support research excellence at HBCUs through two new grants: the HBCU Centers of Excellence Program and the HBCU Faculty Fellowship Program. Now accepting applications: bit.ly/4zu6OdB #science #math #funding
bit.ly
Apply Now: New Grants to Support HBCU Faculty and Research Excellence
Apply Now: New Grants to Support HBCU Faculty and Research Excellence on Simons Foundation
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Ira Zibbu @coolscootre.bsky.social · 30/09/2026
I was once pulled up to an intersection on my bike and a man rolled his window down from his car and told me I shouldn't be in that lane but instead in the bike lane. Ladies and gents there is no bike lane in that 50ft stretch on northbound Abbot Rd south of Saginaw in East Lansing.
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Ira Zibbu @coolscootre.bsky.social · 29/09/2026
Ah, the age old question: do grades matter for graduate school applications and beyond? No. But also yes. irazibbu.substack.com/p/do-grades-...
irazibbu.substack.com
Do Grades Matter for Graduate School?
Short answer: No. But also yes.
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Ira Zibbu @coolscootre.bsky.social · 24/09/2026
I'm so excited!!
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Reposted by Ira Zibbu
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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Reposted by Ira Zibbu
Jesse Raab @jraab.bsky.social · 24/09/2026
Can't decide if this is hilarious or depressing substack.com/home/post/p-...
substack.com
Opinion: I Miss When The NIH Payline Was 40% And We All Mouth-Pipetted Phenol
By Dr. Douglas R. Waverly, Professor Emeritus of Biochemistry, Yale University
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Ira Zibbu @coolscootre.bsky.social · 24/09/2026
www.asimov.press/p/theory-bio...
asimov.press
On the Role of Theory in Biology
Biology is often seen as an experimental science, with theory serving to generalize patterns from empirical data. But history reveals that theory plays a more generative role in discovery itself.
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Ira Zibbu @coolscootre.bsky.social · 16/09/2026
Snakemake has this flag `--keep-going` which tells it to keep running the workflow even if some steps/samples fail. And unironically when I am having a bad day I just say `--keep-going` to myself.
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Reposted by Ira Zibbu
Karen Lloyd @karenlloyd.bsky.social · 16/09/2026
I wrote a blog post about aeornophiles for Small Things Considered. smallthingsconsidered.blog/schaechter/2...
smallthingsconsidered.blog
Aeonophiles
by Karen G. Lloyd — The story behind some extremely long-lived microbial cells.
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Ira Zibbu @coolscootre.bsky.social · 14/09/2026
this panel 1 one rearrangement away from loss
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Reposted by Ira Zibbu
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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Ira Zibbu @coolscootre.bsky.social · 08/09/2026
I think you all deserve a little Weber and Baudrillard as a treat
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Ira Zibbu @coolscootre.bsky.social · 08/09/2026
www.nature.com/articles/s41... fork found in kitchen
nature.com
How contemporary academic structures constrain scientific creativity and hold back early-career researchers - Nature Human Behaviour
In this Perspective, Haubrock et al. argue that today’s scientific structures constrain creativity and that strategic conformity is a rational response. They discuss how this holds back early-career researchers from reaching their full potential as scientists.
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Ira Zibbu @coolscootre.bsky.social · 02/09/2026
How do you make the decision do to a PhD? I had some succinct thoughts: irazibbu.substack.com/p/how-did-i-...
irazibbu.substack.com
How did I know I wanted to do a PhD?
Some thoughts on how to make a crucial decision.
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Reposted by Ira Zibbu
Sean Carroll @seanmcarroll.bsky.social · 29/08/2026
Ever wonder what "information" really means? Here's our new paper, led by @frosas.bsky.social, that lays out the multiple ways the term is used in natural science. rdcu.be/fCDGv
A chart describing four faces of information: Engineering, Statistical, Thermodynamic, and Ontological.
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Ira Zibbu @coolscootre.bsky.social · 31/08/2026
Every time I read the statement "XYZ is poorly understood" it pisses me off. It is a non-statement! Everyone says that about their own research. You can always construct a a gap and the sell yourself as the one to fill it. Anything can be "poorly understood."
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Ira Zibbu @coolscootre.bsky.social · 27/08/2026
arxiv.org/abs/2608.16753 I think it is very important for a field like bioinformatics to reckon with generative AI in the same way. Thank you Terry Tao for this
arxiv.org
Mathematics in the age of AI
An essay, based on a public lecture delivered at the 2026 International Congress of Mathematicians, on how the mathematical community might respond to the arrival of artificial intelligence tools that...
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Ira Zibbu @coolscootre.bsky.social · 27/08/2026
he was a ctrl+F boy i said see your l8r boy he wasn't `grep` enough 4 me
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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 27/08/2026
🙏 #Dolly www.nature.com/articles/d41...
nature.com
Dolly Parton dies aged 80 — researchers celebrate her contributions to science
The country singer was an advocate for vaccines, public health, literacy and marginalized communities.
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Reposted by Ira Zibbu
Rahawa Haile @rahawahaile.bsky.social · 27/08/2026
I wrote about Dolly and Appalachia for this week’s Scratch. www.talkscratch.com/dolly-parton...
talkscratch.com
Dolly Parton Loved Being Dolly Parton
It was one of the most important aspects of her art.
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Reposted by Ira Zibbu
Sarah McAnulty, Ph.D. @sarahmackattack.bsky.social · 25/08/2026
We need YOU to spread the word about @skypeascientist.bsky.social - our *free* program that matches scientists w/classrooms & more! When educators sign up, they can tell us who told them about us. We'll hold a monthly drawing for $150 of science supplies* from the referrers! SkypeAScientist.com
a praying mantis is on the telephone and excited to hear someone on the phone say "Skype a Scientist has a new referral program"
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Ira Zibbu @coolscootre.bsky.social · 21/08/2026
thanks AI
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BejaLabTechnion @bejalab.bsky.social · 19/08/2026
Pervasive phosphorylation by phage T7 kinase disarms bacterial defences www.nature.com/articles/s41...
nature.com
Pervasive phosphorylation by phage T7 kinase disarms bacterial defences - Nature
The T7 bacteriophage deactivates bacterial defence systems through T7K phosphorylation of nearly all host and phage proteins during infection.
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Ira Zibbu @coolscootre.bsky.social · 14/08/2026
Most PhD application advice is either (1) generic advice without examples (2) sample materials without explanation. Here I tried to bridge the gap between these two. If you know somebody applying this cycle and may benefit, please share this! ✨ irazibbu.substack.com/p/a-realisti...
irazibbu.substack.com
A Realistic Guide to Writing a Good PhD Application Essay
I revisit, breakdown and explain my own essay to show you what works (and what doesn't).
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Reposted by Ira Zibbu
derek guy @dieworkwear.bsky.social · 13/08/2026
I enjoyed this. ordinaryabundance.com
ordinaryabundance.com
Ordinary Abundance
A walk through a modern apartment, through the eyes of the people for whom everything in it was new.
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Ira Zibbu @coolscootre.bsky.social · 12/08/2026
I take great pains to never refer to Claude with gendered pronouns, and today it assumed I am a man😔
Screenshot of a terminal that says several
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Claus Wilke @clauswilke.com · 12/08/2026
A new paper challenges how we have used protein language models (pLMs) for protein engineering. It suggests that using pLMs as antipredictors (try mutations the model thinks are bad) can generate the best leads for engineering novel function. blog.genesmindsmachines.com/p/protein-la...
blog.genesmindsmachines.com
Protein language models are overly constrained by covariation
Why good performance on one set of goals can lead to poor performance on another
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Ira Zibbu @coolscootre.bsky.social · 11/08/2026
My personal nightmare is joining a company/institute that forces me to use Windows/macOS on my work laptop and yells at me when I eventually boot whatever linux distro is scratching my itch at that time
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Ira Zibbu @coolscootre.bsky.social · 27/07/2026
This is a lovely measured, nuanced and thoughtful piece. I whole-heartedly agree.
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Evolution Students @ssegrad.bsky.social · 27/07/2026
1/4 In today's funding climate, every grant and fellowship matters. Based on feedback from our GSAC Community Check-In Survey, we're building a growing hub of graduate & postdoctoral funding opportunities and job boards to make them easier to find. 🧵
Funding and job board curated by Dieter Lukas and Pro Manna
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Reposted by Ira Zibbu
Ariadna Morales @ariadnamorales.bsky.social · 09/07/2026
Please consider donating to help fund additional Graduate Research Excellence Grants. Every contribution can help support more student-led research! www.gofundme.com/f/support-st...
gofundme.com
Donate to Support Students on their Scientific Research Journey!, organized by SSE Communications
The Graduate Research Excellence Grants are awarded by the So… SSE Communications needs your support for Support Students on their Scientific Research Journey!
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Ira Zibbu @coolscootre.bsky.social · 12/07/2026
So glad you liked it! It was the most fun I've had in a while giving a talk.
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Ira Zibbu @coolscootre.bsky.social · 24/06/2026
If you're going to be at #SMBE2026, please come by for my talk! I will presenting some very cool results from the long-term evolution experiment concerning unexpected reorganization of their genomes
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Reposted by Ira Zibbu
#1 Lifelong Houston Cougs Fan Brandi 😾 @itsthebrandi.bsky.social · 19/06/2026
If you are under 45 in the US, you should get this. Your gender is irrelevant here. Shout out to my one ex who listened to me after we broke up and was like, "I got the shots" It's a series. I got the series, like, eons ago. If you already have HPV, get the shots. It covers many strains.
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Ira Zibbu @coolscootre.bsky.social · 19/06/2026
I used to live by East Woods Park in Austin and I would often think about how I was standing on the same land as one of the first Juneteenth celebrations.
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Ira Zibbu @coolscootre.bsky.social · 18/06/2026
Does anyone know if the Lake Arrowhead Microbial Genomics meeting may happen this year? #genomics #microbes
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Ira Zibbu @coolscootre.bsky.social · 18/06/2026
I got my first shot this year! It is never too late
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Ira Zibbu @coolscootre.bsky.social · 18/06/2026
Drinking game: Everytime you read a paper about a bioinformatics tool that only exists as a web app and never released binaries for download or source code but now the web app is permanently dead
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Scott Marek @smarek0502.bsky.social · 11/06/2026
What matters most for childhood brain organization? We analyzed 649 variables. The answer: Socioeconomics (SES); with brain patterns pointing at sleep & stress as drivers. Even brain-IQ associations were better explained by SES. In Science today: www.science.org/doi/10.1126/...
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Ira Zibbu @coolscootre.bsky.social · 12/06/2026
I was on my break at work, eating the same meal for a 4th day in a row because it is the cheapest way to cook at home, because it would be irresponsible to get the $10.99 lunch deal at the Chinese place down the road. I was listening to Here & Now, and I heard about the IPO and the man it made rich.
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Grant Sanderson @3blue1brown.com · 10/06/2026
Suppose you wanted to reinvent the idea of Shannon Entropy for yourself. This puzzle is a good place to start (Full video on YouTube).
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Ira Zibbu @coolscootre.bsky.social · 03/06/2026
Getting the vaccine meant I could safely continue volunteering at vaccine camps in Bangalore.. It was such a ray of hope, like angels had come down to earth.
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Ira Zibbu @coolscootre.bsky.social · 02/06/2026
simulation and simulacra hmm
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Your daily John Waters screenshot @johnwatersbot.bsky.social · 02/06/2026
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Ira Zibbu @coolscootre.bsky.social · 29/05/2026
nothing is sacred
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Vaughn Cooper @vscooper.micropopbio.org · 28/05/2026
In celebration of good friends and collaborators Erin Gloag @sirmicrobe.bsky.social, Dan Wozniak and @nanamikubota.bsky.social, here's a cool new study about rapid P. aeruginosa adaptation in wounds, with some hidden phage phun as bonus. journals.asm.org/doi/10.1128/...
journals.asm.org
Pseudomonas aeruginosa biofilm-deficient mutants undergo parallel evolution during chronic infection | Journal of Bacteriology
We demonstrate that in a porcine full-thickness thermal injury wound model, a Pseudomonas aeruginosa mutant deficient in biofilm formation undergoes adaptive evolution by acquiring mutations that alter the outer membrane, either type IV pili (T4P) or lipopolysaccharide (LPS) mutations, that restores the deficient biofilm phenotype. We also observe a striking degree of mutational parallelism, at both the biosynthetic pathway and gene level, indicating the strong selective pressures experienced by these pathways during chronic wound infection.
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Jerome Alexander Horne @jahorne.bsky.social · 20/05/2026
"Sure, not every person and not every trip. Maybe not even as a complete replacement for cars. But as a standard household tool? Absolutely!" Bikes (electric or non) can replace (dare I say it) transit trips. Especially in dense cities depending on where you're going. electrek.co/2026/05/18/w...
electrek.co
Why every American family should have an e-bike at home
There’s a sentence that still sounds slightly radical in much of America, even though millions of people elsewhere in the...
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Ira Zibbu @coolscootre.bsky.social · 20/05/2026
day 4567 of waking up grateful for burrows-wheeler transform
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Ira Zibbu @coolscootre.bsky.social · 18/05/2026
liked this one this morning
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Ira Zibbu @coolscootre.bsky.social · 15/05/2026
Me when I see a new paper on multicellular yeast
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