Pranas Grigaitis

Pranas Grigaitis

@pranasag.bsky.social

helping cells spend their molecular cash wisely | ants, microbes, and combinations of both | biochemist behind a computer @kit.edu | ex @vuamsterdam.bsky.social, @uniheidelberg.bsky.social & U Vilnius | rookie bassist, saxophonist | pranasag.github.io

226 followers426 following50 posts

Pranas Grigaitis reposted

Jürgen Zanghellini
@juergenzanghellini.bsky.social

What kcat predictor is best for systems biology? We predicted yeast growth w/ 6 tools. Benchmark scores failed to predict model performance. One key error can mess up everything Accuracy is global—impact is local Let’s test AI tools beyond benchmarks tinyurl.com/bdznxy8y @univie.ac.at #PROHITS

biorxiv.orgBeyond benchmark accuracy: machine-learning turnover-number predictors require system-level validationEnzyme turnover numbers ( k cat) are essential for kinetic models and enzyme-constrained genome-scale metabolic models (ecGEMs), but measured values are sparse and therefore increasingly estimated usi...

Pranas Grigaitis reposted

ECMTB'26
@ecmtb2026.org

From early morning to late evening; from registration to reception: it's a wrap for the first day of #ECMTB26! Looking forward to more exciting talks, discussions, and the first round of poster presentations tomorrow!

Pranas Grigaitis
@pranasag.bsky.social

Now that the dust has settled. As someone who is not exactly the master of the technique, talking before the audience at the International Metaproteomics Symposium was... an interesting experience, let's put it this way. I have discovered an amazing community

Pranas Grigaitis reposted

Melissah Rowe
@melissahrowe.bsky.social

🐦 Interested in avian reproduction, microbiomes, or reproductive microbiomes? I'm looking for outstanding early-career researchers interested in applying for an NWO Veni grant to join my group at NIOO. Pre-proposals are due after the summer. Email me to discuss ideas. #EarlyCareerResearcher #Postdoc

Pranas Grigaitis
@pranasag.bsky.social

The NWO Life conference was a blast! Great keynotes, very valuable input on our current research, and the cherry on the top was the focus session on socially transferred materials. There I gave a talk on my post-doc shenanigans regarding microbial up-cycling of social fluids in ant colonies...

Pranas Grigaitis
@pranasag.bsky.social

... which means that less complex meals get co-consumed by the host and its microbes, who chip in some small molecules that metazoans cannot produce themselves (some amino acids, vitamins, etc.). Some of these heroes are well known, but some are truly unsung ones. Needs more research!

Pranas Grigaitis
@pranasag.bsky.social

This Friday: microbial superheroes in socially transferred materials! Those who know me can easily guess I will be mostly talking about the feeders, but one just has to appreciate _all_ the microbial goods that circulate in STMs.

Joris M. Koene@joriskoene.bsky.social

With Bart Pollux and @anikokorosi.bsky.social , I will chair the Focus session “Socially Transferred Materials" at NWO Life (28-29 May 2026) 🐜🐸🐌🐄🥚 Invites speakers are @sanjahakala.bsky.social , @pranasag.bsky.social, Peter Kwant and @melissahrowe.bsky.social @socialtransfernet.bsky.social

Pranas Grigaitis
@pranasag.bsky.social

Why to choose between ants and microbes when you can have both? @khadlily.bsky.social, @adriatica.bsky.social and co. have been diving into what's happening in the honeypot ant repletes for years, and the first papers are coming out 🎉 (photo copyright: Smithsonian Institution-NMNH-Insect Zoo)

bioRxiv Genomics@biorxiv-genomic.bsky.social

Genomic insights into bacterial isolates dominating honeypot ant crop microbiomes reveal metabolically distinct Fructilactobacillus sp. https://www.biorxiv.org/content/10.64898/2026.04.09.717501v1

Pranas Grigaitis
@pranasag.bsky.social

Where one finds food, lactobacilli follow - sweet sweet ant honey is not an exception at all. Quoting Oded Rechavi, the father of The Woodstock of Biology, what's the physiological relevance? Here comes the first set of genome- and proteome analysis-driven ideas on what these replete microbes do.

Pranas Grigaitis
@pranasag.bsky.social

The metabolic modeling part of this manuscript is just the beginning of what we set up back in my previous life, last fall in Amsterdam. It was great to host Ian Oiler in the low lands back then, and happy to have laid my finger on this whole endeavor. Stay tuned for more ants AND microbes!

Pranas Grigaitis
@pranasag.bsky.social

Late spring 🌼 is an excellent time to be back in the Lowlands, especially as a part of a great line-up at the STM focus session! Thanks @joriskoene.bsky.social @anikokorosi.bsky.social and Bart for the invitation - looking forward

Joris M. Koene@joriskoene.bsky.social

What do milk, seminal fluid, eggs, and regurgitates have in common? Find out during our Focus Session at NWO Life 2026 “Socially Transferred Materials: Connecting Physiology, Ecology & Evolution” (28-29 May 2026, Egmond aan Zee, NL) 🐜 🐸 🐌 🐄🥚 @socialtransfernet.bsky.social

Pranas Grigaitis reposted

VAAM e.V.
@vaam-microbes.bsky.social

🚀 VAAM Annual Conference 2026, Berlin, 23–25 March Don’t miss out — register now & meet the microbiology community for talks, poster sessions, Research and PhD Awards, and special events for Young Scientists. Connect, learn, and exchange ideas! 👉 Join us & register here: t1p.de/b2vf8 #VAAM2026

Pranas Grigaitis
@pranasag.bsky.social

The book chapter (1st as the last author 😎) is finally "officially" out: doi.org/10.1007/978-... Thanks to the team! (DM for the pdf if you need one)

doi.orgFrom Genome to Function: Metabolism-Wide Models of Lifecycle Stages of ParasitesMetabolism is a complex network of biochemical reactions that cells use to obtain free energy transduced from nutrients and synthesize new cellular components. Understanding the wiring of metabolism c...
Pranas Grigaitis@pranasag.bsky.social

It's a common wisdom that the whole genome is not expressed at the same time. Is trying to make a map of the 'entirety' of the metabolic potential (aka genome-scale model) useless, and potentially reckless? It's only an intermediate stop. Especially for unicellular parasites. doi.org/10.5281/zeno...

doi.orgFrom genome to function: metabolism-wide models of lifecycle stages of parasitesAbstract Metabolism is a complex network of biochemical reactions that cells use to obtain free energy transduced from nutrients and synthesize new cellular components. Understanding the wiring of met...
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Pranas Grigaitis
@pranasag.bsky.social

As a case study, we will consider the recently published GEM for an industrially-relevant NCY Pichia kluyveri, used for the production of alcohol-free beverages, such as alcohol-free beer. I will show how P. kluyveri GEM enabled a comprehensive analysis of physiological and -omics data...

Pranas Grigaitis
@pranasag.bsky.social

... and helped us to reason the metabolic phenotypes and behaviors the NCY P. kluyveri employs. I will make a point for the potential role of reconstructing GEMs in large-scale studies searching for “new biochemistry” in NCYs and beyond.

Pranas Grigaitis
@pranasag.bsky.social

In my talk, I will briefly reflect on the evolution of yeast metabolic modeling in the last 20 years from the first GEM of Saccharomyces cerevisiae published in 2003. I will discuss how the vast amount of knowledge, encoded in the GEM of S. cerevisiae, can be transferred to other yeasts.

Pranas Grigaitis reposted

Jenny Stynoski
@stynoski.bsky.social

🧃☕️ BYOF Seminar | Fri Oct 24 @ 10 am EDT🥛🍹 Bring-Your-Own-Fluid + enjoy 7 min talks about social fluids: 🦈 Viviparity & matrotrophy • Daniel Hughes 🐦 Crop milk • Victoria Farrar 🦂 Sexual stings • Yuqi Reitsema-Wang Email hello@socialtransfer.net for the Zoom link! 🔗 @socialtransfernet.bsky.social

Pranas Grigaitis
@pranasag.bsky.social

Another round of selfish self-promotion: please join us for the best bridging event to your Halloween party if you are nearby Amsterdam on that day (mandatory music reference: youtu.be/vFwYJYl5GUQ?...)

youtu.beType O Negative - Black No. 1 (Little Miss Scare -All) [HD Remaster] [OFFICIAL VIDEO]YouTube video by Roadrunner Records
Pranas Grigaitis@pranasag.bsky.social

Metabolic modeling aficionados in the Netherlands (and close to border), attention please! (promo thread)

Pranas Grigaitis reposted

Ákos T Kovács
@evolvedbiofilm.bsky.social

Metabolic interplay drives population cycles in a cross-feeding microbial community @natcomms.nature.com from @oventurelli2.bsky.social www.nature.com/articles/s41...

nature.comMetabolic interplay drives population cycles in a cross-feeding microbial community - Nature CommunicationsHere the authors leverage a crossfeeding, engineered microbial community to demonstrate that strain abundance cycles are robust across environmental conditions. They pair this with a nonlinear dynamic model to elucidate population cycles.

Pranas Grigaitis reposted

Alex Fedorec
@ajfedorec.bsky.social

I'm going to be advertising for a few positions in my group in the next couple of months for a big project on synthetic microbial communities. I would love to hear from you if you are interested and I'd also appreciate if everyone could share this far and wide!

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Pranas Grigaitis
@pranasag.bsky.social

We’ll explore these questions (and more!) together at the AIMMS Symposium “Modeling metabolism: successes, challenges, and prospects” With talks by: ✨ Djordje Bajić (TUD) ✨ Meike Wortel (UvA) ✨ Ursula Kummer (Uni Heidelberg) ✨ María Suárez Diez (WUR) 🔷 selected early-career researcher talks.

Pranas Grigaitis
@pranasag.bsky.social

🔬 Recent breakthroughs in understanding metabolism, and applying this knowledge, have only been possible thanks to the creative blending of multiple disciplines. Among them, mathematical modeling has become a cornerstone for many successful interdisciplinary studies in the life sciences.

Pranas Grigaitis
@pranasag.bsky.social

Metabolic modeling has advanced over decades, built on the dedication and behind-the-scenes work of countless researchers. But some big questions remain: 💡 What are the biggest challenges ahead? 🚀 What is the next frontier in modeling metabolism?

Pranas Grigaitis
@pranasag.bsky.social

It's a common wisdom that the whole genome is not expressed at the same time. Is trying to make a map of the 'entirety' of the metabolic potential (aka genome-scale model) useless, and potentially reckless? It's only an intermediate stop. Especially for unicellular parasites. doi.org/10.5281/zeno...

doi.orgFrom genome to function: metabolism-wide models of lifecycle stages of parasitesAbstract Metabolism is a complex network of biochemical reactions that cells use to obtain free energy transduced from nutrients and synthesize new cellular components. Understanding the wiring of met...
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Pranas Grigaitis
@pranasag.bsky.social

This text (in another format) will become a chapter in the Euglenozoa book of the Methods in Molecular Biology series soon (details TBD). The copyediting and other formalities are pending; in the meantime, I am very happy to share the manuscript version of the chapter.

Pranas Grigaitis
@pranasag.bsky.social

Embracing computational models in their research feels like crossing the Rubicon for many people, although it should not be so. That was my red thread while overseeing the writing of this manuscript. Modeling is an essential ingredient for the next grand advance(s) of the 21st century biology!

Pranas Grigaitis
@pranasag.bsky.social

It's a common wisdom that the whole genome is not expressed at the same time. Is trying to make a map of the 'entirety' of the metabolic potential (aka genome-scale model) useless, and potentially reckless? It's only an intermediate stop. Especially for unicellular parasites. doi.org/10.5281/zeno...

doi.orgFrom genome to function: metabolism-wide models of lifecycle stages of parasitesAbstract Metabolism is a complex network of biochemical reactions that cells use to obtain free energy transduced from nutrients and synthesize new cellular components. Understanding the wiring of met...
Pranas Grigaitis
@pranasag.bsky.social

We (me and Jurgen Haanstra from the Vrije Universiteit, and colleagues from Uni Sao Paulo in Brazil) spelt some wisdom out on how experimental data becomes some zeros and ones in genome-scale metabolic models (GEMs) - focusing on organisms that exhibit metabolically distinct life stages.