Tomáš Pluskal

Do you have a bold, daring vision how to transform research in biology? Are you a young scientist within 7 years since your PhD? Submit your idea by July 31 to the Dream Biology Award competition and you can win the first prize of €10,000! More details at dreambiologyaward.org

Registration is now open for the 6th Virtual ChemBioTalks on September 29th from 12:00 to 18:00 CEST. We have an amazing program for you highlighted by our keynotes @supertifurgalab.bsky.social and Michelle Chang. Make sure to register to not miss it: events.zoom.us/ev/Ag1AUcW3n...

Come and join us :)

🦠 The #PROTOCELL experiment is heading into space! The project led by @hlouchova-lab.bsky.social & @pluskal-lab.org at IOCB Prague is one of 13 Czech scientific and technological experiments supported by @esa.int that will become part of the now confirmed mission of Czech astronaut Aleš Svoboda.

🔬 This tenure-track position is roughly comparable to an #assistantprofessor at a US university or to a #newinvestigator position at Max Planck Institutes in Germany. See more ► www.uochb.cz/en/open-posi... ⤵️ #openposition #iocbprague #iocb #compchem

Tomas Pluskal @pluskal-lab.org on plants, their products and AI #pps2026

Thanks and congratulations to @jjjvanderhooft.bsky.social, Soha Hassoun @pluskal-lab.org, Stacey Reinke for organizing this landmark #Dagstuhl Computational Metabolomics seminar 26181 ! www.dagstuhl.de/en/seminars/... What an amazing four days with many fruitful discussions and interactions ...

💻 GitHub: github.com/anton-bushui... 📄 Paper: arxiv.org/abs/2411.02109

I am super excited that our paper on inter-laboratory comparability of non-targeted LC–MS/MS analysis of dissolved organic matter was just published in ES&T. pubs.acs.org/doi/10.1021/...

Are you planning to attend the @appliedmldays.bsky.social conference at EPFL? Together with @arianemora.bsky.social we are organizing an ML4Enzymes workshop on Feb 12 morning, including expert presentations and a hands-on coding session. Full program: docs.google.com/document/d/1...

🧬 A new paper from the group of Ed Curtis at IOCB Prague in collab with the @pluskal-lab.org introduces a structure-guided way to explore nucleic acid sequence space that goes beyond traditional random mutagenesis. #research #machinelearning #nucleicacids #chemistry 1/3

📰 @forbescesko.bsky.social ve svém výběru českých vědeckých objevů zmínil také výzkum z našeho ústavu. Vedle dalších projektů upozornil na práce týmu Petra Cíglera a týmu @pluskal-lab.org ► forbes.cz/tricko-proti... 📲 #ceskaveda

Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!

We train machine learning models on millions of proteins. But when it comes to making predictions, do we need them to understand all proteins at once? Often, we need an accurate model for the specific protein we are studying or designing. We address this with ProteinTTT arxiv.org/abs/2411.02109 1/🧵

BIG BIG congratulations to our PhD student @roman-bushuiev.bsky.social for receiving the Google PhD Fellowship 2025 in Health Research! 🎉💰 goo.gle/43wJWw8

Je život ve vesmíru vzácný, nebo se naopak může vyskytovat skoro všude? Odpověď na to hledá projekt #PROTOCELL Kláry Hlouchové a @pluskal-lab.org, který vzniká v @iocbprague.bsky.social. 1/3 #ČeskáCestaDoVesmíru #CzechSpace #CzechSpaceWeek2025 #CzechSpaceWeek #UOCHB #IOCB #IOCBPrague

MSnLib: a large-scale, open multi-stage fragmentation mass spectral library for 30,000 unique small molecules. @robinschmid.bsky.social @pluskal-lab.org www.nature.com/articles/s41...

The first day of our bioML symposium at @iocbprague.bsky.social went very well. It is amazing to see how fast this field is moving forward. Thanks to everyone for the fantastic talks! 🤖🧬

Yesterday @roman-bushuiev.bsky.social visited our lab. He gave a seminar talk about his recent work on DreaMS (www.nature.com/articles/s41...), and provided a hands-on training to my lab members. Looking forward to what we will discover using this awesome tool!

At #ASMS2025, we presented a next-gen workflow pairing the #timsMetabo MoRE (Mobility Range Enhancement) with #mzmine and #DreaMS Compared to conventional LC-MS2, the data delivered: - 84% more detected features - 5.7× more MS² spectra - 3× more spectral matches Read the full poster to learn MoRE

🚨 MetaboART 🎨 2025 – Deadline Extended: 🗓️ Submissions now open until June 13! Two categoried: 👤 Human-Created // 🤖 AI-Generated 🏆Winner @ #MetSoc25 on June 24 Details👉 tinyurl.com/dh37xt78 📩info.emn@metabolomicssociety.org

#mzmine 4.7 is now available! This release brings our most significant improvement in memory efficiency to date, unlocking new capabilities for analyzing large-scale datasets. Join us for a live software demo at our booth today and tomorrow at 12:00/noon during #ASMS2025

Today is the registration deadline for our bioML symposium on Aug 21-22. Last chance to secure your spot! More info at tinyurl.com/bioMLPrague25

⚛️ @pluskal-lab.org from IOCB Prague, together with his student @roman-bushuiev.bsky.social and colleagues from #CIIRC CTU, Josef Šivic and @anton-bushuiev.bsky.social, have developed a machine learning model called #DreaMS – which accelerates the analysis of previously unknown molecules.

Mass spectrometry is a key method to discover and identify molecules in biological and environmental samples. Yet, >90% of mass spectra remain hard to interpret. In our recent paper, we present DreaMS — a foundation model to interpret mass spectra of small molecules. www.nature.com/articles/s41...

This paper represents a great effort by @roman-bushuiev.bsky.social and his brother @anton-bushuiev.bsky.social. The DreaMS foundation model for mass spectra of small molecules now opens lots of avenues for possible downstream applications. It might be a game changer for computational metabolomics.

The Mass Spectrometry Query Language (MassQL) is an open-source language for instrument-independent searching across mass spectrometry data for complex patterns of interest via concise and expressive queries without the need for programming skills. www.nature.com/articles/s41...

Join us for a power-packed software workshop where we’ll be breaking boundaries in multi-vendor MS analysis using #mzmine at #ASMS2015 Led by experts @robinschmid.bsky.social and @ansgarkorf.bsky.social 𝗡𝗼 𝘀𝗶𝗴𝗻–𝘂𝗽 𝗿𝗲𝗾𝘂𝗶𝗿𝗲𝗱, 𝗷𝘂𝘀𝘁 𝗱𝗿𝗼𝗽 𝗯𝘆 𝘁𝗵𝗲 𝗯𝗼𝗼𝘁𝗵 𝗮𝘁 𝟭𝟮 𝗺𝗶𝗱𝗱𝗮𝘆. See you there! 👋

Get Ready! Only 3 weeks to go until #ASMS2025! Our team will be showcasing our latest developments in #mzmine at this year’s conference. Stop by Booth 210 for live demonstrations and insights into how you can streamline your data processing across multiple vendors, adding speed and confidence.

🤝 IOCB Prague is hiring – we are looking for an outstanding Junior Group Leader in Biosciences to join our vibrant scientific community. See more ► www.uochb.cz/en/open-posi... ⤵️ #openposition #iocbprague #iocb #researchjobs #biosciences

Back in July 2023 we organized a small bioML symposium at @iocbprague.bsky.social, and it turned out to be a very pleasant and successful event. This summer we are following up with a great line-up of speakers. Please register for free, deadline May 30. tinyurl.com/bioMLPrague25

#mzmine Rapid MALDI-MS/MS-Based Profiling of Lipid A Species from Gram-Negative Bacteria Utilizing Trapped Ion Mobility Spectrometry and mzmine (Rudt, Froning, @robinschmid.bsky.social, @pluskal-lab.org)–AC: doi.org/10.1021/acs.... @iocbprague.bsky.social @mzmine.bsky.social @uni-muenster.de

We were hosting a MZmine workshop within our INTER-MICRO /Talking microbes/ OP JAK project. Presenters: Zdeněk Kameník (Laboratory of Antibiotic Resistance and Microbial Metabolomics IMIC); Tito Damiani and Joshua Smith (Tomáš Pluskal group @iocbprague.bsky.social) Learning new things #intermicro

This is the first paper from our Piper-series, many more to follow. A great effort by multiple lab members!

🚨 Abstract deadline alert! 🚨 Friendly reminder to submit your oral abstract before March 6 – don’t miss the chance to showcase your work at hashtag#MetSoc2025! Registration is now open: lnkd.in/eFZGi4CK #Metabolomics #EMN

🤝 In April 2024, brothers Roman and Anton Bushuiev from the teams of @pluskal-lab.org @iocbprague.bsky.social and Josef Šivic #CIIRC_CTU initiated a collaboration among 14 research institutes across the globe to benchmark #AI methods for the discovery of molecules from mass spectrometry data. 1/2

We will be hosting the first @mzmine.bsky.social Community Meeting at @iocbprague.bsky.social. Please register if you wish to learn about the latest developments in mzmine. More info: docs.google.com/document/d/1...

New #mzmine release out now! Matching millions of reference spectra against thousands of samples was never faster. Go and test it today. Download: github.com/mzmine/mzmin... youtu.be/AFv55sUn9Lg

MassSpecGym is the largest publicly available collection of mass spectra data with 231K spectra for 29K unique molecular structures. 33% of the dataset was generated from newly measured, in-house data. 🛡️The dataset is now certified on Polaris! polarishub.io/datasets/rom... youtu.be/G8ZnVRm0ogc

The new POMBOX kit is now available from @addgene.bsky.social To plan your cloning with this and other Golden Gate kits, you can try the kit template in #ShareYourCloning 🔗 Visit shareyourcloning.org 👉 Go to Templates > Moclo 🎞️ Full demo video www.youtube.com/watch?v=n0he... #pombe #MoClo

🏆 Cenu #Neuron pro mladé vědce získal v neděli také Dr. Tomáš Pluskal z našeho ústavu. Více na ► www.uochb.cz/cs/novinky/6... ⤵️ #cenaneuron #iocb #iocbprague #uochb #akademievedcr

👏 Hlavní Cenu Neuron 2024 získal tentokrát uznávaný fyzikální chemik prof. Pavel Jungwirth z našeho ústavu. V oboru chemie uspěl také Dr. Tomáš Pluskal z ÚOCHB. Blahopřejeme nejen jim, ale také všem dalším oceněným! Více na ► cenyneuron2024.cz ⤵️

Has Bluesky replaced X for scientists? Take Nature’s poll “The research community has flocked to the social-media platform Bluesky. Tell us about your experience.” www.nature.com/articles/d41...