Varjosalo_Lab
@varjosal.bsky.social
Unveiling the secrets of life through proteomics @helsinkiuni, @HiLIFE_helsinki, @BIOTECH_UH, Proteomics, Genomics, Systems biology 🇫🇮🇨🇳🇧🇩🇭🇷🇮🇳🇮🇹🇹🇷
Reposted by Varjosalo_Lab
Very excited to share that my thesis work is out in Molecular Cell! We trained a Structure and Omics informed Classifier (SPOC) to score binary AlphaFold multimer (AF-M) predictions by structural quality and consistency with experimental omics datasets. www.cell.com/molecular-ce...
Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions
Schmid and Walter train a classifier that discerns functionally relevant structure
predictions in proteome-wide protein-protein interaction (PPI) screens using AlphaFold-Multimer,
and they use this co...
www.cell.com
February 26, 2025 at 6:14 PM
Very excited to share that my thesis work is out in Molecular Cell! We trained a Structure and Omics informed Classifier (SPOC) to score binary AlphaFold multimer (AF-M) predictions by structural quality and consistency with experimental omics datasets. www.cell.com/molecular-ce...
Reposted by Varjosalo_Lab
Exited to share our latest work! Out now in @natcomms.nature.com
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Koina: Democratizing machine learning for proteomics research - Nature Communications
Koina is an open-source, online platform that simplifies access to machine learning models in proteomics, enabling easier integration into analysis tools and helping researchers adopt and reuse ML mod...
www.nature.com
November 11, 2025 at 8:06 PM
Exited to share our latest work! Out now in @natcomms.nature.com
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Reposted by Varjosalo_Lab
A new era for plasma proteomics is on the horizon. 🌅
Get ready for next-generation performance, precision, and simplicity — brought to you by PreOmics® and Biognosys.
✨ www.preomics.com/products/p2-...
#plasmaprep #proteomics #iST #sampleprep #P2-iST
Get ready for next-generation performance, precision, and simplicity — brought to you by PreOmics® and Biognosys.
✨ www.preomics.com/products/p2-...
#plasmaprep #proteomics #iST #sampleprep #P2-iST
November 10, 2025 at 1:35 PM
A new era for plasma proteomics is on the horizon. 🌅
Get ready for next-generation performance, precision, and simplicity — brought to you by PreOmics® and Biognosys.
✨ www.preomics.com/products/p2-...
#plasmaprep #proteomics #iST #sampleprep #P2-iST
Get ready for next-generation performance, precision, and simplicity — brought to you by PreOmics® and Biognosys.
✨ www.preomics.com/products/p2-...
#plasmaprep #proteomics #iST #sampleprep #P2-iST
Reposted by Varjosalo_Lab
I try the newest version of DIA-NN, version 2.3 and its new Infini search approach on some Lumos and tismTOF HT datasets. If you're new to DIA-NN this might be a good video to watch. youtu.be/MIMnDw0loCk
We try the new DIA-NN 2.3 (November 2025)
YouTube video by Brett Phinney
youtu.be
November 3, 2025 at 8:01 PM
I try the newest version of DIA-NN, version 2.3 and its new Infini search approach on some Lumos and tismTOF HT datasets. If you're new to DIA-NN this might be a good video to watch. youtu.be/MIMnDw0loCk
Reposted by Varjosalo_Lab
Science HR in 2026: Smarter, Flexible, and Affordable Job Posting for Scientists and Employers
#science #jobs #recruiting
www.scientific.today/news/1275/sc...
#science #jobs #recruiting
www.scientific.today/news/1275/sc...
Science HR in 2026: Smarter, Flexible, and Affordable Job Posting for Scientists and Employers
www.scientific.today
October 18, 2025 at 5:36 PM
Science HR in 2026: Smarter, Flexible, and Affordable Job Posting for Scientists and Employers
#science #jobs #recruiting
www.scientific.today/news/1275/sc...
#science #jobs #recruiting
www.scientific.today/news/1275/sc...
Reposted by Varjosalo_Lab
BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)
October 15, 2025 at 12:22 PM
BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)
Reposted by Varjosalo_Lab
BREAKING: The Nobel Prize in Physiology or Medicine has been awarded jointly to Mary E. Brunkow, Fred Ramsdell, and Shimon Sakaguchi "for their discoveries concerning peripheral immune tolerance"
Stay tuned for more.
#NobelPrize
Stay tuned for more.
#NobelPrize
October 6, 2025 at 9:34 AM
BREAKING: The Nobel Prize in Physiology or Medicine has been awarded jointly to Mary E. Brunkow, Fred Ramsdell, and Shimon Sakaguchi "for their discoveries concerning peripheral immune tolerance"
Stay tuned for more.
#NobelPrize
Stay tuned for more.
#NobelPrize
Reposted by Varjosalo_Lab
September 27, 2025 at 12:54 AM
Reposted by Varjosalo_Lab
Final countdown! Only 3 days to go until the YPIC Webinar #19: Transition from Academia to Start-Up.
#YPIC #Proteomics #StartUpScience #ScienceCareers #AcademicToIndustry
#YPIC #Proteomics #StartUpScience #ScienceCareers #AcademicToIndustry
September 15, 2025 at 7:12 AM
Final countdown! Only 3 days to go until the YPIC Webinar #19: Transition from Academia to Start-Up.
#YPIC #Proteomics #StartUpScience #ScienceCareers #AcademicToIndustry
#YPIC #Proteomics #StartUpScience #ScienceCareers #AcademicToIndustry
New review w/ Lotta J. Happonen (MCP): “State-of-the-Art and Future Directions in Structural Proteomics.” Integrating XL-MS/HDX-MS/LiP-MS with cryo-EM, NMR, X-ray, SAXS/SANS, native & top-down MS + AI.
Full text: www.mcponline.org/article/S153...
Full text: www.mcponline.org/article/S153...
State-of-the-Art and Future Directions in Structural Proteomics
Structural proteomics has undergone a profound transformation, driven by the convergence
of advanced experimental methodologies and computational innovations. Cutting-edge
mass spectrometry (MS)-based...
www.mcponline.org
September 5, 2025 at 6:09 AM
New review w/ Lotta J. Happonen (MCP): “State-of-the-Art and Future Directions in Structural Proteomics.” Integrating XL-MS/HDX-MS/LiP-MS with cryo-EM, NMR, X-ray, SAXS/SANS, native & top-down MS + AI.
Full text: www.mcponline.org/article/S153...
Full text: www.mcponline.org/article/S153...
Thrilled to share: Helsinki Proteomics Center is installing 3 Thermo Scientific Orbitrap Astral/Astral Zoom mass spectrometers. First Astral Zoom arrived in early Aug—among the first worldwide. Rollout by end of summer 2025. Read more: lnkd.in/d76vpMf6 #proteomics #massspectrometry
August 26, 2025 at 11:41 AM
Thrilled to share: Helsinki Proteomics Center is installing 3 Thermo Scientific Orbitrap Astral/Astral Zoom mass spectrometers. First Astral Zoom arrived in early Aug—among the first worldwide. Rollout by end of summer 2025. Read more: lnkd.in/d76vpMf6 #proteomics #massspectrometry
Reposted by Varjosalo_Lab
Reposted by Varjosalo_Lab
🐧📉 Emperor penguin decline worse than predicted
A new study finds a 22% drop in emperor penguins (2020–2023) in part of Antarctica – far steeper than climate models expected.
This highlights urgent risks from sea ice loss
🔗 www.nature.com/articles/s43...
#SciComm #ClimateChange #Penguins 🧪
A new study finds a 22% drop in emperor penguins (2020–2023) in part of Antarctica – far steeper than climate models expected.
This highlights urgent risks from sea ice loss
🔗 www.nature.com/articles/s43...
#SciComm #ClimateChange #Penguins 🧪
Regional emperor penguin population declines exceed modelled projections - Communications Earth & Environment
The number of emperor penguins in the Bellingshausen and Weddell Sea declined by 22% over the period 2009–2023, a reduction of 1.6% per year, exceeding predictions from population models based on high...
www.nature.com
June 16, 2025 at 4:33 AM
🐧📉 Emperor penguin decline worse than predicted
A new study finds a 22% drop in emperor penguins (2020–2023) in part of Antarctica – far steeper than climate models expected.
This highlights urgent risks from sea ice loss
🔗 www.nature.com/articles/s43...
#SciComm #ClimateChange #Penguins 🧪
A new study finds a 22% drop in emperor penguins (2020–2023) in part of Antarctica – far steeper than climate models expected.
This highlights urgent risks from sea ice loss
🔗 www.nature.com/articles/s43...
#SciComm #ClimateChange #Penguins 🧪
Reposted by Varjosalo_Lab
Luke Brzozowski of @uhn.ca showed how 20+ core facilities are driving hospital-based innovation at #CTLS2025, from genomics to theranostics.
💡 Techna team
🧪 Biobanks & imaging
🏥 Research meets care
#CTLSBrno #CoreFacilities #TranslationalResearch #Stratocore @ctlslifescience.bsky.social
💡 Techna team
🧪 Biobanks & imaging
🏥 Research meets care
#CTLSBrno #CoreFacilities #TranslationalResearch #Stratocore @ctlslifescience.bsky.social
June 10, 2025 at 1:59 PM
Luke Brzozowski of @uhn.ca showed how 20+ core facilities are driving hospital-based innovation at #CTLS2025, from genomics to theranostics.
💡 Techna team
🧪 Biobanks & imaging
🏥 Research meets care
#CTLSBrno #CoreFacilities #TranslationalResearch #Stratocore @ctlslifescience.bsky.social
💡 Techna team
🧪 Biobanks & imaging
🏥 Research meets care
#CTLSBrno #CoreFacilities #TranslationalResearch #Stratocore @ctlslifescience.bsky.social
Back from ASMS 2025 — what a ride!
Tech 💥 Science 🧬 Pirates 🏴☠️ Crabs 🦀 and great conversations with old and new friends.
Grateful for the laughs, the inspiration, and the community.
Already missing Baltimore a bit.
See you next year at ASMS in San Diego! 🌞🌊
#ASMS2025 #massspec #blueskyscience
Tech 💥 Science 🧬 Pirates 🏴☠️ Crabs 🦀 and great conversations with old and new friends.
Grateful for the laughs, the inspiration, and the community.
Already missing Baltimore a bit.
See you next year at ASMS in San Diego! 🌞🌊
#ASMS2025 #massspec #blueskyscience
June 8, 2025 at 9:11 AM
Back from ASMS 2025 — what a ride!
Tech 💥 Science 🧬 Pirates 🏴☠️ Crabs 🦀 and great conversations with old and new friends.
Grateful for the laughs, the inspiration, and the community.
Already missing Baltimore a bit.
See you next year at ASMS in San Diego! 🌞🌊
#ASMS2025 #massspec #blueskyscience
Tech 💥 Science 🧬 Pirates 🏴☠️ Crabs 🦀 and great conversations with old and new friends.
Grateful for the laughs, the inspiration, and the community.
Already missing Baltimore a bit.
See you next year at ASMS in San Diego! 🌞🌊
#ASMS2025 #massspec #blueskyscience
Reposted by Varjosalo_Lab
A potentially very useful tool to assess Cys ligandability on proteins
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
TopCysteineDB: A Cysteinome-wide Database Integrating Structural and Chemoproteomics Data for Cysteine Ligandability Prediction
Development of targeted covalent inhibitors and covalent ligand-first approaches have emerged as a powerful strategy in drug design, with cysteines be…
www.sciencedirect.com
June 4, 2025 at 1:29 AM
A potentially very useful tool to assess Cys ligandability on proteins
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Varjosalo_Lab
DIA-NN 2.2.0 is released! The new DIA-NN 2.2.0 Enterprise achieves up to ~1.6x median speedup on 64-cores under Windows (please see benchmark below). Release notes: github.com/vdemichev/Di..., download (Academia): github.com/vdemichev/Di...
May 30, 2025 at 8:36 AM
DIA-NN 2.2.0 is released! The new DIA-NN 2.2.0 Enterprise achieves up to ~1.6x median speedup on 64-cores under Windows (please see benchmark below). Release notes: github.com/vdemichev/Di..., download (Academia): github.com/vdemichev/Di...
This year’s #ASMS2025 is already off to an unexpected start. Helsinki-Vantaa airport on strike (again).
Luckily, I am ✈️ Icelandair—thanks to @evosep.bsky.social for scheduling me for Saturday🙏
Let’s see how this adventure unfolds. Wish me luck—and hope to see many of you in Baltimore!
Luckily, I am ✈️ Icelandair—thanks to @evosep.bsky.social for scheduling me for Saturday🙏
Let’s see how this adventure unfolds. Wish me luck—and hope to see many of you in Baltimore!
May 30, 2025 at 7:53 AM
This year’s #ASMS2025 is already off to an unexpected start. Helsinki-Vantaa airport on strike (again).
Luckily, I am ✈️ Icelandair—thanks to @evosep.bsky.social for scheduling me for Saturday🙏
Let’s see how this adventure unfolds. Wish me luck—and hope to see many of you in Baltimore!
Luckily, I am ✈️ Icelandair—thanks to @evosep.bsky.social for scheduling me for Saturday🙏
Let’s see how this adventure unfolds. Wish me luck—and hope to see many of you in Baltimore!
Reposted by Varjosalo_Lab
MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics pubs.acs.org/doi/10....
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#proteomics #prot-paper
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#proteomics #prot-paper
May 19, 2025 at 2:40 PM
MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics pubs.acs.org/doi/10....
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#proteomics #prot-paper
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#proteomics #prot-paper
Reposted by Varjosalo_Lab
We present SELPHI 2.0 a machine learning model integrating >40 sequence, omics and structural features to predict kinase-substrate interactions between 420 kinases and 240K phosphosites and improve interpretation of global phosphoproteomics data www.sciencedirect.com/science/arti...
Data-driven extraction of human kinase-substrate relationships from omics datasets
Phosphorylation forms an important part of the signalling system that cells use for decision making and regulation of processes such as cell division …
www.sciencedirect.com
May 16, 2025 at 9:09 AM
We present SELPHI 2.0 a machine learning model integrating >40 sequence, omics and structural features to predict kinase-substrate interactions between 420 kinases and 240K phosphosites and improve interpretation of global phosphoproteomics data www.sciencedirect.com/science/arti...
Reposted by Varjosalo_Lab
University of Helsinki have developed a fully automated #plasma #proteomics workflow—from sample prep to Evotip loading. Achieving >4,200 proteins/sample with high reproducibility and low cost, this workflow is a game-changer for large-scale clinical studies.
Blog post I Automated Plasma Proteomics from Sample to Evotip
New study shows how combining the Evosep One with automated Evotip sample preparation enables scalable, high-throughput plasma proteomics.
www.evosep.com
May 14, 2025 at 12:41 PM
University of Helsinki have developed a fully automated #plasma #proteomics workflow—from sample prep to Evotip loading. Achieving >4,200 proteins/sample with high reproducibility and low cost, this workflow is a game-changer for large-scale clinical studies.
Reposted by Varjosalo_Lab
Happy that our article is Editor´s choice in the May issue of 2025 in @jphysiol.bsky.social.
physoc.onlinelibrary.wiley.com/doi/10.1113/...
physoc.onlinelibrary.wiley.com/doi/10.1113/...
May 13, 2025 at 7:12 PM
Happy that our article is Editor´s choice in the May issue of 2025 in @jphysiol.bsky.social.
physoc.onlinelibrary.wiley.com/doi/10.1113/...
physoc.onlinelibrary.wiley.com/doi/10.1113/...
Reposted by Varjosalo_Lab
Heading to #ASMS2025 in Baltimore? Join us May 31 for the Evosep User Meeting! Markku Varjosalo shares insights on automated plasma workflows.
Connect, learn, and network—refreshments included!
Register here: www.evosep.com/asms2025/
#teammassspec #proteomics #lcms
Connect, learn, and network—refreshments included!
Register here: www.evosep.com/asms2025/
#teammassspec #proteomics #lcms
May 13, 2025 at 12:05 PM
Heading to #ASMS2025 in Baltimore? Join us May 31 for the Evosep User Meeting! Markku Varjosalo shares insights on automated plasma workflows.
Connect, learn, and network—refreshments included!
Register here: www.evosep.com/asms2025/
#teammassspec #proteomics #lcms
Connect, learn, and network—refreshments included!
Register here: www.evosep.com/asms2025/
#teammassspec #proteomics #lcms
Reposted by Varjosalo_Lab
Automated MagNet Enrichment Unlocks Deep and Cost-Effective LC-MS Plasma Proteomics www.biorxiv.org/cont...
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#proteomics #prot-preprint
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#proteomics #prot-preprint
May 12, 2025 at 11:20 AM
Automated MagNet Enrichment Unlocks Deep and Cost-Effective LC-MS Plasma Proteomics www.biorxiv.org/cont...
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#proteomics #prot-preprint
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#proteomics #prot-preprint
Happy to host good candidates!
DM for more info.
DM for more info.
Choose Science. Choose Europe.
A new Marie Skłodowska-Curie Actions Postdoctoral Fellowships 2025 call is now open.
With a budget of €404.3 million, it will support around 1,650 researchers from Europe and beyond.
Apply by 10 September → europa.eu/!fBTMgF
A new Marie Skłodowska-Curie Actions Postdoctoral Fellowships 2025 call is now open.
With a budget of €404.3 million, it will support around 1,650 researchers from Europe and beyond.
Apply by 10 September → europa.eu/!fBTMgF
May 12, 2025 at 10:11 AM
Happy to host good candidates!
DM for more info.
DM for more info.