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Markus Hartl

@hartl.bsky.social
736 followers 335 following 54 posts

Biologist and proteomics specialist at Max Perutz Labs Vienna.

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Reposted by Markus Hartl
Ben Neely @benneely.com · 02/09/2026
So the hackathon projects are open and looking super cool. Obviously I am partial to the one me and @magnuspalmblad.bsky.social are doing on GROUNDING.md, but these other ones look amazing! github.com/EuBIC/EuBIC2...
github.com
EuBIC EuBIC2027 Hackathon Proposals · Discussions
Explore the GitHub Discussions forum for EuBIC EuBIC2027 in the Hackathon Proposals category.
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Magnus Palmblad @magnuspalmblad.bsky.social · 07/07/2026
Tired of AI-generated figures? I asked our talented scientific illustrator Manon Zuurmond to draw some of the instruments and lab equipment we missed in NIH's otherwise fantastic BioArt resource. First batch now available as CC BY. Free for everyone to use in publications: github.com/Center-for-P...
Drawings of various laboratory equipment (liquid chromatography system, mass spectrometers and a centrifuge).
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Michael Okun @michael-okun.bsky.social · 10/06/2026
I’ve officially resigned as Associate Editor for Frontiers in Systems Neuroscience. It used to be a reputable journal, but became a case study in how forced automation destroys academic integrity. 👇
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Reese Richardson @reeserichardson.bsky.social · 05/06/2026
The Thermo Fisher situation keeps getting worse. We've now collected 450+ problematic images presented as verification data in TF's antibody catalog. This includes: 🖌️ Dozens more images with duplications or painting 🖨️ Hundreds of blots that all share the same background (behold slideshow below)
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Markus Hartl @hartl.bsky.social · 08/04/2026
Important groundwork from the Picotti lab. A deep dive into in-source fragmentation.
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Devin Schweppe @dschweppe.bsky.social · 07/04/2026
The next iteration of O-MAP targeting genomic loci is now at eLife!! DNA O-MAP enables proximity labeling at specific DNA loci took a ton of work from many lab members and collaborators, so it's really exciting to wrap up this paper with @oligopain.bsky.social! elifesciences.org/articles/102...
elifesciences.org
DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci
DNA O-MAP enables proximity labeling at specific genomic loci in fixed cells using programmable oligonucleotides, revealing locus-proximal proteomes and chromatin interactions without genetic modifica...
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Cameron Blevins @cblevins.bsky.social · 03/04/2026
This is so, so well-articulated.
People call this friction "grunt work." Schwartz uses exactly that phrase, and he's right that LLMs can remove it. What he doesn't say, because he already has decades of hard-won intuition and doesn't need the grunt work anymore, is that for someone who doesn't yet have that intuition, the grunt work is the work. The boring parts and the important parts are tangled together in a way that you can't separate in advance. You don't know which afternoon of debugging was the one that taught you something fundamental about your data until three years later, when you're working on a completely different problem and the insight surfaces. Serendipity doesn't come from efficiency. It comes from spending time in the space where the problem lives, getting your hands dirty, making mistakes that nobody asked you to make and learning things nobody assigned you to learn.
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AITHYRA Research Institute of the Austrian Academy of Sciences @aithyra.bsky.social · 26/03/2026
AITHYRA is recruiting a LIFE SCIENCE PI We are interested in research questions related to one of our four core disease areas: cancer research, immunological disorders, infectious diseases, neurodevelopment disorders. Job Ad: aithyra.at/fileadmin/do... Apply by 30.4.2026 #StartingPI #LS #AITHYRA
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AITHYRA Research Institute of the Austrian Academy of Sciences @aithyra.bsky.social · 26/03/2026
AITHYRA is recruiting an AI/ML STARTING PI Generative Models, Large Language Models, Agentic AI, Active & Reinforcement Learning, AI-driven Scientific Discovery & Lab Automation, ML-driven molecular simulations... Job Ad: aithyra.at/fileadmin/do... Apply by 30.4.2026 #StartingPI #AI/ML #AITHYRA
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Chris Ashwood @cashwood.proteaglyco.com · 04/03/2026
Acquisition news for bottom up and top down proteomics with Thermo acquiring Proteinaceous and MSAID. Proteinaceous was founded in 2016 (possibly earlier) as a spin out from Neil Kelleher’s lab at Northwestern. MSAID was spun out from Mathias Wilhelm and Bernhardt Kuster’s labs in 2019.
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Alister Burt @alisterburt.bsky.social · 03/03/2026
Wonderful (and fun!) read from @mastroianni.bsky.social which finishes with a clear answer on how to solve the collective action problem of dismantling scientific publishing
open.substack.com
The one science reform we can all agree on, but we're too cowardly to do
OR: the long overdue forest fire
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Yasin Dagdas @plantophagy.bsky.social · 23/02/2026
Really happy to see this one out: www.sciencedirect.com/science/arti... Alibek's drive & great coll w/ friends @gekaragoz.bsky.social & E. Hallacli resulted in a cool story that starts with our beloved #Marchantia and ends with iPSC-derived neurons 🤩🤪 A short 🧵
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Diego del Alamo @delalamo.xyz · 26/12/2025
So 2025 turned out to be a big year for de novo antibody design! Here are thoughts and predictions on the state of de novo antibody design heading into 2026 🧵
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Ming Tommy Tang @tommytang.bsky.social · 17/11/2025
Thread: Multi-omics sounds cool—until you actually try it. Here's are the nuances. 1/ You’ve got RNA-seq. Methylation. Proteomics. Time to “integrate” the data. But how? And why? Let’s break it down.
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Ernst Schmid @ernstschmid.bsky.social · 26/02/2025
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...
cell.com
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...
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Pedro Beltrao @pedrobeltrao.bsky.social · 22/07/2025
Unexpectedly, @jurgjn.bsky.social found that running Alphafold3 predictions for protein interactions can yield ipTM scores that are more predictive of true interactions when run in pools of proteins instead of pairwise predictions. Presumably, this reflects some sort of "competition effect".
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Kusterlab @kusterlab.bsky.social · 09/09/2025
New preprint: We isolate peptide–RNA photo-crosslinks with tunable RNA chains from living cells for mass spec. This maps over 4,700 crosslinking sites across 744 proteins and offers the first glimpse into the RNA sequences in crosslinks by MS. Read here: doi.org/10.1101/2025...
doi.org
Peptide-RNA photo-crosslinks with tunable RNA chain map protein-RNA interfaces
Photo-crosslinking mass spectrometry enables the identification of protein-RNA interactions in living cells, pinpointing interaction interfaces at single-amino acid resolution. However, current isolat...
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Olivia Guest · Ολίβια Γκεστ @olivia.science · 25/10/2025
"Many scholars, including us, have highlighted the threat posed by techno-solutionism in education: Rather than expanding our intellectual horizons, these technologies undermine the very conditions that allow us to think for ourselves." 1/n www.project-syndicate.org/commentary/a...
project-syndicate.org
AI Is Hollowing Out Higher Education
Olivia Guest & Iris van Rooij urge teachers and scholars to reject tools that commodify learning, deskill students, and promote illiteracy.
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Kusterlab @kusterlab.bsky.social · 20/10/2025
Our new review paper about Pathway-Centric PTM Data Analysis is out this week in #Proteomics! We cover databases, enrichment tools, software for pathway reconstruction, and full-fledged platforms that help to interpret high-throughput PTM datasets. Check it out here: doi.org/10.1002/pmic...
doi.org
Computational Approaches for Pathway‐Centric Analysis of Protein Post‐Translational Modifications
Protein function is dynamically modulated by post-translational modifications (PTMs). Many different types of PTMs can nowadays be identified and quantified at a large scale using mass spectrometry. ...
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ypic.bsky.social @ypic.bsky.social · 23/09/2025
🎉 Exciting opportunity for students in proteomics! 🎉 The Student Proteomics Fund (SPF) is back! 📅 Key dates: Call opens: October 1, 2025 Submission deadline: November 30, 2025 Don’t miss your chance to bring your research idea to life! New boost #SPF #YPIC #Proteomics
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Christa Buecker @chribue.bsky.social · 10/09/2025
Just one more week left to get an application in! Starting my lab at the Perutz and the @viennabiocenter.bsky.social has been a fantastic opportunity that shaped me as a scientist!
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Vienna BioCenter Scientific Training @vbcscitraining.bsky.social · 07/09/2025
The Vienna BioCenter PhD program in Molecular BioSciences will offer 20+ fully-funded positions in the Autumn Call which is now open. Have a look at what our campus has to offer: www.vbcphd.at
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Lindsay K Pino @lindsaykpino.com · 06/09/2025
Do you or your lab use the Skyline software for #MassSpectrometry #proteomics? I'm looking for instructors to help with this year's Skyline Online, a virtual workshop/crash-course for all things Skyline! I'm especially looking for early career researchers for this opportunity. Please DM!
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Ben Williamson @benpatrickwill.bsky.social · 07/09/2025
Academic authors, here's a peek into the black box of journal publishing from an journal editor if you can bear it:
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Thilo Muth @drmuth.bsky.social · 26/08/2025
Impressive work from great colleagues at RKI. Ultra-fast virus 🦠 diagnostics with mass spec. Original publication on vPro-MS here: www.nature.com/articles/s41...
nature.com
vPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics - Nature Communications
Proteomics is going viral as a new diagnostic method for untargeted virus identification from patient samples. vPro-MS can be used to simultaneously identify human-pathogenic viruses and analyze the h...
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Alejandro Brenes @ajbrenes.com · 26/08/2025
After the DVP symposium now begins the start of the European Symposium on Single Cell Proteomics #ECSP25 A quick intro from @kmechtler.bsky.social and we kick off two days of exciting science starting with SCP of neutrophils in glioblastoma
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Alexander Hogrebe, PhD @alexhgo.bsky.social · 19/08/2025
A really nice example on how to visually communicate the text contents of a paper on mobile phones
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Christian Kost @kostchristian.bsky.social · 08/08/2025
I am excited to announce that the position of a senior postdoc (3 +3 years) in the field of theoretical biology is available in my group. The position provides the opportunity to closely interact with experimentalists and develop own research projects. Please RT. Details 👇: shorturl.at/iiiOv
shorturl.at
116 FB 5 Research Assistant (m/f/d) field of Theoretical Ecology and Evolution or Computational Biology: Uni Osnabrück
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Andrea Sinz 🧪 @sinzandrea.bsky.social · 15/07/2025
▶️▶️ To all mass spec enthusiasts: A postdoc position (three years) is available in our international group. Please apply if you are interested in structural MS and in developing novel cross-link ing MS workflows!🧪 Thanks @diegofgar.bsky.social for sharing! #teammassspec #AcademicSky #ChemSky
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Andrea Sinz 🧪 @sinzandrea.bsky.social · 25/06/2025
‼️ Job alert 🚨: I have an open 3-year postdoc position in my lab to develop novel crosslinking mass spectrometry workflows. 🧪🧪 So if you want to do cool stuff in protein MS, please apply ! ⬇️ Please RT www.verwaltung.uni-halle.de/dezern3/Auss... #Academicsky #Chemsky #teammassspec
verwaltung.uni-halle.de
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Carl T. Bergstrom @carlbergstrom.com · 25/06/2025
A few months ago, Nature published how-to guide for using ChatGPT to write your peer reviews in 30 minutes. This is, of course, a horrible idea. Here’s my response with @jbakcoleman.bsky.social .
nature.com
AI, peer review and the human activity of science
When researchers cede their scientific judgement to machines, we lose something important.
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Michael MacCoss @maccoss.bsky.social · 16/06/2025
Excited to see this published! It is a good step in the process for people to assess their FDR control in proteomics experiments. Great work from @bo-wen.bsky.social and @urikeich.bsky.social in particular who drove this.
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Ming Tommy Tang @tommytang.bsky.social · 31/05/2025
12/ Bioinformatics isn't just code. It's skepticism. It’s pattern recognition. It’s noticing when something feels off. Your instincts matter. Listen to them. Then verify with data.
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Andrew Burgess @drandrewburgess.bsky.social · 27/05/2025
Love today’s #xkcd comic on #MassSpec 🤣
BEFORE THE BATHROOM SCALE WAS INVENTED, THE ONLY
WAY TO WEIGH PEOPLE WAS MASS SPECTROMETRY.
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Kusterlab @kusterlab.bsky.social · 22/05/2025
🚨Our new paper is online🚨 We use zero-distance⚡photo-crosslinking⚡to reveal direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes. #DNA #Chromatin #Proteomics www.cell.com/cell/fulltex...
cell.com
The human proteome with direct physical access to DNA
Zero-distance photo-crosslinking reveals direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes with single-amino-aci...
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Alexey Nesvizhskii @nesvilab.bsky.social · 15/05/2025
If there any #Sciex decision makers here on Bluesky - I urge you to reconsider. Skyline/Proteowizard support is not only important for your customers using these tools, but it also benefits other bioinformatics efforts that depend on these tools.
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Ass. Prof. Evelyn Rampler @evelynrampler.bsky.social · 30/04/2025
Please apply for this open position for a senior scientist at our faculty. It is the head of the mass spec center and you will be my close colleague! Application Deadline:8.5.2025 jobs.univie.ac.at/job/Senior-S...
jobs.univie.ac.at
Senior Scientist
Senior Scientist
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CZproteo @proteomicscz.bsky.social · 22/04/2025
DIA-MS and targeted #proteomics workshop May 19, 2025, Masaryk University, Brno CZ Organized by CZproteo keynote by Alexey Nesvizhskii @nesvilab.bsky.social Program & Registration: czproteo.cz/workshop-cur...
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Michael Bronstein @mmbronstein.bsky.social · 17/03/2025
Aithyra is hiring! We are looking for multiple starting PIs in life sciences and AI/ML. We offer highly competitive packages and salaries among the highest in Europe. www.oeaw.ac.at/aithyra/news...
oeaw.ac.at
Search for LIFE SCIENCE and AI/ML Starting Principal Investigators (m/f/d) at AITHYRA, Vienna
If you are an ambitious early-career scientist ready to propel your research to new heights, we invite you to be part of AITHYRA’s founding generation of Principal Investigators. Together, we will sha...
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John Gallagher @johnrgallagher.bsky.social · 29/03/2025
I wrote a very long blog post about AI writing. I hope you'll read it. meresophistry.substack.com/p/the-mental...
meresophistry.substack.com
The mental tyranny of AI writing
An arduously long blog post
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Leo Kiss @leokiss.bsky.social · 24/03/2025
Super excited to share our latest work on deciphering the #Ubiquitin Code “𝗨𝗯𝗶𝗥𝗘𝗔𝗗 𝗱𝗲𝗰𝗶𝗽𝗵𝗲𝗿𝘀 𝗽𝗿𝗼𝘁𝗲𝗮𝘀𝗼𝗺𝗮𝗹 𝗱𝗲𝗴𝗿𝗮𝗱𝗮𝘁𝗶𝗼𝗻 𝗰𝗼𝗱𝗲 𝗼𝗳 𝗵𝗼𝗺𝗼𝘁𝘆𝗽𝗶𝗰 𝗮𝗻𝗱 𝗯𝗿𝗮𝗻𝗰𝗵𝗲𝗱 𝗞48 𝗮𝗻𝗱 𝗞63 𝘂𝗯𝗶𝗾𝘂𝗶𝘁𝗶𝗻 𝗰𝗵𝗮𝗶𝗻𝘀” @cp-molcell.bsky.social 1/8 www.cell.com/molecular-ce...
cell.com
UbiREAD deciphers proteasomal degradation code of homotypic and branched K48 and K63 ubiquitin chains
Ubiquitin chains determine the fates of their modified proteins, including proteasomal degradation. Kiss et al. present UbiREAD, a technology to monitor cellular degradation and deubiquitination at hi...
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Michael MacCoss @maccoss.bsky.social · 10/03/2025
2025 Quantitative Proteomics Course in Seattle WA. Space is limited, register now! This is the 11th year of offering this weeklong course. skyline.ms/project/home... #proteomicsky #massspecsky #massspec
skyline.ms
Start Page: /home/software/Skyline/events/2025 UW Course
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Christoph Messner @christophmessner.bsky.social · 22/01/2025
We are expanding our team and looking for a postdoc in Davos! Are you passionate about combining cutting-edge proteomics and immunology to unravel the mechanisms behind human diseases? Join our collaborative and supportive environment in beautiful Davos.
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Marco Hein @marco.heinlab.org · 14/01/2025
Time to share our organelle proteome paper out in @cellcellpress.bsky.social: doi.org/nzwz We created a spatial map of human cells using organelle immunoprecipitation at scale. Locate your fav protein among the 7,600 we mapped across 19 subcellular compartments: organelles.sf.czbiohub.org/ 1/3 🧪
Graphical abstract of the Organelle Profiling paper, showing the workflow:
Endogenously tagged organelle library;
Native IP proteomics;
Data-driven graph clustering;
resulting in a subcellular proteome map with
more than 7,600 proteins localized across 19 subcellular compartments.
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Markus Hartl @hartl.bsky.social · 14/01/2025
Finally, an experienced MS group performed a proper comparison of MS plasma proteomics vs. Olink! Kudos to the Coon lab! Cannot wait to read all the details!
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Max Perutz Labs Vienna @maxperutzlabs.ac.at · 09/01/2025
🚨 Out now! @marcoyannic.bsky.social and his former colleagues at the Chan Zuckerberg Biohub have unveiled a new study in Cell. The team led by Manuel Leonetti mapped the subcellular distribution of thousands of proteins to create an atlas of the human proteome ➡️ tinyurl.com/ypn65duk @univie.ac.at
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Kai Kupferschmidt @kakape.bsky.social · 30/10/2024
I’ve reported on infectious diseases for 15 years, but during the covid-19 pandemic and even more during the global outbreak of mpox clade IIb, I was shocked by the amount of misinformation I was seeing. Misinfo had always been part of any outbreak, but this felt different. 🧪
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Alejandro Brenes @ajbrenes.com · 06/12/2024
Now this is a paper I had long been waiting for! NanoSPLITS is out! Parallel single cell proteomic and transcriptomic measurements from the same cell! Great work from @cajunscience.bsky.social and @nanopots.bsky.social www.nature.com/articles/s41...
nature.com
Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting - Nature Communications
Single-cell multiomics can provide broad insights into gene/protein regulatory networks and cellular diversity. Here, authors develop nanoSPLITS, a nanodroplet splitting approach for global profiling ...
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Mark A. Hanson @hansonmark.bsky.social · 19/11/2024
The strain on scientific publishing: we set out to characterise the remarkable growth of the scientific literature in the last few years, in spite of declining growth in total scientists. What is going on? direct.mit.edu/qss/article/... A 🧵 1/n #AcademicSky #PhDchat #ScientificPublishing #SciPub
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kmechtler.bsky.social @kmechtler.bsky.social · 21/11/2024
It gives me great pleasure to announce our next European Single Cell Proteomics Conference www.apma.at/6thescp/ We would be delighted to receive many abstracts from students so that they have the opportunity to give their first presentation. On behalf of: Erwin, Fabian, Manuel, Fabian and Karl
apma.at
6th ESCP 2025 – APMA
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