Markus Hartl
@hartl.bsky.social
๐ค 716
๐ฅ 335
๐ 54
Biologist and proteomics specialist at Max Perutz Labs Vienna.
Important groundwork from the Picotti lab. A deep dive into in-source fragmentation.
add a skeleton here at some point
about 1 month ago
0
1
0
reposted by
Markus Hartl
Devin Schweppe
about 1 month ago
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...
loading . . .
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...
https://elifesciences.org/articles/102489
1
32
14
reposted by
Markus Hartl
Cameron Blevins
about 1 month ago
This is so, so well-articulated.
add a skeleton here at some point
97
10781
4266
reposted by
Markus Hartl
AITHYRA Research Institute of the Austrian Academy of Sciences
about 2 months ago
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
0
8
14
reposted by
Markus Hartl
AITHYRA Research Institute of the Austrian Academy of Sciences
about 2 months ago
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
1
14
14
reposted by
Markus Hartl
Chris Ashwood
2 months ago
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 Kelleherโs lab at Northwestern. MSAID was spun out from Mathias Wilhelm and Bernhardt Kusterโs labs in 2019.
1
7
3
reposted by
Markus Hartl
Alister Burt
2 months ago
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
loading . . .
The one science reform we can all agree on, but we're too cowardly to do
OR: the long overdue forest fire
https://open.substack.com/pub/experimentalhistory/p/the-one-science-reform-we-can-all?r=bfuf8&utm_medium=ios
0
12
8
reposted by
Markus Hartl
Yasin Dagdas
3 months ago
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 ๐คฉ๐คช A short ๐งต
6
119
60
reposted by
Markus Hartl
Diego del Alamo
5 months ago
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 ๐งต
1
43
17
reposted by
Markus Hartl
Ming Tommy Tang
6 months ago
Thread: Multi-omics sounds coolโuntil you actually try it. Here's are the nuances. 1/ Youโve got RNA-seq. Methylation. Proteomics. Time to โintegrateโ the data. But how? And why? Letโs break it down.
1
14
4
reposted by
Markus Hartl
Ernst Schmid
about 1 year ago
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...
loading . . .
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...
https://www.cell.com/molecular-cell/fulltext/S1097-2765(25)00105-4
3
29
12
reposted by
Markus Hartl
Pedro Beltrao
10 months ago
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".
3
87
34
reposted by
Markus Hartl
Kusterlab
8 months ago
New preprint: We isolate peptideโRNA 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...
loading . . .
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...
https://doi.org/10.1101/2025.09.05.674461
0
24
15
reposted by
Markus Hartl
Olivia Guest ยท ฮฮปฮฏฮฒฮนฮฑ ฮฮบฮตฯฯ
7 months ago
"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...
add a skeleton here at some point
2
223
121
reposted by
Markus Hartl
Kusterlab
7 months ago
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...
loading . . .
Computational Approaches for PathwayโCentric Analysis of Protein PostโTranslational 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. ...
http://doi.org/10.1002/pmic.70055
0
28
13
reposted by
Markus Hartl
8 months ago
๐ Exciting opportunity for students in proteomics! ๐ The Student Proteomics Fund (SPF) is back! ๐ Key dates: Call opens: October 1, 2025 Submission deadline: November 30, 2025 Donโt miss your chance to bring your research idea to life! New boost
#SPF
#YPIC
#Proteomics
0
4
7
reposted by
Markus Hartl
Christa Buecker
8 months ago
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!
add a skeleton here at some point
0
28
27
reposted by
Markus Hartl
Vienna BioCenter Scientific Training
8 months ago
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
loading . . .
1
14
10
reposted by
Markus Hartl
Lindsay K Pino
8 months ago
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!
0
10
12
reposted by
Markus Hartl
Ben Williamson
8 months ago
Academic authors, here's a peek into the black box of journal publishing from an journal editor if you can bear it:
18
1000
575
reposted by
Markus Hartl
Thilo Muth
9 months ago
Impressive work from great colleagues at RKI. Ultra-fast virus ๐ฆ diagnostics with mass spec. Original publication on vPro-MS here:
www.nature.com/articles/s41...
add a skeleton here at some point
0
5
2
reposted by
Markus Hartl
Alejandro Brenes
9 months ago
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
1
13
2
reposted by
Markus Hartl
Alexander Hogrebe, PhD
9 months ago
A really nice example on how to visually communicate the text contents of a paper on mobile phones
add a skeleton here at some point
0
4
3
reposted by
Markus Hartl
Christian Kost
9 months ago
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 ๐:
shorturl.at/iiiOv
loading . . .
116 FB 5 Research Assistant (m/f/d) field of Theoretical Ecology and Evolution or Computational Biology: Uni Osnabrรผck
https://shorturl.at/iiiOv
2
95
123
reposted by
Markus Hartl
Andrea Sinz ๐งช
10 months ago
โถ๏ธโถ๏ธ 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!๐งช Thanks
@diegofgar.bsky.social
for sharing!
#teammassspec
#AcademicSky
#ChemSky
add a skeleton here at some point
1
15
15
reposted by
Markus Hartl
Andrea Sinz ๐งช
11 months ago
โผ๏ธ Job alert ๐จ: I have an open 3-year postdoc position in my lab to develop novel crosslinking mass spectrometry workflows. ๐งช๐งช So if you want to do cool stuff in protein MS, please apply ! โฌ๏ธ Please RT
www.verwaltung.uni-halle.de/dezern3/Auss...
#Academicsky
#Chemsky
#teammassspec
loading . . .
https://www.verwaltung.uni-halle.de/dezern3/Ausschr/25_5_6646_25_H.pdf
0
32
29
reposted by
Markus Hartl
Carl T. Bergstrom
11 months ago
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. Hereโs my response with
@jbakcoleman.bsky.social
.
loading . . .
AI, peer review and the human activity of science
When researchers cede their scientific judgement to machines, we lose something important.
https://www.nature.com/articles/d41586-025-01839-w
16
594
258
reposted by
Markus Hartl
Michael MacCoss
11 months ago
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.
add a skeleton here at some point
2
43
10
reposted by
Markus Hartl
Ming Tommy Tang
12 months ago
12/ Bioinformatics isn't just code. It's skepticism. Itโs pattern recognition. Itโs noticing when something feels off. Your instincts matter. Listen to them. Then verify with data.
1
4
2
reposted by
Markus Hartl
Andrew Burgess
12 months ago
Love todayโs
#xkcd
comic on
#MassSpec
๐คฃ
4
192
63
reposted by
Markus Hartl
Kusterlab
12 months ago
๐จOur new paper is online๐จ We use zero-distanceโกphoto-crosslinkingโกto 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...
loading . . .
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...
https://www.cell.com/cell/fulltext/S0092-8674(25)00507-0
2
85
42
reposted by
Markus Hartl
Alexey Nesvizhskii
about 1 year ago
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.
add a skeleton here at some point
0
25
10
reposted by
Markus Hartl
Ass. Prof. Evelyn Rampler
about 1 year ago
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...
loading . . .
Senior Scientist
Senior Scientist
https://jobs.univie.ac.at/job/Senior-Scientist/1197811201/
1
8
12
reposted by
Markus Hartl
CZproteo
about 1 year ago
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...
0
3
3
reposted by
Markus Hartl
Michael Bronstein
about 1 year ago
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...
loading . . .
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 AITHYRAโs founding generation of Principal Investigators. Together, we will sha...
https://www.oeaw.ac.at/aithyra/news/search-for-life-science-and-ai-ml-starting-principal-investigators-at-aithyra-vienna
2
39
14
reposted by
Markus Hartl
John Gallagher
about 1 year ago
I wrote a very long blog post about AI writing. I hope you'll read it.
meresophistry.substack.com/p/the-mental...
loading . . .
The mental tyranny of AI writing
An arduously long blog post
https://meresophistry.substack.com/p/the-mental-tyranny-of-ai-writing
18
195
83
reposted by
Markus Hartl
Leo Kiss
about 1 year ago
Super excited to share our latest work on deciphering the
#Ubiquitin
Code โ๐จ๐ฏ๐ถ๐ฅ๐๐๐ ๐ฑ๐ฒ๐ฐ๐ถ๐ฝ๐ต๐ฒ๐ฟ๐ ๐ฝ๐ฟ๐ผ๐๐ฒ๐ฎ๐๐ผ๐บ๐ฎ๐น ๐ฑ๐ฒ๐ด๐ฟ๐ฎ๐ฑ๐ฎ๐๐ถ๐ผ๐ป ๐ฐ๐ผ๐ฑ๐ฒ ๐ผ๐ณ ๐ต๐ผ๐บ๐ผ๐๐๐ฝ๐ถ๐ฐ ๐ฎ๐ป๐ฑ ๐ฏ๐ฟ๐ฎ๐ป๐ฐ๐ต๐ฒ๐ฑ ๐48 ๐ฎ๐ป๐ฑ ๐63 ๐๐ฏ๐ถ๐พ๐๐ถ๐๐ถ๐ป ๐ฐ๐ต๐ฎ๐ถ๐ป๐โ
@cp-molcell.bsky.social
1/8
www.cell.com/molecular-ce...
loading . . .
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 etย al. present UbiREAD, a technology to monitor cellular degradation and deubiquitination at hi...
https://www.cell.com/molecular-cell/fulltext/S1097-2765(25)00152-2
16
131
48
reposted by
Markus Hartl
Michael MacCoss
about 1 year ago
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
loading . . .
Start Page: /home/software/Skyline/events/2025 UW Course
https://skyline.ms/project/home/software/Skyline/events/2025%20UW%20Course/begin.view
0
23
10
reposted by
Markus Hartl
Christoph Messner
over 1 year ago
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.
0
8
3
reposted by
Markus Hartl
Marco Hein
over 1 year ago
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 ๐งช
7
196
62
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!
add a skeleton here at some point
over 1 year ago
2
16
3
reposted by
Markus Hartl
Max Perutz Labs Vienna
over 1 year ago
๐จ 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 โก๏ธ
tinyurl.com/ypn65duk
@univie.ac.at
0
22
6
reposted by
Markus Hartl
Kai Kupferschmidt
over 1 year ago
Iโve 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. ๐งช
15
475
116
reposted by
Markus Hartl
Alejandro Brenes
over 1 year ago
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...
loading . . .
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 ...
https://www.nature.com/articles/s41467-024-54099-z
3
66
19
reposted by
Markus Hartl
Mark A. Hanson
over 1 year ago
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 ๐งต 1/n
#AcademicSky
#PhDchat
#ScientificPublishing
#SciPub
45
996
693
reposted by
Markus Hartl
over 1 year ago
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
loading . . .
6th ESCP 2025 โ APMA
https://www.apma.at/6thescp/
0
27
17
reposted by
Markus Hartl
Alejandro Brenes
over 1 year ago
My perspective on CVs for DIA-based
#proteomics
is out in JPR It explores how normalisation, the CV formula and software parameters affect the outputs. It suggests parameters to use for biological and technical studies and provides an R package to calculate CVs.
doi.org/10.1021/acs....
loading . . .
Calculating and Reporting Coefficients of Variation for DIA-Based Proteomics
The coefficient of variation (CV) is a measure that is frequently used to assess data dispersion for mass spectrometry-based proteomics. In the current era of burgeoning technical developments, there ...
https://doi.org/10.1021/acs.jproteome.4c00461
3
66
22
reposted by
Markus Hartl
Richard Unwin
over 1 year ago
I spend a bit of time talking to folk with plasma cohorts about MS vs affinity approaches for discovery. Thought it was worth a thread. Most love the marketing. 5,000 proteins? 10,000 proteins? OLink was used in UK Biobank? Wow, mass spec is sooooo last year. Except life is not that simple.
add a skeleton here at some point
4
35
19
reposted by
Markus Hartl
Jan Schejbal
over 1 year ago
Few quick notes for new followers ๐ฆ Please add some bio โ๏ธ before starting to follow. I still have time to go through new followers and skip those without bio just as a precaution. If you add it later, I (and others) may not return to follow back and I would hate to miss out on great scientists๐ฉโ๐ฌ๐งโ๐ฌ!
1
19
8
Welcome
@kmechtler.bsky.social
to Bluesky! Very glad you join the conversation. Here is Alejandro's starter pack to get started.
go.bsky.app/HH7kqEh
add a skeleton here at some point
over 1 year ago
1
8
1
Load more
feeds!
log in