Daniel Geiszler
@dannygeiszler.bsky.social
You can call me Danny
EMBO Fellow doing Computational Proteomics
Nesvi lab -> Özlü lab
📍İstanbul
https://danny.bio
EMBO Fellow doing Computational Proteomics
Nesvi lab -> Özlü lab
📍İstanbul
https://danny.bio
There’s a big infographic with all of the proteomics startups that occasionally makes rounds. Does anyone know where it can be found?
March 20, 2025 at 6:43 PM
There’s a big infographic with all of the proteomics startups that occasionally makes rounds. Does anyone know where it can be found?
“Seeking Methuselan bioinformatician for methods development”
February 26, 2025 at 12:11 PM
“Seeking Methuselan bioinformatician for methods development”
Reposted by Daniel Geiszler
Our study reconfigures our understanding of the mechanism cells use regulate gene expression.
What was previously reported to have little global impact now is reported to explain up to half of the variation in how protein levels are controlled. Protein degradation matters!
shorturl.at/5wPiS
What was previously reported to have little global impact now is reported to explain up to half of the variation in how protein levels are controlled. Protein degradation matters!
shorturl.at/5wPiS
Protein degradation and growth dependent dilution substantially shape mammalian proteomes
Cellular protein concentrations are maintained through a balance of synthesis and clearance. Clearance occurs through both protein degradation and growth-dependent dilution. At slow growth, clearance ...
www.biorxiv.org
February 25, 2025 at 5:44 PM
Our study reconfigures our understanding of the mechanism cells use regulate gene expression.
What was previously reported to have little global impact now is reported to explain up to half of the variation in how protein levels are controlled. Protein degradation matters!
shorturl.at/5wPiS
What was previously reported to have little global impact now is reported to explain up to half of the variation in how protein levels are controlled. Protein degradation matters!
shorturl.at/5wPiS
Fun little project with OpenCV
February 25, 2025 at 4:06 PM
Fun little project with OpenCV
Reposted by Daniel Geiszler
I created a brief spreadsheet of reductions I've heard of so far. Any additions you know of (especially if you have the links/receipts) would be great: docs.google.com/spreadsheets...
Graduate Reductions Across Biomedical Sciences (2025)
docs.google.com
February 22, 2025 at 1:23 PM
I created a brief spreadsheet of reductions I've heard of so far. Any additions you know of (especially if you have the links/receipts) would be great: docs.google.com/spreadsheets...
I’ve been pretty unimpressed with Deep Research. The actual research is very shallow. It’s missing 50-95% of the relevant info on every case I’ve tested. Is there some sort of magic I haven’t learned?
February 22, 2025 at 3:45 PM
I’ve been pretty unimpressed with Deep Research. The actual research is very shallow. It’s missing 50-95% of the relevant info on every case I’ve tested. Is there some sort of magic I haven’t learned?
Reposted by Daniel Geiszler
It's finally out – actually out and in print! Many thanks to @jcornlab.bsky.social @matthiasmuhar.bsky.social @jakobfarnung.bsky.social and all the fantastic collaborators. What started as pure curiosity lead to an amazing find!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
C-terminal amides mark proteins for degradation via SCF–FBXO31 - Nature
SCF–FBXO31 scans proteins for C-terminal amidation and marks them for subsequent proteasomal degradation.
www.nature.com
February 12, 2025 at 8:23 PM
It's finally out – actually out and in print! Many thanks to @jcornlab.bsky.social @matthiasmuhar.bsky.social @jakobfarnung.bsky.social and all the fantastic collaborators. What started as pure curiosity lead to an amazing find!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Congrats to @alussana.bsky.social and @epetsalaki.bsky.social !
Kinases play a role in many diseases, making them prime targets for therapeutic intervention.
Enter PhosX, a new tool transforming the way researchers analyse and interpret kinase activity.
Read the full article: academic.oup.com/bioinformati...
@alussana.bsky.social @epetsalaki.bsky.social
Enter PhosX, a new tool transforming the way researchers analyse and interpret kinase activity.
Read the full article: academic.oup.com/bioinformati...
@alussana.bsky.social @epetsalaki.bsky.social
PhosX: data-driven kinase activity inference from phosphoproteomics experiments
AbstractSummary. The inference of kinase activity from phosphoproteomics data can point to causal mechanisms driving signalling processes and potential dru
academic.oup.com
January 27, 2025 at 4:54 PM
Congrats to @alussana.bsky.social and @epetsalaki.bsky.social !
Reposted by Daniel Geiszler
Post-translational modifications on proteins can serve as metabolic anchors to target selected proteins for degradation. We are excited to share our study on GlyTACs, a PROTAC modality targeting glycoproteins for proteosomal degradation. Check it out #chembio! chemrxiv.org/engage/chemr...
Self-Assembled PROTACs Enable Glycoproteins Degradation in the Living Cells.
We report here a two-component proteolysis targeting chimeras (PROTACs) strategy selectively targeting O-GalNAcylated and O-GlcNAcylated proteins for proteasomal degradation, which leads to severe tox...
chemrxiv.org
January 16, 2025 at 12:28 PM
Post-translational modifications on proteins can serve as metabolic anchors to target selected proteins for degradation. We are excited to share our study on GlyTACs, a PROTAC modality targeting glycoproteins for proteosomal degradation. Check it out #chembio! chemrxiv.org/engage/chemr...
Reposted by Daniel Geiszler
We are excited to share our new Nature Methods paper describing the Chip-Tip workflow for single-cell proteomics identifying >5,000 proteins in single cells, enabling PTM analysis without enrichment and throughput of up to 120 single cell samples per day: rdcu.be/d6qJe
Enhanced sensitivity and scalability with a Chip-Tip workflow enables deep single-cell proteomics
Nature Methods - Chip-Tip is a label-free quantification-based single-cell proteomics workflow for deep single-cell proteomics, which identifies over 5,000 proteins and 40,000 peptides in single...
rdcu.be
January 16, 2025 at 11:23 AM
We are excited to share our new Nature Methods paper describing the Chip-Tip workflow for single-cell proteomics identifying >5,000 proteins in single cells, enabling PTM analysis without enrichment and throughput of up to 120 single cell samples per day: rdcu.be/d6qJe
Reposted by Daniel Geiszler
🎉 We're happy to announce that our latest project was published in @naturecomms.bsky.social this week: PTMNavigator, a #bioinformatics web platform for in-depth analysis of post-translational modification (PTM) perturbation datasets.
📄 doi.org/10.1038/s414... (1/6)
📄 doi.org/10.1038/s414... (1/6)
PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways - Nature Communications
Post-translational modifications are important regulators of cellular pathways, but our understanding of these processes is limited. Here, the authors present a web tool that integrates various databa...
doi.org
January 10, 2025 at 2:20 PM
🎉 We're happy to announce that our latest project was published in @naturecomms.bsky.social this week: PTMNavigator, a #bioinformatics web platform for in-depth analysis of post-translational modification (PTM) perturbation datasets.
📄 doi.org/10.1038/s414... (1/6)
📄 doi.org/10.1038/s414... (1/6)
Reposted by Daniel Geiszler
Very interesting to see the 50 new drugs that made it to FDA approval in 2024 in one place. A lot of really exciting small molecule chemistry with interesting functional groups, deuterations and covalent warheads. #chemsky #chembio
www.linkedin.com/posts/chrisd...
www.linkedin.com/posts/chrisd...
Chris De Savi on LinkedIn: #medicine #pharmaceuticals #healthcare | 90 comments
FDA Novel Drug Approvals 2024 #medicine
That is a wrap for 2024! And another year of relentless drug discovery!
There you have it, drug-hunting aficionados,… | 90 comments on LinkedIn
www.linkedin.com
January 3, 2025 at 9:00 AM
Very interesting to see the 50 new drugs that made it to FDA approval in 2024 in one place. A lot of really exciting small molecule chemistry with interesting functional groups, deuterations and covalent warheads. #chemsky #chembio
www.linkedin.com/posts/chrisd...
www.linkedin.com/posts/chrisd...
AI creates jobs
Elsevier uses AI to unformat your paper and then real humans have to go through and try to make the paper right again
mathstodon.xyz/@11011110/11...
mathstodon.xyz/@11011110/11...
0xDE (@11011110@mathstodon.xyz)
Buried in a story about yet another Elsevier journal editorial board resigning en masse (Journal of Human Evolution, https://retractionwatch.com/2024/12/27/evolution-journal-editors-resign-en-masse-to...
mathstodon.xyz
December 28, 2024 at 8:48 AM
AI creates jobs
How is it that a 100-author paper from a consortium can be non-open access?
www.nature.com/articles/s41...
www.nature.com/articles/s41...
π-HuB: the proteomic navigator of the human body - Nature
We introduce a major scientific endeavour called π-HuB (proteomic navigator of the human body), its aim being to generate and harness multimodality proteomic datasets to enhance our understanding of h...
www.nature.com
December 26, 2024 at 8:42 PM
How is it that a 100-author paper from a consortium can be non-open access?
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Daniel Geiszler
Nature Methods named spatial proteomics its Method of the Year 2024, highlighting an approach that's transforming our understanding of biological complexity. It’s exciting to see proteomics methods gaining wider recognition in the broader scientific community. Read here: bit.ly/409d77x
Nature methods names spatial proteomics its 'method of the year' for 2024 - IonOpticks
Credit: Modified version of an image by Elham Karimi and Simon Milette, Walsh and Quail Labs, Rosalind and Morris Goodman Cancer Institute In an exciting recognition of cutting-edge biological researc...
bit.ly
December 25, 2024 at 8:48 PM
Nature Methods named spatial proteomics its Method of the Year 2024, highlighting an approach that's transforming our understanding of biological complexity. It’s exciting to see proteomics methods gaining wider recognition in the broader scientific community. Read here: bit.ly/409d77x
Fun fact: if ChatGPT tells you an image is too low quality to process, you can just bully it into processing it anyway.
December 5, 2024 at 11:14 AM
Fun fact: if ChatGPT tells you an image is too low quality to process, you can just bully it into processing it anyway.
Reposted by Daniel Geiszler
Ancient genomics support deep divergence between Eastern and Western Mediterranean Indo-European languages https://www.biorxiv.org/content/10.1101/2024.12.02.626332v1
Ancient genomics support deep divergence between Eastern and Western Mediterranean Indo-European languages https://www.biorxiv.org/content/10.1101/2024.12.02.626332v1
The Indo-European languages are among the most widely spoken in the world, yet their early diversifi
www.biorxiv.org
December 2, 2024 at 10:32 PM
Ancient genomics support deep divergence between Eastern and Western Mediterranean Indo-European languages https://www.biorxiv.org/content/10.1101/2024.12.02.626332v1
Reposted by Daniel Geiszler
🧬 New in @Nature: Our team found that fat cells keep a “memory” of their previous obese state even after weight loss, helping explain why maintaining weight loss is so challenging. Excited to share this work!!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Adipose tissue retains an epigenetic memory of obesity after weight loss - Nature
Stable epigenetic changes indicate the existence of an obesogenic memory in mouse adipocytes that primes cells for pathological responses in an obesogenic environment and potentially contributes to th...
www.nature.com
November 19, 2024 at 5:12 AM
🧬 New in @Nature: Our team found that fat cells keep a “memory” of their previous obese state even after weight loss, helping explain why maintaining weight loss is so challenging. Excited to share this work!!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Nvidia has just open-sourced BioNeMo, a framework for bioinformatics researchers doing machine learning research. Looks like it currently supports (hopefully not only) molecule generation, structure prediction, ligand binding, and representation learning.
nvidia.github.io/bionemo-fram...
nvidia.github.io/bionemo-fram...
BioNeMo Framework
nvidia.github.io
November 19, 2024 at 10:45 AM
Nvidia has just open-sourced BioNeMo, a framework for bioinformatics researchers doing machine learning research. Looks like it currently supports (hopefully not only) molecule generation, structure prediction, ligand binding, and representation learning.
nvidia.github.io/bionemo-fram...
nvidia.github.io/bionemo-fram...