Pipeline release! nf-core/hlatyping v2.1.0 - 2.1.0 - Chewbacca!

Please see the changelog: https://github.com/nf-core/hlatyping/releases/tag/2.1.0

14.04.2025 15:11 — 👍 2    🔁 1    💬 0    📌 0

nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework Author summary We have created nf-core/airrflow, a workflow to help researchers study the immune system in healthy and disease states, such as infections, autoimmunity, and cancer. The adaptive immune...

Do you analyze large BCR and TCR sequencing datasets?

Answer our survey for improving nf-core/airrflow, a Nextflow pipeline to analyze bulk and single-cell AIRRseq data (doi.org/10.1371/jour...). We’re interested in your opinion on useful new features!

yalesurvey.ca1.qualtrics.com/jfe/form/SV_...

31.03.2025 14:41 — 👍 9    🔁 5    💬 0    📌 0

nf-core/detaxizer nf-co.re/detaxizer: A Benchmarking Study for Decontamination from Human Sequences www.biorxiv.org/content/10.1... 🧬🖥️🧪 nextflow github.com/nf-core/deta...

31.03.2025 10:01 — 👍 12    🔁 6    💬 0    📌 0

a cat is sitting in front of a laptop computer on a couch . ALT: a cat is sitting in front of a laptop computer on a couch .

Interested in contributing to @nf-co.re or improving your nf-core pipeline? Register and join the #nf-core hackathon local hub in Tübingen on March 24th-27th if you live nearby! We have snacks and stickers!
nf-co.re/events/2025/...

28.02.2025 14:50 — 👍 3    🔁 0    💬 0    📌 0

TIMS2Rescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MS2Rescore pubs.acs.org/doi/10....

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#proteomics #prot-paper

07.02.2025 08:20 — 👍 1    🔁 1    💬 0    📌 0

Bioinformatician (f/m/d)

We are #hiring! 🚀 Join our #bioinformatics team in a truly #interdisciplinary environment driving #immunopeptidomics analyses and pipeline development with direct impact on advancing patient treatment! Check out the full job description: jobs.medizin.uni-tuebingen.de/Job/5775/Bio...

04.02.2025 06:43 — 👍 0    🔁 1    💬 0    📌 0

Audience in lecture hall

Pavel Sinitcyn presenting

Katerina Nastou presenting

Will Fondrie presenting

The EUBIC-MS Developers Meeting 2025 in Brixen is off to a great start with keynotes by Pavel Sinitcyn, Katerina Nastou, and @willfondrie.com.

#EuBIC2025

03.02.2025 12:59 — 👍 23    🔁 11    💬 1    📌 0

Can’t stress enough about having some code repository (GitHub etc) especially if you are early career and/or looking for a job. If the selection criteria asks for scientific programming skills, everyone claims they can code and use good practice. Show some evidence by providing a link to GitHub etc

01.02.2025 09:13 — 👍 42    🔁 16    💬 2    📌 0

Great Stuff! Thanks for the Thread. Is synchro-PASEF now built-in the Bruker software, or is a Special plugin needed?

28.01.2025 13:40 — 👍 0    🔁 0    💬 1    📌 0

Impact of Local Air Pressure on Ion Mobilities and Data Consistency in diaPASEF-Based High Throughput Proteomics Data-independent acquisition (DIA) on ion mobility mass spectrometers enables deep proteome coverage and high data completeness in large-scale proteomics studies. For advanced acquisition schemes such...

Nice and short technical paper about how air pressure can change ion mobility shifts and peptide quantification! #proteomics
pubs.acs.org/doi/abs/10.1...

28.01.2025 09:51 — 👍 4    🔁 0    💬 0    📌 0

I was forced to do 3h pure copy&pasting excel lists as a student assistant and got sick of it quickly

14.01.2025 22:38 — 👍 0    🔁 0    💬 0    📌 0

Frontiers | Warehouse-based, immunopeptidome-guided design of personalised peptide vaccines shows feasibility in clinical trial evaluation in CLL patients

Phase I trial update: Our warehouse-based cancer peptide vaccine for CLL showed promising safety but limited T cell responses.
Next: Follow-up trial with improved adjuvants & BTK inhibitors underway. Stay tuned! #CancerResearch #Immunopeptidomics #Immunotherapy
🔗 doi.org/10.3389/fimm...

08.01.2025 12:18 — 👍 5    🔁 1    💬 0    📌 0

Nice tiny Xmas gift in the new release 🎄. Percolator feature weights can be simply plotted now with multiQC!

22.12.2024 11:50 — 👍 3    🔁 1    💬 0    📌 0

Leveraging the Human Panproteome to Enhance Peptide and Protein Identification in Proteomics and Metaproteomics www.biorxiv.org/cont...

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#proteomics #prot-preprint

27.11.2024 08:40 — 👍 4    🔁 4    💬 0    📌 0

Nice work! I had a hard time using some of these tools with #immunopeptidomics data some time ago. Do you know/recommend a tool here that is decent in analyzing this data?

23.11.2024 08:46 — 👍 0    🔁 0    💬 1    📌 0

MS2Rescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0 Rescoring of peptide–spectrum matches (PSMs) has emerged as a standard procedure for the analysis of tandem mass spectrometry data. This emphasizes the need for software maintenance and continuous imp...

Happy to announce MS²Rescore v3.0, our much-improved platform for #MachineLearning driven rescoring of #Proteomics search results.

A big thanks to Louise Buur and Viktoria Dorfer for the great collaboration!

Open access full text: biblio.ugent.be/publication/...
Project: github.com/compomics/ms...

19.03.2024 14:58 — 👍 4    🔁 1    💬 0    📌 0

Pipeline release! nf-core/epitopeprediction v2.3.0 - 2.3.0 - Oesterberg!

Please see the changelog: https://github.com/nf-core/epitopeprediction/releases/tag/2.3.0

26.02.2024 11:52 — 👍 3    🔁 2    💬 0    📌 0