Thilo Muth

The Scientific Analysis of Renaissance Recipes: Proteomics, Medicine, and the Body in the Material Renaissance Abstract. Collaborations between the humanities and sciences allow for novel insights into the material world of Renaissance recipe cultures, and in partic

NEW PUBLICATION
Our @historians.org American Historical Review article presents a pathbreaking methodology to analyse the invisible biochemical traces that #earlymodern users left behind on the surface of paper recipes

doi.org/10.1093/ahr/...

Many thanks to wonderful @jenlucpiquant.bsky.social @arstechnica.com for this piece on our @historians.org AHR article on the proteomics analysis of Renaissance recipes. I really enjoyed our conversation!

iPepGen: a modular, immunopeptidogenomic analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates - PubMed Characterizing tumor-specific neoantigen peptides, derived from genomic or transcriptomic aberrations and presented to the immune system, is critical for immuno-oncology studies. To this end, the modular iPepGen immunopeptidogenomics pipeline provides these functions: (1) Neoantigen prediction and p …

iPepGen: a modular, immunopeptidogenomic analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates; Published in Genome Biology:
link.springer.com/article/10.1...

DiNovo enables high-coverage and high-confidence de novo peptide sequencing via mirror proteases and deep learning www.nature.com/artic...

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#proteomics #prot-paper

Systematic Evaluation of Data-independent Acquisition Workflows for High-Throughput and Low-Input Proteomics Analysis with an Astral Mass Spectrometer There is a growing interest in developing high-throughput and high-sensitivity mass spectrometry methods for proteomic profiling of low-input samples, such as sorted cells or spatially resolved tissue samples. Data-independent acquisition mass spectrometry (DIA-MS) coupled with short-gradient liquid chromatography (LC) is gaining significant attention for providing deep proteome coverage in low-input samples, particularly with the recent release of high-speed mass spectrometers. However, the quantification performance of existing DIA workflows for low-input samples has not been extensively evaluated, and there is no consensus on optimal informatics workflows to obtain high-quality quantitative data. As such, we systematically evaluated multiple factors in low-input DIA workflows on an Astral MS, including MS acquisition parameters, data analysis software (DIA-NN, Spectronaut, and FragPipe), LC separation gradient lengths, database searching algorithms, and protein quantification approaches. Using three-species proteome samples (human, yeast, and Escherichia coli) with total input ranging from 0.1 ng to 10 ng and predefined quantity ratios, we focused on proteome coverage, quantification accuracy, and precision, which are the most important considerations when applying these methods in biological applications. Our evaluation suggested a preferred DIA workflow for low-input samples, which involves using a FAIMS interface, DIA-NN-based library-free database search with the enabled match between runs (MBR) function, and MS1-level protein quantification with the maxLFQ algorithm.

Systematic Evaluation of Data-independent Acquisition Workflows for High-Throughput and Low-Input Proteomics Analysis with an Astral Mass Spectrometer | JPR pubs.acs.org/doi/abs/10.1...

Complete Data Analysis Workflow for Quantitative DIA Mass Spectrometry Using Nextflow Data-independent acquisition (DIA) mass spectrometry is a technique used in proteomics to identify and quantify proteins in complex biological samples. While this comprehensive approach yields more co...

Complete Data Analysis Workflow for Quantitative DIA Mass Spectrometry Using Nextflow | Journal of Proteome Research pubs.acs.org/doi/full/10....

An antimicrobial drug recommender system using MALDI-TOF MS and dual-branch neural networks It is possible to accurately recommend antimicrobial drugs from mass spectra using neural networks and large datasets, paving the way for more efficient clinical diagnostics.

An antimicrobial drug recommender system using MALDI-TOF MS and dual-branch neural networks doi.org/10.7554/eLif...

The Virtual Lab of AI agents designs new SARS-CoV-2 nanobodies - Nature Human collaboration with a team of artificial intelligence (AI) agents powered by large language models was used to efficiently design a complex interdisciplinary research project leading to the desig...

The Virtual Lab is there!
www.nature.com/articles/s41...

AI Agents with R Studio, finally: posit.co/products/ai/

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.

The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...

Figure 1 shows they key result

You have my attention... 👀

RNA-seq analysis in seconds using GPUs www.biorxiv.org/content/10.6... 🧬💻🧪 github.com/pachterlab/k...

Staying Current in Data Science and Computational Biology: 2026 Edition Part 3 in a series of posts going back 14 years

Staying Current in Data Science and Computational Biology: 2026 Edition. Part 3 in a series of posts going back 14 years. doi.org/10.59350/2na...

🌱 New preprint with @microbialmarie.bsky.social www.biorxiv.org/content/10.6...
Bacterial Strain Identity and Community Composition Drive the Seed-to-Seedling Microbiota Assembly
We explore which strain traits and community features explain successful bacterial transmission from seed to seedling.⬇️

PROTRIDER: protein abundance outlier detection from mass spectrometry-based proteomics data with a conditional autoencoder AbstractMotivation. Detection of gene regulatory aberrations enhances our ability to interpret the impact of inherited and acquired genetic variation for r

Super cool work!

PROTRIDER: protein abundance outlier detection from mass spectrometry-based proteomics data with a conditional autoencoder url: academic.oup.com/bioinformati...

From articles to code: on-demand generation of core algorithms from scientific publications AbstractMotivation. Scientific software packages impose persistent maintenance costs due to dependency churn, version incompatibilities, and bug triage, ev

Don’t we need to code anymore? 🥹

From articles to code: on-demand generation of core algorithms from scientific publications url: academic.oup.com/bioinformati...

ProteoGyver: a fast, user-friendly tool for routine QC and analysis of MS-based proteomics data Abstract. Mass spectrometry-based proteomics generates increasingly large datasets requiring rapid quality control (QC) and preliminary analysis. Current s

More on the important topic of QC!

ProteoGyver: a fast, user-friendly tool for routine QC and analysis of MS-based #proteomics data url: academic.oup.com/bioinformati...

Multi-scale structural similarity embedding search across entire proteomes AbstractMotivation. The rapid expansion of three-dimensional (3D) biomolecular structure information, driven by breakthroughs in artificial intelligence/de

Multi-scale structural similarity embedding search across entire proteomes url: academic.oup.com/bioinformati...

A dual diffusion model-based representation learning framework for antimicrobial peptides classification AbstractMotivation. The increasing prevalence of antibiotic-resistant bacteria has intensified the demand for novel antimicrobial agents. Antimicrobial pep

Dual diffusion model-based representation learning framework for antimicrobial peptides classification url: academic.oup.com/bioinformati...

SummArIzeR: Simplifying cross-database enrichment result clustering and annotation via large language models AbstractMotivation. Enrichment analysis across multiple databases often results in a high level of redundancy due to overlapping terms, complicating the in

SummArIzeR: Simplifying cross-database enrichment result clustering and annotation via large language models url: academic.oup.com/bioinformati...

De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution - Environmental Microbiome Environmental Microbiome - Protein-based stable isotope probing (Protein-SIP) is a powerful approach that can directly link individual taxa to activity and substrate assimilation, elucidating...

Generation and use of de novo peptide databases protein-SIP in #metaproteomics with up to species-level resolution:
link.springer.com/article/10.1...

Detection of alternative splicing: deep sequencing or deep learning? Abstract. Alternative splicing is a crucial mechanism of gene regulation that enables condition- and tissue-specific expression of gene isoforms. Its dysre

Detection of alternative splicing: deep sequencing or deep learning? url: academic.oup.com/bib/article/...

This IS FUN! Also great to discover other peers in the bubble:
bluesky-map.theo.io?likes=1

Bluesky Map Interactive map of 3.4 million Bluesky users, visualised by their follower pattern.

I made a map of 3.4 million Bluesky users - see if you can find yourself!

bluesky-map.theo.io

I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail

Sometimes I lean towards the assumption that we humans are required to make sense of the data and provide valuable structure, but that might not be true. Chucking raw data at an algorithm and letting it churn for a while as worked out for other tasks

www.incompleteideas.net/IncIdeas/Bit...

The microbial keystone concept is a very cool topic in microbiome ecology. This review summarises mechanisms, prediction methods and implications, with "keystoneness" being highly context/time dependent + new methods approaches suggested. Very nice read!
www.nature.com/articles/s41...

The Metaproteomics Initiative: Five Years of Community-Driven Progress

Preprint here:
chemrxiv.org/doi/full/10....

An LC-Immuno-MRM-MS Winterplex Method Development Framework for Respiratory Viral Screening Reliable large-scale testing for respiratory viruses, including influenza viruses, coronaviruses, such as SARS-CoV-2, and respiratory syncytial virus (RSV) is essential for both endemic surveillance a...

An LC-Immuno-MRM-MS Winterplex Method Development Framework for Respiratory Viral Screening | Analytical Chemistry pubs.acs.org/doi/10.1021/...

Antibiotic resistance detection and concomitant species identification of ESKAPE pathogens by proteomics Antimicrobial resistance (AMR) is an increasing challenge for therapy of bacterial infections. Currently, patient treatment is guided by antimicrobial susceptibility testing (AST) using phenotypic ass...

Antibiotic resistance detection and concomitant species identification of ESKAPE pathogens by proteomics - Molecular & Cellular Proteomics www.mcponline.org/article/S153...

chemrxiv.org/doi/full/10....

Bridging MS2 Spectra and Chemical Space: Advances in Spectral Similarity, Molecular Retrieval, and De Novo Structure Discovery

Ten simple rules for building a collaborative coding culture

From @sciencebanshee.bsky.social @shen4brains.bsky.social @analog-ashley.bsky.social & colleagues in @plos.org #Computational #Biology | Ten simple rules for building a collaborative #coding #culture | #Education #Bioinformatics #PLOSCBTSR #OpenScience 🧬 🖥️ 🧪🔓
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journals.plos.org/ploscompbiol...