Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity

Klemens Fröhlich, Eva Brombacher, Matthias Fahrner, +9

Nature Communications

Galaxy Training: A powerful framework for teaching!

Saskia Hiltemann, Helena Rasche, Simon Gladman, +28

PLoS Computational Biology

EngineeringMachine Learning ToolEducationGalaxy Training MaterialsScience Gateway +16

Identification of tissue damage, extracellular matrix remodeling and bacterial challenge as common mechanisms associated with high-risk cutaneous squamous cell carcinomas

Melanie Christine Föll, Matthias Fahrner, Christine Gretzmeier, +6

Matrix Biology

MedicineCutaneous BiologyPathologyExtracellular Matrix RemodelingWound Healing +11

Netherton syndrome subtypes share IL-17/IL-36 signature with distinct IFN-α and allergic responses

Claire Barbieux, Mathilde Bonnet des Claustres, Matthias Fahrner, +11

Journal of Allergy and Clinical Immunology

Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization

Melanie Christine Föll, Matthias Fahrner, Victor Oginga Oria, +5

Clinical Proteomics

Discovery of a small protein factor involved in the coordinated degradation of phycobilisomes in cyanobacteria

Vanessa Krauspe, Matthias Fahrner, Philipp Spät, +5

Proceedings of the National Academy of Sciences

Depletion of histone methyltransferase KMT9 inhibits lung cancer cell proliferation by inducing non-apoptotic cell death

Hannah Maria Baumert, Eric Metzger, Matthias Fahrner, +4

Cancer Cell International

Targeted and explorative profiling of kallikrein proteases and global proteome biology of pancreatic ductal adenocarcinoma, chronic pancreatitis, and normal pancreas highlights disease-specific proteome remodelling

Janina Werner, Patrick Bernhard, Miguel Cosenza‐Contreras, +7

Neoplasia

MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone

Niko Pinter, Damian Glätzer, Matthias Fahrner, +7

Journal of Proteome Research

EngineeringProteomic TechnologyData ScienceProteomics Quality ControlBiostatistics +16

A Systematic Evaluation of Semispecific Peptide Search Parameter Enables Identification of Previously Undescribed N-Terminal Peptides and Conserved Proteolytic Processing in Cancer Cell Lines

Matthias Fahrner, Lucas Kook, Klemens Fröhlich, +2

Proteomes

Peptide EngineeringMolecular BiologySearch EnginesFuture ReanalysisProtein Folding +17