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Author Details

Julian Uszkoreit
Ruhr University Bochum
2006
43
20
PMIDPaper TitleJournal TitlePublished Year
38038272WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows.J Proteome Res2024
36180966Target formation in muscle fibres indicates reinnervation - A proteomic study in muscle samples from peripheral neuropathies.Neuropathol Appl Neurobiol2023
36979426Quality Control-A Stepchild in Quantitative Proteomics: A Case Study for the Human CSF Proteome.Biomolecules2023
36744821Toward an Integrated Machine Learning Model of a Proteomics Experiment.J Proteome Res2023
36232544Plasma Proteomics Enable Differentiation of Lung Adenocarcinoma from Chronic Obstructive Pulmonary Disease (COPD).Int J Mol Sci2022
35845101Dataset containing physiological amounts of spike-in proteins into murine C2C12 background as a ground truth quantitative LC-MS/MS reference.Data Brief2022
36269744Characterization of peptide-protein relationships in protein ambiguity groups via bipartite graphs.PLoS One2022
33950500Establishing a Custom-Fit Data-Independent Acquisition Method for Label-Free Proteomics.Methods Mol Biol2021
33589928Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases.Brief Bioinform2021
33724838MaCPepDB: A Database to Quickly Access All Tryptic Peptides of the UniProtKB.J Proteome Res2021
34615866A proteomics sample metadata representation for multiomics integration and big data analysis.Nat Commun2021
32112048Spatial proteomics revealed a CX<sub>3</sub>CL1-dependent crosstalk between the urothelium and relocated macrophages through IL-6 during an acute bacterial infection in the urinary bladder.Mucosal Immunol2020
31699904Reproducibility, Specificity and Accuracy of Relative Quantification Using Spectral Library-based Data-independent Acquisition.Mol Cell Proteomics2020
32887649Homozygous expression of the myofibrillar myopathy-associated p.W2710X filamin C variant reveals major pathomechanisms of sarcomeric lesion formation.Acta Neuropathol Commun2020
30474983Protein Inference Using PIA Workflows and PSI Standard File Formats.J Proteome Res2019
31890549Let me infuse this for you - A way to solve the first YPIC challenge.EuPA Open Proteom2019
31890545Proceedings of the EuBIC Winter School 2019.EuPA Open Proteom2019
30395289The PRIDE database and related tools and resources in 2019: improving support for quantification data.Nucleic Acids Res2019
30207155Characterization of Cerebrospinal Fluid via Data-Independent Acquisition Mass Spectrometry.J Proteome Res2018
29864591Proceedings of the EuBIC developer's meeting 2018.J Proteomics2018
27498275In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.J Proteomics2017
28385664Proceedings of the EuBIC Winter School 2017.J Proteomics2017
28379341BioContainers: an open-source and community-driven framework for software standardization.Bioinformatics2017
28515314The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.Mol Cell Proteomics2017
28606611BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication.J Biotechnol2017
27932303One Sample, One Shot - Evaluation of sample preparation protocols for the mass spectrometric proteome analysis of human bile fluid without extensive fractionation.J Proteomics2017
28009083Proteomics of rimmed vacuoles define new risk allele in inclusion body myositis.Ann Neurol2017
26842778New insights into the protein aggregation pathology in myotilinopathy by combined proteomic and immunolocalization analyses.Acta Neuropathol Commun2016
26545397PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.Mol Cell Proteomics2016
27415786Ten Simple Rules for Taking Advantage of Git and GitHub.PLoS Comput Biol2016
25938255PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.J Proteome Res2015
25910694ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.Bioinformatics2015
24284412Amyloid beta a4 precursor protein-binding family B member 1 (FE65) interactomics revealed synaptic vesicle glycoprotein 2A (SV2A) and sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (SERCA2) as new binding proteins in the human brain.Mol Cell Proteomics2014
25521444The bacterial proteogenomic pipeline.BMC Genomics2014
25092112A standardized framing for reporting protein identifications in mzIdentML 1.2.Proteomics2014
23115302A combined laser microdissection and mass spectrometry approach reveals new disease relevant proteins accumulating in aggregates of filaminopathy patients.Mol Cell Proteomics2013
23639843Differential proteomic analysis of abnormal intramyoplasmic aggregates in desminopathy.J Proteomics2013
23599424The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics.Mol Cell Proteomics2013
23651173A combination of two electrophoretical approaches for detailed proteome-based characterization of SCLC subtypes.Arch Physiol Biochem2013
23572515FE65 regulates and interacts with the Bloom syndrome protein in dynamic nuclear spheres - potential relevance to Alzheimer's disease.J Cell Sci2013
22665317Search and decoy: the automatic identification of mass spectra.Methods Mol Biol2012
21978018Sense and nonsense of pathway analysis software in proteomics.J Proteome Res2011
16550739Automated nuclear segmentation in the determination of the Ki-67 labeling index in meningiomas.Clin Neuropathol2006
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Collaborators

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Co-authored papers 10
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European Bioinformatics Institute (EMBL-EBI)
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David L Tabb
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Karl Mechtler
IMP-Institute of Molecular Pathology
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Knut Reinert
Institut fur Informatik, Freie Universitat Berlin
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Jos?? M Fern??ndez
Hospital Universitario y Politecnico la Fe
Co-authored papers 1
Nuno Bandeira
University of California
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Tom J Pollard
Massachusetts Institute of Technology, Scientific Data - Nature, Software Sustainability Institute, University College London, University of Law - London Bloomsbury Centre
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Irene Papatheodorou
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Robert M Flight
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Release 1.2