Marc Vaudel
A5037607788- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Genomics and Phylogenetic Studies
- Birth, Development, and Health
- Bioinformatics and Genomic Networks
- Genetic Associations and Epidemiology
- Machine Learning in Bioinformatics
- Genetics, Bioinformatics, and Biomedical Research
- Pregnancy and preeclampsia studies
- Biomedical Text Mining and Ontologies
- Gene expression and cancer classification
- Pancreatic function and diabetes
- Gestational Diabetes Research and Management
- Microbial Metabolic Engineering and Bioproduction
- Scientific Computing and Data Management
- Advanced Biosensing Techniques and Applications
- Genomics and Rare Diseases
- vaccines and immunoinformatics approaches
- RNA Research and Splicing
- Computational Drug Discovery Methods
- Platelet Disorders and Treatments
- Glycosylation and Glycoproteins Research
- Diabetes and associated disorders
- Cancer-related gene regulation
University of Bergen
2016-2025
Norwegian Institute of Public Health
2022-2024
University of Pennsylvania
2022
Haukeland University Hospital
2016-2020
Leibniz Institute for Analytical Sciences - ISAS
2009-2015
Institute for Biomedicine
2014
Leibniz Institute for Neurobiology
2011
Friedrich Schiller University Jena
2010
BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. allows labs of all sizes to easily install software, maintain multiple versions the same software combine tools into powerful analysis pipelines. based on popular projects Docker rkt frameworks, that allow be installed executed under isolated controlled environment. Also, it infrastructure basic guidelines create, manage...
Abstract The identification of proteins by mass spectrometry is a standard technique in the field proteomics, relying on search engines to perform identifications acquired spectra. Here, we present user‐friendly, lightweight and open‐source graphical user interface called SearchGUI ( http://searchgui.googlecode.com ), for configuring running freely available OMSSA (open algorithm) X!Tandem simultaneously. Freely under permissible Apache2 license, supported Windows, Linux OSX.
Mass-spectrometry-based proteomics has become the standard approach for identifying and quantifying proteins. A vital step consists of analyzing experimentally generated mass spectra to identify underlying peptide sequences later mapping originating We here present latest developments in SearchGUI, a common open-source interface most frequently used freely available search de novo engines that evolved into central component numerous bioinformatics workflows.
Genome-wide association studies of birth weight have focused on fetal genetics, whereas relatively little is known about the role maternal genetic variation. We aimed to identify variants associated with that could highlight potentially relevant determinants growth. meta-analysed data up 8.7 million SNPs in 86 577 women European descent from Early Growth Genetics (EGG) Consortium and UK Biobank. used structural equation modelling (SEM) analyses mother-child pairs quantify separate effects....
Abstract Pubertal timing varies considerably and is associated with later health outcomes. We performed multi-ancestry genetic analyses on ~800,000 women, identifying 1,080 signals for age at menarche. Collectively, these explained 11% of trait variance in an independent sample. Women the top bottom 1% polygenic risk exhibited ~11 ~14-fold higher risks delayed precocious puberty, respectively. identified several genes harboring rare loss-of-function variants ~200,000 including ZNF483 , which...
Abstract Summary Data visualization plays critical roles in proteomics studies, ranging from quality control of MS/MS data to validation peptide identification results. Herein, we present PDV, an integrative viewer that can be used visualize a wide range data, including database search results, de novo sequencing proteogenomics files, mzML/mzXML format and public repositories. PDV is lightweight tool enables intuitive fast exploration diverse, large-scale datasets on standard desktop...
Abstract Infant and childhood growth are dynamic processes with large changes in BMI during development. By performing genome-wide association studies of at 12 time points from birth to eight years (9286 children, 74,105 measurements) the Norwegian Mother, Father, Child Cohort Study, replicated 5235 we identify a transient effect leptin receptor ( LEPR ) locus: no birth, increasing infancy, peaking 6–12 months (rs2767486, P 6m = 2.0 × 10 −21 , β 0.16 sd-BMI), little after age five. We...
Abstract Autoimmune Addison’s disease (AAD) is characterized by the autoimmune destruction of adrenal cortex. Low prevalence and complex inheritance have long hindered successful genetic studies. We here report first genome-wide association study on AAD, which identifies nine independent risk loci ( P < 5 × 10 −8 ). In addition to implicated in lymphocyte function development shared with other diseases such as HLA , BACH2 PTPN22 CTLA4 we associate two protein-coding alterations Regulator...
Summary Infections can lead to persistent or long-term symptoms and diseases such as shingles after varicella zoster, cancers human papillomavirus, rheumatic fever streptococcal infections 1, 2 . Similarly, infection by SARS-CoV-2 result in Long COVID, a condition characterized of fatigue pulmonary cognitive dysfunction 3–5 The biological mechanisms that contribute the development COVID remain be clarified. We leveraged COVID-19 Host Genetics Initiative 6, 7 perform genome-wide association...
Abstract A well-functioning placenta is essential for fetal and maternal health throughout pregnancy. Using placental weight as a proxy growth, we report genome-wide association analyses in the ( n = 65,405), 61,228) paternal 52,392) genomes, yielding 40 independent signals. Twenty-six signals are classified fetal, four three maternal. parent-of-origin effect seen near KCNQ1 . Genetic correlation colocalization reveal overlap with birth genetics, but 12 loci predominantly or only affecting...
Abstract Background The growing interest in the field of proteomics has increased demand for software tools and applications that process analyze resulting data. And even though purpose these can vary significantly, they usually share a basic set features, including handling protein peptide sequences, visualization (and interaction with) spectra chromatograms, parsing results from various search engines. Developers typically spend considerable time effort implementing support structures,...
De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on protein sequence database. Despite the strong potential of de algorithms, their adoption threshold remains quite high. We here present user-friendly and lightweight graphical user interface called DeNovoGUI running parallelized versions freely available software PepNovo+, greatly simplifying use proteomics. Our platform-independent under permissible Apache2 open...
The first stable version of the Proteomics Standards Initiative mzIdentML open data standard (version 1.1) was published in 2012-capturing outputs peptide and protein identification software. In intervening years, has become well-supported both commercial software, as well a submission download format for public repositories. Here we report new release 1.2) that is required to keep pace with emerging practice proteome informatics. New features have been added support: (1) scores associated...