A5063629591- Metabolomics and Mass Spectrometry Studies
- Mass Spectrometry Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Analytical Chemistry and Chromatography
- Health, Environment, Cognitive Aging
- Isotope Analysis in Ecology
- Advanced Chemical Sensor Technologies
- Industrial Vision Systems and Defect Detection
- Control Systems and Identification
- Research Data Management Practices
- Advanced Wireless Communication Techniques
- Analytical chemistry methods development
- Scientific Computing and Data Management
- Nutritional Studies and Diet
- Geological Modeling and Analysis
- Advanced Data Storage Technologies
- Effects and risks of endocrine disrupting chemicals
- BIM and Construction Integration
- Image Processing Techniques and Applications
- AI in cancer detection
- Digital Imaging for Blood Diseases
- Delphi Technique in Research
- Cancer, Hypoxia, and Metabolism
- 3D Modeling in Geospatial Applications
- Toxic Organic Pollutants Impact
Masaryk University
2020-2025
University of Freiburg
2024
RECETOX
2023
Technical University of Munich
2022
Abstract Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public services by platform stability, tool and reference dataset diversity, training, support integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements accessibility, discoverability...
Abstract Mass spectral libraries have proven to be essential for mass spectrum annotation, both library matching and training new machine learning algorithms. A key step in models is the availability of high-quality data. Public spectrometry data that are open user submission often suffer from limited metadata curation harmonization. The resulting variability quality makes challenging. Here we present a cleaning pipeline designed tandem with ease use, flexibility, reproducibility as leading...
The chemical burden on the environment and human population is increasing. Consequently, regulatory risk assessment must keep pace to manage, reduce, prevent adverse impacts environmental health associated with hazardous chemicals. Surveillance of chemicals known, emerging, or potential future concern, entering environment-food-human continuum needed document reality risks posed by ecosystem from a one perspective, feed into early warning systems support public policies for exposure...
Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that used for further downstream analysis new spectra. There many different formats encoding libraries, but none have undergone a standardization process to ensure broad applicability applications. As part Human Proteome Organization Proteomics Standards Initiative (PSI), we developed standardized format called mzSpecLib...
Compound identification and structure annotation from mass spectra is a well-established task widely applied in drug detection, criminal forensics, small molecule biomarker discovery chemical engineering. We propose SpecTUS: Spectral Translator for Unknown Structures, deep neural model that addresses the of structural molecules low-resolution gas chromatography electron ionization (GC-EI-MS). Our analyzes \textit{de novo} manner -- direct translation into 2D-structural representation....
Abstract Various spectrometric methods can be used to conduct metabolomics studies. Nuclear magnetic resonance (NMR) or mass spectrometry (MS) coupled with separation methods, such as liquid gas chromatography (LC and GC, respectively), are the most commonly techniques. Once raw data have been obtained, real challenge lies in bioinformatics required conduct: (i) processing (including preprocessing, normalization, quality control); (ii) statistical analysis for comparative studies (such...
Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that used for further downstream analysis new spectra. There many different formats encoding libraries, but none have undergone a standardization process to ensure broad applicability applications. As part Human Proteome Organization Proteomics Standards Initiative (PSI), we developed standardized format called mzSpecLib...
There is a lack of experimental electron ionization high-resolution mass spectra available to assist compound identification. The in silico generation by quantum chemistry can aid annotation workflows, particular support the identification compounds that reference spectra, such as environmental chemicals. We present an open-source, semiautomated workflow for prediction at 70 eV based on QCxMS software. was applied predict 367 chemicals, and accuracy evaluated comparison acquired. molecular...
Many diseases, such as cancer, are characterized by an alteration of cellular metabolism allowing cells to adapt changes in the microenvironment. Stable isotope-resolved metabolomics (SIRM) and downstream data analyses widely used techniques for unraveling cells' metabolic activity understand altered functioning pathways diseased state. While a number bioinformatic solutions exist differential analysis SIRM data, there is currently no available resource providing comprehensive toolbox.
There is a lack of experimental electron ionization high-resolution mass spectra available to assist compound identification. The in silico generation by quantum chemistry can aid annotation workflows, particular support the identification compounds that reference spectra, such as environmental chemicals. We present an open-source, semi-automated workflow for prediction based on QCxMS software. was applied predict 367 chemicals and accuracy evaluated comparison acquired. molecular...
A novel deep autoencoder architecture is proposed for the analysis of histopathology images. Its purpose to produce a disentangled latent representation in which structure and colour information are confined different subspaces so that stain-independent models may be learned. For this, we introduce two constraints on implemented as classifier an adversarial discriminator. We show how they can used learning across haematoxylin-eosin number immune stains. Finally, demonstrate utility context...
MSMetaEnhancer is a Python software package for the metadata enrichment of records in mass spectral library files commonly used as reference chemical identification via spectrometry.Each record contains information, i.e., peak to charge ratio (m/z) and intensities, alongside & structural metadata, e.g., identifiers.The uses matchms (Huber et al., 2020) data IO supports open, text-based .mspformat.It annotates given spectra file by adding missing such SMILES, InChI, CAS numbers individual...
There is a lack of experimental electron ionization high-resolution mass spectra available to assist compound identification. The in silico generation by quantum chemistry can aid annotation workflows, particular support the identification compounds that reference spectra, such as environmental chemicals. We present an open-source, semi-automated workflow for prediction based on QCxMS software. was applied predict 367 chemicals and accuracy evaluated comparison acquired. molecular...
Identification of experimentally acquired mass spectra unknown compounds presents a~particular challenge because reliable spectral databases do not cover the potential chemical space with sufficient density. Therefore machine learning based \emph{de-novo} methods, which derive molecular structure directly from its spectrum gained attention recently. We present a~novel method in this family, addressing a~specific usecase GC-EI-MS spectra, is particularly hard due to lack additional...
Mass spectral libraries have proven to be essential for mass spectrum annotation, both library matching and training new machine learning algorithms. A key step in models is having high-quality data. Public of spectrometry data that are open user submission often suffer from limited metadata curation harmonization. The resulting variability quality makes challenging. Here we present a cleaning pipeline designed tandem with ease use, flexibility reproducibility as leading principles.
RIAssigner is a software package for the computation of gas chromatographic (GC) retention indices (RI).The uses matchms (Huber et al., 2020) and pandas (The development team, data I/O supports .mspas well as tabular (.csv & .tsv)formats, among others.It multiple keywords identifying time (RT) RI information handling SI units RT.The can be computed using non-isothermal Kováts retention-indexing (from temperature programming, definition van Den Dool Kratz (1963)) or cubic spline interpolation...
Jaud et al., (2022). TUM Open Infra Platform: an open source package for simultaneous viewing and analysis of digital models in the civil engineering domain. Journal Source Software, 7(72), 3061, https://doi.org/10.21105/joss.03061