Author

Katja Ovchinnikova

European Molecular Biology Laboratory

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Bioinformatics· 2 Systems Biology· 2 Molecular Biology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:benchmarking· 3 Assay:metabolomics· 3 Approach:deep learning· 2 Approach:experimental assay· 2 Organism:human· 2 Assay:imaging· 2 Approach:machine learning (classical)· 2 Assay:metagenomics· 2

Frequent Co-Authors

Theodore AlexandroviD· 5 shared Lachlan StuartiD· 4 shared Bernhard SpengleriD· 2 shared Carsten HopfiD· 2 shared Christian JanfeltiD· 2 shared Christopher AndertoniD· 2 shared David C. MuddimaniD· 2 shared Dušan VeličkovićiD· 2 shared

Activity by Year

2019-2024 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

5 shared papersSystems Biology

Theodore AlexandrovORCID

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

Large-Scale Evaluation of Spatial Metabolomics Protocols and Technologies

Veronika Saharuka, Lucas Maciel Vieira, Lachlan Stuart, Måns Ekelöf, Martijn R. Molenaar, Alberto Bailoni, Katja Ovchinnikova, Jens Soltwisch, Tobias Bausbacher, Dennis Jakob, Mary King, Max A. Müller, Janina Oetjen, Crystal L. Pace, Fernanda Endringer Pinto, , Theodore Alexandrov

The paper evaluates spatial metabolomics protocols and technologies, showing extensive metabolite coverage and comparable results across imaging MS methods.

bioRxiv · Jan 29, 2024 · PreprintSystems Biology

Spatial single-cell profiling of intracellular metabolomes in situ

Luca Rappez, Mira Stadler, Sergio Triana, Rose Muthoni Gathungu, Katja Ovchinnikova, Prasad B. Phapale, Mathias F Heikenwälder, Theodore Alexandrov

SpaceM integrates MALDI-imaging mass spectrometry with pre- and post-MALDI microscopy to measure >100 metabolites in >10000 individual cultured cells alongside fluorescence, morphology and spatial context.

Nature Methods · Jul 1, 2021Peer-reviewedMolecular Biology✦ In-depth digest

ColocAI: artificial intelligence approach to quantify co-localization between mass spectrometry images

Katja Ovchinnikova, Alexander Rakhlin, Lachlan Stuart, Sergey Nikolenko, Theodore Alexandrov

ColocAI quantifies co-localization between mass spectrometry images using AI, outperforming existing methods and providing insights into 10,273 molecules from public datasets.

bioRxiv · Sep 8, 2019 · PreprintBioinformatics

METASPACE: A community-populated knowledge base of spatial metabolomes in health and disease

Theodore Alexandrov, Katja Ovchinnikova, Andrew Palmer, Vitaly Kovalev, Artem Tarasov, Lachlan Stuart, Renat Nigmetzianov, Dominik Fay, Key METASPACE contributors, Mathieu Gaudin, Cristina López, Marina Vetter, John G. Swales, Mark T. Bokhart, Mario Kompauer, , Sheerin K. Shahidi-Latham

An open-source cloud engine annotates imaging mass spectrometry data at controlled false discovery rate; publicly shared results reached over 3200 datasets and 6 million metabolite images by January 2019.

bioRxiv · Feb 13, 2019 · PreprintSystems Biology✦ In-depth digest

Recognizing off-sample mass spectrometry images with machine and deep learning

Katja Ovchinnikova, Vitaly Kovalev, Lachlan Stuart, Theodore Alexandrov

The paper develops machine and deep learning methods to identify off-sample ions in mass spectrometry images, achieving high F1 scores.

bioRxiv · Jan 14, 2019 · PreprintBioinformatics