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Friedrich-Alexander-Universität Biomedical Network Science Lab BIONETS
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  1. Friedrich-Alexander-Universität
  2. Technische Fakultät
  3. Department Artificial Intelligence in Biomedical Engineering
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  1. Friedrich-Alexander-Universität
  2. Technische Fakultät
  3. Department Artificial Intelligence in Biomedical Engineering
Friedrich-Alexander-Universität Biomedical Network Science Lab BIONETS
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We develop computational methods for systems and network medicine applications. Problems we are working on include inference of gene regulatory networks, mining of  pathomechanisms in protein-protein interaction networks, dimensionality reduction for high-dimensional molecular data, and detection of differentially abundant cell populations in single-cell data.

Key Publications

  • Bernett J., Krupke D., Sadegh S., Baumbach J., Fekete SP., Kacprowski T., List M., Blumenthal DB.:
    Robust disease module mining via enumeration of diverse prize-collecting Steiner trees
    In: Bioinformatics 38 (2022), p. 1600-1606
    ISSN: 1367-4803
    DOI: 10.1093/bioinformatics/btab876
    URL: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab876/6497106?guestAccessKey=27c2a19b-11b5-4c3c-88d5-f1131e3809a9
  • Sadegh S., Skelton J., Anastasi E., Bernett J., Blumenthal DB., Galindez G., Salgado-Albarran M., Lazareva O., Flanagan K., Cockell S., Nogales C., Casas AI., Schmidt HHHW., Baumbach J., Wipat A., Kacprowski T.:
    Network medicine for disease module identification and drug repurposing with the NeDRex platform
    In: Nature Communications 12 (2021), Article No.: 6848
    ISSN: 2041-1723
    DOI: 10.1038/s41467-021-27138-2
  • Sadegh S., Matschinske J., Blumenthal DB., Galindez G., Kacprowski T., List M., Nasirigerdeh R., Oubounyt M., Pichlmair A., Rose TD., Salgado-Albarran M., Spaeth J., Stukalov A., Wenke NK., Yuan K., Pauling JK., Baumbach J.:
    Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing
    In: Nature Communications 11 (2020), Article No.: 3518
    ISSN: 2041-1723
    DOI: 10.1038/s41467-020-17189-2

We cary out research meta-scientific topics in computational biomedicine. Such topics include (lack of) reproducibility of biomedical AI systems, the effect of data leakage on such systems, and the impact of various forms of biases on data-driven methods in network and systems biology.

Key Publications

  • Sadegh S., Skelton J., Anastasi E., Maier A., Adamowicz K., Möller A., Kriege NM., Kronberg J., Haller T., Kacprowski T., Wipat A., Baumbach J., Blumenthal DB.:
    Lacking mechanistic disease definitions and corresponding association data hamper progress in network medicine and beyond
    In: Nature Communications 14 (2023), Article No.: 1662
    ISSN: 2041-1723
    DOI: 10.1038/s41467-023-37349-4
  • Matschinske J., Benis A., Alcaraz N., Golebiewski M., Grimm DG., Heumos L., Kacprowski T., Lazareva O., List M., Louadi Z., Pauling JK., Pfeifer N., Röttger R., Schwämmle V., Sturm G., Traverso A., Van Steen K., de Freitas MV., Villalba Silva GC., Wee L., Wenke NK., Zanin M., Zolotareva O., Baumbach J., Blumenthal DB.:
    The AIMe registry for artificial intelligence in biomedical research
    In: Nature Methods 18 (2021), p. 1128 - 1131
    ISSN: 1548-7091
    DOI: 10.1038/s41592-021-01241-0
    URL: https://rdcu.be/cv5H7
  • Lazareva O., Baumbach J., List M., Blumenthal DB.:
    On the limits of active module identification
    In: Briefings in Bioinformatics 22 (2021), Article No.: bbab066
    ISSN: 1467-5463
    DOI: 10.1093/bib/bbab066
    URL: https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbab066/6189770?guestAccessKey=1be406a0-6b26-4e15-b32b-505c1ea2b279

We develop privacy-aware methods for problems in computational biomedicine, mainly making use of federated learning. Problems we are working on include federated genome-wide association studies and privacy-aware computation of differentially expressed genes from distributed gene expression data.

Key Publications

  • Zolotareva O., Nasirigerdeh R., Matschinske J., Torkzadehmahani R., Bakhtiari M., Frisch T., Spaeth J., Blumenthal DB., Abbasinejad A., Tieri P., Kaissis G., Rueckert D., Wenke NK., List M., Baumbach J.:
    Flimma: a federated and privacy-aware tool for differential gene expression analysis
    In: Genome Biology 22 (2021), Article No.: 338
    ISSN: 1474-760X
    DOI: 10.1186/s13059-021-02553-2
  • Nasirigerdeh R., Torkzadehmahani R., Baumbach J., Blumenthal DB.:
    On the Privacy of Federated Pipelines
    The 44th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR '21) (Virtual Event, 11/07/2021 - 15/07/2021)
    In: Proceedings of the 44th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR '21), New York, NY, USA: 2021
    DOI: 10.1145/3404835.3462996

We develop graph-based algorithms for applied combinatorial optimization problems. Problems we are working on include the computation of distances between graphs and trees and enumeration of matchings and paths under diversity constraints.

Key Publications

  • Boria N., Kiederle J., Yger F., Blumenthal DB.:
    The edge-preservation similarity for comparing rooted, unordered, node-labeled trees
    In: Pattern Recognition Letters 167 (2023), p. 189-195
    ISSN: 0167-8655
    DOI: 10.1016/j.patrec.2023.02.017
  • Blumenthal DB., Bougleux S., Dignoes A., Gamper J.:
    Enumerating dissimilar minimum cost perfect and error-correcting bipartite matchings for robust data matching
    In: Information Sciences 596 (2022), p. 202-221
    ISSN: 0020-0255
    DOI: 10.1016/j.ins.2022.03.017
  • Blumenthal DB., Boria N., Bougleux S., Brun L., Gamper J., Gaüzère B.:
    Scalable generalized median graph estimation and its manifold use in bioinformatics, clustering, classification, and indexing
    In: Information Systems 100 (2021), Article No.: 101766
    ISSN: 0306-4379
    DOI: 10.1016/j.is.2021.101766
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Biomedical Network Science Lab

Werner-von-Siemens-Str. 61
91052 Erlangen
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