Research Areas

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