SyMBoD
Publications
2023
Adamowicz, K., L. Arend, A. Maier, J. R. Schmidt, B. Kuster, O. Tsoy, O. Zolotareva, J. Baumbach, and T. Laske (2023). "Proteomic meta-study harmonization, mechanotyping and drug repurposing candidate prediction with ProHarMeD." Npj Systems Biology and Applications 9(1). doi.org/10.1038/s41540-023-00311-7.
Del Moral-Morales, A., M. Salgado-Albarrán, Y. Sánchez-Pérez, N. K. Wenke, J. Baumbach, and E. Soto-Reyes (2023). "CTCF and Its Multi-Partner Network for Chromatin Regulation." Cells 12(10): 1357. doi.org/10.3390/cells12101357.
Dondl, P., and M. Zeinhofer (2023). "Lp(I,Cα(Ω)) Regularity for Diffusion Equations with Non-smooth Data." Results Math 78(4): 1–22. doi.org/10.1007/s00025-023-01919-1.
Oubounyt, M., M. L. Elkjaer, T. Laske, A. G. B. Grønning, M. J. Moeller, and J. Baumbach (2023). "De-novo reconstruction and identification of transcriptional gene regulatory network modules differentiating single-cell clusters." NAR Genomics Bioinf. 5(1): lqad018. doi.org/10.1093/nargab/lqad018.
Rogg, M., J. I. Maier, M. Helmstädter, A. Sammarco, F. Kliewe, O. Kretz, L. Weißer, C. Van Wymersch, K. Findeisen, A. L. Koessinger, O. Tsoy, J. Baumbach, M. Grabbert, M. Werner, T. B. Huber, N. Endlich, O. Schilling, and C. Schell (2023). "A YAP/TAZ–ARHGAP29–RhoA Signaling Axis Regulates Podocyte Protrusions and Integrin Adhesions." Cells 12(13): 1795. doi.org/10.3390/cells12131795.
2022
Adamowicz, K., A. Maier, J. Baumbach, and D. B. Blumenthal (2022). "Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST." Briefings in Bioinformatics. doi.org/10.1093/bib/bbac247.
Bernett, J., D. Krupke, S. Sadegh, J. Baumbach, S. P. Fekete, T. Kacprowski, M. List, and D. B. Blumenthal (2022). "Robust disease module mining via enumeration of diverse prize-collecting Steiner trees." Bioinformatics 38(6): 1600–1606. doi.org/10.1093/bioinformatics/btab876.
Biadglegne, F., J. R. Schmidt, K. M. Engel, J. Lehmann, R. T. Lehmann, A. Reinert, B. König, J. Schiller, S. Kalkhof, and U. Sack (2022). "Mycobacterium tuberculosis Affects Protein and Lipid Content of Circulating Exosomes in Infected Patients Depending on Tuberculosis Disease State." Biomedicines 10(4): 783. doi.org/10.3390/biomedicines10040783.
Dias, D. B., R. Fritsche-Guenther, F. Gutmann, G. N. Duda, J. Kirwan, and P. S. P. Poh (2022). "A Comparison of Solvent-Based Extraction Methods to Assess the Central Carbon Metabolites in Mouse Bone and Muscle." Metabolites 12(5): 453. doi.org/10.3390/metabo12050453.
Dondl, P., P. S. P. Poh, and M. Zeinhofer (2022). "An Efficient Model For Scaffold Mediated Bone Regeneration." SIAM J Appl Math. epubs.siam.org/doi/10.1137/21M1401887.
Furesi, G., A. M. de Jesus Domingues, D. Alexopoulou, A. Dahl, M. Hackl, J. R. Schmidt, S. Kalkhof, T. Kurth, H. Taipaleenmaki, S. Conrad, C. Hofbauer, M. Rauner, and L. C. Hofbauer (2022). "Exosomal miRNAs from Prostate Cancer Impair Osteoblast Function in Mice." Int J Mol Sci 23(3). www.ncbi.nlm.nih.gov/pubmed/35163219.
Han, P., G. A. Gomez, G. N. Duda, S. Ivanovski, and P. S. P. Poh (2022). "Scaffold geometry modulation of mechanotransduction and its influence on epigenetics." Acta Biomater. doi.org/10.1016/j.actbio.2022.01.020.
Hartung, M., E. Anastasi, Z. M. Mamdouh, C. Nogales, H. H. H. W. Schmidt, J. Baumbach, O. Zolotareva, and M. List (2022). "Cancer driver drug interaction explorer." Nucleic Acids Res. doi.org/10.1093/nar/gkac384.
Hofmann, J., K. Borcherding, K. Thiel, T. Lingner, U. Sommer, U. Haberkorn, T. N. Bewersdorf, G. Schmidmaier, and T. Grossner (2022). "99mTc-HDP Labeling—A Non-Destructive Method for Real-Time Surveillance of the Osteogenic Differentiation Potential of hMSC during Ongoing Cell Cultures." Int J Mol Sci 23(24): 15874. doi.org/10.3390/ijms232415874.
Jaber, M., P. S. P. Poh, G. N. Duda, and S. Checa (2022). "PCL strut-like scaffolds appear superior to gyroid in terms of bone regeneration within a long bone large defect: An in silico study." Front Bioeng Biotechnol 0. doi.org/10.3389/fbioe.2022.995266.
Perier-Metz, C., G. N. Duda, and S. Checa (2022). "A mechanobiological computer optimization framework to design scaffolds to enhance bone regeneration." Front Bioeng Biotechnol 0. doi.org/10.3389/fbioe.2022.980727.
Poh, P. S., T. Lingner, S. Kalkhof, S. Märdian, J. Baumbach, P. Dondl, G. N. Duda, and S. Checa (2022). "Enabling technologies towards personalization of scaffolds for large bone defect regeneration." Curr Opin Biotechnol 74: 263–270. doi.org/10.1016/j.copbio.2021.12.002.
Rose, T. D., T. Bechtler, O.-A. Ciora, K. A. L. Le, F. Molnar, N. Köhler, J. Baumbach, R. Röttger, and J. K. Pauling (2022). "MoSBi: Automated signature mining for molecular stratification and subtyping." Proceedings of the National Academy of Sciences 119(16): e2118210119. www.pnas.org/doi/abs/10.1073/pnas.2118210119.
Torkzadehmahani, R., R. Nasirigerdeh, D. B. Blumenthal, T. Kacprowski, M. List, J. Matschinske, J. Spaeth, N. K. Wenke, and J. Baumbach (2022). "Privacy-Preserving Artificial Intelligence Techniques in Biomedicine." Methods Inf Med. www.ncbi.nlm.nih.gov/pubmed/35062032.
2021
Lazareva, O., J. Baumbach, M. List and D. B. Blumenthal (2021). "On the limits of active module identification." Brief Bioinform 22(5). SyMBoD, Sys_CARE www.ncbi.nlm.nih.gov/pubmed/33782690.
Manz, Q., O. Tsoy, A. Fenn, J. Baumbach, U. Völker, M. List and T. Kacprowski (2021). "ASimulatoR: splice-aware RNA-Seq data simulation." Bioinformatics 37(18): 3008–3010. SyMBoD & Sys_CARE doi.org/10.1093/bioinformatics/btab142.
Matschinske, J., N. Alcaraz, A. Benis, M. Golebiewski, D. G. Grimm, L. Heumos, T. Kacprowski, O. Lazareva, M. List, Z. Louadi, J. K. Pauling, N. Pfeifer, R. Rottger, V. Schwammle, G. Sturm, A. Traverso, K. Van Steen, M. V. de Freitas, G. C. Villalba Silva, L. Wee, N. K. Wenke, M. Zanin, O. Zolotareva, J. Baumbach and D. B. Blumenthal (2021). "The AIMe registry for artificial intelligence in biomedical research." Nat Methods 18(10): 1128-1131. Sys_CARE & SyMBoD www.ncbi.nlm.nih.gov/pubmed/34433960.
Matschinske, J., N. Alcaraz, A. Benis, M. Golebiewski, D. G. Grimm, L. Heumos, T. Kacprowski, O. Lazareva, M. List, Z. Louadi, J. K. Pauling, N. Pfeifer, R. Rottger, V. Schwammle, G. Sturm, A. Traverso, K. Van Steen, M. V. de Freitas, G. C. Villalba Silva, L. Wee, N. K. Wenke, M. Zanin, O. Zolotareva, J. Baumbach and D. B. Blumenthal (2021). "The AIMe registry for artificial intelligence in biomedical research." Nat Methods 18(10): 1128-1131. Sys_CARE & SyMBoD www.ncbi.nlm.nih.gov/pubmed/34433960.
Müller-Deile, J., G. Sarau, A. M. Kotb, C. Jaremenko, U. E. Rolle-Kampczyk, C. Daniel, S. Kalkhof, S. H. Christiansen and M. Schiffer (2021). "Novel diagnostic and therapeutic techniques reveal changed metabolic profiles in recurrent focal segmental glomerulosclerosis." Sci Rep 11(4577): 1–20. SymBoD doi.org/10.1038/s41598-021-83883-w.
Sadegh, S., J. Skelton, E. Anastasi, J. Bernett, D. B. Blumenthal, G. Galindez, M. Salgado-Albarrán, O. Lazareva, K. Flanagan, S. Cockell, C. Nogales, A. I. Casas, H. H. H. W. Schmidt, J. Baumbach, A. Wipat and T. Kacprowski (2021). "Network medicine for disease module identification and drug repurposing with the NeDRex platform." Nat Commun 12(6848): 1–12. Sys_CARE & SyMBoD doi.org/10.1038/s41467-021-27138-2.
Sarno, F., G. Benincasa, M. List, A. L. Barabasi, J. Baumbach, F. Ciardiello, S. Filetti, K. Glass, J. Loscalzo, C. Marchese, B. A. Maron, P. Paci, P. Parini, E. Petrillo, E. K. Silverman, A. Verrienti, L. Altucci, C. Napoli and C. International Network Medicine (2021). "Clinical epigenetics settings for cancer and cardiovascular diseases: real-life applications of network medicine at the bedside." Clin Epigenetics 13(1): 66. SyMBoD doi.org/10.1186/s13148-021-01047-z.
2020
Sadegh, S., Matschinske, J., Blumenthal, D.B., Galindez, G., Kacprowski, T., List, M., Nasirigerdeh, R., Oubounyt, M., Pichlmair, A., Rose, T.D., Salgado-Albarran, M., Spaeth, J., Stukalov, A., Wenke, N.K., Yuan, K., Pauling, J.K. and Baumbach, J. (2020). "Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing." Nature Communications 11(1). doi.org/10.1038/s41467-020-17189-2.
Weber, P., Pauling, J.K., List, M. and Baumbach, J. (2020). "BALSAM—An Interactive Online Platform for Breath Analysis, Visualization and Classification." Metabolites 10(10): 393. doi.org/10.3390/metabo10100393.