Fenn, A., O. Tsoy, T. Faro, F. L. M. Rößler, A. Dietrich, J. Kersting, Z. Louadi, C. T. Lio, U. Völker, J. Baumbach, T. Kacprowski, and M. List (2023). "Alternative splicing analysis benchmark with DICAST." NAR Genomics Bioinf. 5(2): lqad044. Sys_CARE

Hackl, L. M., A. Fenn, Z. Louadi, J. Baumbach, T. Kacprowski, M. List, and O. Tsoy (2023). "Alternative splicing impacts microRNA regulation within coding regions." NAR Genomics Bioinformatics 5(3): lqad081. Sys_CARE

Lio, C. T., G. Grabert, Z. Louadi, A. Fenn, J. Baumbach, T. Kacprowski, M. List, and O. Tsoy (2023). "Systematic analysis of alternative splicing in time course data using Spycone." Bioinformatics 39(1). SYS_CARE

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. Sys_CARE & SyMBoD

Sadegh, S., J. Skelton, E. Anastasi, A. Maier, K. Adamowicz, A. Möller, N. M. Kriege, J. Kronberg, T. Haller, T. Kacprowski, A. Wipat, J. Baumbach, and D. B. Blumenthal (2023). "Lacking mechanistic disease definitions and corresponding association data hamper progress in network medicine and beyond." Nat Commun 14(1662): 1–15. Sys_CARE


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. Sys_CARE & SyMBoD

Arend, L., J. Bernett, Q. Manz, M. Klug, O. Lazareva, J. Baumbach, D. Bongiovanni and M. List (2022). "A systematic comparison of novel and existing differential analysis methods for CyTOF data." Briefings Bioinf 23(1). Sys_CARE

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. Sys_CARE & SyMBoD

Gress, A., S. K. Srikakulam, S. Keller, V. Ramensky and O. V. Kalinina (2022). "d-StructMAn: Containerized structural annotation on the scale from genetic variants to whole proteomes." GigaScience 11. Sys_CARE

Salgado-Albarran, M., J. Spath, R. Gonzalez-Barrios, J. Baumbach and E. Soto-Reyes (2022). "CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy." NPJ Syst Biol Appl 8(1): 5. Sys_CARE

Tsoy, O. and A. Mushegian (2022). "Florigen and its homologs of FT/CETS/PEBP/RKIP/YbhB family may be the enzymes of small molecule metabolism: review of the evidence." BMC Plant Biol 22(1): 56. Sys_CARE


Blumenthal, D. B., J. Baumbach, M. Hoffmann, T. Kacprowski and M. List (2021). "A framework for modeling epistatic interaction." Bioinformatics 37(12): 1708–1716. Sys_CARE

Bongiovanni, D., M. Klug, O. Lazareva, S. Weidlich, M. Biasi, S. Ursu, S. Warth, C. Buske, M. Lukas, C. D. Spinner, M. v. Scheidt, G. Condorelli, J. Baumbach, K.-L. Laugwitz, M. List and I. Bernlochner (2021). "SARS-CoV-2 infection is associated with a pro-thrombotic platelet phenotype." Cell Death Dis 12(50): 1–10. Sys_CARE

Hoffmann, M., E. Pachl, M. Hartung, V. Stiegler, J. Baumbach, M. H. Schulz and M. List (2021). "SPONGEdb: a pan-cancer resource for competing endogenous RNA interactions." NAR Cancer 3(1). Sys_CARE

Klug, M., O. Lazareva, K. Kirmes, M. Rosenbaum, M. Lukas, S. Weidlich, C. D. Spinner, M. von Scheidt, R. Gosetti, J. Baumbach, J. Ruland, G. Condorelli, K.-L. Laugwitz, M. List, I. Bernlochner and D. Bongiovanni (2021). "Platelet Surface Protein Expression and Reactivity upon TRAP Stimulation after BNT162b2 Vaccination." Thromb Haemost. Sys_CARE

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

Louadi, Z., M. L. Elkjaer, M. Klug, C. T. Lio, A. Fenn, Z. Illes, D. Bongiovanni, J. Baumbach, T. Kacprowski, M. List and O. Tsoy (2021). "Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases." Genome Biol 22(1): 1–22. Sys_CARE

Louadi, Z., K. Yuan, A. Gress, O. Tsoy, O. V. Kalinina, J. Baumbach, T. Kacprowski and M. List (2021). "DIGGER: exploring the functional role of alternative splicing in protein interactions." Nucleic Acids Res 49(D1): D309-D318. SYS_CARE

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

Manz, Q., O. Tsoy, A. Fenn, J. Baumbach, U. Völker, M. List and T. Kacprowski (2021). "splice-aware RNA-Seq data simulation." Bioinformatics. Sys_CARE & SyMBoD

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

Mironov, A., S. Denisov, A. Gress, O. V. Kalinina and D. D. Pervouchine (2021). "An extended catalogue of tandem alternative splice sites in human tissue transcriptomes." PLoS Comput Biol 17(4): e1008329. Sys_CARE

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

Scherer, M., F. Schmidt, O. Lazareva, J. Walter, J. Baumbach, M. H. Schulz and M. List (2021). "Machine learning for deciphering cell heterogeneity and gene regulation." Nat. Comput. Sci. 1(3): 183–191. Sys_CARE

Zolotareva, O., R. Nasirigerdeh, J. Matschinske, R. Torkzadehmahani, M. Bakhtiari, T. Frisch, J. Späth, D. B. Blumenthal, A. Abbasinejad, P. Tieri, G. Kaissis, D. Rückert, N. K. Wenke, M. List and J. Baumbach (2021). "Flimma: a federated and privacy-aware tool for differential gene expression analysis." Genome Biol 22(1): 1–26. Sys_CARE


Sadegh, S., J. Matschinske, D. B. Blumenthal, G. Galindez, T. Kacprowski, M. List, R. Nasirigerdeh, M. Oubounyt, A. Pichlmair, T. D. Rose, M. Salgado-Albarran, J. Spaeth, A. Stukalov, N. K. Wenke, K. Yuan, J. K. Pauling and J. Baumbach (2020). "Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing." Nat Commun 11(1). Sys_CARE & SyMBoD

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