Sys_CARE

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  doi.org/10.1093/nargab/lqad044.

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  doi.org/10.1093/nargab/lqad081.

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  doi.org/10.1093/bioinformatics/btac846.

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  doi.org/10.3390/cells12131795.

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  doi.org/10.1038/s41467-023-37349-4.

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 doi.org/10.1093/bib/bbac247.

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 doi.org/10.1093/bib/bbab471.

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 doi.org/10.1093/bioinformatics/btab876.

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 doi.org/10.1093/gigascience/giac086.

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 www.ncbi.nlm.nih.gov/pubmed/35132075.

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 www.ncbi.nlm.nih.gov/pubmed/35086479.

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 doi.org/10.1093/bioinformatics/btaa990.

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 doi.org/10.1038/s41419-020-03333-9.

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 doi.org/10.1093/narcan/zcaa042.

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 doi.org/10.1055/s-0041-1733934.

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.

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 doi.org/10.1186/s13059-021-02538-1.

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 doi.org/10.1093/nar/gkaa768.

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.

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 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.

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 doi.org/10.1371/journal.pcbi.1008329.

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.

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 doi.org/10.1038/s43588-021-00038-7.

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 doi.org/10.1186/s13059-021-02553-2.

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 doi.org/10.1038/s41467-020-17189-2.