coNfirm
Networks of heart disease: Systems medicine approach to improve heart health
Cardiovascular disease is the leading cause of death in western industrial nations. In Germany, about 40 % of all deaths are caused by diseases of the cardiovascular system. Rising life expectancy is expected to increase the appearance of cardiovascular disease.
The alliance "coNfirm" is part of the networking fonds promoted to intensify the interdisciplinary interactions between the five modules of the research and support concept "e:Med - Establishing systems medicine in Germany". coNfirm is working with conditions of cardiovascular diseases such as heart failure, myocardial infarct and atrial fibrillation. The project aims to identify disease-spanning features and mechanisms using systems medicine approaches to gain profound knowledge of cardiovascular diseases. This is essential for the development of personalized medicine, including diagnostic, preventive and therapeutic measures.
The "coNfirm" network brings together nine e:Med groups, which are combining and evaluating different experimental datasets and clinical information obtained from project partners. To facilitate an efficient data exchange, datasets are harmonized and experimental standards as well as legal requirements are created. The developed tools for combining and exchanging big datasets can be transferred to many different areas to gain more insight in this field. This knowledge will be passed on to the e:Med community in workshops.
Subproject 1: Multi-species and multi-level data resource
Subproject 2: Bioinformatic approaches to generate common signaling pathways of cardiac diseases
Subproject 3: Methods of data exchange within coNfirm: rules, procedures and trust
Publications
Akcan, T. S., S. Vilov, and M. Heinig (2023). "Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures." Nucleic Acids Res. doi.org/10.1093/nar/gkac1272.
Andrieux, G., S. Chakraborty, T. Das, and M. Boerries (2020). "Alteration of Proteotranscriptomic Landscape Reveals the Transcriptional Regulatory Circuits Controlling Key-Signaling Pathways and Metabolic Reprogramming During Tumor Evolution." Front Cell Dev Biol 8. doi.org/10.3389/fcell.2020.586479.
Assum, I., J. Krause, M. O. Scheinhardt, C. Muller, E. Hammer, C. S. Borschel, U. Volker, L. Conradi, B. Geelhoed, T. Zeller, R. B. Schnabel, and M. Heinig (2022). "Tissue-specific multi-omics analysis of atrial fibrillation." Nat Commun 13(1): 441. www.ncbi.nlm.nih.gov/pubmed/35064145.
Bauer, C., M. Quante, W. B. Breunis, C. Regina, M. Schneider, G. Andrieux, O. Gorka, O. Groß, M. Boerries, B. Kammerer, and S. Hettmer (2021). "Lack of Electron Acceptors Contributes to Redox Stress and Growth Arrest in Asparagine-Starved Sarcoma Cells." Cancers 13(3): 412. doi.org/10.3390/cancers13030412.
Bellmann, P., L. Lausser, H. A. Kestler, and F. Schwenker (2022). "A Theoretical Approach to Ordinal Classification: Feature Space-Based Definition and Classifier-Independent Detection of Ordinal Class Structures." Applied Sciences 12(4): 1815. www.mdpi.com/2076-3417/12/4/1815.
Bellmann, P., P. Thiam, H. A. Kestler, and F. Schwenker (2022). "Machine Learning-based Pain Intensity Estimation: Where Pattern Recognition meets Chaos Theory – An Example based on the BioVid Heat Pain Database." IEEE Access: 1. doi.org/10.1109/ACCESS.2022.3208905.
Beyes, S., G. Andrieux, M. Schrempp, D. Aicher, J. Wenzel, P. Anton-Garcia, M. Boerries, and A. Hecht (2019). "Genome-wide mapping of DNA-binding sites identifies stemness-related genes as directly repressed targets of SNAIL1 in colorectal cancer cells." Oncogene. www.ncbi.nlm.nih.gov/pubmed/31391555.
Buhler, A., B. M. Gahr, D. D. Park, A. Bertozzi, A. Boos, M. Dalvoy, A. Pott, F. Oswald, R. A. Kovall, B. Kuhn, G. Weidinger, W. Rottbauer, and S. Just (2021). "Histone deacetylase 1 controls cardiomyocyte proliferation during embryonic heart development and cardiac regeneration in zebrafish." PLoS Genet 17(11): e1009890. www.ncbi.nlm.nih.gov/pubmed/34723970.
Chakraborty, S., G. Andrieux, A. M. M. Hasan, M. Ahmed, M. I. Hosen, T. Rahman, M. A. Hossain, and M. Boerries (2019). "Harnessing the tissue and plasma lncRNA-peptidome to discover peptide-based cancer biomarkers." Sci Rep 9(1): 12322. www.ncbi.nlm.nih.gov/pubmed/31444383.
Chakraborty, S., G. Andrieux, P. Kastl, L. Adlung, S. Altamura, M. E. Boehm, L. E. Schwarzmüller, Y. Abdullah, M.-C. Wagner, B. Helm, H.-J. Gröne, W. D. Lehmann, M. Boerries, H. Busch, M. U. Muckenthaler, M. Schilling, and U. Klingmüller (2022). "Erythropoietin-driven dynamic proteome adaptations during erythropoiesis prevent iron overload in the developing embryo." Cell Reports 40(12): 111360. doi.org/10.1016/j.celrep.2022.111360.
Dicks, S., L. Jürgensen, F. Leuschner, D. Hassel, G. Andrieux, and M. Boerries (2020). "Cardiac Regeneration and Tumor Growth—What Do They Have in Common?" Frontiers in Genetics 11. doi.org/10.3389/fgene.2020.586658.
Diofano, F., K. Weinmann, I. Schneider, K. D. Thiessen, W. Rottbauer, and S. Just (2020). "Genetic compensation prevents myopathy and heart failure in an in vivo model of Bag3 deficiency." Plos Genetics 16(11): 24. www.ncbi.nlm.nih.gov/pubmed/33137814.
Dittman, J., T. Haydn, P. Metzger, G. A. Ward, M. Boerries, M. Vogler, and S. Fulda (2020). "Next-generation hypomethylating agent SGI-110 primes acute myeloid leukemia cells to IAP antagonist by activating extrinsic and intrinsic apoptosis pathways." Cell Death Differ 27(6): 1878–1895. doi.org/10.1038/s41418-019-0465-8.
Frey, P., A. Devisme, M. Schrempp, G. Andrieux, M. Boerries, and A. Hecht (2020). "Canonical BMP Signaling Executes Epithelial-Mesenchymal Transition Downstream of SNAIL1." J Cancers 12(4): 1019. doi.org/10.3390/cancers12041019.
Gross, A., B. Kracher, J. M. Kraus, S. D. Kuhlwein, A. S. Pfister, S. Wiese, K. Luckert, O. Potz, T. Joos, D. Van Daele, L. De Raedt, M. Kuhl, and H. A. Kestler (2019). "Representing dynamic biological networks with multi-scale probabilistic models." Commun Biol 2: 21. www.ncbi.nlm.nih.gov/pubmed/30675519.
Hamarsheh, S. a., L. Osswald, B. S. Saller, S. Unger, D. De Feo, J. M. Vinnakota, M. Konantz, F. M. Uhl, H. Becker, M. Lübbert, K. Shoumariyeh, C. Schürch, G. Andrieux, N. Venhoff, A. Schmitt-Graeff, S. Duquesne, D. Pfeifer, M. A. Cooper, C. Lengerke, M. Boerries, J. Duyster, C. M. Niemeyer, M. Erlacher, B. R. Blazar, B. Becher, O. Groß, T. Brummer, and R. Zeiser (2020). "Oncogenic KrasG12D causes myeloproliferation via NLRP3 inflammasome activation." Nat Commun 11(1659): 1–17. doi.org/10.1038/s41467-020-15497-1.
Hammoud, Z., and F. Kramer (2020). "Multilayer networks: aspects, implementations, and application in biomedicine." Big Data Anal 5(1): 1–18. doi.org/10.1186/s41044-020-00046-0.
--- (2020). "Multipath: An R Package to Generate Integrated Reproducible Pathway Models." Biology 9(12): 483. doi.org/10.3390/biology9120483.
Haring, E., F. M. Uhl, G. Andrieux, M. Proietti, A. Bulashevska, B. Sauer, L. M. Braun, E. de Vega Gomez, P. R. Esser, S. F. Martin, D. Pfeifer, M. Follo, A. Schmitt-Graeff, J. Buescher, J. Duyster, B. Grimbacher, M. Boerries, E. L. Pearce, R. Zeiser, and P. Apostolova (2021). "Bile acids regulate intestinal antigen presentation and reduce graft-versus-host disease without impairing the graft-versus-leukemia effect." Haematologica 106(8): 2131–2146. doi.org/10.3324/haematol.2019.242990.
Hawe, J. S., A. Saha, M. Waldenberger, S. Kunze, S. Wahl, M. Müller-Nurasyid, H. Prokisch, H. Grallert, C. Herder, A. Peters, K. Strauch, F. J. Theis, C. Gieger, J. Chambers, A. Battle, and M. Heinig (2022). "Network reconstruction for trans acting genetic loci using multi-omics data and prior information." Genome Med 14(1): 1–21. doi.org/10.1186/s13073-022-01124-9.
Hawe, J. S., F. J. Theis, and M. Heinig (2019). "Inferring Interaction Networks From Multi-Omics Data." Front Genet 10: 535. www.ncbi.nlm.nih.gov/pubmed/31249591.
Heinig, M. (2018). "Using Gene Expression to Annotate Cardiovascular GWAS Loci." Front. Cardiovasc. Med 5. www.frontiersin.org/articles/10.3389/fcvm.2018.00059/full.
Ho, J. G., D. Schmidt, T. Lowinus, J. Ryoo, E.-P. Dopfer, N. Gonzalo Nunez, S. Costa-Pereira, C. Toffalori, M. Punta, V. Fetsch, T. Wertheimer, M.-C. Rittmann, L. M. Braun, M. Follo, C. Briere, J. M. Vinnakota, M. Langenbach, F. Koppers, K. Shoumariyeh, H. Engel, T. Rückert, M. Märklin, S. J. Holzmayer, A. L. Illert, F. Magon, G. Andrieux, S. Duquesne, D. Pfeifer, J. Staniek, M. Rizzi, C. Miething, N. Köhler, J. Duyster, H. D. Menssen, M. Boerries, J. Buescher, N. Cabezas-Wallscheid, B. R. Blazar, P. Apostolova, L. Vago, E. Pearce, B. Becher, and R. Zeiser (2022). "Targeting MDM2 enhances anti-leukemia immunity after allogeneic transplantation via MHC-II and TRAIL-R1/2 upregulation." Blood. doi.org/10.1182/blood.2022016082.
Hofeichner, J., B. M. Gahr, M. Huber, A. Boos, W. Rottbauer, and S. Just (2023). "CRISPR/Cas9-mediated nexilin deficiency interferes with cardiac contractile function in zebrafish in vivo." Scientific Reports 13. doi.org/10.1038/s41598-023-50065-9.
Hussung, S., D. Akhoundova, J. Hipp, M. Follo, R. F. U. Klar, U. Philipp, F. Scherer, N. von Bubnoff, J. Duyster, M. Boerries, U. Wittel, and R. M. Fritsch (2021). "Longitudinal analysis of cell-free mutated KRAS and CA 19–9 predicts survival following curative resection of pancreatic cancer." BMC Cancer 21(1): 49. doi.org/10.1186/s12885-020-07736-x.
Hussung, S., M. Follo, R. F. U. Klar, S. Michalczyk, K. Fritsch, F. Nollmann, J. Hipp, J. Duyster, F. Scherer, N. von Bubnoff, M. Boerries, U. Wittel, and R. M. Fritsch (2020). "Development and clinical validation of discriminatory multi-target digital droplet PCR assays for the detection of hot spot KRAS and NRAS mutations in cell-free DNA." J Mol Diagn. doi.org/10.1016/j.jmoldx.2020.04.206.
Ikonomi, N., S. D. Kuehlwein, J. D. Schwab, and H. A. Kestler (2020). "Awakening the HSC: Dynamic Modeling of HSC Maintenance Unravels Regulation of the TP53 Pathway and Quiescence." Front Physiol 11(848). doi.org/10.3389/fphys.2020.00848.
Ketterer, S., J. Mitschke, A. Ketscher, M. Schlimpert, W. Reichardt, N. Baeuerle, M. E. Hess, P. Metzger, M. Boerries, C. Peters, B. Kammerer, T. Brummer, F. Steinberg, and T. Reinheckel (2020). "Cathepsin D deficiency in mammary epithelium transiently stalls breast cancer by interference with mTORC1 signaling." Nat Commun 11(5133): 1–18. doi.org/10.1038/s41467-020-18935-2.
Kläsener, K., J. Jellusova, G. Andrieux, U. Salzer, C. Böhler, S. N. Steiner, J. B. Albinus, M. Cavallari, B. Süß, R. E. Voll, M. Boerries, B. Wollscheid, and M. Reth (2021). "CD20 as a gatekeeper of the resting state of human B cells." Proc Natl Acad Sci U.S.A 118(7): e2021342118. doi.org/10.1073/pnas.2021342118.
Klett, H., L. Jürgensen, P. Most, M. Busch, F. Günther, G. Dobreva, F. Leuschner, D. Hassel, H. Busch, and M. Boerries (2018). "Delineating the Dynamic Transcriptome Response of mRNA and microRNA during Zebrafish Heart Regeneration." Biomolecules 9(1). doi.org/10.3390/biom9010011.
Kozyra, E. J., V. B. Pastor, S. Lefkopoulos, S. S. Sahoo, H. Busch, R. K. Voss, M. Erlacher, D. Lebrecht, E. A. Szvetnik, S. Hirabayashi, R. Pasaulienė, L. Pedace, M. Tartaglia, C. Klemann, P. Metzger, M. Boerries, A. Catala, H. Hasle, V. de Haas, K. Kállay, R. Masetti, B. De Moerloose, M. Dworzak, M. Schmugge, O. Smith, J. Starý, E. Mejstrikova, M. Ussowicz, E. Morris, P. Singh, M. Collin, M. Derecka, G. Göhring, C. Flotho, B. Strahm, F. Locatelli, C. M. Niemeyer, E. Trompouki, M. W. Wlodarski, and E. W. G. o. M. i. Childhood (2020). "Synonymous GATA2 mutations result in selective loss of mutated RNA and are common in patients with GATA2 deficiency." Leukemia: 1–15. doi.org/10.1038/s41375-020-0899-5.
Krause, J., A. Nickel, A. Madsen, H. M. Aitken-Buck, A. S. Stoter, J. Schrapers, F. Ojeda, K. Geiger, M. Kern, M. Kohlhaas, E. Bertero, P. Hofmockel, F. Hübner, I. Assum, M. Heinig, C. Müller, A. Hansen, T. Krause, D.-D. Park, S. Just, D. Aïssi, D. Börnigen, D. Lindner, N. Friedrich, K. Alhussini, C. Bening, R. B. Schnabel, M. Karakas, L. Iacoviello, V. Salomaa, A. Linneberg, H. Tunstall-Pedoe, K. Kuulasmaa, P. Kirchhof, S. Blankenberg, T. Christ, T. Eschenhagen, R. R. Lamberts, C. Maack, J. Stenzig, and T. Zeller (2023). "An arrhythmogenic metabolite in atrial fibrillation." Journal of Translational Medicine 21(1): 566. doi.org/10.1186/s12967-023-04420-z.
Langenbach, M., S. Giesler, S. Richtsfeld, S. Da Costa-Pereira, L. Rindlisbacher, T. Wertheimer, L. M. Braun, G. Andrieux, S. Duquesne, D. Pfeifer, N. M. Woessner, H. D. Menssen, S. Taromi, J. Duyster, M. Boerries, T. Brummer, B. R. Blazar, S. Minguet, P. Turko, M. P. Levesque, B. Becher, and R. Zeiser (2023). "MDM2 inhibition enhances immune checkpoint inhibitor efficacy by increasing IL-15 and MHC class II production." Mol Cancer Res. doi.org/10.1158/1541-7786.MCR-22-0898.
Lausser, L., L. M. Schäfer, S. D. Kühlwein, A. M. R. Kestler, and H. A. Kestler (2020). "Detecting Ordinal Subcascades." Neural Process Lett 52(3): 2583–2605. doi.org/10.1007/s11063-020-10362-0.
Lausser, L., L. M. Schafer, L. R. Schirra, R. Szekely, F. Schmid, and H. A. Kestler (2019). "Assessing phenotype order in molecular data." Sci Rep 9(1): 11746. www.ncbi.nlm.nih.gov/pubmed/31409831.
Lausser, L., L. Siegle, W. Rottbauer, D. Frank, S. Just, and H. A. Kestler (2018). "Semantic Multi-Classifier Systems Identify Predictive Processes in Heart Failure Models across Species." Biomolecules 8(4). www.ncbi.nlm.nih.gov/pubmed/30486323.
Lausser, L., R. Szekely, V. Kessler, F. Schwenker, and H. A. Kestler. 2018. "Selecting Features from Foreign Classes." 2018/09//.
Lausser, L., R. Szekely, and H. A. Kestler (2020). "Chained correlations for feature selection." Advances in Data Analysis and Classification: 1–14. ideas.repec.org/a/spr/advdac/vyid10.1007_s11634-020-00397-5.html.
Lausser, L., R. Szekely, A. Klimmek, F. Schmid, and H. A. Kestler (2020). "Constraining classifiers in molecular analysis: invariance and robustness." Journal of the Royal Society Interface 17(163): 14. www.ncbi.nlm.nih.gov/pubmed/32019472.
Maccari, M. E., S. Fuchs, P. Kury, G. Andrieux, S. Völkl, B. Bengsch, M. R. Lorenz, M. Heeg, J. Rohr, S. Jägle, C. N. Castro, M. Groß, U. Warthorst, C. König, I. Fuchs, C. Speckmann, J. Thalhammer, F. G. Kapp, M. G. Seidel, G. Dückers, S. Schönberger, C. Schütz, M. Führer, R. Kobbe, D. Holzinger, C. Klemann, P. Smisek, S. Owens, G. Horneff, R. Kolb, N. Naumann-Bartsch, M. Miano, J. Staniek, M. Rizzi, T. Kalina, P. Schneider, A. Erxleben, R. Backofen, A. Ekici, C. M. Niemeyer, K. Warnatz, B. Grimbacher, H. Eibel, A. Mackensen, A. P. Frei, K. Schwarz, M. Boerries, S. Ehl, and A. Rensing-Ehl (2021). "A distinct CD38+CD45RA+ population of CD4+, CD8+, and double-negative T cells is controlled by FAS." J Exp Med 218(2). doi.org/10.1084/jem.20192191.
Marschner, D., M. Falk, N. R. Javorniczky, K. Hanke-Müller, J. Rawluk, A. Schmitt-Graeff, F. Simonetta, E. Haring, S. Dicks, M. Ku, S. Duquesne, K. Aumann, D. Rafei-Shamsabadi, F. Meiss, P. Marschner, M. Boerries, R. S. Negrin, J. Duyster, R. Zeiser, and N. Köhler (2020). "MicroRNA-146a regulates immune-related adverse events caused by immune checkpoint inhibitors." JCI Insight 5(6). insight.jci.org/articles/view/132334.
Martinez-Hernandez, J. E., Z. Hammoud, A. M. de Sousa, F. Kramer, R. L. do Monte-Neto, V. Maracaja-Coutinho, and A. J. M. Martin (2021). "Network-Based Approaches Reveal Potential Therapeutic Targets for Host-Directed Antileishmanial Therapy Driving Drug Repurposing." Microbiology Spectrum 9(2). journals.asm.org/doi/10.1128/Spectrum.01018-21.
Müller, A., L. Lausser, A. Wilhelm, T. Ropinski, M. Platzer, H. Neumann, and H. A. Kestler (2020). "A perceptually optimised bivariate visualisation scheme for high-dimensional fold-change data." Adv Data Anal Classif: 1–18. doi.org/10.1007/s11634-020-00416-5.
Müssel, C., N. Ikonomi, S. D. Werle, F. M. Weidner, M. Maucher, J. D. Schwab, and H. A. Kestler (2022). "CANTATA—prediction of missing links in Boolean networks using genetic programming." Bioinformatics. doi.org/10.1093/bioinformatics/btac623.
Norona, J., P. Apostolova, D. Schmidt, R. Ihlemann, N. Reischmann, G. Taylor, N. Köhler, J. de Heer, S. Heeg, G. Andrieux, B. A. Siranosian, A. Schmitt-Graeff, D. Pfeifer, A. Catalano, I. Frew, M. Proietti, B. Grimbacher, A. Bulashevska, A. S. Bhatt, T. Brummer, T. S. Clauditz, T. Zabelina, N. Kroeger, B. R. Blazar, M. Boerries, F. Ayuk, and R. Zeiser (2020). "Glucagon like peptide-2 for Intestinal stem cell and Paneth cell repair during graft-versus-host disease in mice and humans." Blood. doi.org/10.1182/blood.2020005957.
Osswald, L., S. a. Hamarsheh, F. M. Uhl, G. Andrieux, C. Klein, C. Dierks, S. Duquesne, L. M. Braun, A. Schmitt-Graeff, J. Duyster, M. Boerries, T. Brummer, and R. Zeiser (2021). "Oncogenic KrasG12D Activation in the Nonhematopoietic Bone Marrow Microenvironment Causes Myelodysplastic Syndrome in Mice." Mol Cancer Res 19(9): 1596–1608. doi.org/10.1158/1541-7786.MCR-20-0275.
Park, D.-D., B. M. Gahr, J. Krause, W. Rottbauer, T. Zeller, and S. Just (2021). "Long-Chain Acyl-Carnitines Interfere with Mitochondrial ATP Production Leading to Cardiac Dysfunction in Zebrafish." Int J Mol Sci 22(16): 8468. doi.org/10.3390/ijms22168468.
Pott, A., W. Rottbauer, and S. Just (2020). "Streamlining drug discovery assays for cardiovascular disease using zebrafish." Expert Opin Drug Discov 15(1): 27-37. www.ncbi.nlm.nih.gov/pubmed/31570020.
Pott, A., M. Shahid, D. Köhler, C. Pylatiuk, K. Weinmann, S. Just, and W. Rottbauer (2018). "Therapeutic Chemical Screen Identifies Phosphatase Inhibitors to Reconstitute PKB Phosphorylation and Cardiac Contractility in ILK-Deficient Zebrafish." Biomolecules 8(4). doi.org/10.3390/biom8040153.
R Mathew, N., J. M. Vinnakota, P. Apostolova, D. Erny, S. a. Hamarsheh, G. Andrieux, J.-S. Kim, K. Hanke, T. Goldmann, L. Chappell-Maor, N. El-Khawanky, G. Ihorst, D. Schmidt, J. Duyster, J. Finke, T. Blank, M. Boerries, B. R. Blazar, S. Jung, M. Prinz, and R. Zeiser (2020). "Graft-versus-host disease of the CNS is mediated by TNF upregulation in microglia." J. Clin. Invest. 130(3): 1315-1329. www.ncbi.nlm.nih.gov/pubmed/31846439.
Rattka, M., S. Westphal, B. M. Gahr, S. Just, and W. Rottbauer (2021). "Spen deficiency interferes with Connexin 43 expression and leads to heart failure in zebrafish." Journal of Molecular and Cellular Cardiology 155: 25-35. doi.org/10.1016/j.yjmcc.2021.01.006.
Reischmann, N., G. Andrieux, R. Griffin, T. Reinheckel, M. Boerries, and T. Brummer (2020). "BRAFV600E drives dedifferentiation in small intestinal and colonic organoids and cooperates with mutant p53 and Apc loss in transformation." Oncogene: 1–18. doi.org/10.1038/s41388-020-01414-9.
Saleva-Stateva, M., M. Hess, K. Technau-Hafsi, L. Weibel, M.-A. Badea, M. d. C. Boente, M. Theiler, M. J. Fiandrino, P. Hoeger, A. Zimmer, D. Rafei-Shamsabadi, M. Balabanova, J. Fischer, M. Boerries, and C. Has (2021). "Molecular characterization and natural history of linear porokeratosis: A case series." Journal of the American Academy of Dermatology 85(6): 1603–1606. doi.org/10.1016/j.jaad.2020.11.061.
Sanchez-Gonzalez, I., A. Bobien, C. Molnar, S. Schmid, M. Strotbek, M. Boerries, H. Busch, and M. A. Olayioye (2020). "miR-149 suppresses breast cancer metastasis by blocking paracrine interactions with macrophages." Cancer Res 80(6): 1330-1341. www.ncbi.nlm.nih.gov/pubmed/31911555.
Schumacher, D., G. Andrieux, K. Boehnke, M. Keil, A. Silvestri, M. Silvestrov, U. Keilholz, J. Haybaeck, G. Erdmann, C. Sachse, M. Templin, J. Hoffmann, M. Boerries, R. Schafer, and C. R. A. Regenbrecht (2019). "Heterogeneous pathway activation and drug response modelled in colorectal-tumor-derived 3D cultures." PLoS Genet 15(3): e1008076. www.ncbi.nlm.nih.gov/pubmed/30925167.
Schwab, J. D., and H. A. Kestler (2018). "Automatic Screening for Perturbations in Boolean Networks." Frontiers in Physiology 9: 431. www.ncbi.nlm.nih.gov/pubmed/29740342.
Schwab, J. D., S. D. Kühlwein, N. Ikonomi, M. Kühl, and H. A. Kestler (2020). "Concepts in Boolean network modeling: What do they all mean?" Computational and Structural Biotechnology Journal. www.sciencedirect.com/science/article/pii/S200103701930460X.
Seifert, S., S. Gundlach, O. Junge, and S. Szymczak (2020). "Integrating biological knowledge and gene expression data using pathway guided random forests: A benchmarking study." Bioinformatics. doi.org/10.1093/bioinformatics/btaa483.
Siegle, L., J. D. Schwab, S. D. Kühlwein, L. Lausser, S. Tümpel, A. S. Pfister, M. Kühl, and H. A. Kestler (2018). "A Boolean network of the crosstalk between IGF and Wnt signaling in aging satellite cells." PloS One 13(3): e0195126. www.ncbi.nlm.nih.gov/pubmed/29596489.
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Thiam, P., H. Hihn, D. A. Braun, H. A. Kestler, and F. Schwenker (2021). "Multi-Modal Pain Intensity Assessment Based on Physiological Signals: A Deep Learning Perspective." Front Physiol 12: 720464. www.ncbi.nlm.nih.gov/pubmed/34539444.
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