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Consortium Publications
Peer-reviewed papers published by the consortium members in cancer and immunity since the project initiation
2022
Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence. Vera J, Lai X, Baur A, Erdmann M, Gupta S, Guttà C, Heinzerling L, Heppt MV, Kazmierczak PM, Kunz M, Lischer C, Pützer BM, Rehm M, Ostalecki C, Retzlaff J, Witt S, Wolkenhauer O, Berking C. Brief Bioinform. doi: 10.1093/bib/bbac433
Development of Lymphopenia during Therapy with Immune Checkpoint Inhibitors Is Associated with Poor Outcome in Metastatic Cutaneous Melanoma Tomsitz D, Schlaak M, Zierold S, Pesch G, Schulz TU, Müller G, Zecha C, French LE, Heinzerling L. Cancers (Basel). 2022 Jul 5;14(13):3282. doi: 10.3390/cancers14133282. PMID: 35805052
Persistent immune-related adverse events after cessation of checkpoint inhibitor therapy: Prevalence and impact on patients' health-related quality of life. Schulz TU, Zierold S, Sachse MM, Pesch G, Tomsitz D, Schilbach K, Kähler KC, French LE, Heinzerling L. . Eur J Cancer. 2022 Nov;176:88-99. doi: 10.1016/j.ejca.2022.08.029. Epub 2022 Oct 2. PMID: 36198246.
Characteristics of immune checkpoint inhibitor-induced encephalitis and comparison with HSV-1 and anti-LGI1 encephalitis: A retrospective multicentre cohort study. Müller-Jensen L, Zierold S, Versluis JM, Boehmerle W, Huehnchen P, Endres M, Mohr R, Compter A, Blank CU, Hagenacker T, Meier F, Reinhardt L, Gesierich A, Salzmann M, Hassel JC, Ugurel S, Zimmer L, Banks P, Spain L, Soon JA, Enokida T, Tahara M, Kähler KC, Seggewiss-Bernhardt R, Harvey C, Long GV, Schöberl F, von Baumgarten L, Hundsberger T, Schlaak M, French LE, Knauss S, Heinzerling LM. Eur J Cancer. 2022 Nov;175:224-235. doi: 10.1016/j.ejca.2022.08.009. Epub 2022 Sep 22. PMID: 36155116.
Bin-based visualization of cytokine-co-expression patterns of IL-10-producing CD4 T cell subsets. Mohr E, Hinnenthal T, Gryzik S, Hoang Y, Lischke T, Retzlaff J, Mekonnen A, Paul F, Valleriani A, Radbruch A, Vera J, Baumgrass R. BEur J Immunol. doi: 10.1002/eji.202249829.
Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps. Hoch M, Smita S, Cesnulevicius K, Lescheid D, Schultz M, Wolkenhauer O, Gupta S. NPJ Syst Biol Appl. https://www.nature.com/articles/s41540-022-00222-z
A network medicine approach for identifying diagnostic and prognostic biomarkers and exploring drug repurposing in human cancer. L Zhang, S Fan, J Vera, X Lai (2022), Computational and Structural Biotechnology Journal. https://doi.org/10.1016/j.csbj.2022.11.037
Artificial intelligence in cancer target identification and drug discovery. You Y, Lai X, Pan Y, Zheng H, Vera J, Liu S, Deng S, Zhang L. . Signal Transduct Target Ther. 2022 May 10;7(1):156. www.nature.com/articles/s41392-022-00994-0
Multi-Level Computational Modeling of Anti-Cancer Dendritic Cell Vaccination Utilized to Select Molecular Targets for Therapy Optimization. Lai X, Keller C, Santos G, Schaft N, Dörrie J, Vera J (2022). Front Cell Dev Biol. ;9:746359. doi.org/10.3389/fcell.2021.746359
Artificial intelligence in cancer target identification and drug discovery. You Y, Lai X, Pan Y, Zheng H, Vera J, Liu S, Deng S, Zhang L (2022). Signal Transduct Target Ther. 2022 May 10;7(1):156. doi: 10.1038/s41392-022-00994-0
PRI: Re-Analysis of a Public Mass Cytometry Dataset Reveals Patterns of Effective Tumor Treatments, Y Hoang, S Gryzik, I Hoppe, A Rybak, M Schädlich, I Kadner, D Walther, J Vera, A Radbruch, D Groth, S Baumgart, R Baumgrass (2022). Front. Immunol. https://doi.org/10.3389/fimmu.2022.849329
2021
A disease network-based deep learning approach for characterizing melanoma. X Lai , J Zhou , A Wessely, M Heppt, A Maier, C Berking, J Vera, L Zhang. Int J Cancer. https://doi.org/10.1002/ijc.33860
Inflammatory markers in autoimmunity induced by checkpoint inhibitors. Husain B, Kirchberger MC, Erdmann M, Schüpferling S, Abolhassani AR, Fröhlich W, Berking C, Heinzerling L.. J Cancer Res Clin Oncol. 2021 Jun;147(6):1623-1630. doi: 10.1007/s00432-021-03550-5. Epub 2021 Apr 10. PMID: 33837821;
Structure-function relationships explain CTCF zinc finger mutation phenotypes in cancer. Bailey CG, Gupta S, Metierre C, Amarasekera PMS, O'Young P, Kyaw W, Laletin T, Francis H, Semaan C, Sharifi Tabar M, Singh KP, Mullighan CG, Wolkenhauer O, Schmitz U, Rasko JEJ. . Cell Mol Life Sci. doi: 10.1007/s00018-021-03946-z
Interleukin-33-induced metabolic reprogramming controls the differentiation of alternatively activated macrophages and the resolution of inflammation. Faas S, Ipseiz N, Ackermann J, Culemann S, Grüneboom A, Schröder F, Rothe T, Scholtysek C, Eberhardt M, Böttcher M Kirchner P, Stoll C, Ekici A, Fuchs M, Kunz M, Weigmann B, Wirtz S, Lang R, Hofmann J, Vera J, Voehringer D, Montelucci A, Mougiakakos D, Uderhardt S, Schett G, Krönke G. Immunity 54, 1–16. https://doi.org/10.1016/j.immuni.2021.09.010
Network- and systems-based re-engineering of dendritic cells with non-coding RNAs for cancer immunotherapy. Lai, X., F. S. Dreyer, M. Cantone, M. Eberhardt, K. F. Gerer, T. Jaitly, S. Uebe, C. Lischer, A. Ekici, J. Wittmann, H. M. Jack, N. Schaft,J. Dorrie, and J. Vera (2021). Theranostics 11(3): 1412-1428. doi.org/10.7150/thno.53092.
Mathematical Modelling in Biomedicine: A Primer for the Curious and the Skeptic. Vera, J., C. Lischer, M. Nenov, S. Nikolov, X. Lai, and M. Eberhardt (2021). Int J Mol Sci 22(2): 547. doi.org/10.3390/ijms22020547.
Inflammatory markers in autoimmunity induced by checkpoint inhibitors. Husain B, Kirchberger MC, Erdmann M, Schüpferling S, Abolhassani A, Fröhlich W, Berking C, Heinzerling L. J Cancer Res Clin Oncol, 147(6):1623-30. https://doi.org/10.1007/s00432-021-03550-5
2020
LncRNA-SLC16A1-AS1 induces metabolic reprogramming during Bladder Cancer progression as target and co-activator of E2F1. Logotheti, S., S. Marquardt, S. K. Gupta, C. Richter, B. A. H. Edelhäuser, D. Engelmann, J. Brenmoehl, C. Söhnchen, N. Murr, M. Alpers, K. P. Singh, O. Wolkenhauer, D. Heckl, A. Spitschak, and B. M. Pützer (2020). "." Theranostics 10(21). doi.org/10.7150/thno.44176.
Neural Networks Recapitulation by Cancer Cells Promotes Disease Progression: A Novel Role of p73 Isoforms in Cancer-Neuronal Crosstalk. Logotheti, S., S. Marquardt, C. Richter, R. Sophie Hain, N. Murr, I. Takan, A. Pavlopoulou, and B. M. Pützer (2020). "." Cancers (Basel) 12(12): 3789. doi.org/10.3390/cancers12123789.
The Atlas of Inflammation Resolution (AIR). Serhan, C. N., S. K. Gupta, M. Perretti, C. Godson, E. Brennan, Y. Li, O. Soehnlein, T. Shimizu, O. Werz, V. Chiurchiù, A. Azzi, M. Dubourdeau, S. S. Gupta, P. Schopohl, M. Hoch, D. Gjorgevikj, F. M. Khan, D. Brauer, A. Tripathi, K. Cesnulevicius, D. Lescheid, M. Schultz, E. Särndahl, D. Repsilber, R. Kruse, A. Sala, J. Z. Haeggström, B. D. Levy, J. G. Filep, and O. Wolkenhauer (2020). "." Mol Aspects Med 74: 100894. doi.org/10.1016/j.mam.2020.100894.
An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma. Singh, N., M. Eberhardt, O. Wolkenhauer, J. Vera, and S. K. Gupta (2020). "." BMC Bioinformatics 21(1): 1–17. doi.org/10.1186/s12859-020-03656-6.
2019
Curatopes Melanoma: A Database of Predicted T-cell Epitopes from Overly Expressed Proteins in Metastatic Cutaneous Melanoma. C Lischer, M Eberhardt, T Jaitly , C Schinzel , N Schaft , J Dörrie , G Schuler , J Vera (2019). Cancer Res 79(20):5452-5456. doi.org/10.1158/0008-5472.CAN-19-0296.
Locally renewing resident synovial macrophages provide a protective barrier for the join. S Culemann, AGrüneboom, JA Nicolás-Ávila , D Weidner, K F Lämmle, T Roth, J A Quintana, P Kirchner, B Krljanac, M Eberhardt, F Ferrazzi, E Kretzschmar, M Schicht, K Fischer, K Gelse, M Faas, R Pfeifle, J A Ackermann, M Pachowsky, N Renner, D Simon, R F Haseloff, A B Ekici, T Bäuerle, I E Blasig, J Vera, D Voehringe, A Kleyer, F Paulsen, G Schett , A Hidalgo, G Krönke (2019) . Nature ;572(7771):670-675. doi: 10.1038/s41586-019-1471-1
Drug repositioning inferred from E2F1-coregulator interactions studies for the prevention and treatment of metastatic cancers. Goody D*, Gupta SK*, Engelmann D, Spitschak A, Marquardt S, Mikkat S, Meier C, Hauser C, Gundlach J-P, Egberts J-H, Martin H, Schumacher T, Trauzold A, Wolkenhauer O, Logotheti S, Pützer BM. Theranostics 2019; 9(5):1490-1509. doi:10.7150/thno.29546.
2022
Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence. Vera J, Lai X, Baur A, Erdmann M, Gupta S, Guttà C, Heinzerling L, Heppt MV, Kazmierczak PM, Kunz M, Lischer C, Pützer BM, Rehm M, Ostalecki C, Retzlaff J, Witt S, Wolkenhauer O, Berking C. Brief Bioinform. doi: 10.1093/bib/bbac433
Development of Lymphopenia during Therapy with Immune Checkpoint Inhibitors Is Associated with Poor Outcome in Metastatic Cutaneous Melanoma Tomsitz D, Schlaak M, Zierold S, Pesch G, Schulz TU, Müller G, Zecha C, French LE, Heinzerling L. Cancers (Basel). 2022 Jul 5;14(13):3282. doi: 10.3390/cancers14133282. PMID: 35805052
Persistent immune-related adverse events after cessation of checkpoint inhibitor therapy: Prevalence and impact on patients' health-related quality of life. Schulz TU, Zierold S, Sachse MM, Pesch G, Tomsitz D, Schilbach K, Kähler KC, French LE, Heinzerling L. . Eur J Cancer. 2022 Nov;176:88-99. doi: 10.1016/j.ejca.2022.08.029. Epub 2022 Oct 2. PMID: 36198246.
Characteristics of immune checkpoint inhibitor-induced encephalitis and comparison with HSV-1 and anti-LGI1 encephalitis: A retrospective multicentre cohort study. Müller-Jensen L, Zierold S, Versluis JM, Boehmerle W, Huehnchen P, Endres M, Mohr R, Compter A, Blank CU, Hagenacker T, Meier F, Reinhardt L, Gesierich A, Salzmann M, Hassel JC, Ugurel S, Zimmer L, Banks P, Spain L, Soon JA, Enokida T, Tahara M, Kähler KC, Seggewiss-Bernhardt R, Harvey C, Long GV, Schöberl F, von Baumgarten L, Hundsberger T, Schlaak M, French LE, Knauss S, Heinzerling LM. Eur J Cancer. 2022 Nov;175:224-235. doi: 10.1016/j.ejca.2022.08.009. Epub 2022 Sep 22. PMID: 36155116.
Bin-based visualization of cytokine-co-expression patterns of IL-10-producing CD4 T cell subsets. Mohr E, Hinnenthal T, Gryzik S, Hoang Y, Lischke T, Retzlaff J, Mekonnen A, Paul F, Valleriani A, Radbruch A, Vera J, Baumgrass R. BEur J Immunol. doi: 10.1002/eji.202249829.
Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps. Hoch M, Smita S, Cesnulevicius K, Lescheid D, Schultz M, Wolkenhauer O, Gupta S. NPJ Syst Biol Appl. https://www.nature.com/articles/s41540-022-00222-z
A network medicine approach for identifying diagnostic and prognostic biomarkers and exploring drug repurposing in human cancer. L Zhang, S Fan, J Vera, X Lai (2022), Computational and Structural Biotechnology Journal. https://doi.org/10.1016/j.csbj.2022.11.037
Artificial intelligence in cancer target identification and drug discovery. You Y, Lai X, Pan Y, Zheng H, Vera J, Liu S, Deng S, Zhang L. . Signal Transduct Target Ther. 2022 May 10;7(1):156. www.nature.com/articles/s41392-022-00994-0
Multi-Level Computational Modeling of Anti-Cancer Dendritic Cell Vaccination Utilized to Select Molecular Targets for Therapy Optimization. Lai X, Keller C, Santos G, Schaft N, Dörrie J, Vera J (2022). Front Cell Dev Biol. ;9:746359. doi.org/10.3389/fcell.2021.746359
Artificial intelligence in cancer target identification and drug discovery. You Y, Lai X, Pan Y, Zheng H, Vera J, Liu S, Deng S, Zhang L (2022). Signal Transduct Target Ther. 2022 May 10;7(1):156. doi: 10.1038/s41392-022-00994-0
PRI: Re-Analysis of a Public Mass Cytometry Dataset Reveals Patterns of Effective Tumor Treatments, Y Hoang, S Gryzik, I Hoppe, A Rybak, M Schädlich, I Kadner, D Walther, J Vera, A Radbruch, D Groth, S Baumgart, R Baumgrass (2022). Front. Immunol. https://doi.org/10.3389/fimmu.2022.849329
2021
A disease network-based deep learning approach for characterizing melanoma. X Lai , J Zhou , A Wessely, M Heppt, A Maier, C Berking, J Vera, L Zhang. Int J Cancer. https://doi.org/10.1002/ijc.33860
Inflammatory markers in autoimmunity induced by checkpoint inhibitors. Husain B, Kirchberger MC, Erdmann M, Schüpferling S, Abolhassani AR, Fröhlich W, Berking C, Heinzerling L.. J Cancer Res Clin Oncol. 2021 Jun;147(6):1623-1630. doi: 10.1007/s00432-021-03550-5. Epub 2021 Apr 10. PMID: 33837821;
Structure-function relationships explain CTCF zinc finger mutation phenotypes in cancer. Bailey CG, Gupta S, Metierre C, Amarasekera PMS, O'Young P, Kyaw W, Laletin T, Francis H, Semaan C, Sharifi Tabar M, Singh KP, Mullighan CG, Wolkenhauer O, Schmitz U, Rasko JEJ. . Cell Mol Life Sci. doi: 10.1007/s00018-021-03946-z
Interleukin-33-induced metabolic reprogramming controls the differentiation of alternatively activated macrophages and the resolution of inflammation. Faas S, Ipseiz N, Ackermann J, Culemann S, Grüneboom A, Schröder F, Rothe T, Scholtysek C, Eberhardt M, Böttcher M Kirchner P, Stoll C, Ekici A, Fuchs M, Kunz M, Weigmann B, Wirtz S, Lang R, Hofmann J, Vera J, Voehringer D, Montelucci A, Mougiakakos D, Uderhardt S, Schett G, Krönke G. Immunity 54, 1–16. https://doi.org/10.1016/j.immuni.2021.09.010
Network- and systems-based re-engineering of dendritic cells with non-coding RNAs for cancer immunotherapy. Lai, X., F. S. Dreyer, M. Cantone, M. Eberhardt, K. F. Gerer, T. Jaitly, S. Uebe, C. Lischer, A. Ekici, J. Wittmann, H. M. Jack, N. Schaft,J. Dorrie, and J. Vera (2021). Theranostics 11(3): 1412-1428. doi.org/10.7150/thno.53092.
Mathematical Modelling in Biomedicine: A Primer for the Curious and the Skeptic. Vera, J., C. Lischer, M. Nenov, S. Nikolov, X. Lai, and M. Eberhardt (2021). Int J Mol Sci 22(2): 547. doi.org/10.3390/ijms22020547.
Inflammatory markers in autoimmunity induced by checkpoint inhibitors. Husain B, Kirchberger MC, Erdmann M, Schüpferling S, Abolhassani A, Fröhlich W, Berking C, Heinzerling L. J Cancer Res Clin Oncol, 147(6):1623-30. https://doi.org/10.1007/s00432-021-03550-5
2020
LncRNA-SLC16A1-AS1 induces metabolic reprogramming during Bladder Cancer progression as target and co-activator of E2F1. Logotheti, S., S. Marquardt, S. K. Gupta, C. Richter, B. A. H. Edelhäuser, D. Engelmann, J. Brenmoehl, C. Söhnchen, N. Murr, M. Alpers, K. P. Singh, O. Wolkenhauer, D. Heckl, A. Spitschak, and B. M. Pützer (2020). "." Theranostics 10(21). doi.org/10.7150/thno.44176.
Neural Networks Recapitulation by Cancer Cells Promotes Disease Progression: A Novel Role of p73 Isoforms in Cancer-Neuronal Crosstalk. Logotheti, S., S. Marquardt, C. Richter, R. Sophie Hain, N. Murr, I. Takan, A. Pavlopoulou, and B. M. Pützer (2020). "." Cancers (Basel) 12(12): 3789. doi.org/10.3390/cancers12123789.
The Atlas of Inflammation Resolution (AIR). Serhan, C. N., S. K. Gupta, M. Perretti, C. Godson, E. Brennan, Y. Li, O. Soehnlein, T. Shimizu, O. Werz, V. Chiurchiù, A. Azzi, M. Dubourdeau, S. S. Gupta, P. Schopohl, M. Hoch, D. Gjorgevikj, F. M. Khan, D. Brauer, A. Tripathi, K. Cesnulevicius, D. Lescheid, M. Schultz, E. Särndahl, D. Repsilber, R. Kruse, A. Sala, J. Z. Haeggström, B. D. Levy, J. G. Filep, and O. Wolkenhauer (2020). "." Mol Aspects Med 74: 100894. doi.org/10.1016/j.mam.2020.100894.
An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma. Singh, N., M. Eberhardt, O. Wolkenhauer, J. Vera, and S. K. Gupta (2020). "." BMC Bioinformatics 21(1): 1–17. doi.org/10.1186/s12859-020-03656-6.
2019
Curatopes Melanoma: A Database of Predicted T-cell Epitopes from Overly Expressed Proteins in Metastatic Cutaneous Melanoma. C Lischer, M Eberhardt, T Jaitly , C Schinzel , N Schaft , J Dörrie , G Schuler , J Vera (2019). Cancer Res 79(20):5452-5456. doi.org/10.1158/0008-5472.CAN-19-0296.
Locally renewing resident synovial macrophages provide a protective barrier for the join. S Culemann, AGrüneboom, JA Nicolás-Ávila , D Weidner, K F Lämmle, T Roth, J A Quintana, P Kirchner, B Krljanac, M Eberhardt, F Ferrazzi, E Kretzschmar, M Schicht, K Fischer, K Gelse, M Faas, R Pfeifle, J A Ackermann, M Pachowsky, N Renner, D Simon, R F Haseloff, A B Ekici, T Bäuerle, I E Blasig, J Vera, D Voehringe, A Kleyer, F Paulsen, G Schett , A Hidalgo, G Krönke (2019) . Nature ;572(7771):670-675. doi: 10.1038/s41586-019-1471-1
Drug repositioning inferred from E2F1-coregulator interactions studies for the prevention and treatment of metastatic cancers. Goody D*, Gupta SK*, Engelmann D, Spitschak A, Marquardt S, Mikkat S, Meier C, Hauser C, Gundlach J-P, Egberts J-H, Martin H, Schumacher T, Trauzold A, Wolkenhauer O, Logotheti S, Pützer BM. Theranostics 2019; 9(5):1490-1509. doi:10.7150/thno.29546.
