We disseminate our research in peer-reviewed journal articles ranging from contributions in basic science to applied interdisciplinary science. The articles were published in prominent journals, such as Nucleic Acids Research, Theranostics, Bioinformatics, Cancer Research, Signal Transduction and Targeted Therapy etc. In addition, we regularly receive invitations to publish chapters in books related to systems biology and systems medicine. In 2019, we published a book titled “Computational Biology of Non-Coding RNA” and the second edition of the book is to appear in 2024. So far, we have reported on our research in the form of an oral presentation in 30+ in international conferences (such as ISMB/ECCB, ICSB, and GCB), workshops, and summer schools. The figures below show publications and citations per year, and more statistics and information about our publications can be found at Google Scholar, Web of Science, and Scopus.
Journal Articles
Zhang, L., Fan, S., Vera, J. & Lai, X. A network medicine approach for identifying diagnostic and prognostic biomarkers and exploring drug repurposing in human cancer. Comput Struct Biotechnol J 21, 34–45 (2023).
Retzlaff, J., Lai, X., Berking, C. & Vera, J. Integration of transcriptomics data into agent-based models of solid tumor metastasis. Comput Struct Biotechnol J 21, 1930–1941 (2023).
Vera, J., Lai, X., Baur, A., Erdmann, M., Gupta, S., Guttà, C., Heinzerling, L., Heppt, M. V., Kazmierczak, P. M., Kunz, M., Lischer, C., Pützer, B. M., Rehm, M., Ostalecki, C., Retzlaff, J., Witt, S., Wolkenhauer, O. & Berking, C. Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence. Brief Bioinform 23, bbac433 (2022).
You, Y., Lai, X., Pan, Y., Zheng, H., Vera, J., Liu, S., Deng, S. & Zhang, L. Artificial intelligence in cancer target identification and drug discovery. Sig Transduct Target Ther 7, 1–24 (2022).
Lai, X., Zhou, J., Wessely, A., Heppt, M., Maier, A., Berking, C., Vera, J. & Zhang, L. A disease network-based deep learning approach for characterizing melanoma. Int J Cancer 150, 1029–1044 (2022).
Lai, X., Keller, C., Santos, G., Schaft, N., Dörrie, J. & Vera, J. Multi-Level Computational Modeling of Anti-Cancer Dendritic Cell Vaccination Utilized to Select Molecular Targets for Therapy Optimization. Front Cell Dev Biol 9, 746359 (2021).
Lai, X., Dreyer, F. S., Cantone, M., Eberhardt, M., Gerer, K. F., Jaitly, T., Uebe, S., Lischer, C., Ekici, A., Wittmann, J., Jäck, H.-M., Schaft, N., Dörrie, J. & Vera, J. Network- and systems-based re-engineering of dendritic cells with non-coding RNAs for cancer immunotherapy. Theranostics 11, 1412–1428 (2021).
Vera, J., Lischer, C., Nenov, M., Nikolov, S., Lai, X. & Eberhardt, M. Mathematical Modelling in Biomedicine: A Primer for the Curious and the Skeptic. Int J Mol Sci 22, (2021).
Wach, S., Taubert, H., Weigelt, K., Hase, N., Köhn, M., Misiak, D., Hüttelmaier, S., Stöhr, C. G., Kahlmeyer, A., Haller, F., Vera, J., Hartmann, A., Wullich, B. & Lai, X. RNA Sequencing of Collecting Duct Renal Cell Carcinoma Suggests an Interaction between miRNA and Target Genes and a Predominance of Deregulated Solute Carrier Genes. Cancers 12, 64 (2020).
Naderi-Meshkin, H., Lai, X., Amirkhah, R., Vera, J., Rasko, J. E. J. & Schmitz, U. Exosomal lncRNAs and cancer: connecting the missing links. Bioinformatics 35, 352–360 (2019).
Lee, J.-H., Dindorf, J., Eberhardt, M., Lai, X., Ostalecki, C., Koliha, N., Gross, S., Blume, K., Bruns, H., Wild, S., Schuler, G., Vera-Gonzales, J. & Baur, A. S. Innate extracellular vesicles from melanoma patients suppress β-catenin in tumor cells by miRNA-34a. Life Science Alliance 2, e201800205 (2019).
Lai, X., Eberhardt, M., Schmitz, U. & Vera, J. Systems biology-based investigation of cooperating microRNAs as monotherapy or adjuvant therapy in cancer. Nucleic Acids Res 47, 7753–7766 (2019).
Cantone, M., Küspert, M., Reiprich, S., Lai, X., Eberhardt, M., Göttle, P., Beyer, F., Azim, K., Küry, P., Wegner, M. & Vera, J. A gene regulatory architecture that controls region-independent dynamics of oligodendrocyte differentiation. Glia 67, 825–843 (2019).
Lieb, V., Weigelt, K., Scheinost, L., Fischer, K., Greither, T., Marcou, M., Theil, G., Klocker, H., Holzhausen, H.-J., Lai, X., Vera, J., Ekici, A. B., Horninger, W., Fornara, P., Wullich, B., Taubert, H. & Wach, S. Serum levels of miR-320 family members are associated with clinical parameters and diagnosis in prostate cancer patients. Oncotarget 9, 10402–10416 (2018).
Santos, G., Lai, X., Eberhardt, M. & Vera, J. Bacterial Adherence and Dwelling Probability: Two Drivers of Early Alveolar Infection by Streptococcus pneumoniae Identified in Multi-Level Mathematical Modeling. Front Cell Infect Microbiol 8, 159 (2018).
Lai, X., Gupta, S. K., Schmitz, U., Marquardt, S., Knoll, S., Spitschak, A., Wolkenhauer, O., Pützer, B. M. & Vera, J. MiR-205-5p and miR-342-3p cooperate in the repression of the E2F1 transcription factor in the context of anticancer chemotherapy resistance. Theranostics 8, 1106–1120 (2018).
Cantone, M., Santos, G., Wentker, P., Lai, X. & Vera, J. Multiplicity of Mathematical Modeling Strategies to Search for Molecular and Cellular Insights into Bacteria Lung Infection. Front Physiol 8, 645 (2017).
Nolte, E., Wach, S., Silva, I. T., Lukat, S., Ekici, A. B., Munkert, J., Müller-Uri, F., Kreis, W., Oliveira Simões, C. M., Vera, J., Wullich, B., Taubert, H. & Lai, X. A new semisynthetic cardenolide analog 3β-[2-(1-amantadine)- 1-on-ethylamine]-digitoxigenin (AMANTADIG) affects G2/M cell cycle arrest and miRNA expression profiles and enhances proapoptotic survivin-2B expression in renal cell carcinoma cell lines. Oncotarget 8, 11676–11691 (2017).
Schulz, C., Lai, X., Bertrams, W., Jung, A. L., Sittka-Stark, A., Herkt, C. E., Janga, H., Zscheppang, K., Stielow, C., Schulte, L., Hippenstiel, S., Vera, J. & Schmeck, B. THP-1-derived macrophages render lung epithelial cells hypo-responsive to Legionella pneumophila - a systems biology study. Sci Rep 7, 11988 (2017).
Santos, G., Nikolov, S., Lai, X., Eberhardt, M., Dreyer, F. S., Paul, S., Schuler, G. & Vera, J. Model-based genotype-phenotype mapping used to investigate gene signatures of immune sensitivity and resistance in melanoma micrometastasis. Sci Rep 6, 24967 (2016).
Lai, X., Wolkenhauer, O. & Vera, J. Understanding microRNA-mediated gene regulatory networks through mathematical modelling. Nucleic Acids Res 44, 6019–6035 (2016).
Schmitz, U., Lai, X., Winter, F., Wolkenhauer, O., Vera, J. & Gupta, S. K. Cooperative gene regulation by microRNA pairs and their identification using a computational workflow. Nucleic Acids Res. 42, 7539–7552 (2014).
Sittka, A., Vera, J., Lai, X. & Schmeck, B. T. Asthma phenotyping, therapy, and prevention: what can we learn from systems biology? Pediatr. Res. 73, 543–552 (2013).
Vera, J., Schmitz, U., Lai, X., Engelmann, D., Khan, F. M., Wolkenhauer, O. & Pützer, B. M. Kinetic modeling-based detection of genetic signatures that provide chemoresistance via the E2F1-p73/DNp73-miR-205 network. Cancer Res. 73, 3511–3524 (2013).
Lai, X., Bhattacharya, A., Schmitz, U., Kunz, M., Vera, J. & Wolkenhauer, O. A systems’ biology approach to study microRNA-mediated gene regulatory networks. Biomed Res Int 2013, 703849 (2013).
Lai, X., Schmitz, U., Gupta, S. K., Bhattacharya, A., Kunz, M., Wolkenhauer, O. & Vera, J. Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs. Nucleic Acids Res. 40, 8818–8834 (2012).
Vera, J., Nikolov, S., Lai, X., Singh, A. & Wolkenhauer, O. Model-based investigation of the transcriptional activity of p53 and its feedback loop regulation via 14-3-3σ. IET Syst Biol 5, 293–307 (2011).
Gupta, S. K., Gupta, S. K., Smita, S., Srivastava, M., Lai, X., Schmitz, U., Rahman, Q., Wolkenhauer, O. & Vera, J. Computational analysis and modeling the effectiveness of ‘Zanamivir’ targeting neuraminidase protein in pandemic H1N1 strains. Infect. Genet. Evol. 11, 1072–1082 (2011).
Nikolov, S., Lai, X., Liebal, U. W., Wolkenhauer, O. & Vera, J. Integration of sensitivity and bifurcation analysis to detect critical processes in a model combining signalling and cell population dynamics. International Journal of Systems Science 41, 81–105 (2010).
Lai, X., Nikolov, S., Wolkenhauer, O. & Vera, J. A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis. Comput Biol Chem 33, 312–324 (2009).
Lai, X. Time delay and protein modulation analysis in a model of RNA silencing. Communications of SIWN 6, 111–117 (2009).
Book and Book Chapters
Book
Lai, X., Gupta, S., & Vera, J. Computational Biology of Non-Coding RNA: Methods and Protocols the Second Edition. In press, Humana Press.
Lai, X., Gupta, S., & Vera, J. (2019) Computational Biology of Non-Coding RNA: Methods and Protocols. ISBN: 978-1-4939-8981-2, Humana Press.
Book chapters
Lai,X., Schmitz,U. and Vera,J. (2022) The Role of MicroRNAs in Cancer Biology and Therapy from a Systems Biology Perspective. Adv. Exp. Med. Biol., 1385, 1–22.
Jendrek,S., Lai,X., Riemekasten,G., Vera-González,J., Schmeck,B. and Bertrams,W. (2020) Sepsis and Autoimmune Disease: Pathology, Systems Medicine, and Artificial Intelligence. In Systems Medicine: Integrative, Qualitative and Computational Approaches: Volume 1-3. Elsevier, pp. 581–592.
Schmeck,B., Bertrams,W., Lai,X. and Vera,J. (2016) Systems Medicine for Lung Diseases: Phenotypes and Precision Medicine in Cancer, Infection, and Allergy. Methods Mol. Biol., 1386, 119–133.
Eberhardt,M., Lai,X., Tomar,N., Gupta,S., Schmeck,B., Steinkasserer,A., Schuler,G. and Vera,J. (2016) Third-Kind Encounters in Biomedicine: Immunology Meets Mathematics and Informatics to Become Quantitative and Predictive. Methods Mol. Biol., 1386, 135–179.
Vera,J., Lai,X., Schmitz,U. and Wolkenhauer,O. (2013) MicroRNA-regulated networks: the perfect storm for classical molecular biology, the ideal scenario for systems biology. Adv. Exp. Med. Biol., 774, 55–76.
Vera,J., Nikolov,S. and Lai,X. (2013) Nonlinear Dynamics, miRNA Circuits. Encyclopedia of Systems Biology. Springer New York, pp. 1541–1545.
Nikolov,S., Lai,X. and Vera,J. (2013) MicroRNA Regulation, Time Delay. Encyclopedia of Systems Biology. Springer New York, pp. 1331–1334.
Lai,X. and Vera,J. (2013) Target Hub. Encyclopedia of Systems Biology. Springer New York, pp. 2134–2138.
Lai,X. and Vera,J. (2013) MicroRNA Regulation, Feed-Forward Loops. Encyclopedia of Systems Biology. Springer New York, pp. 1324–1328.
Lai,X. and Vera,J. (2013) MicroRNA Clusters. Encyclopedia of Systems Biology. Springer New York, pp. 1310–1314.
Lai,X., Wolkenhauer,O. and Vera,J. (2012) Modeling miRNA regulation in cancer signaling systems: miR-34a regulation of the p53/Sirt1 signaling module. Methods Mol. Biol., 880, 87–108.
Oral Presentation
Invited talks
The China-Germany-Finland Life Science Forum, Chengdu, China, 2-5 August 2024.
1st International Caparica Conference on Prescriptomics & Precision Medicine, Lisbon-Caparica, Portugal, 10–13 May 2024. [Event Photos]
MET Research Day at Tampere University, Tampere, Finland, 30 November - 1 December 2023. [Event Video]
Finland RNA Salon (FiRNASalon), Turku, Finland, 29 September 2023.
Young scientist retreat in 32nd German skin oncology congress (ADO2022 Nachwunchs Retreat), Hannover, Germany, 13-14 September 2022
2022 2nd International Symposium on Biomedical Engineering and Computational Biology (BECB2022), Nanchang Hangkong University, China, 13-15 August 2022.
Curious 2022-future insight, Darmstadt, Germany, 12-14 July 2022. [Presentation Video]
2021 International Symposium on Biomedical Engineering and Computational Biology (BECB2021), Nanchang Hangkong University, China, 13-15 August 2021.
The 16th International Conference on Molecular Systems Biology (ICMSB2019), Manila, Philippines, 28-30 October 2019.
e:Med summer school “Forging Trails from Cells to Hospitals – Linking Systems Biology and Precision Medicine in the Black Forest (ForCeHLSByMed)”, Freiburg, Germany, 14-17 May 2019.
The 3rd OpenMultiMed Training School: Multi-scale and Multi-level Modelling in Biomedicine, Erlangen, Germany, 21-23 February 2018.
The 5th Annual Meeting of Zhejiang Bioinformatics Society & "Big Data and Precision Medicine" International Workshop, Ningbo, China, 13-15 October 2017.
Summer School on The Integration of Data and Models in Medicine (IDaMo), Rostock, Germany, 17-20 May 2016.
Sino-German Workshop on Multiscale Spatial Computational Systems Biology (MSCSB2015), Beijing, China, 8-10 October 2015.
Workshop of IT for Life Science @ Bayer, Leverkusen, Germany, 15-16 December 2014.
Contributed talks
The 20th International Symposium on Bioinformatics Research and Application (ISBRA 2024), Kunming, China, 19-21 July, 2024.
Finnish Bioinformatics Day 2024, Helsinki, Finland, 6 June 2024.
Cancer Research Day, Tampere University, 21 March 2024.
The German Conference on Bioinformatics 2023 (GCB2023), Hamburg, Germany, 10-14 September 2023. [Event Photo]
The 21st International Conference on Systems Biology (ICSB2022), Berlin, Germany, 8-12 October 2022.
The German Conference on Bioinformatics 2021 (GCB2021), Halle, Germany, 6-9 September 2021.
The 29th Conference on Intelligence Systems for Molecular Biology and the 20th European Conference on Computational Biology (ISMB/ECBB 2021), 25-30 July 2021.
The German Conference on Bioinformatics 2019 (GCB2019), Heidelberg, Germany, 17-19 September 2019.
The 27th Conference on Intelligence Systems for Molecular Biology and the 18th European Conference on Computational Biology (ISMB/ECBB 2019), Basel, Switzerland, 21-25 July 2019.
The 19th International Conference on Systems Biology (ICSB2018), Lyon, France, 28 October-1 November 2018.
The 15th International Symposium on Dendritic Cells (DC2018), Aachen, Germany, 10–14 June 2018.
Workshop on Computational Models in Biology and Medicine, Regensburg, Germany, 8-9 March 2018.
The 15th International Conference on Molecular Systems Biology (ICMSB2017), Raitenhaslach, Germany, 26-28 July 2017.
Workshop on Computational Models in Biology and Medicine, Leipzig, Germany, 10-11 September 2015.
The 2nd International Conference on Bioinformatics and Systems Biology (BSB), Leipzig, Germany, 23-25 March 2009.
The 6th International Conference on Computational Methods in Systems Biology (CMSB), Rostock, Germany, 12-15 October 2008.