Publications and communications of Liesbet Geris

Books and journal issues published as editor or director

Geris, L., & Gomez-Cabrero, D. (Eds.). (2015). Uncertainty in biology: a computational modeling approach. Springer.

Book chapters or contributions to a collective book as author or co-author

Papantoniou, I., Lambrechts, T., Gupta, P., de Bournonville, S., Loverdou, N., Geris, L., & Aerts, J. (2022). Bioreactor Sensing and Monitoring for Cell Therapy Manufacturing. In: Bioreactors for Stem Cell Expansion and Differentiation. In Bioreactors for Stem Cell Expansion and Differentiation. CRC Press.

Reina-Romo, E., Papantoniou, I., Bloemen, V., & Geris, L. (2019). 4 - Computational design of tissue engineering scaffolds. In M. Mozafari, F. Sefat, ... A. Atala (Eds.), Woodhead Publishing Series in Biomaterials. Woodhead Publishing. doi:10.1016/B978-0-08-102563-5.00004-6

Van schepdael, Carlier, A., & Geris, L. (2016). Sensitivity analysis by design of experiments. In L. Geris & D. Gomez-Cabrero (Eds.), Uncertainty in Biology: a computational modeling approach (pp. 327-366). Springer.

Geris, L., & Gomez-Cabrero, D. (2015). An introduction to uncertainty in the development of computational models of biological processes. In Modeling under uncertainty: a computational modeling approach. Springer.

Gomez-Cabrero, D., Tegner, J., & Geris, L. (2015). Computational modeling under uncertainty: challenges and opportunities. In Modeling under uncertainty: a computational modeling approach. Springer.

papantoniou, I., mantalaris, A., sonnaert, M., lambrechts, T., aerts, J.-M., Geris, L., & schrooten, J. (2015). Product and Process Design: Toward Industrial TE Manufacturing. In C. Van Blitterswijk (Ed.), Tissue Engineering. Elsevier.

van oosterwyck, H., Geris, L., & Garcia-Aznar, J.-M. (2015). Cell Mechanics and Mechanobiology. In M. Doblare & J. Merodio, Component Encyclopedia of PHYSICAL SCIENCES, ENGINEERING AND TECHNOLOGY RESOURCES, Biomechanics (pp. 271-300). United Kingdom: Eolss Publishers/UNESCO.

Geris, L. (2013). In Vivo, In Vitro, In Silico: Computational Tools for Product and Process Design in Tissue Engineering. In Computational modeling in tissue engineering. Springer.

Articles accepted in reviewed journal

Joiret, M., Kerff, F., Rapino, F., Close, P., & Geris, L. (31 May 2024). Reversing the relative time courses of the peptide bond reaction with oligopeptides of different lengths and charged amino acid distributions in the ribosome exit tunnel. Computational and Structural Biotechnology Journal, 23, 2453-2464. doi:10.1016/j.csbj.2024.05.045

Salar Amoli, M., Anand, R., EzEldeen, M., Geris, L., Jacobs, R., & Bloemen, V. (12 February 2024). Development of 3D Printed pNIPAM-Chitosan Scaffolds for Dentoalveolar Tissue Engineering. Gels (Basel, Switzerland), 10 (2). doi:10.3390/gels10020140

Decoene, I., Nasello, G., Madeiro de Costa, R. F., Nilsson Hall, G., Pastore, A., Van Hoven, I., Ribeiro Viseu, S., Verfaillie, C., Geris, L., Luyten, F. P., & Papantoniou, I. (2024). Robotics-Driven Manufacturing of Cartilaginous Microtissues for Skeletal Tissue Engineering Applications. Stem Cells Translational Medicine. doi:10.1093/stcltm/szad091

Liang, B., Sadeghian Dehkord, E., Van hede, D., Barzegari, M., Verlee, B., Pirson, J., Nolens, G., Lambert, F., & Geris, L. (03 December 2023). Model-Based Design to Enhance Neotissue Formation in Additively Manufactured Calcium-Phosphate-Based Scaffolds. Journal of Functional Biomaterials, 14 (563), 22. doi:10.3390/jfb14120563

Crump, K. B.* , Alminnawi, A.* , Bermudez-Lekerika, P., Compte, R., Gualdi, F., McSweeney, T., Muñoz-Moya, E., Nüesch, A., Geris, L., Dudli, S., Karppinen, J., Noailly, J., Le Maitre, C., & Gantenbein, B. (2023). Cartilaginous endplates: A comprehensive review on a neglected structure in intervertebral disc research. JOR Spine. doi:10.1002/jsp2.1294
* These authors have contributed equally to this work.

Viceconti, M., De Vos, M., Mellone, S., & Geris, L. (11 October 2023). Position paper From the digital twins in healthcare to the Virtual Human Twin: a moon-shot project for digital health research. IEEE Journal of Biomedical and Health Informatics, PP. doi:10.1109/JBHI.2023.3323688

Sadeghian Dehkord, E., Kerckhofs, G., Compère, P., Lambert, F., & Geris, L. (22 July 2023). An Empirical Model Linking Physico-Chemical Biomaterial Characteristics to Intra-Oral Bone Formation. Journal of Functional Biomaterials, 14 (7), 388. doi:10.3390/jfb14070388

Joiret, M., Kerff, F., Rapino, F., Close, P., & Geris, L. (July 2023). A simple geometrical model of the electrostatic environment around the catalytic center of the ribosome and its significance for the elongation cycle kinetics. Computational and Structural Biotechnology Journal, 21, 3768-3795. doi:10.1016/j.csbj.2023.07.016

Stein, M., Elefteriou, F., Busse, B., Fiedler, I. A., Kwon, R. Y., Farrell, E., Ahmad, M., Ignatius, A., Grover, L., Geris, L., & Tuckermann, J. (2023). Why Animal Experiments Are Still Indispensable in Bone Research: A Statement by the European Calcified Tissue Society. Journal of Bone and Mineral Research. doi:10.1002/jbmr.4868

Sremački, I., Asadian, M., De Geyter, N., Leys, C., Geris, L., & Nikiforov, A. (08 May 2023). Potentials of a Plasma-Aerosol System for Wound Healing Advanced by Drug Introduction: An In Vitro Study. ACS Biomaterial Science and Engineering, 9 (5), 2392 - 2407. doi:10.1021/acsbiomaterials.2c01391

Joiret, M., Leclercq, M., Lambrechts, G., Rapino, F., Close, P., Louppe, G., & Geris, L. (06 April 2023). Cracking the genetic code with neural networks. Frontiers in Artificial Intelligence, 6. doi:10.3389/frai.2023.1128153

Borgiani, E., Nasello, G., Ory, L., Herpelinck, T., GROENEVELDT, L., Bucher, C. H., Schmidt-Bleek, K., & Geris, L. (2023). COMMBINI: an experimentally-informed COmputational Model of Macrophage dynamics in the Bone INjury Immunoresponse. Frontiers in Immunology, 14, 1231329. doi:10.3389/fimmu.2023.1231329

Lesage, R., Van Oudheusden, M., Schievano, S., Van Hoyweghen, I., Geris, L., & Capelli, C. (2023). Mapping the use of computational modelling and simulation in clinics: A survey. Frontiers in Medical Technology, 5, 1125524. doi:10.3389/fmedt.2023.1125524

Schamberger, B., Roschger, A., Ziege, R., Anselme, K., Amar, M. B., Bykowski, M., Castro, A. P. G., Cipitria, A., Coles, R., Dimova, R., Eder, M., Ehrig, S., Escudero, L. M., Evans, M. E., Fernandes, P. R., Fratzl, P., Geris, L., Gierlinger, N., Hannezo, E., ... Dunlop, J. W. C. (2022). Curvature in Biological Systems: Its quantification, Emergence and Implications Across the Scales. Advanced Materials, 2206110. doi:10.1002/adma.202206110

Lesage, R., Ferrao Blanco, M. N., Narcisi, R., Welting, T., van Osch, G. J. V. M., & Geris, L. (09 November 2022). An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis. BMC Biology, 20 (1), 253. doi:10.1186/s12915-022-01451-8

Kanapeckaitė, A., Mažeikienė, A., Geris, L., Burokienė, N., Cottrell, G. S., & Widera, D. (November 2022). Computational pharmacology: New avenues for COVID-19 therapeutics search and better preparedness for future pandemic crises. Biophysical Chemistry, 290, 106891. doi:10.1016/j.bpc.2022.106891

Pappalardo, F., Wilkinson, J., Busquet, F., Bril, A., Palmer, M., Walker, B., Curreli, C., Russo, G., Marchal, T., Toschi, E., Alessandrello, R., Costignola, V., Klingmann, I., Contin, M., Staumont, B., Woiczinski, M., Kaddick, C., Salvatore, V. D., Aldieri, A., ... Viceconti, M. (November 2022). Toward A Regulatory Pathway for the Use of in Silico Trials in the CE Marking of Medical Devices. IEEE Journal of Biomedical and Health Informatics, 26 (11), 5282-5286. doi:10.1109/JBHI.2022.3198145

Hall, G. N., Chandrakar, A., Pastore, A., Ioannidis, K., Moisley, K., Cirstea, M., Geris, L., Moroni, L., Luyten, F. P., Wieringa, P., & Papantoniou, I. (2022). Engineering bone-forming biohybrid sheets through the integration of melt electrowritten membranes and cartilaginous microspheroids. Acta Biomaterialia. doi:10.1016/j.actbio.2022.10.037

Corradi, M. P. F., de Haan, A. M., Staumont, B., Piersma, A. H., Geris, L., Pieters, R. H. H., Krul, C. A. M., & Teunis, M. A. T. (August 2022). Natural language processing in toxicology: Delineating adverse outcome pathways and guiding the application of new approach methodologies. Biomaterials and Biosystems, 7, 100061. doi:10.1016/j.bbiosy.2022.100061

Salar Amoli, M., Anand, R., EzEldeen, M., Amorim, P. A., Geris, L., Jacobs, R., & Bloemen, V. (01 August 2022). The development of a 3D printable chitosan-based copolymer with tunable properties for dentoalveolar regeneration. Carbohydrate Polymers, 289, 119441. doi:10.1016/j.carbpol.2022.119441

Anand, R., Salar Amoli, M., Huysecom, A.-S., Amorim, P. A., Agten, H., Geris, L., & Bloemen, V. (24 June 2022). A tunable gelatin-hyaluronan dialdehyde/methacryloyl gelatin interpenetrating polymer network hydrogel for additive tissue manufacturing. Biomedical Materials, 17 (4), 045027. doi:10.1088/1748-605X/ac78b8

Barzegari, M., & Geris, L. (14 June 2022). BioDeg: A finite element software for the simulation ofthe corrosion and biodegradation process in metallicbiomaterials. Journal of Open Source Software, 7 (74), 4281. doi:10.21105/joss.04281

Bekisz, S., Baudin, L., Buntinx, F., Noël, A., & Geris, L. (16 March 2022). In Vitro, In Vivo, and In Silico Models of Lymphangiogenesis in Solid Malignancies. Cancers, 14 (6), 1525. doi:10.3390/cancers14061525

Barzegari, M., & Geris, L. (March 2022). Highly scalable numerical simulation of coupled reaction–Diffusion systems with moving interfaces. International Journal of High Performance Computing Applications, 36 (2), 198 - 213. doi:10.1177/10943420211045939

Sermeus, Y., Vangheel, J., Geris, L., Smeets, B., & Tylzanowski, P. (26 January 2022). Mechanical Regulation of Limb Bud Formation. Cells, 11 (3). doi:10.3390/cells11030420

Joiret, M., Kerff, F., Rapino, F., Close, P., & Geris, L. (13 January 2022). Ribosome exit tunnel electrostatics. Physical Review. E, 105 (1), 014409-1 - 014409-43. doi:10.1103/PhysRevE.105.014409

Bermudez-Lekerika, P., Crump, K. B., Tseranidou, S., Nüesch, A., Kanelis, E., Alminnawi, A., Baumgartner, L., Muñoz-Moya, E., Compte, R., Gualdi, F., Alexopoulos, L. G., Geris, L., Wuertz-Kozak, K., Le Maitre, C. L., Noailly, J., & Gantenbein, B. (2022). Immuno-Modulatory Effects of Intervertebral Disc Cells. Frontiers in Cell and Developmental Biology, 10, 924692. doi:10.3389/fcell.2022.924692

Lammens, J., Maréchal, M., Delport, H., Geris, L., & Luyten, F. P. (2022). A Flowchart for the Translational Research of CellBased Therapy in the Treatment of Long Bone Defects. Journal of Regenerative Medicine, 10 (1).

Loverdou, N., Cuvelier, M., Nilsson Hall, G., Christiaens, A.-S., Decoene, I., Bernaerts, K., Smeets, B., Ramon, H., Luyten, F. P., Geris, L., & Papantoniou, I. (2022). Stirred culture of cartilaginous microtissues promotes chondrogenic hypertrophy through exposure to intermittent shear stress. Bioengineering and Translational Medicine. doi:10.1002/btm2.10468

Perez-Boerema, F., Barzegari, M., & Geris, L. (2022). A flexible and easy-to-use open-source tool for designing functionally graded 3D porous structures. Virtual and Physical Prototyping, 17 (3), 682 - 699. doi:10.1080/17452759.2022.2048956

Elahi, S. A., Tanska, P., Mukherjee, S., Korhonen, R. K., Geris, L., Jonkers, I., & Famaey, N. (December 2021). Guide to mechanical characterization of articular cartilage and hydrogel constructs based on a systematic in silico parameter sensitivity analysis. Journal of the Mechanical Behavior of Biomedical Materials, 124, 104795. doi:10.1016/j.jmbbm.2021.104795

Farzin, A., Hassan, S., Teixeira, L. S. M., Gurian, M., Crispim, J. F., Manhas, V., Carlier, A., Bae, H., Geris, L., Noshadi, I., Shin, S. R., & Leijten, J. (14 October 2021). Self-Oxygenation of Tissues Orchestrates Full-Thickness Vascularization of Living Implants. Advanced Functional Materials, 31 (42). doi:10.1002/adfm.202100850

Viceconti, M., Emili, L., Afshari, P., Courcelles, E., Curreli, C., Famaey, N., Geris, L., Horner, M., Jori, M. C., Kulesza, A., Loewe, A., Neidlin, M., Reiterer, M., Rousseau, C. F., Russo, G., Sonntag, S. J., Voisin, E. M., & Pappalardo, F. (October 2021). Possible Contexts of Use for In Silico Trials Methodologies: A Consensus-Based Review. IEEE Journal of Biomedical and Health Informatics, 25 (10), 3977-3982. doi:10.1109/JBHI.2021.3090469

Tam, W. L., Freitas Mendes, L., Chen, X., Lesage, R., Van Hoven, I., Leysen, E., Kerckhofs, G., Bosmans, K., Chai, Y. C., Yamashita, A., Tsumaki, N., Geris, L., Roberts, S. J., & Luyten, F. P. (25 September 2021). Human pluripotent stem cell-derived cartilaginous organoids promote scaffold-free healing of critical size long bone defects. Stem Cell Research and Therapy, 12 (1), 513. doi:10.1186/s13287-021-02580-7

Nilsson Hall, G., Rutten, I., Lammertyn, J., Eberhardt, J., Geris, L., Luyten, F. P., & Papantoniou, I. (21 September 2021). Cartilaginous spheroid-assembly design considerations for endochondral ossification: towards robotic-driven biomanufacturing. Biofabrication, 13 (4). doi:10.1088/1758-5090/ac2208

Barzegari, M., Mei, D., Lamaka, S. V., & Geris, L. (September 2021). Computational modeling of degradation process of biodegradable magnesium biomaterials. Corrosion Science, 190, 109674. doi:10.1016/j.corsci.2021.109674

Musuamba, F. T., Skottheim Rusten, I., Lesage, R., Russo, G., Bursi, R., Emili, L., Wangorsch, G., Manolis, E., Karlsson, K. E., Kulesza, A., Courcelles, E., Boissel, J.-P., Rousseau, C. F., Voisin, E. M., Alessandrello, R., Curado, N., Dall'ara, E., Rodriguez, B., Pappalardo, F., & Geris, L. (August 2021). Scientific and regulatory evaluation of mechanistic in silico drug and disease models in drug development: Building model credibility. CPT: Pharmacometrics and Systems Pharmacology, 10 (8), 804-825. doi:10.1002/psp4.12669

Vinken, M., Benfenati, E., Busquet, F., Castell, J., Clevert, D.-A., de Kok, T. M., Dirven, H., Fritsche, E., Geris, L., Gozalbes, R., Hartung, T., Jennen, D., Jover, R., Kandarova, H., Kramer, N., Krul, C., Luechtefeld, T., Masereeuw, R., Roggen, E., ... Piersma, A. H. (30 June 2021). Safer chemicals using less animals: kick-off of the European ONTOX project. Toxicology, 458, 152846. doi:10.1016/j.tox.2021.152846

Barzegari, M., & Geris, L. (27 June 2021). An open source crash course on parameter estimation of computational models using a Bayesian optimization approach. Journal of Open Source Education, 4 (40), 89. doi:10.21105/jose.00089

Hall, G. N., Tam, W. L., Andrikopoulos, K. S., Casas-Fraile, L., Voyiatzis, G. A., Geris, L., Luyten, F. P., & Papantoniou, I. (June 2021). Patterned, organoid-based cartilaginous implants exhibit zone specific functionality forming osteochondral-like tissues in vivo. Biomaterials, 273, 120820. doi:10.1016/j.biomaterials.2021.120820

de Bournonville, S., Geris, L., & Kerckhofs, G. (02 February 2021). Micro computed tomography with and without contrast enhancement for the characterization of microcarriers in dry and wet state. Scientific Reports, 11 (1), 2819. doi:10.1038/s41598-021-81998-8

Gorgun, C., Ceresa, D., Lesage, R., Villa, F., Reverberi, D., Balbi, C., Santamaria, S., Cortese, K., Malatesta, P., Geris, L., Quarto, R., & Tasso, R. (February 2021). Dissecting the effects of preconditioning with inflammatory cytokines and hypoxia on the angiogenic potential of mesenchymal stromal cell (MSC)-derived soluble proteins and extracellular vesicles (EVs). Biomaterials, 269, 120633. doi:10.1016/j.biomaterials.2020.120633

Papantoniou, I., Nilsson Hall, G., Loverdou, N., Lesage, R., Herpelinck, T., Mendes, L., & Geris, L. (February 2021). Turning Nature's own processes into design strategies for living bone implant biomanufacturing: a decade of Developmental Engineering. Advanced Drug Delivery Reviews, 169, 22-39. doi:10.1016/j.addr.2020.11.012

Gallez, A., Blacher, S., Maquoi, E., Konradowski, E., Joiret, M., Primac, I., Gérard, C., Taziaux, M., Houtman, R., Geris, L., Lenfant, F., Marangoni, E., Sounni, N. E., Foidart, J.-M., Noël, A., & Pequeux, C. (2021). Estetrol combined to progestogen for menopause or contraception indication is neutral on breast cancer. Cancers. doi:10.3390/cancers13102486

Khurana, S., Schivo, S., Plass, J. R. M., Mersinis, N., Scholma, J., Kerkhofs, J., Zhong, L., van de Pol, J., Langerak, R., Geris, L., Karperien, M., & Post, J. N. (2021). An ECHO of Cartilage: In Silico Prediction of Combinatorial Treatments to Switch Between Transient and Permanent Cartilage Phenotypes With Ex Vivo Validation. Frontiers in Bioengineering and Biotechnology, 9, 732917. doi:10.3389/fbioe.2021.732917

Lafuente-Gracia, L., Borgiani, E., Nasello, G., & Geris, L. (2021). Towards in silico Models of the Inflammatory Response in Bone Fracture Healing. Frontiers in Bioengineering and Biotechnology, 9, 703725. doi:10.3389/fbioe.2021.703725

Rapino, F.* , ZHOU, Z.* , RONCERO SANCHEZ, A. M.* , Joiret, M., Seca, C., El Hachem, N., Valenti, G., Latini, S., Shostak, K., Geris, L., Li, P., Huang, G., Mazzucchelli, G., Baiwir, D., Desmet, C., Chariot, A., Georges, M., & Close, P. (2021). Wobble tRNA modification and hydrophilic amino acid patterns dictate protein fate. Nature Communications, 12 (1), 2170. doi:10.1038/s41467-021-22254-5
* These authors have contributed equally to this work.

Reina Romo, E.* , Mandal, S.* , Amorim, P., Bloemen, V., Ferraris, E., & Geris, L. (2021). Towards the Experimentally-Informed In Silico Nozzle Design Optimization for Extrusion-Based Bioprinting of Shear-Thinning Hydrogels. Frontiers in Bioengineering and Biotechnology, 9, 701778. doi:10.3389/fbioe.2021.701778
* These authors have contributed equally to this work.

Van de Velde, M., Ebroin, M., Durré, T., Joiret, M., Gillot, L., Blacher, S., Geris, L., Kridelka, F., & Noël, A. (2021). Tumor exposed-lymphatic endothelial cells promote primary tumor growth via IL6. Cancer Letters, 497, 154-164. doi:10.1016/j.canlet.2020.10.020

Corral-Acero, J., Margara, F., Marciniak, M., Rodero, C., Loncaric, F., Feng, Y., Gilbert, A., Fernandes, J. F., Bukhari, H. A., Wajdan, A., Martinez, M. V., Santos, M. S., Shamohammdi, M., Luo, H., Westphal, P., Leeson, P., DiAchille, P., Gurev, V., Mayr, M., ... Lamata, P. (21 December 2020). The 'Digital Twin' to enable the vision of precision cardiology. European Heart Journal, 41 (48), 4556-4564. doi:10.1093/eurheartj/ehaa159

Bekisz, S., & Geris, L. (October 2020). Cancer modeling: From mechanistic to data-driven approaches, and from fundamental insights to clinical applications. Journal of Computational Science, 46 (101198). doi:10.1016/j.jocs.2020.101198

Lammens, J., Maréchal, M., Delport, H., Geris, L., Oppermann, H., Vukicevic, S., & Luyten, F. P. (September 2020). A cell-based combination product for the repair of large bone defects. BONE, 138, 115511. doi:10.1016/j.bone.2020.115511

Musuamba, F. T., Bursi, R., Manolis, E., Karlsson, K., Kulesza, A., Courcelles, E., Boissel, J.-P., Lesage, R., Crozatier, C., Voisin, E. M., Rousseau, C. F., Marchal, T., Alessandrello, R., & Geris, L. (April 2020). Verifying and Validating Quantitative Systems Pharmacology and In Silico Models in Drug Development: Current Needs, Gaps, and Challenges. CPT: Pharmacometrics and Systems Pharmacology, 9 (4), 195-197. doi:10.1002/psp4.12504

Schivo, S., Khurana, S., Govindaraj, K., Scholma, J., Kerkhofs, J., Zhong, L., Huang, X., van de Pol, J., Langerak, R., van Wijnen, A. J., Geris, L., Karperien, M., & Post, J. N. (April 2020). ECHO, the executable CHOndrocyte: A computational model to study articular chondrocytes in health and disease. Cellular Signalling, 68, 109471. doi:10.1016/j.cellsig.2019.109471

Bolander, J., Herpelinck, T., Chaklader, M., Gklava, C., Geris, L., & Luyten, F. P. (March 2020). Single-cell characterization and metabolic profiling of in vitro cultured human skeletal progenitors with enhanced in vivo bone forming capacity. Stem Cells Translational Medicine, 9 (3), 389-402. doi:10.1002/sctm.19-0151

Kamperman, T., Teixeira, L. M., Salehi, S. S., Kerckhofs, G., Guyot, Y., Geven, M., Geris, L., Grijpma, D., Blanquer, S., & Leijten, J. (07 February 2020). Engineering 3D parallelized microfluidic droplet generators with equal flow profiles by computational fluid dynamics and stereolithographic printing. Lab on a Chip, 20 (3), 490-495. doi:10.1039/c9lc00980a

Groeneveldt, L. C., Herpelinck, T., Maréchal, M., Politis, C., van IJcken, W. F. J., Huylebroeck, D., Geris, L., Mulugeta, E., & Luyten, F. P. (2020). The Bone-Forming Properties of Periosteum-Derived Cells Differ Between Harvest Sites. Frontiers in Cell and Developmental Biology, 8, 554984. doi:10.3389/fcell.2020.554984

Mehrian, M., & Geris, L. (2020). Optimizing neotissue growth inside perfusion bioreactors with respect to culture and labor cost: a multi-objective optimization study using evolutionary algorithms. Computer Methods in Biomechanics and Biomedical Engineering, 23 (7), 285-294. doi:10.1080/10255842.2020.1719081

Mehrian, M., Lambrechts, T., Marechal, M., Luyten, F. P., Papantoniou, I., & Geris, L. (2020). Predicting in vitro human mesenchymal stromal cell expansion based on individual donor characteristics using machine learning. Cytotherapy, 22 (2), 82-90. doi:10.1016/j.jcyt.2019.12.006

Mehrian, M., Lambrechts, T., Papantoniou, I., & Geris, L. (2020). Computational Modeling of Human Mesenchymal Stromal Cell Proliferation and Extra-Cellular Matrix Production in 3D Porous Scaffolds in a Perfusion Bioreactor: The Effect of Growth Factors. Frontiers in Bioengineering and Biotechnology, 8, 376. doi:10.3389/fbioe.2020.00376

Mukherjee, S., Nazemi, M., Jonkers, I., & Geris, L. (2020). Use of Computational Modeling to Study Joint Degeneration: A Review. Frontiers in Bioengineering and Biotechnology, 8, 93. doi:10.3389/fbioe.2020.00093

Nilsson Hall, G., Mendes, L. F., Gklava, C., Geris, L., Luyten, F. P., & Papantoniou, I. (2020). Developmentally Engineered Callus Organoid Bioassemblies Exhibit Predictive In Vivo Long Bone Healing. Advanced Science, 7 (2), 1902295. doi:10.1002/advs.201902295

Zappia, J., Joiret, M., Sanchez, C., Lambert, C., Geris, L., Muller, M., & Henrotin, Y. (2020). From translation to protein degradation as mechanisms for regulating biological functions: A review on the SLRP family in skeletal tissues. Biomolecules, 10, 80. doi:10.3390/biom10010080

Van Sint Jan, S., & Geris, L. (December 2019). Modelling towards a more holistic medicine: The Virtual Physiological Human (VPH). Morphologie, 103 (343), 127-130. doi:10.1016/j.morpho.2019.10.044

Grivas, K. N., Vavva, M. G., Polyzos, D., Carlier, A., Geris, L., Van Oosterwyck, H., & Fotiadis, D. I. (February 2019). Effect of ultrasound on bone fracture healing: A computational mechanobioregulatory model. Journal of the Acoustical Society of America, 145 (2), 1048. doi:10.1121/1.5089221

Brekelmans, C., Hollants, S., De Groote, C., Sohier, N., Marechal, M., Geris, L., Luyten, F. P., Ginckels, L., Sciot, R., de Ravel, T., De Smet, L., Lammens, J., Legius, E., & Brems, H. (2019). Neurofibromatosis type 1-related pseudarthrosis: Beyond the pseudarthrosis site. Human Mutation. doi:10.1002/humu.23783

de Bournonville, S., Lambrechts, T., Vanhulst, J., Luyten, F. P., Papantoniou, I., & Geris, L. (2019). Towards Self-Regulated Bioprocessing: A Compact Benchtop Bioreactor System for Monitored and Controlled 3D Cell and Tissue Culture. Biotechnology Journal, 1800545. doi:10.1002/biot.201800545

Geris, L., & Papantoniou, I. (2019). The Third Era of Tissue Engineering: Reversing the Innovation Drivers. Tissue Engineering. Part A, 25 (11-12), 821-826. doi:10.1089/ten.TEA.2019.0064

Gupta, P., Hall, G. N., Geris, L., Luyten, F. P., & Papantoniou, I. (2019). Human Platelet Lysate Improves Bone Forming Potential of Human Progenitor Cells Expanded in Microcarrier-Based Dynamic Culture. Stem Cells Translational Medicine. doi:10.1002/sctm.18-0216

Verbeeck, L., Geris, L., Tylzanowski, P., & Luyten, F. P. (2019). Uncoupling of in-vitro identity of embryonic limb derived skeletal progenitors and their in-vivo bone forming potential. Scientific Reports, 9 (1). doi:10.1038/s41598-019-42259-x

Carlier, A., Vasilevich, A., de Boer, J., Geris, L., & Maréchal, M. (Other coll.). (2018). In silico clinical trials for pediatric orphan diseases. Scientific Reports, 8 (1), 2465. doi:10.1038/s41598-018-20737-y

Hoekstra, A. G., Bavel, E. V., Siebes, M., Gijsen, F., & Geris, L. (2018). Virtual physiological human 2016: Translating the virtual physiological human to the clinic. Interface Focus, 8 (1). doi:10.1098/rsfs.2017.0067

Lang, A., Volkamer, A., Behm, L., Roblitz, S., Ehrig, R., Schneider, M., Geris, L., Wichard, J., & Buttgereit, F. (2018). In silico methods - Computational alternatives to animal testing. ALTEX: Alternatives to Animal Experimentation, 35 (1), 124-126. doi:10.14573/altex.1712031

Lesage, R., Kerkhofs, J., & Geris, L. (2018). Computational Modeling and Reverse Engineering to Reveal Dominant Regulatory Interactions Controlling Osteochondral Differentiation: Potential for Regenerative Medicine. Frontiers in Bioengineering and Biotechnology, 6, 165. doi:10.3389/fbioe.2018.00165

Mendes, L. F., Katagiri, H., Tam, W. L., Chai, Y. C., Geris, L., Roberts, S. J., & Luyten, F. P. (2018). Advancing osteochondral tissue engineering: bone morphogenetic protein, transforming growth factor, and fibroblast growth factor signaling drive ordered differentiation of periosteal cells resulting in stable cartilage and bone formation in vivo. Stem Cell Research and Therapy, 9 (1), 42. doi:10.1186/s13287-018-0787-3

Vavva, M. G., Grivas, K. N., Carlier, A., Polyzos, D., Geris, L., Van Oosterwyck, H., & Fotiadis, D. I. (2018). Effect of ultrasound on bone fracture healing: A computational bioregulatory model. Computers in Biology and Medicine, 100, 74-85. doi:10.1016/j.compbiomed.2018.06.024

Manhas, V., Guyot, Y., Kerckhofs, G., Chai, Y. C., & Geris, L. (2016). Computational modelling of local calcium ions release from calcium phosphate-based scaffolds. Biomechanics and Modeling in Mechanobiology. doi:10.1007/s10237-016-0827-9

Bolander, J., Ji, W., Geris, L., Bloemen, V., Chai, Y. C., Schrooten, J., & Luyten, F. P. (2016). The combined mechanism of bone morphogenetic protein- and calcium phosphate-induced skeletal tissue formation by human periosteum derived cells. European Cells and Materials, 31, 11-25. doi:10.22203/eCM.v031a02

carlier, A., brems, H., ashbourn, J. M. A., nica, I., legius, E., & Geris, L. (2016). Capturing the wide variety of impaired fracture healing phenotypes in Neurofibromatosis Type 1 with eight key factors: a computational study. Scientific Reports, 7, 20010. doi:10.1038/srep20010

Guyot, Y., Papantoniou, I., Luyten, F. P., & Geris, L. (2016). Coupling curvature-dependent and shear stress-stimulated neotissue growth in dynamic bioreactor cultures: a 3D computational model of a complete scaffold. Biomechanics and Modeling in Mechanobiology, 15 (1), 169-80. doi:10.1007/s10237-015-0753-2

Guyot, Y., Smeets, B., Odenthal, T., Subramani, R., Luyten, F. P., Ramon, H., Papantoniou, I., & Geris, L. (2016). Immersed Boundary Models for Quantifying Flow-Induced Mechanical Stimuli on Stem Cells Seeded on 3D Scaffolds in Perfusion Bioreactors. PLoS Computational Biology, 12 (9), 1005108. doi:10.1371/journal.pcbi.1005108

Kerckhofs, G., Durand, M., Vangoitsenhoven, R., Marin, C., Van der Schueren, B., Carmeliet, G., Luyten, F. P., Geris, L., & Vandamme, K. (2016). Changes in bone macro- and microstructure in diabetic obese mice revealed by high resolution microfocus X-ray computed tomography. Scientific Reports, 6, 35517. doi:10.1038/srep35517

Kerkhofs, J., Leijten, J., Bolander, J., Luyten, F. P., Post, J. N., & Geris, L. (2016). A Qualitative Model of the Differentiation Network in Chondrocyte Maturation: A Holistic View of Chondrocyte Hypertrophy. PLoS ONE, 11 (8), 0162052. doi:10.1371/journal.pone.0162052

Kerkhofs, J., & Geris, L. (11 June 2015). A semiquantitative framework for gene regulatory networks: increasing the time and quantitative resolution of Boolean networks. PLoS ONE, 10 (6), 0130033. doi:10.1371/journal.pone.0130033

Carlier, A., Geris, L., Gastel, N. V., Carmeliet, G., & Van Oosterwyck, H. (2015). Oxygen as a critical determinant of bone fracture healing-a multiscale model. Journal of Theoretical Biology, 365, 247-64. doi:10.1016/j.jtbi.2014.10.012

Carlier, A., Geris, L., Lammens, J., & Van Oosterwyck, H. (2015). Bringing computational models of bone regeneration to the clinic. Wiley Interdisciplinary Reviews. Systems Biology and Medicine, 7 (4), 183-94. doi:10.1002/wsbm.1299

Carlier, A., Lammens, J., Van Oosterwyck, H., & Geris, L. (2015). Computational modeling of bone fracture non-unions: four clinically relevant case studies. In Silico Cell and Tissue Science, 2, 1. doi:10.1186/s40482-015-0004-x

Guyot, Y., Luyten, F. P., Schrooten, J., Papantoniou, I., & Geris, L. (2015). A Three-Dimensional Computational Fluid Dynamics Model Of Shear Stress Distribution During Neotissue Growth In A Perfusion Bioreactor. Biotechnology and Bioengineering. doi:10.1002/bit.25672

Sonnaert, M., Kerckhofs, G., Papantoniou, I., Van Vlierberghe, S., Boterberg, V., Dubruel, P., Luyten, F. P., Schrooten, J., & Geris, L. (2015). Multifactorial Optimization of Contrast-Enhanced Nanofocus Computed Tomography for Quantitative Analysis of Neo-Tissue Formation in Tissue Engineering Constructs. PLoS ONE, 10 (6), 0130227. doi:10.1371/journal.pone.0130227

Vavva, M. G., Grivas, K. N., Carlier, A., Polyzos, D., Geris, L., Van Oosterwyck, H., & Fotiadis, D. I. (2015). A mechano-regulatory model for bone healing predictions under the influence of ultrasound. Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2015, 921-4. doi:10.1109/EMBC.2015.7318513

Carlier, A., van Gastel, N., Geris, L., Carmeliet, G., & Van Oosterwyck, H. (2014). Size does matter: an integrative in vivo-in silico approach for the treatment of critical size bone defects. PLoS Computational Biology, 10 (11), 1003888. doi:10.1371/journal.pcbi.1003888

Chai, Y. C., Geris, L., Bolander, J., Pyka, G., Van Bael, S., Luyten, F. P., & Schrooten, J. (2014). In vivo ectopic bone formation by devitalized mineralized stem cell carriers produced under mineralizing culture condition. BioResearch Open Access, 3 (6), 265-77. doi:10.1089/biores.2014.0050

Geris, L. (2014). Regenerative orthopaedics: in vitro, in vivo ... in silico. International Orthopaedics, 38 (9), 1771-8. doi:10.1007/s00264-014-2419-6

Kerckhofs, G., Sainz, J., Maréchal, M., Wevers, M., Van de Putte, T., Schrooten, J., & Geris, L. (2013). Contrast-enhanced nanofocus X-ray computed tomography allows virtual 3D histopathology and morphometric analysis of osteoarthritis in small animal models. Cartilage. doi:10.1177/1947603513501175

Papantoniou, I., Sonnaert, M., Geris, L., Luyten, F. P., Schrooten, J., & Kerckhofs, G. (2013). Three dimensional characterization of tissue-engineered constructs by contrast enhanced nanofocus computed tomography. Tissue Engineering. Part C, Methods. doi:10.1089/ten.tec.2013.0041

Kerkhofs, J., Roberts, S. J., Luyten, F. P., Van Oosterwyck, H., & Geris, L. (2012). Relating the Chondrocyte Gene Network to Growth Plate Morphology: From Genes to Phenotype. PLoS ONE. doi:10.1371/journal.pone.0034729

Ashbourn, J., Miller, J., Reumers, V., Baekelandt, V., & Geris, L. (2012). A mathematical model of adult subventricular neurogenesis. Journal of the Royal Society, Interface. doi:10.1098/rsif.2012.0193

Bolander, J., Roberts, S., Eyckmans, J., Geris, L., & Luyten, F. (2012). The Effect of Activating Fibroblast Growth Factor Receptor 3 Mutations on Osteogenic Differentiation and Ectopic Bone Formation by Human Periosteal Derived Cells. Journal of Tissue Science and Engineering, 2. doi:10.4172/2157-7552.S2-003

Carlier, A., Geris, L., Bentley, K., Carmeliet, G., Carmeliet, P., & Van Oosterwyck, H. (2012). MOSAIC: a multiscale model of osteogenesis and sprouting angiogenesis with lateral inhibition of endothelial cells. PLoS Computational Biology, 8 (10), 1002724. doi:10.1371/journal.pcbi.1002724

Geris, L., Reed, A. A. C., Vander Sloten, J., Simpson, A. H. R. W., & Van Oosterwyck, H. (September 2010). Occurrence and Treatment of Bone Atrophic Non-Unions Investigated by an Integrative Approach. PLoS Computational Biology, 6 (9), 1000915. doi:10.1371/journal.pcbi.1000915

Articles accepted in journal without reviewing

Geris, L. (2020). In silico tools predict effects of drugs on bone remodelling. Nature Reviews Rheumatology. doi:10.1038/s41584-020-0457-6

Articles accepted in conference proceedings

Barnes, D., Irvine, A., Gamba, A., Maia Ladeira, L. C., Staumont, B., Yang, H., Steffensen, I.-L., Geris, L., Janssen, M., & Masereeuw, R. (2022). Development of an adverse outcome pathway for kidney tubular necrosis. In Helena Kandarova & João Barroso, 21st International Congress ESTIV Abstract Book. Bratslava, Slovakia: ESTIV.

Berkhout, J., Piersma, A., Legler, J., Gamba, A., Maia Ladeira, L. C., Staumont, B., Lesage, R. L., Geris, L., & Heuseinkveld, H. (2022). Computational modelling of neural tube closure defects. In Helena Kandarova & João Barroso, 21st International Congress ESTIV Abstract Book. Bratslava, Slovakia: ESTIV.

Maia Ladeira, L. C., Gamba, A., Lesage, R. L., Verhoeven, A., van Ertvelde, J., Jiang, J., Roodzant, D. L., Teunis, M., Jover, R., Vanhaecke, T., Vinken, M., Heuseinkveld, H., Geris, L., & Staumont, B. (2022). Designing physiological maps as a tool to study liver toxicology. In Helena Kandarova & João Barroso, 21st International Congress ESTIV Abstract Book. Bratslava, Slovakia: ESTIV.

Gamba, A., Maia Ladeira, L. C., Lesage, R. L., Roodzant, D. L., Barnes, D. A., Janssen, M. J., Teunis, M., Masereeuw, R., Geris, L., & Staumont, B. (2022). From Physiological Map to Ontology Unravelling Kidney Toxicity From Physiological Map to Ontology Unravelling Kidney Toxicity. In VPHi, VPH2022 Virtual Physiological Human Conference. Brussels, Belgium: VPHi.

Maia Ladeira, L. C., Gamba, A., Lesage, R. L., Verhoeven, A., Jiang, J., van Ertvelde, J., Jover, R., Vanhaecke, T., Mathieu, V., Geris, L., & Staumont, B. (2022). Developing a physiological map as a framework to study chemical- induced liver steatosis. In VPHi, VPH2022 Virtual Physiological Human Conference. Brussels, Belgium: VPHi.

Drion, P., Tirelli, E., Geris, L., & Rentier, B. (2018). InfOPAL_Les actes du Colloque_De l'engagement des chercheurs au service de l'animal et de la recherche. In OPAL, Les actes du Colloque (pp. 26-37). Paris, France: Opal.

Geris, L., Van Oosterwyck, H., Duyck, J., De Cooman, M., Puers, R., Naert, I., & Vander Sloten, J. (2004). The mechanobiology of tissue differentiation around immediately loaded implants: a bone chamber experiment. In Proceedings of the 14th conference of the European Society of Biomechanics. Netherlands: s’Hertogenbosch.