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

Authors: Marc Joiret, Frederic Kerff, Francesca Rapino, Pierre Close, Liesbet Geris

Source: Computational and Structural Biotechnology Journal, Vol 23, Iss , Pp 2453-2464 (2024)

Subject Terms: Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037024001910; https://doaj.org/toc/2001-0370

Access URL: https://doaj.org/article/724f2b0efb594b5aa4ac512751a11362

Immune digital twins for complex human pathologies: applications, limitations, and challenges

Authors: Anna Niarakis, Reinhard Laubenbacher, Gary An, Yaron Ilan, Jasmin Fisher, Åsmund Flobak, Kristin Reiche, María Rodríguez Martínez, Liesbet Geris, Luiz Ladeira, Lorenzo Veschini, Michael L. Blinov, Francesco Messina, Luis L. Fonseca, Sandra Ferreira, Arnau Montagud, Vincent Noël, Malvina Marku, Eirini Tsirvouli, Marcella M. Torres, Leonard A. Harris, T. J. Sego, Chase Cockrell, Amanda E. Shick, Hasan Balci, Albin Salazar, Kinza Rian, Ahmed Abdelmonem Hemedan, Marina Esteban-Medina, Bernard Staumont, Esteban Hernandez-Vargas, Shiny Martis B, Alejandro Madrid-Valiente, Panagiotis Karampelesis, Luis Sordo Vieira, Pradyumna Harlapur, Alexander Kulesza, Niloofar Nikaein, Winston Garira, Rahuman S. Malik Sheriff, Juilee Thakar, Van Du T. Tran, Jose Carbonell-Caballero, Soroush Safaei, Alfonso Valencia, Andrei Zinovyev, James A. Glazier

Source: npj Systems Biology and Applications, Vol 10, Iss 1, Pp 1-14 (2024)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/2056-7189

Access URL: https://doaj.org/article/c925f2072b8448f08b5b01c6a74dc959

A multi-model approach identifies ALW-II-41-27 as a promising therapy for osteoarthritis-associated inflammation and endochondral ossification

Authors: Mauricio N. Ferrao Blanco, Raphaelle Lesage, Nicole Kops, Niamh Fahy, Fjodor T. Bekedam, Athina Chavli, Yvonne M. Bastiaansen-Jenniskens, Liesbet Geris, Mark G. Chambers, Andrew A. Pitsillides, Roberto Narcisi, Gerjo J.V.M. van Osch

Source: Heliyon, Vol 10, Iss 23, Pp e40871- (2024)

Subject Terms: Chondrocyte hypertrophy, Inflammation, Kinase inhibitor, Virtual cell, Drug target, Author e-mails, Science (General), Q1-390, Social sciences (General), H1-99

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2405844024169022; https://doaj.org/toc/2405-8440

Access URL: https://doaj.org/article/48e3461e9a244cc184140f61e1073ffe

Influence of physicochemical characteristics of calcium phosphate-based biomaterials in cranio-maxillofacial bone regeneration. A systematic literature review and meta-analysis of preclinical models

Authors: Ehsan Sadeghian Dehkord, Bruno De Carvalho, Marie Ernst, Adelin Albert, France Lambert, Liesbet Geris

Source: Materials Today Bio, Vol 26, Iss , Pp 101100- (2024)

Subject Terms: Calcium phosphate, Biomaterials, Physicochemical, Cranio-maxillofacial, Intra-oral bone formation, Preclinical, Medicine (General), R5-920, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2590006424001595; https://doaj.org/toc/2590-0064

Access URL: https://doaj.org/article/b4ab42235de2409f8b2f77335af906bb

A simple geometrical model of the electrostatic environment around the catalytic center of the ribosome and its significance for the elongation cycle kinetics

Authors: Marc Joiret, Frederic Kerff, Francesca Rapino, Pierre Close, Liesbet Geris

Source: Computational and Structural Biotechnology Journal, Vol 21, Iss , Pp 3768-3795 (2023)

Subject Terms: Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037023002568; https://doaj.org/toc/2001-0370

Access URL: https://doaj.org/article/edc77a47b63d45179c2a014bca29d8b4

Cartilaginous endplates: A comprehensive review on a neglected structure in intervertebral disc research

Authors: Katherine B. Crump, Ahmad Alminnawi, Paola Bermudez‐Lekerika, Roger Compte, Francesco Gualdi, Terence McSweeney, Estefano Muñoz‐Moya, Andrea Nüesch, Liesbet Geris, Stefan Dudli, Jaro Karppinen, Jérôme Noailly, Christine Le Maitre, Benjamin Gantenbein

Source: JOR Spine, Vol 6, Iss 4, Pp n/a-n/a (2023)

Subject Terms: biologic therapies, biomechanics, degeneration, pre‐clinical models, Orthopedic surgery, RD701-811

File Description: electronic resource

Relation: https://doaj.org/toc/2572-1143

Access URL: https://doaj.org/article/5b4478ce19fc4886978a62ecc9211dac

COMMBINI: an experimentally-informed COmputational Model of Macrophage dynamics in the Bone INjury Immunoresponse

Authors: Edoardo Borgiani, Gabriele Nasello, Liesbeth Ory, Tim Herpelinck, Lisanne Groeneveldt, Christian H. Bucher, Katharina Schmidt-Bleek, Liesbet Geris

Source: Frontiers in Immunology, Vol 14 (2023)

Subject Terms: bone fracture healing, inflammatory phase, macrophages, in silico model, multiscale model, sensitivity analysis, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2023.1231329/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/5e0252e1af884dfbacc52a35256b0162

An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis

Authors: Raphaëlle Lesage, Mauricio N. Ferrao Blanco, Roberto Narcisi, Tim Welting, Gerjo J. V. M. van Osch, Liesbet Geris

Source: BMC Biology, Vol 20, Iss 1, Pp 1-25 (2022)

Subject Terms: Network of signal transduction, Computational modeling, Drug targets, Osteoarthritis, Chondrocyte hypertrophy, In vitro validation, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1741-7007

Access URL: https://doaj.org/article/2fb86faad3ea4fd497c909d3f48ce2c2

A flexible and easy-to-use open-source tool for designing functionally graded 3D porous structures

Authors: Fernando Perez-Boerema, Mojtaba Barzegari, Liesbet Geris

Source: Virtual and Physical Prototyping, Vol 17, Iss 3, Pp 682-699 (2022)

Subject Terms: tissue engineering, scaffolds, functional materials, tpms, additive manufacturing, Science, Manufactures, TS1-2301

File Description: electronic resource

Relation: https://doaj.org/toc/1745-2759; https://doaj.org/toc/1745-2767

Access URL: https://doaj.org/article/2d7018e50b1e4baebd93becb7ce5bcd9

Development of 3D Printed pNIPAM-Chitosan Scaffolds for Dentoalveolar Tissue Engineering

Authors: Mehdi Salar Amoli, Resmi Anand, Mostafa EzEldeen, Liesbet Geris, Reinhilde Jacobs, Veerle Bloemen

Source: Gels, Vol 10, Iss 2, p 140 (2024)

Subject Terms: pNIPAM, chitosan, degradability, 3D printing, dental pulp stem cells, Science, Chemistry, QD1-999, Inorganic chemistry, QD146-197, General. Including alchemy, QD1-65

File Description: electronic resource

Relation: https://www.mdpi.com/2310-2861/10/2/140; https://doaj.org/toc/2310-2861

Access URL: https://doaj.org/article/55f74d4fb5734f28bc59ba1aa26d7fc6

Stirred culture of cartilaginous microtissues promotes chondrogenic hypertrophy through exposure to intermittent shear stress

Authors: Niki Loverdou, Maxim Cuvelier, Gabriella Nilsson Hall, An‐Sofie Christiaens, Isaak Decoene, Kristel Bernaerts, Bart Smeets, Herman Ramon, Frank P. Luyten, Liesbet Geris, Ioannis Papantoniou

Source: Bioengineering & Translational Medicine, Vol 8, Iss 3, Pp n/a-n/a (2023)

Subject Terms: bioreactor, cartilage microtissues, exometabolomics, mathematical modeling, shear stress, Chemical engineering, TP155-156, Biotechnology, TP248.13-248.65, Therapeutics. Pharmacology, RM1-950

File Description: electronic resource

Relation: https://doaj.org/toc/2380-6761

Access URL: https://doaj.org/article/9f08099a700446d4b6e19b34041ce55d

Cracking the genetic code with neural networks

Authors: Marc Joiret, Marine Leclercq, Gaspard Lambrechts, Francesca Rapino, Pierre Close, Gilles Louppe, Liesbet Geris

Source: Frontiers in Artificial Intelligence, Vol 6 (2023)

Subject Terms: Artificial Intelligence, genetic code deciphering, codon usage, codon embedding, deep neural network, data efficiency, Electronic computers. Computer science, QA75.5-76.95

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/frai.2023.1128153/full; https://doaj.org/toc/2624-8212

Access URL: https://doaj.org/article/5953f6390c294c27883db9ffb648b52e

Mapping the use of computational modelling and simulation in clinics: A survey

Authors: Raphaëlle Lesage, Michiel Van Oudheusden, Silvia Schievano, Ine Van Hoyweghen, Liesbet Geris, Claudio Capelli

Source: Frontiers in Medical Technology, Vol 5 (2023)

Subject Terms: in silico medicine, computer modelling, simulations, clinicians, translation, trust in technology, Medical technology, R855-855.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmedt.2023.1125524/full; https://doaj.org/toc/2673-3129

Access URL: https://doaj.org/article/5e7e60489aa142559bd1e7f2f473e051

Model-Based Design to Enhance Neotissue Formation in Additively Manufactured Calcium-Phosphate-Based Scaffolds

Authors: Bingbing Liang, Ehsan Sadeghian Dehkord, Dorien Van Hede, Mojtaba Barzegari, Bruno Verlée, Justine Pirson, Grégory Nolens, France Lambert, Liesbet Geris

Source: Journal of Functional Biomaterials, Vol 14, Iss 12, p 563 (2023)

Subject Terms: bone tissue engineering, dental bone regeneration, porous scaffold, biomaterials, 3D printing, computer modeling and simulation, Biotechnology, TP248.13-248.65, Medicine (General), R5-920

File Description: electronic resource

Relation: https://www.mdpi.com/2079-4983/14/12/563; https://doaj.org/toc/2079-4983

Access URL: https://doaj.org/article/0da639fdfd304929a77c5dc5965d825e

Human pluripotent stem cell-derived cartilaginous organoids promote scaffold-free healing of critical size long bone defects

Authors: Wai Long Tam, Luís Freitas Mendes, Xike Chen, Raphaëlle Lesage, Inge Van Hoven, Elke Leysen, Greet Kerckhofs, Kathleen Bosmans, Yoke Chin Chai, Akihiro Yamashita, Noriyuki Tsumaki, Liesbet Geris, Scott J. Roberts, Frank P. Luyten

Source: Stem Cell Research & Therapy, Vol 12, Iss 1, Pp 1-16 (2021)

Subject Terms: Stem cell technology, Organoid biology, Bone tissue engineering, Induced pluripotent stem cells, Endochondral ossification, Cartilage, Medicine (General), R5-920, Biochemistry, QD415-436

File Description: electronic resource

Relation: https://doaj.org/toc/1757-6512

Access URL: https://doaj.org/article/e0bbc5cdaf7747208d680c993e153392

Scientific and regulatory evaluation of mechanistic in silico drug and disease models in drug development: Building model credibility

Authors: Flora T. Musuamba, Ine Skottheim Rusten, Raphaëlle Lesage, Giulia Russo, Roberta Bursi, Luca Emili, Gaby Wangorsch, Efthymios Manolis, Kristin E. Karlsson, Alexander Kulesza, Eulalie Courcelles, Jean‐Pierre Boissel, Cécile F. Rousseau, Emmanuelle M. Voisin, Rossana Alessandrello, Nuno Curado, Enrico Dall’ara, Blanca Rodriguez, Francesco Pappalardo, Liesbet Geris

Source: CPT: Pharmacometrics & Systems Pharmacology, Vol 10, Iss 8, Pp 804-825 (2021)

Subject Terms: Therapeutics. Pharmacology, RM1-950

File Description: electronic resource

Relation: https://doaj.org/toc/2163-8306

Access URL: https://doaj.org/article/97e2e67f5a5b4314bf9e9f73a5497dde

An Empirical Model Linking Physico-Chemical Biomaterial Characteristics to Intra-Oral Bone Formation

Authors: Ehsan Sadeghian Dehkord, Greet Kerckhofs, Philippe Compère, France Lambert, Liesbet Geris

Source: Journal of Functional Biomaterials, Vol 14, Iss 7, p 388 (2023)

Subject Terms: empirical modeling, intra-oral bone formation, calcium phosphate, physico-chemical, biomaterials, Biotechnology, TP248.13-248.65, Medicine (General), R5-920

File Description: electronic resource

Relation: https://www.mdpi.com/2079-4983/14/7/388; https://doaj.org/toc/2079-4983

Access URL: https://doaj.org/article/7fe7227a405249ce95f80aab8307a9d1

Wobble tRNA modification and hydrophilic amino acid patterns dictate protein fate

Authors: Francesca Rapino, Zhaoli Zhou, Ana Maria Roncero Sanchez, Marc Joiret, Christian Seca, Najla El Hachem, Gianluca Valenti, Sara Latini, Kateryna Shostak, Liesbet Geris, Ping Li, Gang Huang, Gabriel Mazzucchelli, Dominique Baiwir, Christophe J. Desmet, Alain Chariot, Michel Georges, Pierre Close

Source: Nature Communications, Vol 12, Iss 1, Pp 1-14 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/c065fd32e605402394e0d38dfe8266a8

Engineering bone-forming callus organoid implants in a xenogeneic-free differentiation medium

Authors: Isaak Decoene, Tim Herpelinck, Liesbet Geris, Frank P. Luyten, Ioannis Papantoniou

Source: Frontiers in Chemical Engineering, Vol 4 (2022)

Subject Terms: advanced therapy medicinal products, skeletal tissue engineering, scalability, manufacturing, spheroid culture, cartilage microtissue, Technology, Chemical technology, TP1-1185

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fceng.2022.892190/full; https://doaj.org/toc/2673-2718

Access URL: https://doaj.org/article/37819762e8dd418ba29802c6fa75dae7

Natural language processing in toxicology: Delineating adverse outcome pathways and guiding the application of new approach methodologies

Authors: Marie P.F. Corradi, Alyanne M. de Haan, Bernard Staumont, Aldert H. Piersma, Liesbet Geris, Raymond H.H. Pieters, Cyrille A.M. Krul, Marc A.T. Teunis

Source: Biomaterials and Biosystems, Vol 7, Iss , Pp 100061- (2022)

Subject Terms: Natural Language Processing, Adverse Outcome Pathways, New Approach Methodologies, Toxicology, Medical technology, R855-855.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S266653442200023X; https://doaj.org/toc/2666-5344

Access URL: https://doaj.org/article/aa0f32b77c024ebd9017437a87e31bbf