Innovations to accelerate vaccine development and manufacture

Risultati finali

Scientific consensus docon new challenge influenza strains
Roadmap document prioritizing RSV immune assays for development and standardization
Report of regulatory workshop 1
Prepare SOPs for handling open calls process
Workshops with stakeholders implemented
Open call process launched

Launch of web site

Pubblicazioni

Training data composition determines machine learning generalization and biological rule discovery

Autori: Eugen Ursu, Aygul Minnegalieva, Puneet Rawat, Maria Chernigovskaya, Robi Tacutu, Geir Kjetil Sandve, Philippe A. Robert, Victor Greiff
Pubblicato in: bioRxiv, 2024, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.06.17.599333

Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning

Autori: Maria Chernigovskaya, Milena Pavlović, Chakravarthi Kanduri, Sofie Gielis, Philippe A. Robert, Lonneke Scheffer, Andrei Slabodkin, Ingrid Hobæk Haff, Pieter Meysman, Gur Yaari, Geir Kjetil Sandve, Victor Greiff
Pubblicato in: bioRxiv, 2023, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.10.20.562936

Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases

Autori: Maria Chernigovskaya, Khang Lê Quý, Maria Stensland, Sachin Singh, Rowan Nelson, Melih Yilmaz, Konstantinos Kalogeropoulos, Pavel Sinitcyn, Anand Patel, Natalie Castellana, Stefano Bonissone, Stian Foss, Jan Terje Andersen, Geir Kjetil Sandve, Timothy Patrick Jenkins, William S. Noble, Tuula A. Nyman, Igor Snapkow, Victor Greiff
Pubblicato in: bioRxiv, 2024, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.11.11.622451

Weakly supervised identification and generation of adaptive immune receptor sequences associated with immune disease status

Autori: Andrei Slabodkin, Ludvig M. Sollid, Geir Kjetil Sandve, Philippe A. Robert, Victor Greiff
Pubblicato in: bioRxiv, 2024, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.09.24.558823

InSilicoSeq 2.0: Simulating realistic amplicon-based sequence reads

Autori: Stefan H. Lelieveld, Thijs Maas, Tessa C. X. Duk, Hadrien Gourlé, Henk-Jan van den Ham
Pubblicato in: bioRxiv, 2024, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.02.16.580469

Identification of a type 1 diabetes-associated T cell receptor repertoire signature from the human peripheral blood

Autori: Puneet Rawat, Melanie R. Shapiro, Leeana D. Peters, Michael Widrich, Koshlan Mayer-Blackwell, Keshav Motwani, Milena Pavlović, Ghadi al Hajj, Amanda L. Posgai, Chakravarthi Kanduri, Giulio Isacchini, Maria Chernigovskaya, Lonneke Scheffer, Kartik Motwani, Leandro Octavio Balzano-Nogueira, Camryn M. Pettenger-Willey, Sebastiaan Valkiers, Laura M. Jacobsen, Michael J. Haller, Desmond A. Schatz, Cli
Pubblicato in: medRxiv, 2025, ISSN 3067-2007
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.12.10.24318751

Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning

Autori: Timothy J. O’Donnell, Chakravarthi Kanduri, Giulio Isacchini, Julien P. Limenitakis, Rebecca A. Brachman, Raymond A. Alvarez, Ingrid H. Haff, Geir K. Sandve, Victor Greiff
Pubblicato in: Cell Systems, Numero 15, 2024, Pagina/e 1168-1189, ISSN 2405-4712
Editore: Elsevier BV
DOI: 10.1016/j.cels.2024.11.006

Symptoms and adverse events in controlled human infection models

Autori: Karen Götz, Poleta Luga, Jörg Rengel, Mei Masur, Marcela Juárez-Hernández, Isabelle Bekeredjian-Ding
Pubblicato in: Frontiers in Medicine, Numero 12, 2025, ISSN 2296-858X
Editore: Frontiers Media SA
DOI: 10.3389/fmed.2025.1578560

Comparison of air-liquid interface transwell and airway organoid models for human respiratory virus infection studies

Autori: Camilla T. Ekanger, Nilima Dinesh Kumar, Rosanne W. Koutstaal, Fan Zhou, Martin Beukema, Joanna Waldock, Simon P. Jochems, Noa Mulder, Cécile A. C. M. van Els, Othmar G. Engelhardt, Nathalie Mantel, Kevin P. Buno, Karl Albert Brokstad, Agnete S. T. Engelsen, Rebecca J. Cox, Barbro N. Melgert, Anke L. W. Huckriede, Puck B. van Kasteren
Pubblicato in: Frontiers in Immunology, Numero 16, 2025, ISSN 1664-3224
Editore: Frontiers Media SA
DOI: 10.3389/fimmu.2025.1532144

Inno4Vac Workshop Report Part 1: Controlled Human Influenza Virus Infection Model (CHIVIM) Strain Selection and Immune Assays for CHIVIM Studies, November 2021, MHRA, UK

Autori: Joanna Waldock, Rebecca J. Cox, Christopher Chiu, Kanta Subbarao, Adrian Wildfire, Wendy Barclay, Puck B. van Kasteren, John McCauley, Colin A. Russell, Derek Smith, Ryan S. Thwaites, John S. Tregoning, Othmar G. Engelhardt
Pubblicato in: Influenza and Other Respiratory Viruses, Numero 18, 2024, ISSN 1750-2640
Editore: Blackwell Publishing Inc.
DOI: 10.1111/irv.70014

Advancing regulatory dialogue: In silico models for improved vaccine biomanufacturing - an expert meeting report

Autori: Irina Meln, Wim Van Molle, Mónica Perea Vélez, Greger Abrahamsen, Koen Brusselmans, Eric Calvosa, Antonio Gaetano Cardillo, Didier Clénet, Caroline Forestieri, Krist V. Gernaey, Marcel Hoefnagel, John Bagterp Jorgensen, Pierre Lebrun, Laurent Natalis, Bernt Nilsson, Volker Öppling, Julius Carl Pollinger, Andrea C.M.E. Rayat, Daniel Reem, Michelle Rubbrecht, Johannes Schmölder, Timothy Schofie
Pubblicato in: Vaccine, Numero 56, 2025, Pagina/e 127170, ISSN 0264-410X
Editore: Elsevier BV
DOI: 10.1016/j.vaccine.2025.127170

CADET-Julia: Efficient and versatile, open-source simulator for batch chromatography in Julia

Autori: Jesper Frandsen, Jan Michael Breuer, Johannes Schmölder, Jakob Kjøbsted Huusom, Krist V. Gernaey, Jens Abildskov, Eric von Lieres
Pubblicato in: Computers & Chemical Engineering, Numero 192, 2024, Pagina/e 108913, ISSN 0098-1354
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.compchemeng.2024.108913

Fourth Controlled Human Infection Model (CHIM) meeting – CHIMs in endemic countries, May 22–23, 2023

Autori: Melissa Kapulu, Lucinda Manda-Taylor, Shobana Balasingam, Gary Means, Mikal Ayiro Malungu, Philip Bejon, Primus Che Chi, Christopher Chiu, E. Chandler Church, Rodrigo Correa-Oliveira, Nicholas Day, Anna Durbin, Moses Egesa, Claudia Emerson, Kondwani Jambo, Roli Mathur, Wolfram Metzger, Noni Mumba, Winfred Nazziwa, Ally Olotu, Jacqueline Rodgers, Frank Sinyiza, Kawsar Talaat, Ingrid Kamerling, Char
Pubblicato in: Biologicals, Numero 85, 2024, Pagina/e 101747, ISSN 1045-1056
Editore: Academic Press
DOI: 10.1016/j.biologicals.2024.101747

Solving crystallization/precipitation population balance models in CADET, part I: Nucleation growth and growth rate dispersion in batch and continuous modes on nonuniform grids

Autori: Wendi Zhang, Todd Przybycien, Johannes Schmölder, Samuel Leweke, Eric von Lieres
Pubblicato in: Computers & Chemical Engineering, Numero 183, 2024, Pagina/e 108612, ISSN 0098-1354
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.compchemeng.2024.108612

Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling

Autori: Khang Lê Quý, Maria Chernigovskaya, Maria Stensland, Sachin Singh, Jinwoo Leem, Santiago Revale, David A. Yadin, Francesca L. Nice, Chelsea Povall, Danielle H. Minns, Jacob D. Galson, Tuula A. Nyman, Igor Snapkow, Victor Greiff
Pubblicato in: npj Systems Biology and Applications, Numero 10, 2024, ISSN 2056-7189
Editore: Springer Nature
DOI: 10.1038/s41540-024-00402-z

NetTCR-struc, a structure driven approach for prediction of TCR-pMHC interactions

Autori: Sebastian N. Deleuran, Morten Nielsen
Pubblicato in: Frontiers in Immunology, Numero 16, 2025, ISSN 1664-3224
Editore: Frontiers Media SA
DOI: 10.3389/fimmu.2025.1616328

Biophysical cartography of the native and human-engineered antibody landscapes quantifies the plasticity of antibody developability

Autori: Habib Bashour, Eva Smorodina, Matteo Pariset, Jahn Zhong, Rahmad Akbar, Maria Chernigovskaya, Khang Lê Quý, Igor Snapkow, Puneet Rawat, Konrad Krawczyk, Geir Kjetil Sandve, Jose Gutierrez-Marcos, Daniel Nakhaee-Zadeh Gutierrez, Jan Terje Andersen, Victor Greiff
Pubblicato in: Communications Biology, Numero 7, 2024, ISSN 2399-3642
Editore: Springer Nature
DOI: 10.1038/s42003-024-06561-3

How to develop a controlled human infection model for Clostridioides difficile

Autori: Annefleur D.O. Hensen, Maria J.G.T. Vehreschild, Dale N. Gerding, Oleg Krut, Wilbur Chen, Vincent B. Young, Saul Tzipori, Philipp Solbach, Malick Mahdi Gibani, Christopher Chiu, Sigrid C.J. de Keersmaecker, Dileep Dasyam, Sandra Morel, Jeanne-Marie Devaster, Nicoletta Corti, Ed J. Kuijper, Meta Roestenberg, Wiep Klaas Smits
Pubblicato in: Clinical Microbiology and Infection, Numero 31, 2025, Pagina/e 373-379, ISSN 1198-743X
Editore: Blackwell Publishing Inc.
DOI: 10.1016/j.cmi.2024.08.025

High-Performance C++ and Julia solvers in CADET for weakly and strongly coupled continuous chromatography problems

Autori: Jesper Frandsen, Jan Michael Breuer, Johannes Schmölder, Jens Abildskov, Jakob Kjøbsted Huusom, Krist V. Gernaey, Eric von Lieres
Pubblicato in: Computers & Chemical Engineering, Numero 202, 2025, Pagina/e 109295, ISSN 0098-1354
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.compchemeng.2025.109295

Organ-on-chip models for infectious disease research

Autori: Raquel Alonso-Roman, Alexander S. Mosig, Marc Thilo Figge, Kai Papenfort, Christian Eggeling, Felix H. Schacher, Bernhard Hube, Mark S. Gresnigt
Pubblicato in: Nature Microbiology, Numero 9, 2024, Pagina/e 891-904, ISSN 2058-5276
Editore: Nature Microbiology
DOI: 10.1038/s41564-024-01645-6

Hybrid Optimization Methods for Parameter Estimation of Reactive Transport Systems

Autori: Marcus Johan Schytt, Halldór Gauti Pétursson, John Bagterp Jørgensen
Pubblicato in: IFAC-PapersOnLine, Numero 59, 2025, Pagina/e 163-168, ISSN 2405-8963
Editore: Elsevier BV
DOI: 10.1016/j.ifacol.2025.07.139

Accelerating vaccine manufacturing development through model-based approaches: current advances and future opportunities

Autori: Elham Ramin, Antonio Gaetano Cardillo, Reinhard Liebers, Johannes Schmölder, Eric von Lieres, Wim Van Molle, Bastian Niebel, Laurent Natalis, Irina Meln, Mónica Perea-Vélez, Didier Clénet, John Bagterp Jørgensen, Bernt Nilsson, Daniel G. Bracewell, Krist V. Gernaey
Pubblicato in: Current Opinion in Chemical Engineering, Numero 43, 2024, Pagina/e 100998, ISSN 2211-3398
Editore: Elsevier BV
DOI: 10.1016/j.coche.2023.100998

Regulatory workshop on challenge strain development and GMP manufacture – A stakeholder meeting report

Autori: Nicoletta Corti, Christopher Chiu, Rebecca J. Cox, Clarisse Demont, Jeanne-Marie Devaster, Othmar G. Engelhardt, Andrew Gorringe, Khaole Hassan, Marcel Hoefnagel, Ingrid Kamerling, Oleg Krut, Chelsea Lane, Reinhard Liebers, Catherine Luke, Wim Van Molle, Sandra Morel, Pieter Neels, Meta Roestenberg, Michelle Rubbrecht, Wiep Klaas Smits, Daniel Stoughton, Kawsar Talaat, Maria J.G.T. Vehreschild, Ad
Pubblicato in: Biologicals, Numero 85, 2024, Pagina/e 101746, ISSN 1045-1056
Editore: Academic Press
DOI: 10.1016/j.biologicals.2024.101746

Solving crystallization/precipitation population balance models in CADET, Part II: Size-based Smoluchowski coagulation and fragmentation equations in batch and continuous modes

Autori: Wendi Zhang, Todd Przybycien, Jan Michael Breuer, Eric von Lieres
Pubblicato in: Computers & Chemical Engineering, Numero 192, 2024, Pagina/e 108860, ISSN 0098-1354
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.compchemeng.2024.108860

Inno4Vac Workshop Report Part 2: RSV‐Controlled Human Infection Model (CHIM) Strain Selection and Immune Assays for RSV CHIM Studies, November 2021, MHRA, UK

Autori: Joanna Waldock, Rebecca J. Cox, Othmar G. Engelhardt, Stephanie Ascough, Albert Osterhaus, Guus F. Rimmelzwaan, Martin Ludlow, John S. Tregoning, Jacqueline U. McDonald, Ursula J. Buchholz, Rienk E. Jeeninga, Charles. Sande, Christopher Chiu
Pubblicato in: Influenza and Other Respiratory Viruses, Numero 18, 2024, ISSN 1750-2640
Editore: Blackwell Publishing Inc.
DOI: 10.1111/irv.70013

Ethical approval for controlled human infectious model clinical trial protocols – A workshop report

Autori: Euzebiusz Jamrozik, Katherine Littler, Irina Meln, Wim Van Molle, Sandra Morel, Ole F. Olesen, Michelle Rubbrecht, Shobana Balasingam, Pieter Neels
Pubblicato in: Biologicals, Numero 85, 2024, Pagina/e 101748, ISSN 1045-1056
Editore: Academic Press
DOI: 10.1016/j.biologicals.2024.101748

Spatial discontinuous Galerkin spectral element method for a family of chromatography models in CADET

Autori: Jan Michael Breuer, Samuel Leweke, Johannes Schmölder, Gregor Gassner, Eric von Lieres
Pubblicato in: Computers & Chemical Engineering, 2023, Pagina/e 108340, ISSN 0098-1354
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.compchemeng.2023.108340

Fourth Controlled Human Infection Model (CHIM) meeting, CHIM regulatory issues, May 24, 2023

Autori: Marco Cavaleri, David Kaslow, Eric Boateng, Wilbur H. Chen, Christopher Chiu, Robert K.M. Choy, Rodrigo Correa-Oliveira, Anna Durbin, Moses Egesa, Malick Gibani, Melissa Kapulu, Melba Katindi, Ally Olotu, Pongphaya Pongsuwan, Michelo Simuyandi, Bruno Speder, Kawsar R. Talaat, Charlie Weller, Bridget Wills, Marc Baay, Shobana Balasingam, Ole F. Olesen, Pieter Neels
Pubblicato in: Biologicals, Numero 85, 2024, Pagina/e 101745, ISSN 1045-1056
Editore: Academic Press
DOI: 10.1016/j.biologicals.2024.101745

Immunocompetent PDMS‐Free Organ‐on‐Chip Model of Cervical Cancer Integrating Patient‐Specific Cervical Fibroblasts and Neutrophils

Autori: Elena Kromidas, Alicia Geier, Adrian Weghofer, Hui‐Yu Liu, Martin Weiss, Peter Loskill
Pubblicato in: Advanced Healthcare Materials, Numero 13, 2024, ISSN 2192-2640
Editore: John Wiley and Sons Ltd
DOI: 10.1002/adhm.202302714

Deciphering respiratory viral infections by harnessing organ-on-chip technology to explore the gut–lung axis

Autori: Hristina Koceva, Mona Amiratashani, Parastoo Akbarimoghaddam, Bianca Hoffmann, Gaukhar Zhurgenbayeva, Mark S. Gresnigt, Vanessa Rossetto Marcelino, Christian Eggeling, Marc Thilo Figge, Maria-João Amorim, Alexander S. Mosig
Pubblicato in: Open Biology, Numero 15, 2025, ISSN 2046-2441
Editore: Royal Society Publishing
DOI: 10.1098/rsob.240231

modsim/CADET: Version 4.4.0

Autori: Samuel Leweke, Johannes Schmölder, Eric von Lieres, Jayghosh Rao, Jazib Hassan, William Heymann, Jan Breuer, Jonathan Rocher, & Salah Azzouzi
Pubblicato in: 2023, ISSN 1082-9873
Editore: Zenodo
DOI: 10.5281/zenodo.8179016

Advancing In Silico Tools for Vaccine Development and Process Modeling

Autori: Irina Meln, Gunnveig Grødeland, Daniel G. Bracewell, Meta Roestenberg, Cécile van Els, Kimberly Veenstra and Ole Olesen
Pubblicato in: BioProcess International, 2022
Editore: Informa Connect Limited

Risultati finali

Pubblicazioni

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