Publications
This is a list of publications related to the work of the Inno4Vac Consortium published in scientific journals. Please contact us for more information, or if a relevant publication is missing: daniel.reem@euvaccine.eu
A cloud-enabled digital twin platform for upstream processing in biotechnology: Integrating CFD, compartmentalization, and reaction kinetics
2025
Xiyan Li, Sebastian L. Jensen, Noah B. Christiansen, Elham Ramin, Johan le Nepvou de Carfort, Johannes Schmölder, Eric von Lieres, Krist V. Gernaey
Computers & Chemical Engineering, 109488
Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases
2025
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
Cell Systems Volume 16, Issue 11101449
Symptoms and adverse events in controlled human infection models.
2025
Götz K, Luga P, Rengel J, Masur M, Juárez-Hernández M, Bekeredjian-Ding I.
Front Med (Lausanne). 2025 Aug 14;12:1578560
Hybrid Optimization Methods for Parameter Estimation of Reactive Transport Systems
2025
Marcus Johan Schytt, Halldór Gauti Pétursson, John Bagterp Jørgensen
IFAC-PapersOnLine Volume 59, Issue 6, 2025, Pages 163-168
High-Performance C++ and Julia solvers in CADET for weakly and strongly coupled continuous chromatography problems
2025
Jesper Frandsen, Jan Michael Breuer, Johannes Schmölder, Kjøbsted Huusom, Krist V. Gernaey, Eric von Lieres
Computers & Chemical Engineering Volume 202, November 2025, 109295
NetTCR-struc, a structure driven approach for prediction of TCR-pMHC interactions
2025
Sebastian N Deleuran and Morten Nielsen
Front. Immunol. Volume 16 - 2025
Advancing regulatory dialogue: In silico models for improved vaccine biomanufacturing - an expert meeting report.
2025
Meln I, Van Molle W, Vélez MP, Abrahamsen G, Brusselmans K, Calvosa E, Cardillo AG, Clénet D, Forestieri C, Gernaey KV, Hoefnagel M, Jorgensen JB, Lebrun P, Natalis L, Nilsson B, Öppling V, Pollinger JC, Rayat ACME, Reem D, Rubbrecht M, Schmölder J, Schofield T, Smith D, Timmins S, von Lieres E, Welin M, Bracewell DG.
Vaccine. 2025 Apr 26;56:127170.
Deciphering respiratory viral infections by harnessing organ-on-chip technology to explore the gut–lung axis
2025
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
Open Biology, Volume 15, Issue 3
Identification of a type 1 diabetes-associated T cell receptor repertoire signature from the human peripheral blood
2025
Puneet Rawat, Melanie R. Shapiro, Michael Widrich, Koshlan Mayer-Blackwell, Keshav Motwani, Leeana D. Peters, Ghadi al Hajj, Milena Pavlović, Amanda L. Posgai, Mark A. Atkinson, Michael J. Haller, Desmond A.
Schatz, Maria Chernigkovskaya, Lonneke Scheffer, Kartik Motwani, Leandro Octavio Balzano-Nogueira, Camryn Pettenger-Willey, Sebastiaan Valkiers, Sepp Hochreiter, Giulio isacchini, Chakravarthi Kanduri, Clive H. Wasserfall, Andrew J Fiore-Gartland, Erik Yusko, Alex Dahmani, and Ryan O. Emerson, Günter Klambauer, Dr. Philip Bradley , Geir Kjetil Sandve, Victor Greiff and Todd M. Brusko
medRxiv 2024.12.10.24318751
Comparison of air-liquid interface transwell and airway organoid models for human respiratory virus infection studies
2025
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, and Puck B. van Kasteren
Front. Immunol. Volume 16 - 2025
Regulatory workshop on standardisation of clinical procedures, endpoints and data robustness of human challenge studies - A stakeholder meeting report
2025
Irina Meln, Victor Cnossen, Nicoletta Corti, Arno Andeweg, Marc Baay, Christopher Chiu, John Coia, Oliver Cornely, Rebecca J Cox, Dileep Dasyam, Sigrid C J De Keersmaecker, Meagan Deming, Joanna Waldock, Othmar G Engelhardt, Manman Guo, Okba Haj-Ali Saflo, Annefleur Hensen, Rienk Jeeninga, Simon Kolstoe, Oleg Krut, Ed J Kuijper, Lorna Leal, Natalie Mazur, Kristin G I Mohn, Sandra Morel, Ab Osterhaus, Augustin Portela Moreira, Wiep Klaas Smits, Saranya Sridhar, Danny Toomey, Joop van Gerven, Maria J G T Vehreschild, Juan Pablo Yarzabal, Paul Zimmer-Harwood, Pieter Neels, Ole F Olesen, Meta Roestenberg, Ingrid M C Kamerling
Biologicals 2025 May:90:101818
CADET-Julia: Efficient and versatile, open-source simulator for batch chromatography in Julia
2025
Frandsen, J, Breuer, J, Schmölder, J, Huusom JK, Gernaey KV, Abildskov J, von Lieres E.
Computers & Chemical Engineering (192), Jan 2025, 108913
Solving crystallization/precipitation population balance models in CADET, Part II: Size-based Smoluchowski coagulation and fragmentation equations in batch and continuous modes
2025
Zhang, W, Przybycien, T. Breuer, JM, von Lieres E.
Computers & Chemical Engineering 2025 (192), Jan 2025, 108860
Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning
2024
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
Cell Systems Volume 15, Issue 12p1168-1189
modsim/CADET: Version 4.4.0
2024
Leweke S, Schmölder J, von Lieres E, Rao J, Hassan J, Heymann W, Breuer J, Rocher J, Azzouzi S.
Zenodo
Inno4Vac Workshop Report Part 1: Controlled Human Influenza Virus Infection Model (CHIVIM) Strain Selection and Immune Assays for CHIVIM Studies, November 2021, MHRA, UK.
2024
Waldock J, Cox RJ, Chiu C, Subbarao K, Wildfire A, Barclay W, van Kasteren PB, McCauley J, Russell CA, Smith D, Thwaites RS, Tregoning JS, Engelhardt OG.
Influenza Other Respir Viruses. 2024 Nov;18(11):e70014.
Inno4Vac Workshop Report Part 2: RSV-Controlled Human Infection Model (CHIM) Strain Selection and Immune Assays for RSV CHIM Studies, November 2021, MHRA, UK.
2024
Waldock J, Cox RJ, Engelhardt OG, Ascough S, Osterhaus A, Rimmelzwaan GF, Ludlow M, Tregoning JS, McDonald JU, Buchholz UJ, Jeeninga RE, Sande C, Chiu C.
Influenza Other Respir Viruses. 2024 Oct;18(10):e70013.
How to develop a controlled human infection model for Clostridioides difficile.
2024
Hensen ADO, Vehreschild MJGT, Gerding DN, Krut O, Chen W, Young VB, Tzipori S, Solbach P, Gibani MM, Chiu C, de Keersmaecker SCJ, Dasyam D, Morel S, Devaster JM, Corti N, Kuijper EJ, Roestenberg M, Smits WK.
Clin Microbiol Infect. 2024 Aug 29:S1198-743X(24)00425-7.
Immunocompetent PDMS-Free Organ-on-Chip Model of Cervical Cancer Integrating Patient-Specific Cervical Fibroblasts and Neutrophils.
2024
Kromidas E, Geier A, Weghofer A, Liu HY, Weiss M, Loskill P.
Adv Healthc Mater. 2024 Aug;13(21):e2302714. .
Biophysical cartography of the native and human-engineered antibody landscapes quantifies the plasticity of antibody developability.
2024
Bashour H, Smorodina E, Pariset M, Zhong J, Akbar R, Chernigovskaya M, Lê Quý K, Snapkow I, Rawat P, Krawczyk K, Sandve GK, Gutierrez-Marcos J, Gutierrez DN, Andersen JT, Greiff V.
Commun Biol. 2024 Jul 31;7(1):922.
Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling.
2024
Lê Quý K, Chernigovskaya M, Stensland M, Singh S, Leem J, Revale S, Yadin DA, Nice FL, Povall C, Minns DH, Galson JD, Nyman TA, Snapkow I, Greiff V.
NPJ Syst Biol Appl. 2024 Jul 12;10(1):73.
Training data composition determines machine learning generalization and biological rule discovery
2024
Ursu E, Minnegalieva A, Rawat P, Chernigovskaya M, Tacutu R, Sandve GK, Robert PA, Greiff V.
bioRxiv 2024.06.17.599333
Solving the crystallization/precipitation population balance model in CADET part I: nucleation growth and growth rate dispersion in batch and continuous modes on a nonuniform grid
2024
Zhang, W, Przybycien, T, Schmölder, J, Leweke, S, von Lieres, E.
Computers & Chemical Engineering, 2024 (183), 2024, 108612
Accelerating vaccine manufacturing development through model-based approaches: current advances and future opportunities
2024
Ramin E, Cardillo AG, Liebers R, Schmölder J, von Lieres E, Van Molle W, Niebel B, Natalis L, Meln I, Perea-Vélez M, Clénet D, Jørgensen JB, Nilsson B, Bracewell DG, Gernaey KV.
Current Opinion in Chemical Engineering 2024. (43), March 2024, 100998
InSilicoSeq 2.0: Simulating realistic amplicon-based sequence reads
2024
Stefan H. Lelieveld, Thijs Maas, Tessa C. X. Duk, Hadrien Gourlé, Henk-Jan van den Ham
bioRxiv 2024.02.16.580469
Fourth Controlled Human Infection Model (CHIM) meeting - CHIMs in endemic countries, May 22-23, 2023.
2024
Kapulu M, Manda-Taylor L, Balasingam S, Means G, Ayiro Malungu M, Bejon P, Chi PC, Chiu C, Church EC, Correa-Oliveira R, Day N, Durbin A, Egesa M, Emerson C, Jambo K, Mathur R, Metzger W, Mumba N, Nazziwa W, Olotu A, Rodgers J, Sinyiza F, Talaat K, Kamerling I, Weller C, Baay M, Neels P.
Biologicals. 2024 Feb;85:101747.
Ethical approval for controlled human infectious model clinical trial protocols - A workshop report.
2024
Jamrozik E, Littler K, Meln I, Van Molle W, Morel S, Olesen OF, Rubbrecht M, Balasingam S, Neels P.
Biologicals. 2024 Feb;85:101748.
Fourth Controlled Human Infection Model (CHIM) meeting, CHIM regulatory issues, May 24, 2023.
2024
Cavaleri M, Kaslow D, Boateng E, Chen WH, Chiu C, Choy RKM, Correa-Oliveira R, Durbin A, Egesa M, Gibani M, Kapulu M, Katindi M, Olotu A, Pongsuwan P, Simuyandi M, Speder B, Talaat KR, Weller C, Wills B, Baay M, Balasingam S, Olesen OF, Neels P.
Biologicals. 2024 Feb;85:101745.
Regulatory workshop on challenge strain development and GMP manufacture - A stakeholder meeting report.
2024
Corti N, Chiu C, Cox RJ, Demont C, Devaster JM, Engelhardt OG, Gorringe A, Hassan K, Hoefnagel M, Kamerling I, Krut O, Lane C, Liebers R, Luke C, Van Molle W, Morel S, Neels P, Roestenberg M, Rubbrecht M, Klaas Smits W, Stoughton D, Talaat K, Vehreschild MJGT, Wildfire A, Meln I, Olesen OF.
Biologicals. 2024 Feb;85:101746.
Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling
2023
Khang Lê Quý, Maria Chernigovskaya, Maria Stensland, Sachin Singh, Jinwoo Leem, Santiago Revale, Jacob D. Galson, Tuula A. Nyman, Igor Snapkow, Victor Greiff
bioRxiv 2023.11.01.565093
Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning
2023
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
bioRxiv 2023.10.20.562936
Weakly supervised identification and generation of adaptive immune receptor sequences associated with immune disease status
2023
Slabodkin A, Sollid LM, Sandve GK, Robert PA, Greiff V.
bioRxiv 2023.09.24.558823
Spatial discontinuous Galerkin spectral element method for a family of chromatography models in CADET
2023
Breuer JM, Leweke S, Schmölder J, Gassner G, von Lieres E.
Computers & Chemical Engineering. 2023 Sept 2023 (117), 108340
Reference-based comparison of adaptive immune receptor repertoires.
2022
Weber CR, Rubio T, Wang L, Zhang W, Robert PA, Akbar R, Snapkov I, Wu J, Kuijjer ML, Tarazona S, Conesa A, Sandve GK, Liu X, Reddy ST, Greiff V.
Cell Rep Methods. 2022 Aug 22;2(8):100269.
In Press:
Author(s): Irina Meln, Xiyan Li, Antonio Gaetano Cardillo, Krist V Gernaey
Published in: Vaccine Insights, 2025
Publisher: Bioinsights Publishing Limited
Advancing In Silico Tools for Vaccine Development and Process Modeling
Author(s): Irina Meln, Gunnveig Grødeland, Daniel G. Bracewell, Meta Roestenberg, Cécile van Els, Kimberly Veenstra and Ole Olesen
Published in: BioProcess International, 2022
Publisher: Informa Connect Limited