Publications

This is a list of publications related to the work of the Inno4Vac Consortium published in scientific journals. Please contact the Project Leader for more information, or if a relevant publication is missing: irina.meln@euvaccine.eu

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

Doi:

https://doi.org/10.1016/j.compchemeng.2024.108913

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

Doi:

https://doi.org/10.1016/j.compchemeng.2024.108860

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

Doi:

https://zenodo.org/doi/10.5281/zenodo.8179015

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.

Doi:

https://doi.org/10.1111/irv.70014

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.

Doi:

https://doi.org/10.1111/irv.70013

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.

Doi:

https://doi.org/10.1016/j.cmi.2024.08.025

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. .

Doi:

http://doi: 10.1002/adhm.202302714. Epub 2024 Jan 8. PMID: 38029413

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.

Doi:

https://doi.org/10.1038/s42003-024-06561-3

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.

Doi:

https://doi.org/10.1038/s41540-024-00402-z

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

Doi:

https://doi.org/10.1101/2024.06.17.599333

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

Doi:

https://doi.org/10.1016/j.compchemeng.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

Doi:

https://doi.org/10.1016/j.coche.2023.100998

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

Doi:

http:// https://doi.org/10.1101/2024.02.16.580469

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.

Doi:

https://doi.org/10.1016/j.biologicals.2024.101747

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.

Doi:

https://doi.org/10.1016/j.biologicals.2024.101748

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.

Doi:

https://doi.org/10.1016/j.biologicals.2024.101745

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.

Doi:

https://doi.org/10.1016/j.biologicals.2024.101746

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

Doi:

https://doi.org/10.1101/2023.11.01.565093

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

Doi:

https://doi.org/10.1101/2023.10.20.562936

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

Doi:

https://doi.org/10.1101/2023.09.24.558823

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

Doi:

https://doi.org/10.1016/j.compchemeng.2023.108340

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 M,ethods. 2022 Aug 22;2(8):100269.

Doi:

http://doi: 10.1016/j.crmeth.2022.100269.

Other(s)

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

Publications

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

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

modsim/CADET: Version 4.4.0

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

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

How to develop a controlled human infection model for Clostridioides difficile.

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

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

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

Training data composition determines machine learning generalization and biological rule discovery

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

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

InSilicoSeq 2.0: Simulating realistic amplicon-based sequence reads

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

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

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

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

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

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

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

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

Reference-based comparison of adaptive immune receptor repertoires.

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