Ghent University Academic Bibliography

Journal Article
A1
open access

PathwayPilot : a user-friendly tool for visualizing and navigating metabolic pathways

Tibo Vande Moortele (UGent) , Pieter Verschaffelt (UGent) , Qingyao Huang, Nadezhda T. Doncheva, Tanja Holstein (UGent) , Caroline Jachmann (UGent) , Peter Dawyndt (UGent) , Lennart Martens (UGent) , Bart Mesuere (UGent) and Tim Van Den Bossche (UGent)

(2025) MOLECULAR & CELLULAR PROTEOMICS. 24(3).

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Journal Article
A1
open access

The microbiologist's guide to metaproteomics

Tim Van Den Bossche (UGent) , Jean Armengaud, Dirk Benndorf, Jose Alfredo Blakeley‐Ruiz, Madita Brauer, Kai Cheng, Marybeth Creskey, Daniel Figeys, Lucia Grenga, Timothy J. Griffin, et al.

(2025) IMETA. 4(3).

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Miscellaneous
open access

Metaproteomics in the One Health framework for unraveling microbial effectors in microbiomes

Robert Heyer, Maximilian Wolf, Dirk Benndorf, Sergio Uzzau, Jana Seifert, Lucia Grenga, Martin Pabst, Heike Schmitt, Bart Mesuere (UGent) , Tim Van Den Bossche (UGent) , et al.

(2025) MICROBIOME. 13(1).

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Journal Article
A1
open access

Unipept in 2024 : expanding metaproteomics analysis with support for missed cleavages and semitryptic and nontryptic peptides

Tibo Vande Moortele (UGent) , Bram Devlaminck, Simon Van de Vyver (UGent) , Tim Van Den Bossche (UGent) , Lennart Martens (UGent) , Peter Dawyndt (UGent) , Bart Mesuere (UGent) and Pieter Verschaffelt (UGent)

(2025) JOURNAL OF PROTEOME RESEARCH. 24(2). p.949-954

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Journal Article
A1
open access

Critical Assessment of MetaProteome Investigation 2 (CAMPI-2) : multi-laboratory assessment of sample processing methods to stabilize fecal microbiome for functional analysis

Alessandro Tanca, Kay Schallert, Lucia Grenga, Samantha L. Peters, Marcello Abbondio, Laura De Diego, Maria Antonietta Deledda, Sven-Bastiaan Haange, Guylaine Miotello, Johan S. Sáenz, et al.

(2025) MICROBIOME. 13(1).

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Journal Article
A1
open access

Proceedings of the EuBIC-MS developers meeting 2023

Pedro Beltrao, Tim Van Den Bossche (UGent) , Ralf Gabriels (UGent) , Tanja Holstein (UGent) , Tobias Kockmann, Alireza Nameni (UGent) , Christian Panse, Ralph Schlapbach, Ludwig Lautenbacher, Matthias Mattanovich, et al.

(2024) JOURNAL OF PROTEOMICS. 305.

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Book Chapter

Biodiversity analysis of metaproteomics samples with Unipept : a comprehensive tutorial

Tim Van Den Bossche (UGent) , Pieter Verschaffelt (UGent) , Tibo Vande Moortele (UGent) , Peter Dawyndt (UGent) , Lennart Martens (UGent) and Bart Mesuere (UGent)

(2024) Protein bioinformatics. In Methods in Molecular Biology 2836. p.183-215

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Journal Article
A1
open access

Investigation of the human-gut-kidney axis by fecal proteomics, highlights molecular mechanisms affected in CKD

Sonnal Lohia, Sophie Valkenburg (UGent) , Rafael Stroggilos, Vasiliki Lygirou, Manousos Makridakis, Jerome Zoidakis, Francis Verbeke (UGent) , Griet Glorieux (UGent) and Antonia Vlahou

(2024) HELIYON. 10(12).

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Journal Article
A1
open access

Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species

Lydia Kipping, Nico Jehmlich, Julia Moll, Matthias Noll, Martin M Gossner, Tim Van Den Bossche (UGent) , Pascal Edelmann, Werner Borken, Martin Hofrichter and Harald Kellner

(2024) ISME JOURNAL. 18(1).

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Journal Article
A1
open access

Unipept Desktop 2.0 : construction of targeted reference protein databases for metaproteogenomics analyses

Pieter Verschaffelt (UGent) , Alessandro Tanca, Marcello Abbondio, Tim Van Den Bossche (UGent) , Tibo Vande Moortele (UGent) , Peter Dawyndt (UGent) , Lennart Martens (UGent) and Bart Mesuere (UGent)

(2023) JOURNAL OF PROTEOME RESEARCH. 22(8). p.2620-2628

Academic Bibliography

PathwayPilot : a user-friendly tool for visualizing and navigating metabolic pathways

The microbiologist's guide to metaproteomics

Metaproteomics in the One Health framework for unraveling microbial effectors in microbiomes

Unipept in 2024 : expanding metaproteomics analysis with support for missed cleavages and semitryptic and nontryptic peptides

Critical Assessment of MetaProteome Investigation 2 (CAMPI-2) : multi-laboratory assessment of sample processing methods to stabilize fecal microbiome for functional analysis

Proceedings of the EuBIC-MS developers meeting 2023

Biodiversity analysis of metaproteomics samples with Unipept : a comprehensive tutorial

Investigation of the human-gut-kidney axis by fecal proteomics, highlights molecular mechanisms affected in CKD

Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species

Unipept Desktop 2.0 : construction of targeted reference protein databases for metaproteogenomics analyses

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