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Translational control in infection biology: riboproteogenomics of bacterial pathogens

Publications

Gasdermin D independent canonical inflammasome responses cooperate with caspase-8 to establish host defense against gastrointestinal Citrobacter rodentium infection

Author(s): Elien Eeckhout, Lisa Hamerlinck, Veronique Jonckheere, Petra Van Damme, Geert van Loo, Andy Wullaert
Published in: Cell Death & Disease, 2023, ISSN 2041-4889
Publisher: Nature Publishing Group
DOI: 10.1038/s41419-023-05801-4

Use of Hybrid Data-Dependent and -Independent Acquisition Spectral Libraries Empowers Dual-Proteome Profiling

Author(s): Patrick Willems, Ursula Fels, An Staes, Kris Gevaert, Petra Van Damme
Published in: Journal of Proteome Research, Issue 20/2, 2021, Page(s) 1165-1177, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.0c00350

Rhizogenic Agrobacterium protein RolB interacts with the TOPLESS repressor proteins to reprogram plant immunity and development

Author(s): Lore Gryffroy; Evi Ceulemans; Nicolás Manosalva Pérez; Jhon Venegas-Molina; Ana Cristina Jaramillo-Madrid; Savio D. Rodrigues; Liesbeth De Milde; Veronique Jonckheere; Marc Van Montagu; Barbara De Coninck; Klaas Vandepoele; Petra Van Damme; Alain Goossens
Published in: Proceedings of the National Academy of Sciences of the United States of America, Issue 3, 2023, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2210300120

Recent Advancements in Tracking Bacterial Effector Protein Translocation

Author(s): Julie Braet, Dominiek Catteeuw, Petra Van Damme
Published in: Microorganisms, 2022, ISSN 2076-2607
Publisher: MDPI
DOI: 10.3390/microorganisms10020260

Lost and Found: Re-searching and Re-scoring Proteomics Data Aids Genome Annotation and Improves Proteome Coverage

Author(s): Patrick Willems, Igor Fijalkowski, Petra Van Damme
Published in: mSystems, Issue 5/5, 2020, ISSN 2379-5077
Publisher: American Society for Microbiology
DOI: 10.1128/msystems.00833-20

Expanded in vivo substrate profile of the yeast N-terminal acetyltransferase NatC

Author(s): Petra Van Damme; Camilla Osberg; Veronique Jonckheere; Nina Glomnes; Kris Gevaert; Thomas Arnesen; Henriette Aksnes
Published in: Journal of Biological Chemistry, Issue 4, 2023, ISSN 0021-9258
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.jbc.2022.102824

Hidden in plain sight : challenges in proteomics detection of small ORF-encoded polypeptides

Author(s): Igor Fijalkowski; Patrick Willems; Veronique Jonckheere; Laure Simoens; Petra Van Damme
Published in: microLife, Issue 2, 2022, ISSN 2633-6693
Publisher: Oxford University Press
DOI: 10.1093/femsml/uqac005

Keeping in Touch with Type-III Secretion System Effectors: Mass Spectrometry-Based Proteomics to Study Effector–Host Protein–Protein Interactions

Author(s): Margaux De Meyer, Joren De Ryck, Sofie Goormachtig, Petra Van Damme
Published in: International Journal of Molecular Sciences, Issue 21/18, 2020, Page(s) 6891, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms21186891

From prediction to function : current practices and challenges towards the functional characterization of type III effectors

Author(s): Joren De Ryck; Petra Van Damme; Sofie Goormachtig
Published in: Frontiers in Microbiology, Issue 5, 2023, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2023.1113442

Capturing Salmonella SspH2 Host Targets in Virus-Like Particles

Author(s): Margaux De Meyer, Igor Fijalkowski, Veronique Jonckheere, Delphine De Sutter, Sven Eyckerman, Petra Van Damme
Published in: Frontiers in Medicine, Issue 8, 2021, ISSN 2296-858X
Publisher: Lausanne: Frontiers Media S.A., 2014-
DOI: 10.3389/fmed.2021.725072

To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in Arabidopsis Thaliana

Author(s): Patrick Willems, Elvis Ndah, Veronique Jonckheere, Frank Van Breusegem, Petra Van Damme
Published in: Frontiers in Plant Science, 2022, ISSN 1664-462X
Publisher: Frontiers Media S. A.
DOI: 10.3389/fpls.2021.778804

Establishment of Proximity-dependent Biotinylation Approaches in Different Plant Model Systems

Author(s): Deepanksha Arora, Nikolaj B. Abel, Chen Liu, Petra Van Damme, Klaas Yperman, Dominique Eeckhout, Lam Dai Vu, Jie Wang, Anna Tornkvist, Francis Impens, Barbara Korbei, Jelle Van Leene, Alain Goossens, Geert De Jaeger, Thomas Ott, Panagiotis Nikolaou Moschou, Daniel Van Damme
Published in: The Plant Cell, 2020, Page(s) tpc.00235.2020, ISSN 1040-4651
Publisher: American Society of Plant Biologists
DOI: 10.1105/tpc.20.00235

Seeking the interspecies crosswalk for filamentous microbe effectors

Author(s): Naomi Stuer, Petra Van Damme, Sofie Goormachtig, Judith Van Dingenen
Published in: Trends in Plant Science, 2023, ISSN 1360-1385
Publisher: Elsevier BV
DOI: 10.1016/j.tplants.2023.03.017

Shift in vacuolar to cytosolic regime of infecting Salmonella from a dual proteome perspective

Author(s): Ursula Fels, Patrick Willems, Margaux De Meyer, Kris Gevaert, Petra Van Damme
Published in: PLoS Pathogens, 2023, ISSN 1553-7366
Publisher: Public Library of Science
DOI: 10.1371/journal.ppat.1011183

PROTEOFORMER 2.0: further developments in the ribosome profiling-assisted proteogenomic hunt for new proteoforms

Author(s): Steven Verbruggen, Elvis Ndah, Wim Van Criekinge, Siegfried Gessulat, Bernhard Kuster, Mathias Wilhelm, Petra Van Damme, Gerben Menschaert
Published in: Molecular & Cellular Proteomics, 2019, Page(s) mcp.RA118.001218, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.ra118.001218

Bacterial riboproteogenomics: the era of N-terminal proteoform existence revealed

Author(s): Daria Fijalkowska, Igor Fijalkowski, Patrick Willems, Petra Van Damme
Published in: FEMS Microbiology Reviews, 2020, ISSN 1574-6976
Publisher: Oxford academic
DOI: 10.1093/femsre/fuaa013

Small Protein Enrichment Improves Proteomics Detection of sORF Encoded Polypeptides

Author(s): Igor Fijalkowski, Marlies Peeters, Petra Van Damme
Published in: Frontiers in Genetics, 2021, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2021.713400

Exposing the small protein load of bacterial life

Author(s): Laure Simoens, Igor Fijalkowski, Petra Van Damme
Published in: FEMS Microbiology Reviews, 2023, ISSN 0168-6445
Publisher: Blackwell
DOI: 10.1093/femsre/fuad063

Selective ribosome profiling reveals a role for SecB in the co-translational inner membrane protein biogenesis

Author(s): Lena Eismann; Igor Fijalkowski; Carla Verónica Galmozzi; Jiří Koubek; Frank Tippmann; Petra Van Damme; Günter Kramer
Published in: Cell Reports, Issue 7, 2022, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2022.111776

Bacterial Genetic Engineering by Means of Recombineering for Reverse Genetics

Author(s): Ursula Fels, Kris Gevaert, Petra Van Damme
Published in: Frontiers in Microbiology, Issue 11, 2020, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2020.548410

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