P. Van Damme

发表

REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes

Gerben Menschaert, Elvis Ndah, Petra Van Damme, 2017, bioRxiv.

Deep Proteome Coverage Based on Ribosome Profiling Aids Mass Spectrometry-based Protein and Peptide Discovery and Provides Evidence of Alternative Translation Products and Near-cognate Translation Initiation Events*

K. Gevaert, W. Van Criekinge, A. Koch, 2013, Molecular & Cellular Proteomics.

A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites

B. Shen, K. Gevaert, W. Van Criekinge, 2014, Proteomics.

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

P. Willems, P. Van Damme, Daria Fijałkowska, 2020, FEMS microbiology reviews.

Omics Assisted N-terminal Proteoform and Protein Expression Profiling On Methionine Aminopeptidase 1 (MetAP1) Deletion*

V. Jonckheere, P. Van Damme, Daria Fijałkowska, 2018, Molecular & Cellular Proteomics.

Ribosome signatures aid bacterial translation initiation site identification

Eivind Valen, Elvis Ndah, V. Jonckheere, 2017, BMC Biology.

N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana

P. Willems, F. Van Breusegem, K. Gevaert, 2017, Molecular & Cellular Proteomics.

A Unique Ribosome Signature Reveals Bacterial Translation Initiation Sites

Eivind Valen, Elvis Ndah, V. Jonckheere, 2016, bioRxiv.

A Role for Human N-alpha Acetyltransferase 30 (Naa30) in Maintaining Mitochondrial Integrity*

T. Arnesen, J. Varhaug, K. Gevaert, 2016, Molecular & Cellular Proteomics.

Positional proteomics reveals differences in N‐terminal proteoform stability

K. Gevaert, Elvis Ndah, P. Van Damme, 2016, Molecular systems biology.

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

W. Van Criekinge, A. Koch, T. De Meyer, 2014, Nucleic acids research.

Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects

N. Reuter, J. Swensen, T. Arnesen, 2014, Human molecular genetics.

An organellar nα-acetyltransferase, naa60, acetylates cytosolic N termini of transmembrane proteins and maintains Golgi integrity.

T. Arnesen, K. Gevaert, P. Van Damme, 2015, Cell reports.

Holistic view on the extended substrate specificities of orthologous granzymes.

S. Maurer-Stroh, K. Gevaert, P. Van Damme, 2014, Journal of proteome research.

A Saccharomyces cerevisiae Model Reveals In Vivo Functional Impairment of the Ogden Syndrome N-Terminal Acetyltransferase NAA10 Ser37Pro Mutant*

T. Arnesen, K. Gevaert, P. Van Damme, 2014, Molecular & Cellular Proteomics.

Identification of Serpinb6b as a Species-specific Mouse Granzyme A Inhibitor Suggests Functional Divergence between Human and Mouse Granzyme A

S. E. Stewart, K. Gevaert, P. Bird, 2014, The Journal of Biological Chemistry.

Substrate specificities of the granzyme tryptases A and K.

K. Gevaert, P. Van Damme, H. Demol, 2014, Journal of proteome research.

N-terminal Proteomics and Ribosome Profiling Provide a Comprehensive View of the Alternative Translation Initiation Landscape in Mice and Men*

W. Van Criekinge, G. Menschaert, P. Van Damme, 2014, Molecular & Cellular Proteomics.

Contemporary positional proteomics strategies to study protein processing.

K. Gevaert, P. Van Damme, K. Plasman, 2013, Current opinion in chemical biology.

Protein N-terminal Acetyltransferases Act as N-terminal Propionyltransferases In Vitro and In Vivo*

R. Evjenth, T. Arnesen, K. Gevaert, 2012, Molecular & Cellular Proteomics.

Protein alpha‐N‐acetylation studied by N‐terminomics

T. Arnesen, K. Gevaert, P. Van Damme, 2011, The FEBS journal.

Proteome-wide Identification of HtrA2/Omi Substrates.

P. Vandenabeele, K. Gevaert, M. Lamkanfi, 2007, Journal of proteome research.

Improved recovery of proteome‐informative, protein N‐terminal peptides by combined fractional diagonal chromatography (COFRADIC)

K. Gevaert, A. Staes, P. Van Damme, 2008, Proteomics.

Targeted Peptidecentric Proteomics Reveals Caspase-7 as a Substrate of the Caspase-1 Inflammasomes *S

T. Vanden Berghe, P. Vandenabeele, K. Gevaert, 2008, Molecular & Cellular Proteomics.

Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans

R. Evjenth, J. Lillehaug, T. Arnesen, 2009, Proceedings of the National Academy of Sciences.

Analysis of Protein Processing by N-terminal Proteomics Reveals Novel Species-specific Substrate Determinants of Granzyme B Orthologs *S

S. Maurer-Stroh, F. Rousseau, J. van Durme, 2009, Molecular & Cellular Proteomics.

Proteome-wide Substrate Analysis Indicates Substrate Exclusion as a Mechanism to Generate Caspase-7 Versus Caspase-3 Specificity*

J. Verspurten, P. Vandenabeele, F. Rousseau, 2009, Molecular & Cellular Proteomics.

Structure of granzyme C reveals an unusual mechanism of protease autoinhibition

J. Whisstock, J. Irving, A. Buckle, 2009, Proceedings of the National Academy of Sciences of the United States of America.

The substrate specificity profile of human granzyme A

F. Eisenhaber, S. Maurer-Stroh, K. Gevaert, 2010, Biological chemistry.

MS‐driven protease substrate degradomics

K. Gevaert, F. Impens, P. Van Damme, 2010, Proteomics.

Diagonal reverse-phase chromatography applications in peptide-centric proteomics: ahead of catalogue-omics?

K. Gevaert, L. Martens, P. Van Damme, 2005, Analytical biochemistry.

Proteome-derived Peptide Libraries Allow Detailed Analysis of the Substrate Specificities of Nα-acetyltransferases and Point to hNaa10p as the Post-translational Actin Nα-acetyltransferase*

R. Evjenth, J. Lillehaug, T. Arnesen, 2011, Molecular & Cellular Proteomics.

A la carte proteomics with an emphasis on gel‐free techniques

Lennart Martens, Francis Impens, Kris Gevaert, 2007, Proteomics.

Bacterial Genetic Engineering by Means of Recombineering for Reverse Genetics

K. Gevaert, P. Van Damme, Ursula Fels, 2020, Frontiers in Microbiology.

Establishment of Proximity-Dependent Biotinylation Approaches in Different Plant Model Systems[OPEN]

Jelle Van Leene, D. Eeckhout, G. De Jaeger, 2020, Plant Cell.

Stable isotopic labeling in proteomics

Francis Impens, Kris Gevaert, Petra Van Damme, 2008, Proteomics.

Applications of diagonal chromatography for proteome‐wide characterization of protein modifications and activity‐based analyses

K. Gevaert, F. Impens, B. Ghesquière, 2007, The FEBS journal.

Recent Advancements in Tracking Bacterial Effector Protein Translocation

D. Catteeuw, P. Van Damme, Julie Braet, 2022, Microorganisms.

REPARATION: Ribosome Profiling Assisted (Re-)Annotation of Bacterial genomes

Eivind Valen, G. Menschaert, Elvis Ndah, 2017, bioRxiv.

Proteomic Identification of Cysteine Cathepsin Substrates Shed from the Surface of Cancer Cells*

K. Gevaert, V. Turk, M. Fonović, 2015, Molecular & Cellular Proteomics.

Protein processing and other modifications analyzed by diagonal peptide chromatography.

K. Gevaert, B. Ghesquière, P. Van Damme, 2006, Biochimica et biophysica acta.

The Chaperone-Like Protein HYPK Acts Together with NatA in Cotranslational N-Terminal Acetylation and Prevention of Huntingtin Aggregation

H. Dinh, R. Evjenth, T. Arnesen, 2010, Molecular and Cellular Biology.

Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation.

S. Degroeve, T. Arnesen, K. Gevaert, 2011, Journal of proteome research.

N-terminal Acetylation Levels Are Maintained During Acetyl-CoA Deficiency in Saccharomyces cerevisiae*

T. Arnesen, K. Gevaert, F. Impens, 2018, Molecular & Cellular Proteomics.

Poly-beta-hydroxybutyrate-accumulating bacteria protect gnotobiotic Artemia franciscana from pathogenic Vibrio campbellii.

W. Verstraete, T. van de Wiele, N. Boon, 2007, FEMS microbiology ecology.

Extracellular Vesicles from Follicular and Ampullary Fluid Isolated by Density Gradient Ultracentrifugation Improve Bovine Embryo Development and Quality

A. Hendrix, A. Van Soom, P. Van Damme, 2021, International journal of molecular sciences.

Cell-Intrinsic Control of Interneuron Migration Drives Cortical Morphogenesis

Mohit H. Adhikari, L. Nguyen, N. Kessaris, 2018, Cell.

Transcriptional activation of the NF‐κB p65 subunit by mitogen‐ and stress‐activated protein kinase‐1 (MSK1)

G. Haegeman, L. Vermeulen, P. Van Damme, 2003, The EMBO journal.

Caspase-14 is required for filaggrin degradation to natural moisturizing factors in the skin.

P. Vandenabeele, S. Kežić, G. Puppels, 2011, The Journal of investigative dermatology.

Noncoding after All: Biases in Proteomics Data Do Not Explain Observed Absence of lncRNA Translation Products.

Lennart Martens, Gerben Menschaert, Kris Gevaert, 2017, Journal of proteome research.

eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs

G. Menschaert, Elvis Ndah, V. Jonckheere, 2017, Nucleic acids research.

The proteome under translational control

K. Gevaert, P. Van Damme, Daria Gawron, 2014, Proteomics.

T‐cell receptor‐induced JNK activation requires proteolytic inactivation of CYLD by MALT1

K. Gevaert, R. Beyaert, P. Van Damme, 2011, The EMBO journal.

Importance of extended protease substrate recognition motifs in steering BNIP-2 cleavage by human and mouse granzymes B

S. Maurer-Stroh, Giel Vandemoortele, K. Gevaert, 2014, BMC Biochemistry.

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

T. Arnesen, K. Gevaert, V. Jonckheere, 2022, The Journal of biological chemistry.

Abolition of stress-induced protein synthesis sensitizes leukemia cells to anthracycline-induced death.

Ø. Bruserud, J. Vandekerckhove, S. Døskeland, 2008, Blood.

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

S. Goormachtig, P. Van Damme, Joren De Ryck, 2023, Frontiers in Microbiology.

N-terminal acetylation modulates Bax targeting to mitochondria.

M. Côrte-Real, S. Manon, V. Jonckheere, 2018, The international journal of biochemistry & cell biology.

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

S. Goormachtig, P. Van Damme, Margaux De Meyer, 2020, International journal of molecular sciences.

Conservation of the Extended Substrate Specificity Profiles Among Homologous Granzymes Across Species*

Fernanda L. Sirota, S. Maurer-Stroh, K. Gevaert, 2013, Molecular & Cellular Proteomics.

Proximity Mapping of CCP6 Reveals Its Association with Centrosome Organization and Cilium Assembly

A. Candiota, F. Avilés, J. Lorenzo, 2023, International journal of molecular sciences.

Charting the N-Terminal Acetylome: A Comprehensive Map of Human NatA Substrates

P. Van Damme, 2021, International journal of molecular sciences.

Absence of N-terminal acetyltransferase diversification during evolution of eukaryotic organisms

A. Faustino, C. Cox, P. Van Damme, 2016, Scientific Reports.

N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB

Kris Gevaert, Petra Van Damme, Jesus Prieto, 2012, Proceedings of the National Academy of Sciences.

N-terminal acetylation and other functions of Nα-acetyltransferases

Kris Gevaert, Petra Van Damme, K. Gevaert, 2012, Biological chemistry.

The Human N-Alpha-Acetyltransferase 40 (hNaa40p/hNatD) Is Conserved from Yeast and N-Terminally Acetylates Histones H2A and H4

J. Lillehaug, T. Arnesen, J. Varhaug, 2011, PloS one.

Small Protein Enrichment Improves Proteomics Detection of sORF Encoded Polypeptides

P. Van Damme, Igor Fijałkowski, Marlies K. R. Peeters, 2021, Frontiers in Genetics.

NatF Contributes to an Evolutionary Shift in Protein N-Terminal Acetylation and Is Important for Normal Chromosome Segregation

T. Arnesen, K. Gevaert, P. Van Damme, 2011, PLoS genetics.

N-Terminal Acetyltransferase Naa40p Whereabouts Put into N-Terminal Proteoform Perspective

V. Jonckheere, P. Van Damme, 2021, International journal of molecular sciences.

Mechanisms of Congenital Heart Disease Caused by NAA15 Haploinsufficiency

Craig C. Benson, W. Chung, J. Seidman, 2021, Circulation research.

Degradomics Reveals That Cleavage Specificity Profiles of Caspase-2 and Effector Caspases Are Alike*

P. Vandenabeele, K. Gevaert, F. Impens, 2012, The Journal of Biological Chemistry.

Disentanglement of protease substrate repertoires

K. Gevaert, P. Van Damme, J. Vandekerckhove, 2008, Biological chemistry.

Crossbreeding effect of double-muscled cattle on in vitro embryo development and quality.

A. Van Soom, P. Van Damme, G. Opsomer, 2020, Reproductive biology.

Human and mouse granzyme M display divergent and species-specific substrate specificities.

C. Craik, K. Gevaert, N. Bovenschen, 2011, The Biochemical journal.

Probing the Efficiency of Proteolytic Events by Positional Proteomics*

K. Gevaert, P. Bird, F. Impens, 2010, Molecular & Cellular Proteomics.

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

Patrick Willems, Igor Fijalkowski, Petra Van Damme, 2020, mSystems.

Lost and found: re-searching and re-scoring proteomics data aids the discovery of bacterial proteins and improves proteome coverage

Patrick Willems, Igor Fijalkowski, Petra Van Damme, 2019, bioRxiv.

Proteogenomics in Aid of Host–Pathogen Interaction Studies: A Bacterial Perspective

Kris Gevaert, Petra Van Damme, K. Gevaert, 2017, Proteomes.

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

G. Kramer, P. Van Damme, Igor Fijałkowski, 2022, Cell reports.

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

F. Van Breusegem, Elvis Ndah, V. Jonckheere, 2022, Frontiers in Plant Science.

The Arabidopsis METACASPASE9 Degradome[C][W]

F. Van Breusegem, K. Gevaert, E. Timmerman, 2013, Plant Cell.

Dissecting apoptosis the omics way

P. Van Damme, 2013, eLife.

Establishment of Proximity-Dependent Biotinylation Approaches in Different Plant Model Systems[OPEN]

Jelle Van Leene, D. Eeckhout, G. De Jaeger, 2019, The Plant Cell.

The human platelet proteome mapped by peptide‐centric proteomics: A functional protein profile

Lennart Martens, An Staes, Kris Gevaert, 2005, Proteomics.

Big fish, little fish: N-terminal acetyltransferase Naa40p proteoforms caught in the act

V. Jonckheere, P. Van Damme, 2021, bioRxiv.

PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms*

Mathias Wilhelm, Gerben Menschaert, Bernhard Kuster, 2019, Molecular & Cellular Proteomics.

Follicular fluid during individual oocyte maturation enhances cumulus expansion and improves embryo development and quality in a dose-specific manner.

A. Van Soom, P. Van Damme, A. Raes, 2021, Theriogenology.

Caspase substrates: easily caught in deep waters?

Kris Gevaert, Petra Van Damme, Wim Declercq, 2009, Trends in biotechnology.

Capturing Salmonella SspH2 Host Targets in Virus-Like Particles

Delphine De Sutter, S. Eyckerman, V. Jonckheere, 2021, Frontiers in Medicine.

A review of COFRADIC techniques targeting protein N-terminal acetylation

K. Gevaert, A. Staes, J. Van Damme, 2009, BMC proceedings.

C-terminomics Screen for Natural Substrates of Cytosolic Carboxypeptidase 1 Reveals Processing of Acidic Protein C termini*

F. Avilés, K. Gevaert, Olivia Tort, 2014, Molecular & Cellular Proteomics.

Limitless translation limits translation

P. Van Damme, P. Damme, 2018, Nature.

Protease Substrate Profiling by N-Terminal COFRADIC.

K. Gevaert, Elisabeth Stes, F. Impens, 2017, Methods in molecular biology.

Antigenic peptides: Reviving nuclear translation.

G. Menschaert, P. Van Damme, 2013, Nature chemical biology.

Proteome-derived Peptide Libraries to Study the Substrate Specificity Profiles of Carboxypeptidases*

S. Degroeve, F. Avilés, K. Gevaert, 2013, Molecular & Cellular Proteomics.

AggA is required for aggregation and increased biofilm formation of a hyper-aggregating mutant of Shewanella oneidensis MR-1.

W. Verstraete, Jizhong Zhou, N. Boon, 2006, Microbiology.

Effect of lycopene supplementation to bovine oocytes exposed to heat shock during in vitro maturation.

Budiono, A. Van Soom, P. Van Damme, 2021, Theriogenology.

Geometric isomers of sex pheromone components do not affect attractancy of Conopomorpha cramerella in cocoa plantations

P. Van Damme, W. Vanhove, A. Zhang, 2015 .

Identification of Plant Protein-Metabolite Interactions by Limited Proteolysis-Coupled Mass Spectrometry (LiP-MS).

P. Van Damme, A. Goossens, Jhon Venegas-Molina, 2023, Methods in molecular biology.

Seeking the interspecies crosswalk for filamentous microbe effectors.

S. Goormachtig, P. Van Damme, J. Van Dingenen, 2023, Trends in plant science.

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

V. Jonckheere, P. Van Damme, Igor Fijałkowski, 2022, microLife.

Ribosome signatures aid bacterial translation initiation site identification

Eivind Valen, Elvis Ndah, V. Jonckheere, 2017, BMC Biology.

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

M. Van Montagu, K. Vandepoele, V. Jonckheere, 2023, Proceedings of the National Academy of Sciences of the United States of America.

Tracking the sources of psychrotrophic bacteria contaminating chicken cuts during processing.

F. Devlieghere, P. Van Damme, M. Cnockaert, 2018, Food microbiology.

Preparation of Arabidopsis thaliana seedling proteomes for identifying metacaspase substrates by N-terminal COFRADIC.

F. Van Breusegem, K. Gevaert, P. Van Damme, 2014, Methods in molecular biology.

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

K. Gevaert, P. Van Damme, P. Damme, 2023, bioRxiv.

PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms

B. Kuster, Mathias Wilhelm, Siegfried Gessulat, 2019, Molecular & Cellular Proteomics.

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

G. van Loo, A. Wullaert, V. Jonckheere, 2023, Cell death & disease.

Protein processing characterized by a gel-free proteomics approach.

K. Gevaert, F. Impens, P. Van Damme, 2008, Methods in molecular biology.

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

P. Willems, K. Gevaert, A. Staes, 2021, Journal of proteome research.

A review of COFRADIC techniques targeting protein N-terminal acetylation

K. Gevaert, A. Staes, P. Van Damme, 2009, BMC proceedings.

Ablation of elongation factor 2 kinase enhances heat-shock protein 90 chaperone expression and protects cells under proteotoxic stress

C. Proud, P. Van Damme, J. Xie 谢, 2019, The Journal of Biological Chemistry.

Caspase substrates: easily caught in deep waters?

T. Vanden Berghe, P. Vandenabeele, K. Gevaert, 2009, Trends in biotechnology.