Willems Patrick

Willems Patrick - Postdoctoral fellow
Joined the group in 2019

Patrick Willems obtained his master degree at Ghent University after plant studying cold stress signaling in plants during six months in the Vaughan Hurry lab in Umeå (Sweden). Afterwards, he continued studying plant abiotic stress signaling during his PhD in the oxidative stress signaling group of Frank Van Breusegem in collaboration with the proteomics group of Kris Gevaert. This led to multiple first-author papers and several co-authorships, mostly entailing integrative –OMICS analysis of transcriptome, proteome or other datasets. As a postdoctoral researcher, he was shortly active in the proteogenomic annotation of microbial species. More recently, he is focusing on studying post-translational modifications (PTMs) in plants. Recently published work on this topic incudes the characterization of S-sulfenylation at a site-specific level in Arabidopsis and the development of an integrative plant PTM database, ‘The Plant PTM Viewer’. The bridging theme in his research is the integration and interpretation of large (multi-)omics data to make new discoveries or help addressing specific biological research questions.

43. Scywalker: scalable end-to-end data analysis workflow for nanopore single-cell transcriptome sequencing

Peter De Rijk, Tijs Watzeels, Fahri Küçükali, Jasper Van Dongen, Júlia Faura, Patrick Willems, Lara De Deyn, Lena Duchateau, Carolin Grones, Thomas Eekhout, Tim De Pooter, Geert Joris, Stephane Rombauts, Bert De Rybel, Rosa Rademakers, Frank Van Breusegem, Mojca Strazisar, Kristel Sleegers, Wouter De Coster

(2024) -

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42. Mutation of Arabidopsis SME1 and Sm core assembly improves oxidative stress resilience

Patrick Willems, Valerie Van Ruyskensvelde, Takanori Maruta, Robin Pottie, Álvaro D. Fernández-Fernández, Jarne Pauwels, Matthew A. Hannah, Kris Gevaert, Frank Van Breusegem, Katrien Van der Kelen

(2023) - Free Radical Biology and Medicine

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41. Functionally annotating cysteine disulfides and metal binding sites in the plant kingdom using AlphaFold2 predicted structures

Patrick Willems, Jingjing Huang, Joris Messens, Frank Van Breusegem

(2023) - Free Radical Biology and Medicine

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40. Cysteine thiol-based post-translational modification: What do we know about transcription factors?

Heng Zhou, Jingjing Huang, Patrick Willems, Frank Van Breusegem, Yanjie Xie

(2023) - Trends in Plant Science

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39. CysQuant: simultaneous quantification of cysteine oxidation and protein abundance using data dependent or independent acquisition mass spectrometry

Jingjing Huang, An Staes, Francis Impens, Vadim Demichev, Frank Van Breusegem, Kris Gevaert, Patrick Willems

(2023) -

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38. Interactome of Arabidopsis ATG5 Suggests Functions beyond Autophagy

Pernilla H. Elander, Sanjana Holla, Igor Sabljić, Emilio Gutierrez-Beltran, Patrick Willems, Peter V. Bozhkov, Elena A. Minina

(2023) - International Journal of Molecular Sciences

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

Fels U, Willems P, De Meyer M, Gevaert K, Van Damme P

(2023) - PLoS pathogens

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36. CysQuant: Simultaneous quantification of cysteine oxidation and protein abundance using data dependent or independent acquisition mass spectrometry

Jingjing Huang, An Staes, Francis Impens, Vadim Demichev, Frank Van Breusegem, Kris Gevaert, Patrick Willems

(2023) - Redox Biology

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

No contributors listed

(2022) - Frontiers in Plant Science

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34. Editorial: Plant protein termini: Their generation, modification and function

Patrick Willems, Patrick Willems, Pitter F. Huesgen, Iris Finkemeier, Emmanuelle Graciet, Thierry Meinnel, Frank Van Breusegem

(2022) - Frontiers in Plant Science

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33. Exploring Posttranslational Modifications with the Plant PTM Viewer.

Patrick Willems, Willems P

(2022) - Methods in molecular biology (Clifton, N.J.)

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32. Analysis of ROS-Triggered Changes in the Transcriptome.

Patrick Willems, Willems P

(2022) - Methods in molecular biology (Clifton, N.J.)

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31. Mutation of Arabidopsis SME1 and Sm core assembly improves oxidative stress resilience

Patrick Willems, Valerie Van Ruyskensvelde, Takanori Maruta, Robin Pottie, Álvaro Daniel Fernández-Fernández, Jarne Pauwels, Matthew A. Hannah, Kris Gevaert, Frank Van Breusegem, Katrien Van der Kelen

(2022) -

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

No contributors listed

(2022) - microLife

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

Patrick Willems, Ursula Fels, An Staes, Kris Gevaert, Petra Van Damme

(2021) - Journal of Proteome Research

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28. Phototropin 1 and 2 Influence Photosynthesis, UV-C Induced Photooxidative Stress Responses, and Cell Death

Anna Rusaczonek, Weronika Czarnocka, Patrick Willems, Marzena Sujkowska-Rybkowska, Frank Van Breusegem, Stanisław Karpiński

(2021) - Cells

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27. Contemporary proteomic strategies for cysteine redoxome profiling

Patrick Willems, Frank Van Breusegem, Jingjing Huang

(2021) - Plant Physiology

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26. The Arabidopsis mediator complex subunit 8 regulates oxidative stress responses

Huaming He, Jordi Denecker, Katrien Van Der Kelen, Patrick Willems, Robin Pottie, Su Yin Phua, Matthew A Hannah, Didier Vertommen, Frank Van Breusegem, Amna Mhamdi

(2021) - The Plant Cell

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25. Novel Role of JAC1 in Influencing Photosynthesis, Stomatal Conductance, and Photooxidative Stress Signalling Pathway in Arabidopsis thaliana

No contributors listed

(2020) - Frontiers in Plant Science

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24. Identification of Sulfenylated Cysteines in Arabidopsis thaliana Proteins Using a Disulfide-Linked Peptide Reporter.

No contributors listed

(2020) - Frontiers in plant science

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

No contributors listed

(2020) - FEMS Microbiology Reviews

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

No contributors listed

(2020) - mSystems

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21. Chemical Genetics Approach Identifies Abnormal Inflorescence Meristem 1 as a Putative Target of a Novel Sulfonamide That Protects Catalase2-Deficient Arabidopsis against Photorespiratory Stress

Tom van der Meer, Arno Verlee, Patrick Willems, Francis Impens, Kris Gevaert, Christa Testerink, Christian V. Stevens, Frank Van Breusegem, Pavel Kerchev

(2020) - Cells

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20. Damage on plants activates Ca 2+ -dependent metacaspases for release of immunomodulatory peptides

Tim Hander, Álvaro D. Fernández-Fernández, Robert P. Kumpf, Patrick Willems, Hendrik Schatowitz, Debbie Rombaut, An Staes, Jonah Nolf, Robin Pottie, Panfeng Yao, Amanda Gonçalves, Benjamin Pavie, Thomas Boller, Kris Gevaert, Frank Van Breusegem, Sebastian Bartels, Simon Stael

(2019) - Science

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19. The Plant PTM Viewer, a central resource for exploring plant protein modifications.

No contributors listed

(2019) - The Plant journal : for cell and molecular biology

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18. Extracellular peptide Kratos restricts cell death during vascular development and stress in Arabidopsis.

Escamez S, Stael S, Vainonen J, Willems P, Jin H, Kimura S, Van Breusegem F, Gevaert K, Wrzaczek M, Tuominen H

(2019) - Journal of experimental botany

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17. Mining for protein S-sulfenylation in Arabidopsis uncovers redox-sensitive sites

No contributors listed

(2019) - Proceedings of the National Academy of Sciences

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16. Pathways crossing mammalian and plant sulfenomic landscapes.

Huang J, Willems P, Van Breusegem F, Messens J

(2018) - Free radical biology & medicine

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15. In vivo detection of protein cysteine sulfenylation in plastids

Barbara De Smet, Patrick Willems, Alvaro D. Fernandez-Fernandez, Saleh Alseekh, Alisdair R. Fernie, Joris Messens, Frank Van Breusegem

(2018) - The Plant Journal

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14. N-terminomics Proteogenomics

No contributors listed

(2017) -

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13. The dual role of LESION SIMULATING DISEASE 1 as a condition-dependent scaffold protein and transcription regulator.

No contributors listed

(2017) - Plant, cell & environment

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12. Measurement of Transcripts Associated with Photorespiration and Related Redox Signaling.

Patrick Willems, Amna Mhamdi, Pavel Kerchev, Willems P, Noctor G, Frank Van Breusegem

(2017) - Methods in molecular biology (Clifton, N.J.)

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

Patrick Willems, Elvis Ndah, Veronique Jonckheere, Simon Stael, Adriaan Sticker, Lennart Martens, Frank Van Breusegem, Kris Gevaert, Petra Van Damme

(2017) - Molecular & Cellular Proteomics

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10. The Transcription Factor MYB29 Is a Regulator of ALTERNATIVE OXIDASE1a

Xinhua Zhang, Aneta Ivanova, Klaas Vandepoele, Jordan Radomiljac, Jan Van de Velde, Oliver Berkowitz, Patrick Willems, Yue Xu, Sophia Ng, Olivier Van Aken, Owen Duncan, Botao Zhang, Veronique Storme, Kai Xun Chan, Dries Vaneechoutte, Barry James Pogson, Frank Van Breusegem, James Whelan, Inge De Clercq

(2017) - Plant Physiology

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9. The ROS Wheel: Refining ROS Transcriptional Footprints

Patrick Willems, Amna Mhamdi, Simon Stael, Veronique Storme, Pavel Kerchev, Graham Noctor, Kris Gevaert, Frank Van Breusegem

(2016) - Plant Physiology

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8. The ROS Wheel: refining ROS transcriptional footprints in Arabidopsis.

Willems P, Mhamdi A, Simon S, Storme V, Kerchev PI, Noctor G, Gevaert K, Van Breusegem F

(2016) -

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7. Lack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient Arabidopsis.

Kerchev PI, Waszczak C, Lewandowska A, Willems P, Shapiguzov A, Li Z, Alseekh S, Mühlenbock P, Hoebrichts F, Huang JJ, Van Der Kelen K, Kangasjärvi J, Fernie AR, De Smet R, Van de Peer Y, Messens J, Van Breusegem F

(2016) -

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6. SHORT-ROOT Deficiency Alleviates the Cell Death Phenotype of the Arabidopsis catalase2 Mutant under Photorespiration-Promoting Conditions

Cezary Waszczak, Pavel I. Kerchev, Per Mühlenbock, Frank A. Hoeberichts, Katrien Van Der Kelen, Amna Mhamdi, Patrick Willems, Jordi Denecker, Robert P. Kumpf, Graham Noctor, Joris Messens, Frank Van Breusegem

(2016) - The Plant Cell

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5. Lack of GLYCOLATE OXIDASE1, but Not GLYCOLATE OXIDASE2, Attenuates the Photorespiratory Phenotype of CATALASE2-Deficient Arabidopsis

Pavel Kerchev, Cezary Waszczak, Aleksandra Lewandowska, Patrick Willems, Alexey Shapiguzov, Zhen Li, Saleh Alseekh, Per Mühlenbock, Frank A. Hoeberichts, Jingjing Huang, Katrien Van Der Kelen, Jaakko Kangasjärvi, Alisdair R. Fernie, Riet De Smet, Yves Van de Peer, Joris Messens, Frank Van Breusegem

(2016) - Plant Physiology

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4. Protein Methionine Sulfoxide Dynamics in Arabidopsis thaliana under Oxidative Stress.

Jacques S, Ghesquière B, De Bock PJ, Demol H, Wahni K, Willems P, Messens J, Van Breusegem F, Gevaert K

(2015) -

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3. Plant innate immunity--sunny side up?

Stael S, Kmiecik P, Willems P, Van Der Kelen K, Coll NS, Teige M, Van Breusegem F

(2015) -

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2. Selection for Improved Energy Use Efficiency and Drought Tolerance in Canola Results in Distinct Transcriptome and Epigenome Changes

Aurine Verkest, Marina Byzova, Cindy Martens, Patrick Willems, Tom Verwulgen, Bram Slabbinck, Debbie Rombaut, Jan Van de Velde, Klaas Vandepoele, Evi Standaert, Marrit Peeters, Mieke Van Lijsebettens, Frank Van Breusegem, Marc De Block

(2015) - Plant Physiology

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1. Anterograde and retrograde regulation of nuclear genes encoding mitochondrial proteins during growth, development, and stress.

Ng S, De Clercq I, Van Aken O, Law SR, Ivanova A, Willems P, Giraud E, Van Breusegem F, Whelan J

(2014) -

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