Research Explorer

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Researcher

Patrick Willems

Awards & Distinctions

45 Results

2025

Maximizing immunopeptidomics-based bacterial epitope discovery by multiple search engines and rescoring

Patrick WillemsFabien Henri TheryLaura Van MoortelMargaux De MeyerAn StaesAdillah GulLyudmila KovalchukeArthur DeclercqRobbe DevreeseRobbin Bouwmeester et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2024

Immunopeptidomics mapping of Listeria monocytogenes T cell epitopes in mice

Adillah GulLecia L. PewePatrick WillemsRupert MayerFabien Henri TheryCaroline AsselmanIlke AernoutRein VerbekeDenzel EggermontLaura Van Moortel et al.

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Scywalker : scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing

Peter De RijkTijs WatzeelsFahri KüçükaliJasper Van DongenJúlia FauraPatrick WillemsLara De DeynLena DuchateauCarolin SeyfferthThomas Eekhout et al.

A1 Journal Article in BIOINFORMATICS

TermineR : extracting information on endogenous proteolytic processing from shotgun proteomics data

Miguel Cosenza‐ContrerasAdrianna SeredynskaDaniel VogeleNiko PinterEva BrombacherRuth Fiestas CuetoThien‐Ly Julia DinhPatrick BernhardManuel RoggJunwei Liu et al.

A1 Journal Article in PROTEOMICS

The Plant PTM Viewer 2.0 : in-depth exploration of plant protein modification landscapes

Patrick WillemsLieven SterckAvilien DardJingjing HuangIve De SmetKris GevaertFrank Van Breusegem

A1 Journal Article in JOURNAL OF EXPERIMENTAL BOTANY

2023

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

Jingjing HuangAn StaesFrancis ImpensVadim DemichevFrank Van BreusegemKris GevaertPatrick Willems

A1 Journal Article in REDOX BIOLOGY

Cysteine thiol–based post-translational modification : what do we know about transcription factors?

Heng ZhouJingjing HuangPatrick WillemsFrank Van BreusegemYanjie Xie

A1 Journal Article in TRENDS IN PLANT SCIENCE

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

Patrick WillemsJingjing HuangJoris MessensFrank Van Breusegem

A1 Journal Article in FREE RADICAL BIOLOGY AND MEDICINE

Interactome of Arabidopsis ATG5 suggests functions beyond autophagy

Pernilla H. ElanderSanjana HollaIgor SabljićEmilio Gutierrez-BeltranPatrick WillemsPeter V. BozhkovElena A. Minina

A1 Journal Article in INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

Patrick WillemsValerie Van RuyskensveldeTakanori MarutaRobin PottieÁlvaro Daniel Fernández FernándezJarne PauwelsMatthew A. HannahKris GevaertFrank Van BreusegemKatrien Van Der Kelen

A1 Journal Article in FREE RADICAL BIOLOGY AND MEDICINE

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

Ursula FelsPatrick WillemsMargaux De MeyerKris GevaertPetra Van Damme

A1 Journal Article in PLOS PATHOGENS

2022

Analysis of ROS-triggered changes in the transcriptome

Patrick Willems

Bookchapter in Reactive oxygen species in plants : methods and protocols

Cysteine-based redox switches in plant stress response

Jingjing HuangPatrick WillemsZeya ChenLindsy De VeirmanFrank Van Breusegem

Editorial : plant protein termini : their generation, modification and function

Patrick WillemsPitter F. HuesgenIris FinkemeierEmmanuelle GracietThierry MeinnelFrank Van Breusegem

Editorial material

Exploring posttranslational modifications with the Plant PTM Viewer

Patrick Willems

Bookchapter in Plant proteases and plant cell death : methods and protocols

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

Igor FijalkowskiPatrick WillemsVeronique JonckheereLaure SimoensPetra Van Damme

A2 Journal Article in MICROLIFE

To new beginnings : riboproteogenomics discovery of N-terminal proteoforms in Arabidopsis thaliana

Patrick WillemsElvis NdahVeronique JonckheereFrank Van BreusegemPetra Van Damme

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

2021

Contemporary proteomic strategies for cysteine redoxome profiling

Patrick WillemsFrank Van BreusegemJingjing Huang

A1 Journal Article in PLANT PHYSIOLOGY

Phototropin 1 and 2 influence photosynthesis, UV-C induced photooxidative stress responses, and cell death

Anna RusaczonekWeronika CzarnockaPatrick WillemsMarzena Sujkowska-RybkowskaFrank Van BreusegemStanisław Karpiński

A1 Journal Article in CELLS

The Arabidopsis mediator complex subunit 8 regulates oxidative stress responses

Huaming HeJordi DeneckerKatrien Van Der KelenPatrick WillemsRobin PottieSu Yin PhuaMatthew A. HannahDidier VertommenFrank Van BreusegemAmna M'Hamdi

A1 Journal Article in PLANT CELL

Use of hybrid data-dependent and -independent acquisition spectral libraries empowers dual-proteome profiling

Patrick WillemsUrsula FelsAn StaesKris GevaertPetra Van Damme

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2020

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

Daria FijalkowskaIgor FijalkowskiPatrick WillemsPetra Van Damme

A1 Journal Article in FEMS MICROBIOLOGY REVIEWS

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 MeerArno VerleePatrick WillemsFrancis ImpensKris GevaertChrista TesterinkChristian StevensFrank Van BreusegemPavel Kerchev

A1 Journal Article in CELLS

Identification of sulfenylated cysteines in Arabidopsis thaliana proteins using a disulfide-linked peptide reporter

Bo WeiPatrick WillemsJingjing HuangCaiping TianJing YangJoris MessensFrank Van Breusegem

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

Lost and found : re-searching and re-scoring proteomics data aids genome annotation and improves proteome coverage

Patrick WillemsIgor FijalkowskiPetra Van Damme

A1 Journal Article in MSYSTEMS

Novel role of JAC1 in influencing photosynthesis, stomatal conductance, and photooxidative stress signalling pathway in Arabidopsis thaliana

Weronika CzarnockaAnna RusaczonekPatrick WillemsMarzena Sujkowska-RybkowskaFrank Van BreusegemStanisław Karpiński

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

2019

Damage on plants activates Ca2+-dependent metacaspases for release of immunomodulatory peptides

Tim HanderÁlvaro Daniel Fernández FernándezRobert KumpfPatrick WillemsHendrik SchatowitzDebbie RombautAn StaesJonah NolfRobin PottiePanfeng Yao et al.

A1 Journal Article in SCIENCE

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

Sacha EscamezSimon StaelJulia P VainonenPatrick WillemsHuiting JinSachie KimuraFrank Van BreusegemKris GevaertMichael WrzaczekHannele Tuominen

A1 Journal Article in JOURNAL OF EXPERIMENTAL BOTANY

In vivo detection of protein cysteine sulfenylation in plastids

Barbara De SmetPatrick WillemsÁlvaro Daniel Fernández FernándezSaleh AlseekhAlisdair R FernieJoris MessensFrank Van Breusegem

A1 Journal Article in PLANT JOURNAL

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

Jingjing HuangPatrick WillemsBo WeiCaiping TianRenan B FerreiraNandita BodraSantiago Agustín Martínez GacheKhadija WahniKeke LiuDidier Vertommen et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Patrick WillemsAlison HorneThomas Van ParysSofie GoormachtigIve De SmetAlexander BotzkiFrank Van BreusegemKris Gevaert

A1 Journal Article in PLANT JOURNAL

2018

Pathways crossing mammalian and plant sulfenomic landscapes

Jingjing HuangPatrick WillemsFrank Van BreusegemJoris Messens

A1 Journal Article in FREE RADICAL BIOLOGY AND MEDICINE

Plant redox biology with an -omics perspective

Patrick WillemsFrank Van BreusegemKris Gevaert

2017

Measurement of transcripts associated with photorespiration and related redox signaling

Amna M'HamdiPavel KerchevPatrick WillemsGraham NoctorFrank Van Breusegem

Bookchapter in Photorespiration : methods and protocols

N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana

Patrick WillemsElvis NdahVeronique JonckheereSimon StaelAdriaan StickerLennart MartensFrank Van BreusegemKris GevaertPetra Van Damme

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

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

Weronika CzarnockaKatrien Van Der KelenPatrick WillemsMagdalena Szechynska-HebdaSara Shahnejat-BushehriSalma BalazadehAnna RusaczonekBernd Mueller-RoeberFrank Van BreusegemStanislaw Karpiński

A1 Journal Article in PLANT CELL AND ENVIRONMENT

The transcription factor MYB29 is a regulator of ALTERNATIVE OXIDASE1a

Xinhua ZhangAneta IvanovaKlaas VandepoeleJordan RadomiljacJan Van de VeldeOliver BerkowitzPatrick WillemsYue XuSophia NgOlivier Van Aken et al.

A1 Journal Article in PLANT PHYSIOLOGY

2016

Lack of GLYCOLATE OXIDASE1, but not GLYCOLATE OXIDASE2, attenuates the photorespiratory phenotype of CATALASE2-deficient Arabidopsis

Pavel KerchevCezary WaszczakAleksandra LewandowskaPatrick WillemsAlexey ShapiguzovZhen LiSaleh AlseekhPer MühlenbockFrank HoeberichtsJingjing Huang et al.

A1 Journal Article in PLANT PHYSIOLOGY

SHORT-ROOT deficiency alleviates the cell death phenotype of the Arabidopsis catalase2 mutant under photorespiration-promoting conditions

Cezary WaszczakPavel KerchevPer MühlenbockFrank HoeberichtsKatrien Van Der KelenAmna MhamdiPatrick WillemsJordi DeneckerRobert KumpfGraham Noctor et al.

A1 Journal Article in PLANT CELL

The ROS wheel: refining ROS transcriptional footprints

Patrick WillemsAmna M'HamdiSimon StaelVeronique StormePavel KerchevGraham NoctorKris GevaertFrank Van Breusegem

A1 Journal Article in PLANT PHYSIOLOGY

2015

Plant innate immunity: sunny side up?

Simon StaelPrzemyslaw KmiecikPatrick WillemsKatrien Van Der KelenNuria S CollMarkus TeigeFrank Van Breusegem

A1 Journal Article in TRENDS IN PLANT SCIENCE

Protein methionine sulfoxide dynamics in Arabidopsis thaliana under oxidative stress

Silke JacquesBart GhesquièrePieter-Jan De BockHans DemolKhadija WahniPatrick WillemsJoris MessensFrank Van BreusegemKris Gevaert

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Selection for improved energy use efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes

Aurine VerkestMarina ByzovaCindy MartensPatrick WillemsTom VerwulgenBram SlabbinckDebbie RombautJan Van de VeldeKlaas VandepoeleEvi Standaert et al.

A1 Journal Article in PLANT PHYSIOLOGY

2014

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

Sophia NgInge De ClercqOlivier Van AkenSimon R LawAneta IvanovaPatrick WillemsEstelle GiraudFrank Van BreusegemJames Whelan

A1 Journal Article in MOLECULAR PLANT

2013

Mechanics of overground accelerated running vs. running on an accelerated treadmill

Ine Van CaekenbergheVeerle SegersPatrick WillemsThierry GosseyePeter AertsDirk De Clercq

A1 Journal Article in GAIT & POSTURE