Research Explorer

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Project

Proteomics-derived epitopes for dramatically improved anticancer and antibacterial vaccine development

Outputs and Outcomes

Publications

MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0

Louise M. BuurArthur DeclercqMarina StroblRobbin BouwmeesterSven DegroeveLennart MartensViktoria DorferRalf Gabriels

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Considerations on the design of lipid-based mRNA vaccines against cancer

Sofie MeulewaeterYao ZhangAbishek WadhwaKevin FoxIne LentackerKenneth W. HarderPieter R. CullisStefaan De SmedtMiffy H.Y. ChengRein Verbeke

A1 Journal Article in JOURNAL OF MOLECULAR BIOLOGY

msqrob2PTM : differential abundance and differential usage analysis of MS-based proteomics data at the post-translational modification and peptidoform level

Nina DemeulemeesterMarie GébelinLucas Caldi GomesPaul LingorChristine CarapitoLennart MartensLieven Clement

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Ionmob : a Python package for prediction of peptide collisional cross-section values

David TeschnerDavid Gomez-ZepedaArthur DeclercqMateusz K ŁąckiSeymen AvciKonstantin BobUte DistlerThomas MichnaLennart MartensStefan TenzerAndreas HildebrandtJonathan Wren et al.

A1 Journal Article in BIOINFORMATICS

Updated MS²PIP web server supports cutting-edge proteomics applications

Arthur DeclercqRobbin BouwmeesterCristina ChivaEduard SabidoAurelie HirschlerChristine CarapitoLennart MartensSven DegroeveRalf Gabriels

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Nanobody-mediated SPECT/CT imaging reveals the spatiotemporal expression of programmed death-ligand 1 in response to a CD8+ T cell and iNKT cell activating mRNA vaccine

Thomas ErtveldtSofie MeulewaeterYannick De VlaeminckOscar OlarteKatrijn BroosSerge Van CalenberghStephanie BourgeoisJoke DeprezYves HeremansCleo GoyvaertsWillem StaelsStefaan De SmedtHeleen DewitteNick DevoogdtMarleen KeyaertsRein VerbekeKurt BarbéIne LentackerKarine Breckpot et al.

A1 Journal Article in THERANOSTICS

lesSDRF is more : maximizing the value of proteomics data through streamlined metadata annotation

Tine ClaeysTim Van Den BosscheYasset Perez-RiverolKris GevaertJuan Antonio VizcaínoLennart Martens

A1 Journal Article in NATURE COMMUNICATIONS

Transport by circulating myeloid cells drives liposomal accumulation in inflamed synovium

Joke DeprezRein VerbekeSofie MeulewaeterIlke AernoutHeleen DewitteTine DecruyJulie CoudenysJulie Van DuyseGert Van IsterdaelDan PeerRoy van der MeelStefaan De SmedtPeggy JacquesDirk ElewautIne Lentacker et al.

A1 Journal Article in NATURE NANOTECHNOLOGY

Single-cell profiling identifies a novel human polyclonal unconventional T cell lineage

Lore BillietLaurenz De CockGuillem Sanchez SanchezRupert MayerGlenn GoetgelukStijn De MunterMelissa PilleJoline IngelsHanne JansenKarin WeeningEva PascalKillian RaesSarah BonteTessa KerreNiels VandammeRuth SeurinckJana RoelsMarieke LavaertFilip Van NieuwerburghGeorges LeclercqTom TaghonFrancis ImpensBjörn MentenDavid VermijlenBart Vandekerckhove et al.

A1 Journal Article in JOURNAL OF EXPERIMENTAL MEDICINE

Continuous freeze-drying of messenger RNA lipid nanoparticles enables storage at higher temperatures

Sofie MeulewaeterGust NuyttenMiffy H.Y. ChengStefaan De SmedtPieter R. CullisThomas De BeerIne LentackerRein Verbeke

A1 Journal Article in JOURNAL OF CONTROLLED RELEASE

Quality control for the target decoy approach for peptide identification

Elke DebrieMilan MalfaitRalf GabrielsArthur DeclercqAdriaan StickerLennart MartensLieven Clement

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Machine learning on large-scale proteomics data identifies tissue and cell-type specific proteins

Tine ClaeysMaxime MenuRobbin BouwmeesterKris GevaertLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Cells responding to closely related cholesterol-dependent cytolysins release extracellular vesicles with a common proteomic content including membrane repair proteins

S AlvesJM PereiraRupert MayerADA GonçalvesFrancis ImpensD CabanesS Sousa

A1 Journal Article in TOXINS

psm_utils : a high-level python API for parsing and handling peptide-spectrum matches and proteomics search results

Ralf GabrielsArthur DeclercqRobbin BouwmeesterSven DegroeveLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Innate immune mechanisms of mRNA vaccines

Rein VerbekeMichael J. HoganKarin LoréNorbert Pardi

A1 Journal Article in IMMUNITY

An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia

Lien ProvezBart Van PuyveldeLaura CorveleynNina DemeulemeesterSigrid VerhelstBeatrice LintermansSimon DaledJuliette RoelsLieven ClementLennart MartensDieter DeforcePieter Van VlierbergheMaarten Dhaenens et al.

A1 Journal Article in SCIENTIFIC DATA

Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes

Rupert MayerRein VerbekeCaroline AsselmanIlke AernoutAdillah GulDenzel EggermontKatie BoucherFabien Henri TheryTeresa MaiaHans DemolRalf GabrielsLennart MartensChristophe BécavinStefaan De SmedtBart VandekerckhoveIne LentackerFrancis Impens et al.

A1 Journal Article in NATURE COMMUNICATIONS

Sensitive and specific spectral library searching with CompOmics Spectral library Searching tool and Percolator

Genet Abay ShiferawRalf GabrielsRobbin BouwmeesterTim Van Den BosscheElien VandermarliereLennart MartensPieter-Jan Volders

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Moyamoya disease emerging as an immune-related angiopathy

Caroline AsselmanDimitri HemelsoetDenzel EggermontBart DermautFrancis Impens

A1 Journal Article in TRENDS IN MOLECULAR MEDICINE

MS2Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

Arthur DeclercqRobbin BouwmeesterAurélie HirschlerChristine CarapitoSven DegroeveLennart MartensRalf Gabriels

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Small-scale manufacturing of neoantigen-encoding messenger RNA for early-phase clinical trials

Joline IngelsLaurenz De CockRupert MayerPam DevrekerKarin WeeningKelly HeynsNele LootensSaskia De SmetMarieke BrusseelStijn De MunterMelissa PilleLore BillietGlenn GoetgelukSarah BonteHanne JansenSandra Van LintGeorges LeclercqTom TaghonBjörn MentenKarim VermaelenFrancis ImpensBart Vandekerckhove et al.

A1 Journal Article in CYTOTHERAPY

Nanoparticle mediated targeting of toll-like receptors to treat colorectal cancer

Ragna HaegebaertMaxime KempersWim CeelenIne LentackerKatrien Remaut

A1 Journal Article in EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS

DeepLC can predict retention times for peptides that carry as-yet unseen modifications

Robbin BouwmeesterRalf GabrielsNiels HulstaertLennart MartensSven Degroeve

A1 Journal Article in NATURE METHODS

Strategies for controlling the innate immune activity of conventional and self-amplifying mRNA therapeutics : getting the message across

An-Katrien MinnaertHelena VanlucheneRein VerbekeIne LentackerStefaan De SmedtKoen RaemdonckNiek SandersKatrien Remaut

A1 Journal Article in ADVANCED DRUG DELIVERY REVIEWS