Publications
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Selected publications
To showcase the world-class scientific research of the VIB Nucleomics Core, you can discover their scientific papers in more detail.
Counting more than beans : A different take on key performance indicators for core facilities.
Ghazavi, F., Botzki, A., Derveaux, S., Durinx, C., Van Isterdael, G., Van Minnebruggen, G., & Lippens, S. (2026). Counting more than beans : A different take on key performance indicators for core facilities. EMBO reports, 27(9), 2156–2159.
The complexome contextualizes proteomics data to fingerprint biological states and highlight perturbed functional modules in disease
Guharoy, M., Adant, I., Bird, M., Botzki, A., Collier, J., Dehairs, J., Derveaux, S., Devos, S., Goeminne, G., Impens, F., Jáñez Pedrayes, A., Janky, R., Maes, R., Magalhães, P., Maia, T. M., Meersseman, W., Rymen, D., Swinnen, J. V., Van Haver, D., Verdegem, D., … Ghesquiere, B. (2026). The complexome contextualizes proteomics data to fingerprint biological states and highlight perturbed functional modules in disease. NPJ systems biology and applications
Soma-localized Rab39 inhibits synaptic autophagy by controlling trafficking of Atg9 vesicles
Kilic, A., Ozturan, G., Vandekerkhove, D., Kuenen, S., Swerts, J., Muñoz Pedrazo, E., Calatayud Aristoy, C., Escamilla Ayala, A., Corthout, N., Hernández Varas, P., Plaisance, S., Uytterhoeven, V., Nachman, E., & Verstreken, P. (2025). Soma-localized Rab39 inhibits synaptic autophagy by controlling trafficking of Atg9 vesicles. The EMBO journal, 44(20), 5662–5693.
Sporadic ALS hiPSC-derived motor neurons show axonal defects linked to altered axon guidance pathways.
Ye L, Dittlau KS, Sicart A, Janky R, Van Damme P, Van Den Bosch L. (2025) Sporadic ALS hiPSC-derived motor neurons show axonal defects linked to altered axon guidance pathways. Neurobiol Dis. 2025 Mar;206:106815. . Epub 2025 Jan 28. PMID: 39884586
An Improved Chromosome-scale Genome Assembly and Population Genetics resource for Populus tremula.
Robinson, K. M., Schiffthaler, B., Liu, H., Rydman, S. M., Rendón-Anaya, M., Kalman, T. A., Kumar, V., Canovi, C., Bernhardsson, C., Delhomme, N., Jenkins, J., Wang, J., Mähler, N., Richau, K. H., Stokes, V., A'Hara, S., Cottrell, J., Coeck, K., Diels, T., Vandepoele, K., Mannapperuma C., Park E.J., Plaisance S., Jansson S., Ingvarsson P.K., Street, N. R. (2024). An Improved Chromosome-scale Genome Assembly and Population Genetics resource for Populus tremula. Physiologia plantarum, 176(5), e14511.
The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars.
Salojärvi J, Rambani A, Yu Z, Guyot R, Strickler S, Lepelley M, Wang C, Rajaraman S, Rastas P, Zheng C, Muñoz DS, Meidanis J, Paschoal AR, Bawin Y, Krabbenhoft TJ, Wang ZQ, Fleck SJ, Aussel R, Bellanger L, Charpagne A, Fournier C, Kassam M, Lefebvre G, Métairon S, Moine D, Rigoreau M, Stolte J, Hamon P, Couturon E, Tranchant-Dubreuil C, Mukherjee M, Lan T, Engelhardt J, Stadler P, Correia De Lemos SM, Suzuki SI, Sumirat U, Wai CM, Dauchot N, Orozco-Arias S, Garavito A, Kiwuka C, Musoli P, Nalukenge A, Guichoux E, Reinout H, Smit M, Carretero-Paulet L, Filho OG, Braghini MT, Padilha L, Sera GH, Ruttink T, Henry R, Marraccini P, Van de Peer Y, Andrade A, Domingues D, Giuliano G, Mueller L, Pereira LF, Plaisance S, Poncet V, Rombauts S, Sankoff D, Albert VA, Crouzillat D, de Kochko A, Descombes P. The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nat Genet. 2024 Apr;56(4):721-731. Epub 2024 Apr 15. PMID: 38622339; PMCID: PMC11018527.
A bispecific Clec9A-PD-L1 targeted type I interferon profoundly reshapes the tumor microenvironment towards an antitumor state.
Van Lint, S., Van Parys, A., Van Den Eeckhout, B., Vandamme, N., Plaisance, S., Verhee, A., Catteeuw, D., Rogge, E., De Geest, J., Vanderroost, N., Roels, J., Saeys, Y., Uzé, G., Kley, N., Cauwels, A., & Tavernier, J. (2023). A bispecific Clec9A-PD-L1 targeted type I interferon profoundly reshapes the tumor microenvironment towards an antitumor state. Molecular cancer, 22(1), 191.
FUS-ALS hiPSC-derived astrocytes impair human motor units through both gain-of-toxicity and loss-of-support mechanisms
Stoklund Dittlau, K., Terrie, L., Baatsen, P., Kerstens, A., De Swert, L., Janky, R., Corthout, N., Masrori, P., Van Damme, P., Hyttel, P., Meyer, M., Thorrez, L., Freude, K. and Van Den Bosch, L. (2023) FUS-ALS hiPSC-derived astrocytes impair human motor units through both gain-of-toxicity and loss-of-support mechanisms. Mol Neurodegeneration 18, 5 (2023).
The bacterial quorum sensing peptide iAM373 is a novel inducer of sarcopenia
De Spiegeleer, A., Wynendaele, E., Descamps, A., Debunne, N., Braeckman, B.P., De Mey, M., Coudenys, J., Crombez, L., Verbeke, F., Janssens, Y., Janky, R., Goossens, E., Vlaeminck, C., Duchi, D., Andries, V., Dumas, E., Petrovic, M., Van de Wiele, T., Knappe, D., Hoffmann, R., Mouly, V., Bigot, A., Vereecke, L., Van Immerseel, F., Van Den Noortgate, N., De Spiegeleer, B. and Elewaut, D. (2022), The bacterial quorum sensing peptide iAM373 is a novel inducer of sarcopenia. Clin. Transl. Med., 12: e1053.
CRISPR/Cas9 screen in human iPSC-derived cortical neurons identifies NEK6 as a novel disease modifier of C9orf72 poly(PR) toxicity
Guo W, Wang H, Kumar Tharkeshwar A, Couthouis J, Braems E, Masrori P, Van Schoor E, Fan Y, Ahuja K, Moisse M, Jacquemyn M, Furtado Madeiro da Costa R, Gajjar M, Balusu S, Tricot T, Fumagalli L, Hersmus N, Janky R, Impens F, Vanden Berghe P, Ho R, Thal DR, Vandenberghe R, Hegde ML, Chandran S, De Strooper B, Daelemans D, Van Damme P, Van Den Bosch L, Verfaillie C.
Alzheimers Dement. 2022 Aug 22.
Unraveling the Molecular Basis of the Dystrophic Process in Limb-Girdle Muscular Dystrophy LGMD-R12 by Differential Gene Expression Profiles in Diseased and Healthy Muscles
Depuydt CE, Goosens V, Janky R, D'Hondt A, De Bleecker JL, Noppe N, Derveaux S, Thal DR, Claeys KG.
Cells. 2022 Apr 30;11(9):1508.
Selective IL-1 activity on CD8+ T cells empowers antitumor immunity and synergizes with neovasculature-targeted TNF for full tumor eradication
Van Den Eeckhout B, Huyghe L, Van Lint S, Burg E, Plaisance S, Peelman F, Cauwels A, Uzé G, Kley N, Gerlo S, Tavernier J.
J Immunother Cancer. 2021 Nov;9(11):e003293.
Single-cell Transcriptomics Uncover a Novel Role of Myeloid Cells and T-lymphocytes in the Fibrotic Microenvironment in Peyronie's Disease
Milenkovic U, Boeckx B, Lambrechts D, Janky R, Hatzichristodoulou G, Van R, Gevaert T, Cellek S, Bivalacqua T, De R, Albersen M
Eur Urol Focus. 2021 May 4;S2405-4569(21)00118-8.
Chloroplast Electron Chain, ROS Production, and Redox Homeostasis Are Modulated by COS-OGA Elicitation in Tomato (Solanum lycopersicum) Leaves.
Moreau S, Van Aubel G, Janky R, Van Cutsem P
Front Plant Sci. 2020 Dec 14;11:597589.
Gemcitabine Recruits M2-Type Tumor-Associated Macrophages into the Stroma of Pancreatic Cancer.
Bulle A, Dekervel J, Deschuttere L, Nittner D, Libbrecht L, Janky R, Plaisance S, Topal B, Coosemans A, Lambrechts D, Van Cutsem E, Verslype C, van Pelt J.
Transl Oncol. 2020 Mar;13(3):100743. Epub 2020 Mar 4.
Nuclear import of the DSCAM-cytoplasmic domain drives signaling capable of inhibiting synapse formation.
Sachse SM, Lievens S, Ribeiro LF, Dascenco D, Masschaele D, Horré K, Misbaer A, Vanderroost N, De Smet AS, Salta E, Erfurth ML, Kise Y, Nebel S, Van Delm W, Plaisance S, Tavernier J, De Strooper B, De Wit J, Schmucker D.
EMBO J. 2019 Mar 15;38(6):e99669.
High-throughput sequencing identifies aetiology-dependent differences in ductular reaction in human chronic liver disease.
Govaere O, Cockell S, Van Haele M, Wouters J, Van Delm W, Van den Eynde K, Bianchi A, van Eijsden R, Van Steenbergen W, Monbaliu D, Nevens F, Roskams T.
J Pathol. 2019 May;248(1):66-76.
Dysregulation of Macropinocytosis Processes in Glioblastomas May Be Exploited to Increase Intracellular Anti-Cancer Drug Levels: The Example of Temozolomide
Colin M, Delporte C, Janky R, Lechon AS, Renard G, Van Antwerpen P, Maltese WA, Mathieu V.
Cancers (Basel). 2019 Mar 22;11(3):411.
Challenges in the Structural-Functional Characterization of Multidomain, Partially Disordered Proteins CBP and p300: Preparing Native Proteins and Developing Nanobody Tools
Bekesi A, Abdellaoui S, Holroyd N, Van Delm W, Pardon E, Pauwels J, Gevaert K, Steyaert J, Derveaux S, Borysik A, Tompa P.
Methods Enzymol. 2018;611:607-675.
OMSim: a simulator for optical map data
Miclotte G, Plaisance S, Rombauts S, Van de Peer Y, Audenaert P, Fostier J.
Bioinformatics. 2017 Sep 1;33(17):2740-2742.
Nuclear inclusion bodies of mutant and wild-type p53 in cancer: a hallmark of p53 inactivation and proteostasis remodelling by p53 aggregation
De Smet F, Saiz Rubio M, Hompes D, Naus E, De Baets G, Langenberg T, Hipp MS, Houben B, Claes F, Charbonneau S, Delgado Blanco J, Plaisance S, Ramkissoon S, Ramkissoon L, Simons C, van den Brandt P, Weijenberg M, Van England M, Lambrechts S, Amant F, D'Hoore A, Ligon KL, Sagaert X, Schymkowitz J, Rousseau F.
J Pathol. 2017 May;242(1):24-38.