2025

Nanopore sequencing enables tissue-of-origin and pathogen detection in plasma cell-free DNA from critically ill patients
C. Willemart, M. Strazisar, T. De Pooter, T. Stroobants, T. Demuyser, P. Jorens, E. Hoste, G. Menschaert and T. Vanden Berghe
(2025) CELL DEATH DISCOVERY, 11, 484

Unravelling the hidden side of laundry : malodour, microbiome and pathogenome
C. Diez Lopez, F. Van Herreweghen, B. De Pessemier, Y. Minnebo, S. Taelman, K. Judge, K. Ransley, C. Hammond, M. Batson, M. Stock, W. Van Criekinge, T. Van de Wiele, A. Macmaster and C. Callewaert
(2025) BMC BIOLOGY, 23, 40

Pre-trained Maldi Transformers improve MALDI-TOF MS-based prediction
G. De Waele, G. Menschaert, P. Vandamme and W. Waegeman
(2025) COMPUTERS IN BIOLOGY AND MEDICINE, 186, 109695

Comprehensive analysis of the melanoma DNA methylome identifies LY75 methylation as an independent marker predicting poor clinical outcome
K. van den Hurk, K. Lommen, L. Coussement, D. van den Kerkhof, M. Beckers, G. Trooskens, L. Van Neste, M. Oosterhof, R. van Doorn, J. van den Oord, T. Kerkhofs, M. Aarts, B. Ramaekers, M. Joore, V. Winnepenninckx, W. Van Criekinge, W. Gallagher, T. De Meyer, K. Smits and M. van Engeland
(2025) JOURNAL OF INVESTIGATIVE DERMATOLOGY, 0,

Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants : a randomized controlled trial
L. Deng, S. Taelman, M. Olm, L. Toe, E. Balini, W. Ouedraogo, Y. Bastos Moreira, A. Alemayehu, K. Hadush, E. Sonnenburg, G. Hanley-Cook, M. Ouédraogo, R. Ganaba, W. Van Criekinge, L. Huybregts, M. Stock, P. Kolsteren, J. Sonnenburg, C. Lachat and T. Dailey-Chwalibóg
(2025) NATURE COMMUNICATIONS, 16, 2683

Dual lipid modulation overcomes ferroptosis resistance in high-risk neuroblastoma
I. Koeken, M. Walravens, R. Fernández-Acosta, R. Van Hoyweghen, I. Vintea, Y. Kong, B. Golba, J. Dehairs, A. Talebi, J. Swinnen, K. Durinck, A. Mañas, S. Toyokuni, G. Menschaert, M. Fedorova, B. De Geest, B. Hassannia and T. Vanden Berghe
(2025) CELL DEATH AND DIFFERENTIATION, 0,

Population-level allelic dispersion modeling by maelstRom yields genome-wide maps of allele-specific dysregulation during early carcinogenesis
C. Stroobandt, L. Coussement, T. Goovaerts, F. De Graeve, J. Galle, W. Van Criekinge and T. De Meyer
(2025) GIGASCIENCE, 14, giaf125

Independent genetic mapping experiments identify diverse molecular determinants of host adaptation in a generalist herbivore
E. Villacis Perez, F. De Graeve, B. De Beer, S. Alshami, R. De Jong, T. De Meyer and T. Van Leeuwen
(2025) MOLECULAR ECOLOGY, 0, e17618

Reannotation of cancer mutations based on expressed RNA transcripts reveals functional non-coding mutations in melanoma
D. Pepe, X. Janssens, K. Timcheva, G. Marron-Linares, B. Verbelen, V. Konstantakos, D. De Groote, J. De Bie, A. Verhasselt, B. Dewaele, A. Godderis, C. Cools, M. Franco-Tolsau, J. Royaert, J. Verbeeck, K. Kampen, K. Subramanian, D. Granados, G. Menschaert and K. De Keersmaecker
(2025) AMERICAN JOURNAL OF HUMAN GENETICS, 112,

Translon : a single term for translated regions
M. Świrski, J. Tierney, M. Albà, D. Andreev, J. Aspden, J. Atkins, M. Bassani-Sternberg, M. Berry, S. Biffo, K. Boris-Lawrie, M. Borodovsky, I. Brierley, M. Brook, M. Brunet, J. Bujnicki, N. Caliskan, L. Calviello, A. Carvunis, J. Cate, C. Cenik, K. Chang, Y. Chen, S. Chothani, J. Choudhary, P. Clark, J. Clauwaert, L. Cooley, E. Dassi, K. Dean, J. Diaz, C. Dieterich, R. Dikstein, J. Dinman, S. Dmitriev, O. Dontsova, C. Dunham, S. Eswarappa, P. Farabaugh, P. Faridi, I. Fierro-Monti, A. Firth, D. Gatfield, F. Gebauer, M. Gelfand, N. Gray, R. Green, C. Hill, Y. Hou, N. Hübner, Z. Ignatova, P. Ivanov, S. Iwasaki, R. Johnson, A. Jomaa, M. Jovanovic, I. Jungreis, M. Kellis, J. Kieft, A. Kochetov, E. Koonin, A. Korostelev, J. Kufel, I. Kulakovskiy, L. Kurian, D. Lafontaine, O. Larsson, G. Loughran, J. Lukeš, M. Mariotti, E. Martens-Uzunova, T. Martinez, A. Matsumoto, J. McManus, J. Medenbach, S. Melnikov, G. Menschaert, C. Merchante, M. Mikl, W. Miller, O. Mühlemann, O. Namy, D. Nedialkova, J. Nosek, S. Orchard, P. Ozretić, M. Pertea, D. Pervouchine, L. Romão, D. Ron, X. Roucou, M. Rubtsova, J. Ruiz-Orera, A. Saghatelian, S. Salzberg, L. Seale, C. Seoighe, P. Sergiev, P. Shah, N. Shirokikh, S. Slavoff, N. Sonenberg, T. Stasevich, R. Szczesny, T. Tamm, M. Tchórzewski, I. Topisirovic, M. Tremblay, T. Tuller, I. Ulitsky, L. Valášek, P. Van Damme, G. Viero, J. Vizcaino, C. Vogel, E. Wallace, J. Weissman, E. Westhof, N. Whiffin, D. Wilson, Z. Xie, J. Yewdell, M. Yordanova, C. Yu, V. Yurchenko, B. Zagrovic, [. TRANSLACORE, M. Almeida, N. Atabey, N. Balatsos, P. Baranov, A. Bojan, T. Choli-Papadopoulou, P. Close, V. Cowling, E. Dassi, A. David, K. Dean, J. Diaz, A. Eftimov, F. Gebauer, M. Helm, C. Iuga, D. Jurkovičová, A. Kanopka, D. Lafontaine, E. Martens-Uzunova, L. Messingerová, H. Nielsen, P. Ozretić, M. Ozturk, V. Pelechano, M. Penzo, P. Podszywalow-Bartnicka, L. Pojskić, J. Le Quesne, L. Romão, B. Rotblat, A. Stanhill, G. Stoecklin, T. Tamm, M. Tchorzewski, V. Trajković, L. Valasek, E. Valen, S. Volarevic, L. Vucicevic, K. Watt, A. Willis, M. Zdralevic, T. Ramuta, E. Valen and P. Baranov
(2025) NATURE METHODS, 22,