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Berrio, RT, Verstaen, K, Vandamme, N, Pevernagie, J, Achon, I, Van Duyse, J, Van Isterdael, G, Saeys, Y, De Veylder, L, Inze, D, Dubois, M.
Single-Cell Transcriptomics Sheds Light on the Identity and Metabolism of Developing Leaf Cells
Plant Physiol 188, 898-918, 2022. (Epub 2021 Oct 23)

Bues, J, Biocanin, M, Pezoldt, J, Dainese, R, Chrisnandy, A, Rezakhani, S, Saelens, W, Gardeux, V, Gupta, R, Sarkis, R, Russeil, J, Saeys, Y, Amstad, E, Claassen, M, Lutolf, MP, Deplancke, B.
Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition
Nat Methods 19, 323330, 2022. (Epub 2022 Feb 14)

Couckuyt, A, Seurinck, R, Emmaneel, A, Quintelier, K, Novak, D, Van Gassen, S, Saeys, Y.
Challenges in translational machine learning
Human Genetics 141, 14511466, 2022. (Epub 2022 Mar 4)

Dubouchet, L, Todorov, H, Seurinck, R, Vallet, N, Van Gassen, S, Corneau, A, Blanc, C, Zouali, H, Boland, A, Deleuze, JF, Ingram, B, de Latour, RP, Saeys, Y, Socie, G, Michonneau, D.
Operational tolerance after hematopoietic stem cell transplantation is characterized by distinct transcriptional, phenotypic, and metabolic signatures
Sci Transl Med 14, eabg3083, 2022. (Epub 2022 Feb 23)

Emmaneel, A, Quintelier, K, Sichien, D, Rybakowska, P, Maranon, C, Alarcon-Riquelme, ME, Van Isterdael, G, Van Gassen, S, Saeys, Y.
PeacoQC: Peak-based selection of high quality cytometry data
Cytometry A 101, 325-338, 2022. (Epub 2021 Sep 22)

Franchina, DG, Kurniawan, H, Grusdat, M, Binsfeld, C, Guerra, L, Bonetti, L, Soriano-Baguet, L, Ewen, A, Kobayashi, T, Farinelle, S, Minafra, AR, Vandamme, N, Carpentier, A, Borgmann, FK, Jager, C, Chen, Y, Kleinewietfeld, M, Vasiliou, V, Mittelbronn, M, et al..
Glutathione-dependent redox balance characterizes the distinct metabolic properties of follicular and marginal zone B cells
Nat Commun 13, 1789, 2022. (Epub 2022 Apr 4)

Guilliams, M, Bonnardel, J, Haest, B, Vanderborght, B, Wagner, C, Remmerie, A, Bujko, A, Martens, L, Thone, T, Browaeys, R, De Ponti, FF, Vanneste, B, Zwicker, C, Svedberg, FR, Vanhalewyn, T, Goncalves, A, Lippens, S, Devriendt, B, Cox, E, et al..
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
Cell 185, 379-396, 2022. (Epub 2022 Jan 22)

Hoste, L, Roels, L, Naesens, L, Bosteels, V, Vanhee, S, Dupont, S, Bosteels, C, Browaeys, R, Vandamme, N, Verstaen, K, Roels, J, Van Damme, KFA, Maes, B, De Leeuw, E, Declercq, J, Aegerter, H, Seys, L, Smole, U, De Prijck, S, et al..
TIM3+ TRBV11-2 T cells and IFNgamma signature in patrolling monocytes and CD16+ NK cells delineate MIS-C
J Exp Med 219, e20211381, 2022. (Epub 2021 Dec 16)

Loret, N, Vandamme, N, De Coninck, J, Taminau, J, De Clercq, K, Blancke, G, Jonckheere, S, Goossens, S, Lemeire, K, De Prijck, S, Verstaen, K, Seurinck, R, Van Dorpe, J, Weyers, S, Denys, H, Van de Vijver, K, Lambrecht, BN, Tummers, P, Saeys, Y, et al..
Distinct transcriptional programs in ascitic and solid cancer cells induce different responses to chemotherapy in high-grade serous ovarian cancer
Mol Cancer Res , in press, 2022. (Epub 2022 Jun 24)

Murgaski, A, Kiss, M, Van Damme, H, Kancheva, D, Vanmeerbeek, I, Keirsse, J, Hadadi, E, Brughmans, J, Arnouk, SM, Hamouda, AEI, Debraekeleer, A, Bosteels, V, Elkrim, Y, Boon, L, Hoves, S, Vandamme, N, Deschoemaeker, S, Janssens, S, Garg, AD, et al..
Efficacy of CD40 agonists is mediated by distinct cDC subsets and subverted by suppressive macrophages
Cancer Res , in press, 2022. (Epub 2022 Aug 18)

Mylka, V, Matetovici, I, Poovathingal, S, Aerts, J, Vandamme, N, Seurinck, R, Verstaen, K, Hulselmans, G, Van den Hoecke, S, Scheyltjens, I, Movahedi, K, Wils, H, Reumers, J, Van Houdt, J, Aerts, S, Saeys, Y.
Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq
Genome Biol 23, 55, 2022. (Epub 2022 Feb 16)

Scheyltjens, I, Van Hove, H, De Vlaminck, K, Kancheva, D, Bastos, J, Vara-Perez, M, Pombo Antunes, AR, Martens, L, Scott, CL, Van Ginderachter, JA, Saeys, Y, Guilliams, M, Vandamme, N, Movahedi, K.
Single-cell RNA and protein profiling of immune cells from the mouse brain and its border tissues
Nat Protoc , in press, 2022. (Epub 2022 Aug 5)

Todorov, H, Prieux, M, Laubreton, D, Bouvier, M, Wang, S, de Bernard, S, Arpin, C, Cannoodt, R, Saelens, W, Bonnaffoux, A, Gandrillon, O, Crauste, F, Saeys, Y, Marvel, J.
CD8 memory precursor cell generation is a continuous process
iScience 25, 104927, 2022. (Epub 2022 Aug 13)

Van Coillie, S, Van San, E, Goetschalckx, I, Wiernicki, B, Mukhopadhyay, B, Tonnus, W, Choi, SM, Roelandt, R, Dumitrascu, C, Lamberts, L, Dams, G, Weyts, W, Huysentruyt, J, Hassannia, B, Ingold, I, Lele, S, Meyer, E, Berg, M, Seurinck, R, et al..
Targeting ferroptosis protects against experimental (multi)organ dysfunction and death
Nat Commun 13, 1046, 2022. (Epub 2022 Feb 24)

Vandaele, R, Kang, B, De Bie, T, Saeys, Y.
The Curse Revisited: When are Distances Informative for the Ground Truth in Noisy High-Dimensional Data?
International Conference on Artificial Intelligence and Statistics, Vol 151 151, 2158-2172, 2022. (Epub 2022 May 3)

Vanneste, D, Staal, J, Haegman, M, Driege, Y, Carels, M, Van Nuffel, E, De Bleser, P, Saeys, Y, Beyaert, R, Afonina, IS.
CARD14 Signalling Ensures Cell Survival and Cancer Associated Gene Expression in Prostate Cancer Cells
Biomedicines 10, 2008, 2022. (Epub 2022 Aug 18)

Baldan, FJ, Peralta, D, Saeys, Y, Benitez, JM.
SCMFTS: Scalable and Distributed Complexity Measures and Features for Univariate and Multivariate Time Series in Big Data Environments
International Journal of Computational Intelligence Systems 14, 186, 2021. (Epub 2021 Nov 2)

Cannoodt, R, Saelens, W, Deconinck, L, Saeys, Y.
Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells
Nat Commun 12, 3942, 2021. (Epub 2021 Jun 24)

Catrysse, L, Maes, B, Mehrotra, P, Martens, A, Hoste, E, Martens, L, Maueroder, C, Remmerie, A, Bujko, A, Slowicka, K, Sze, M, Vikkula, H, Ghesquiere, B, Scott, CL, Saeys, Y, van de Sluis, B, Ravichandran, K, Janssens, S, van Loo, G.
A20 deficiency in myeloid cells protects mice from diet-induced obesity and insulin resistance due to increased fatty acid metabolism
Cell Rep 36, 109748, 2021. (Epub 2021 Sep 21)

Deconinck, L, Cannoodt, R, Saelens, W, Deplancke, B, Saeys, Y.
Recent advances in trajectory inference from single-cell omics data
Current Opinion in Systems Biology 27, 100344, 2021. (Epub 2021 Sep)

Desmet, S, Saeys, Y, Verstaen, K, Dauwe, R, Kim, H, Niculaes, C, Fukushima, A, Goeminne, G, Vanholme, R, Ralph, J, Boerjan, W, Morreel, K.
Maize specialized metabolome networks reveal organ-preferential mixed glycosides
Comput Struct Biotechnol J 19, 1127-1144, 2021. (Epub 2021 jan 26)

Di Grande, A, Peirs, S, Donovan, PD, Van Trimpont, M, Morscio, J, Lintermans, B, Reunes, L, Vandamme, N, Goossens, S, Nguyen, HA, Lavie, A, Lock, RB, Prehn, JHM, Van Vlierberghe, P, Ni Chonghaile, T.
The spleen as a sanctuary site for residual leukemic cells following ABT-199 monotherapy in ETP-ALL
Blood Adv 5, 1963-1976, 2021. (Epub 2021 Apr 13)

Duetz, C, Van Gassen, S, Westers, TM, van Spronsen, MF, Bachas, C, Saeys, Y, van de Loosdrecht, AA.
Computational flow cytometry as a diagnostic tool in suspected-myelodysplastic syndromes
Cytometry A 99, 814-824, 2021. (Epub 2021 May 3)

Geeraerts, X, Fernandez-Garcia, J, Hartmann, FJ, de Goede, KE, Martens, L, Elkrim, Y, Debraekeleer, A, Stijlemans, B, Vandekeere, A, Rinaldi, G, De Rycke, R, Planque, M, Broekaert, D, Meinster, E, Clappaert, E, Bardet, P, Murgaski, A, Gysemans, C, Nana, FA, et al..
Macrophages are metabolically heterogeneous within the tumor microenvironment
Cell Rep 37, 110171, 2021. (Epub 2021 Dec 28)

Hoste, E, Lecomte, K, Annusver, K, Vandamme, N, Roels, J, Maschalidi, S, Verboom, L, Vikkula, HK, Sze, M, Van Hove, L, Verstaen, K, Martens, A, Hochepied, T, Saeys, Y, Ravichandran, K, Kasper, M, van Loo, G.
OTULIN maintains skin homeostasis by controlling keratinocyte death and stem cell identity
Nat Commun 12, 5913, 2021. (Epub 2021 Oct 8)

Liechti, T, Weber, LM, Ashhurst, TM, Stanley, N, Prlic, M, Van Gassen, S, Mair, F.
An updated guide for the perplexed: cytometry in the high-dimensional era
Nat Immunol 22, 1190-1197, 2021. (Epub 2021 Oct)

Lorenzi, L, Chiu, HS, Avila Cobos, F, Gross, S, Volders, PJ, Cannoodt, R, Nuytens, J, Vanderheyden, K, Anckaert, J, Lefever, S, Tay, AP, de Bony, EJ, Trypsteen, W, Gysens, F, Vromman, M, Goovaerts, T, Hansen, TB, Kuersten, S, Nijs, N, et al..
The RNA Atlas expands the catalog of human non-coding RNAs
Nat Biotechnol 39, 1467-1467, 2021. (Epub 2021 Jun 17)

Meireson, A, Tavernier, SJ, Van Gassen, S, Sundahl, N, Demeyer, A, Spaas, M, Kruse, V, Ferdinande, L, Van Dorpe, J, Hennart, B, Allorge, D, Haerynck, F, Decaestecker, K, Rottey, S, Saeys, Y, Ost, P, Brochez, L.
Immune Monitoring in Melanoma and Urothelial Cancer Patients Treated with Anti-PD-1 Immunotherapy and SBRT Discloses Tumor Specific Immune Signatures
Cancers (Basel) 13, 2630, 2021. (Epub 2021 May 27)

Moerkerke, B, Seurinck, R.
Discussion on "distributional independent component analysis for diverse neuroimaging modalities" by Ben Wu, Subhadip Pal, Jian Kang, and Ying Guo
Biometrics , in press, 2021. (Epub 2021 Nov 15)

Penttila, PA, Van Gassen, S, Panovska, D, Vanderbeke, L, Van Herck, Y, Quintelier, K, Emmaneel, A, Filtjens, J, Malengier-Devlies, B, Ahmadzadeh, K, Van Mol, P, Borras, DM, Antoranz, A, Bosisio, FM, Wauters, E, Martinod, K, Matthys, P, Saeys, Y, Garg, AD, et al..
High dimensional profiling identifies specific immune types along the recovery trajectories of critically ill COVID19 patients
Cell Mol Life Sci 78, 3987-4002, 2021. (Epub 2021 Mar 13)

Peralta, D, Tang, L, Lippeveld, M, Saeys, Y.
A study on the calibration of fingerprint classifiers
2021 Ieee International Conference on Big Data (Big Data) , 698-704, 2021. (Epub 2021 Dec)

Pombo Antunes, AR, Scheyltjens, I, Lodi, F, Messiaen, J, Antoranz, A, Duerinck, J, Kancheva, D, Martens, L, De Vlaminck, K, Van Hove, H, Kjolner Hansen, SS, Bosisio, FM, Van der Borght, K, De Vleeschouwer, S, Sciot, R, Bouwens, L, Verfaillie, M, Vandamme, N, Vandenbroucke, RE, et al..
Single-cell profiling of myeloid cells in glioblastoma across species and disease stage reveals macrophage competition and specialization
Nat Neurosci 24, 595-610, 2021. (Epub 2021 Mar 29)

Quintelier, K, Couckuyt, A, Emmaneel, A, Aerts, J, Saeys, Y, Van Gassen, S.
Analyzing high-dimensional cytometry data using FlowSOM
Nat Protoc 16, 3775-3801, 2021. (Epub 2021 Jun 25)

Roszak, P, Heo, JO, Blob, B, Toyokura, K, Sugiyama, Y, de Luis Balaguer, MA, Lau, WWY, Hamey, F, Cirrone, J, Madej, E, Bouatta, AM, Wang, X, Guichard, M, Ursache, R, Tavares, H, Verstaen, K, Wendrich, J, Melnyk, CW, Oda, Y, et al..
Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization
Science 374, eaba5531, 2021. (Epub 2021 Dec 24)

Rybakowska, P, Burbano, C, Van Gassen, S, Varela, N, Aguilar-Quesada, R, Saeys, Y, Alarcon-Riquelme, ME, Maranon, C.
Stabilization of human whole blood samples for multi-center and retrospective immunophenotyping studies
Cytometry A 99, 524-537, 2021. (Epub 2020 Oct 18)

Rybakowska, P, Van Gassen, S, Quintelier, K, Saeys, Y, Alarcon-Riquelme, ME, Maranon, C.
Data processing workflow for large-scale immune monitoring studies by mass cytometry
Comput Struct Biotechnol J 19, 3160-3175, 2021. (Epub 2021 May 21)

Scheenstra, MR, Martinez-Botia, P, Acebes-Huerta, A, Brouwer, RWW, Caballero-Sanchez, N, Gillemans, N, De Bleser, P, Nota, B, De Cuyper, IM, Salunkhe, V, Woltman, AM, van de Laar, L, Rijkers, E, Demmers, JAA, van, IWFJ, Philipsen, S, van den Berg, TK, Kuijpers, TW, Gutierrez, L.
Comparison of the PU.1 transcriptional regulome and interactome in human and mouse inflammatory dendritic cells
J Leukoc Biol 110, 735-751, 2021. (Epub 2020 Dec 2)

Seyfferth, C, Renema, J, Wendrich, JR, Eekhout, T, Seurinck, R, Vandamme, N, Blob, B, Saeys, Y, Helariutta, Y, Birnbaum, KD, De Rybel, B.
Advances and Opportunities of Single-Cell Transcriptomics for Plant Research
Annu Rev Plant Biol 72, 847-866, 2021. (Epub 2021 Mar 17)

Sipieter, F, Cappe, B, Leray, A, De Schutter, E, Bridelance, J, Hulpiau, P, Van Camp, G, Declercq, W, Heliot, L, Vincent, P, Vandenabeele, P, Riquet, FB.
Characteristic ERK1/2 signaling dynamics distinguishes necroptosis from apoptosis
iScience 24, 103074, 2021. (Epub 2021 Sep 24)

Vandaele, R, Rieck, B, Saeys, Y, De Bie, T.
Stable topological signatures for metric trees through graph approximations
Pattern Recognition Letters 147, 85-92, 2021. (Epub 2021 April 14)

Vandaele, R, Saeys, Y, De Bie, T.
Graph approximations to geodesics on metric graphs
2020 25TH INTERNATIONAL CONFERENCE ON PATTERN RECOGNITION (ICPR) , 7328-7334, 2021. (Epub )

Van Damme, H, Dombrecht, B, Kiss, M, Roose, H, Allen, E, Van Overmeire, E, Kancheva, D, Martens, L, Murgaski, A, Bardet, PMR, Blancke, G, Jans, M, Bolli, E, Martins, MS, Elkrim, Y, Dooley, J, Boon, L, Schwarze, JK, Tacke, F, Movahedi, K, Vandamme, N, Neyns, B, Ocak, S, Scheyltjens, I, Vereecke, L, Nana, FA, Merchiers, P, Laoui, D, Van Ginderachter, JA.
Therapeutic depletion of CCR8(+) tumor-infiltrating regulatory T cells elicits antitumor immunity and synergizes with anti-PD-1 therapy
J Immunother Cancer 9, e001749, 2021. (Epub 2021 Feb)

Vanderbeke, L, Van Mol, P, Van Herck, Y, De Smet, F, Humblet-Baron, S, Martinod, K, Antoranz, A, Arijs, I, Boeckx, B, Bosisio, FM, Casaer, M, Dauwe, D, De Wever, W, Dooms, C, Dreesen, E, Emmaneel, A, Filtjens, J, Gouwy, M, Gunst, J, et al..
Monocyte-driven atypical cytokine storm and aberrant neutrophil activation as key mediators of COVID-19 disease severity
Nat Commun 12, 4117, 2021. (Epub 2021 Jul 5)

Vanderkerken, M, Baptista, AP, De Giovanni, M, Fukuyama, S, Browaeys, R, Scott, CL, Norris, PS, Eberl, G, Di Santo, JP, Vivier, E, Saeys, Y, Hammad, H, Cyster, JG, Ware, CF, Tumanov, AV, De Trez, C, Lambrecht, BN.
ILC3s control splenic cDC homeostasis via lymphotoxin signaling
J Exp Med 218, e20190835, 2021. (Epub 2021 Mar 16)

Van Hove, L, Lecomte, K, Roels, J, Vandamme, N, Vikkula, HK, Hoorens, I, Ongenae, K, Hochepied, T, Donati, G, Saeys, Y, Quist, SR, Watt, FM, van Loo, G, Hoste, E.
Fibrotic enzymes modulate wound-induced skin tumorigenesis
EMBO Rep , e51573, 2021. (Epub 2021 Mar 29)

Yang, B, Minne, M, Brunoni, F, Plackova, L, Petrik, I, Sun, Y, Nolf, J, Smet, W, Verstaen, K, Wendrich, JR, Eekhout, T, Hoyerova, K, Van Isterdael, G, Haustraete, J, Bishopp, A, Farcot, E, Novak, O, Saeys, Y, De Rybel, B.
Non-cell autonomous and spatiotemporal signalling from a tissue organizer orchestrates root vascular development
Nat Plants 7, 1485-1494, 2021. (Epub 2021 Nov 15)

Bosteels, C, Neyt, K, Vanheerswynghels, M, van Helden, MJ, Sichien, D, Debeuf, N, De Prijck, S, Bosteels, V, Vandamme, N, Martens, L, Saeys, Y, Louagie, E, Lesage, M, Williams, DL, Tang, SC, Mayer, JU, Ronchese, F, Scott, CL, Hammad, H, et al..
Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection
Immunity 52, 1039-1056, 2020. (Epub 2020 May 4)

Browaeys, R, Saelens, W, Saeys, Y.
NicheNet: modeling intercellular communication by linking ligands to target genes
Nat Methods 17, 159-162, 2020. (Epub 2019 Dec 9)

Bruneel, K, Verstappe, J, Vandamme, N, Berx, G.
Intrinsic Balance between ZEB Family Members Is Important for Melanocyte Homeostasis and Melanoma Progression
Cancers (Basel) 12, 2248, 2020. (Epub 2020 Aug 11)

Grootaert, H, Van Landuyt, L, Hulpiau, P, Callewaert, N.
Functional exploration of the GH29 fucosidase family
Glycobiology 30, 735-745, 2020. (Epub 2020 Aug 20)

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