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Todorov, H, Cannoodt, R, Saelens, W, Saeys, Y.
Network Inference from Single-Cell Transcriptomic Data
Methods Mol Biol 1883, 235-249, 2019. (Epub 2018 Dec 14)

Venken, K, Jacques, P, Mortier, C, Labadia, ME, Decruy, T, Coudenys, J, et al., Van Gassen, S, Martens, L, Smith, D, Harcken, C, Wahle, J, Wang, CT, Verheugen, E, Schryvers, N, Varkas, G, Cypers, H, et al.,Van den Bosch, F, Saeys, Y, Nabozny, G, Elewaut D.
RORgammat inhibition selectively targets IL-17 producing iNKT and gammadelta-T cells enriched in Spondyloarthritis patients
Nat Commun 10, 9, 2019. (Epub 2019 Jan 2)

Cannoodt, R, Ruyssinck, J, Ramon, J, De Preter, K, Saeys, Y.
IncGraph: Incremental graphlet counting for topology optimisation
PLoS One 13, e0195997, 2018. (Epub 2018 Apr 26)

De Keuckelaere, E, Hulpiau, P, Saeys, Y, Berx, G, van Roy, F.
Nanos genes and their role in development and beyond
Cell Mol Life Sci 75, 1929-1946, 2018. (Epub 2018 Feb 3)

Govindarajan, S, Gaublomme, D, Van der Cruyssen, R, Verheugen, E, Van Gassen, S, Saeys, Y, Tavernier, S, Iwawaki, T, Bloch, Y, Savvides, SN, Lambrecht, BN, Janssens, S, Elewaut, D, Drennan, MB.
Stabilization of cytokine mRNAs in iNKT cells requires the serine-threonine kinase IRE1alpha
Nat Commun 9, 5340, 2018. (Epub 2018 Dec 17)

Gul, IS, Staal, J, Hulpiau, P, De Keuckelaere, E, Kamm, K, Deroo, T, Sanders, E, Staes, K, Driege, Y, Saeys, Y, Beyaert, R, Technau, U, Schierwater, B, Van Roy, F.
GC content of early metazoan genes and its impact on gene expression levels in mammalian cell lines
Genome biology and Evolution 10, 909–917, 2018. (Epub 2018 Feb 21)

Kiss, M, Van Gassen, S, Movahedi, K, Saeys, Y, Laoui, D.
Myeloid cell heterogeneity in cancer: not a single cell alike
Cell Immunol 330, 188-201, 2018. (Epub 2018 Feb 14)

Milani, G, Matthijssens, F, Van Loocke, W, Durinck, K, Roels, J, Peirs, S, Thenoz, M, Pieters, T, Reunes, L, Lintermans, B, Vandamme, N, Lammens, T, Van Roy, N, Van Nieuwerburgh, F, Deforce, D, Schwab, C, Raimondi, S, Dalla Pozza, L, Carroll, AJ, 3rd, et al..
Genetic characterization and therapeutic targeting of MYC-rearranged T cell acute lymphoblastic leukaemia
Br J Haematol , in press, 2018. (Epub 2018 Jun 25)

Roels, J, Aelterman, J, Luong, HQ, Lippens, S, Pizurica, A, Saeys, Y, Philips, W.
An overview of state-of-the-art image restoration in electron microscopy
J Microsc 271, 239-254, 2018. (Epub 2018 jun 8)

Saelens, W, Cannoodt, R, Saeys, Y.
A comprehensive evaluation of module detection methods for gene expression data
Nat Commun 9, 1090, 2018. (Epub 2018 Mar 15)

Saeys, Y, Van Gassen, S, Lambrecht, B.
Response to Orlova et al. "Science not art: statistically sound methods for identifying subsets in multi-dimensional flow and mass cytometry data sets"
Nat Rev Immunol 18, 78, 2018. (Epub 2017 Dec 22)

Scott, CL, T'Jonck, W, Martens, L, Todorov, H, Sichien, D, Soen, B, Bonnardel, J, De Prijck, S, Vandamme, N, Cannoodt, R, Saelens, W, Vanneste, B, Toussaint, W, De Bleser, P, Takahashi, N, Vandenabeele, P, et al., Lambrecht, BN, De Baetselier, P, Milling, SWF, Van Ginderachter, JA, Malissen, B, Berx, G, Beschin, A, Saeys, Y, Guilliams, M.
The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages
Immunity 49, 312-325, 2018. (Epub 2018 Jul 31)

Staal, J, Driege, Y, Haegman, M, Borghi, A, Hulpiau, P, Lievens, L, Gul, IS, Sundararaman, S, Goncalves, A, Dhondt, I, Pinzon, JH, Braeckman, BP, Technau, U, Saeys, Y, van Roy, F, Beyaert, R.
Ancient Origin of the CARD-Coiled Coil/Bcl10/MALT1-Like Paracaspase Signaling Complex Indicates Unknown Critical Functions
Front Immunol 9, 1136, 2018. (Epub 2018 May 24)

Todorov, H, Saeys, Y.
Computational approaches for high-throughput single-cell data analysis
FEBS J , in press, 2018. (Epub 2018 Jul 30)

Van der Borght, K, Scott, CL, Martens, L, Sichien, D, Van Isterdael, G, Nindl, V, Saeys, Y, Boon, L, Ludewig, B, Gillebert, TC, Lambrecht, BN.
Myocarditis Elicits Dendritic Cell and Monocyte Infiltration in the Heart and Self-Antigen Presentation by Conventional Type 2 Dendritic Cells
Front Immunol 9, 2714, 2018. (Epub 2018 Nov 21)

Vluymans, S, Cornelis, C, Herrera, F, Saeys, Y.
Multi-label classification using a fuzzy rough neighborhood consensus
Information Sciences 433-434, 96–114, 2018. (Epub 2017 Dec 25)

Vluymans, S, Fernández, A, Saeys, Y, Cornelis, C, Herrera, F.
Dynamic affinity-based classification of multi-class imbalanced data with one-versus-one decomposition: a fuzzy rough set approach
KNOWLEDGE AND INFORMATION SYSTEMS 56, 55-84, 2018. (Epub 2017 Oct 22)

Zuallaert, J, Godin, F, Kim, M, Soete, A, Saeys, Y, De Neve, W.
SpliceRover: Interpretable Convolutional Neural: Networks for Improved Splice Site Prediction
Bioinformatics 34, 4180-4188, 2018. (Epub 2018 Jun 21)

Zuallaert, J, Kim, M, Soete, A, Saeys, Y, De Neve, W.
TISRover: ConvNets learn biologically relevant features for effective translation initiation site prediction
International Journal of Data Mining and Bioinformatics 20, 267-284, 2018. (Epub 2018)

Aghaeepour, N, Ganio, EA, McIlwain, D, Tsai, AS, Tingle, M, Van Gassen, S, Gaudilliere, DK, Baca, Q, McNeil, L, Okada, R, Ghaemi, MS, Furman, D, Wong, RJ, Winn, VD, Druzin, ML, El-Sayed, YY, Quaintance, C, Gibbs, R, Darmstadt, GL, et al..
An immune clock of human pregnancy
Sci Immunol 2, 15, 2017. (Epub 2017 Sep 1)

Aguilar, D, Pinart, M, Koppelman, GH, Saeys, Y, Nawijn, MC, Postma, DS, Akdis, M, Auffray, C, Ballereau, S, Benet, M, Garcia-Aymerich, J, Gonzalez, JR, Guerra, S, Keil, T, Kogevinas, M, Lambrecht, B, Lemonnier, N, Melen, E, Sunyer, J, et al..
Computational analysis of multimorbidity between asthma, eczema and rhinitis
PLoS One 12, e0179125, 2017. (Epub 2017 Jun 9)

Anto, JM, Bousquet, J, Akdis, M, Auffray, C, Keil, T, Momas, I, Postma, DS, Valenta, R, Wickman, M, Cambon-Thomsen, A, Haahtela, T, Lambrecht, BN, et al., Saeys, Y, Schuijs, MJ, et al., Annesi-Maesano, I, Arno, A, Bindslev-Jensen, C, et al..
Mechanisms of the Development of Allergy (MeDALL): Introducing novel concepts in allergy phenotypes
J Allergy Clin Immunol 139, 388-399, 2017. (Epub 2017 Feb)

Bain, CC, Montgomery, J, Scott, CL, Kel, JM, Girard-Madoux, MJH, Martens, L, Zangerle-Murray, TFP, Ober-Blobaum, J, Lindenbergh-Kortleve, D, Samsom, JN, Henri, S, Lawrence, T, Saeys, Y, Malissen, B, Dalod, M, Clausen, BE, Mowat, AM.
TGFbetaR signalling controls CD103+CD11b+ dendritic cell development in the intestine
Nat Commun 8, 620, 2017. (Epub 2017 Sep 20)

Claeys, S, Denecker, G, Cannoodt, R, Kumps, C, Durinck, K, Speleman, F, De Preter, K.
Early and late effects of pharmacological ALK inhibition on the neuroblastoma transcriptome
Oncotarget 8, 106820-106832, 2017. (Epub 2017 Nov 6)

Cole, JH, Underwood, J, Caan, MW, De Francesco, D, van Zoest, RA, Leech, R, Wit, FW, Portegies, P, Geurtsen, GJ, Schmand, BA, Schim van der Loeff, MF, Franceschi, C, Sabin, CA, Majoie, CB, Winston, A, Reiss, P, Sharp, DJ, collaboration, C.
Increased brain-predicted aging in treated HIV disease
Neurology 88, 1349-1357, 2017. (Epub 2017 Mar 3)

De Smet, R, Sabaghian, E, Li, Z, Saeys, Y, Van de Peer, Y.
Coordinated Functional Divergence of Genes after Genome Duplication in Arabidopsis thaliana
Plant Cell 29, 2786-2800, 2017. (Epub 2017 Oct 27)

Gul, IS, Hulpiau, P, Saeys, Y, van Roy, F.
Metazoan evolution of the armadillo repeat superfamily
Cell Mol Life Sci 74, 525–541, 2017. (Epub 2016 Aug 6)

Kreft, L, Soete, A, Hulpiau, P, Botzki, A, Saeys, Y, De Bleser, P.
ConTra v3: a tool to identify transcription factor binding sites across species, update 2017
Nucleic Acids Res 45, W490-W494, 2017. (Epub 2017 May 4)

Mamantopoulos, M, Ronchi, F, Van Hauwermeiren, F, Vieira-Silva, S, Yilmaz, B, Martens, L, Saeys, Y, Drexler, SK, Yazdi, AS, Raes, J, Lamkanfi, M, McCoy, KD, Wullaert, A.
Nlrp6- and ASC-Dependent Inflammasomes Do Not Shape the Commensal Gut Microbiota Composition
Immunity 47, 339-348, 2017. (Epub 2017 Aug 15)

Meysman, P, Saeys, Y, Sabaghian, E, Bittremieux, W, van de Peer, Y, Goethals, B, Laukens, K.
Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph
IEEE/ACM Trans Comput Biol Bioinform , in press, 2017. (Epub 2016 Jun 7)

Peck, J, Saeys, Y, Goossens, B, Roels, J.
Lower bounds on the robustness to adversarial perturbations
Proc of Neural Information Processing Systems 30, , 2017. (Epub 2017)

Peralta, D, Triguero, I, García, S, Saeys, Y, Benítez, JM, Herrera, F.
On the use of convolutional neural networks for robust classification of multiple fingerprint captures
Computer Vision and Pattern Recognition 33, 213-230, 2017. (Epub 2017 Nov 14)

Peralta, D, Triguero, I, Garcia, S, Saeys, Y, Benitez, JM, Herrera, F.
Distributed incremental fingerprint identification with reduced database penetration rate using a hierarchical classification based on feature fusion and selection
Knowledge-Based Systems 126, 91-103, 2017. (Epub 2017 Jun 15)

Roels, J, De Vylder, J, Aelterman, J, Saeys, Y, Philips, W.
Convolutional neural network pruning to accelerate membrane segmentation in electron microscopy
IEEE Xplore , 633-637, 2017. (Epub 2017 Jun 19)

Van Acker, A, Gronke, K, Biswas, A, Martens, L, Saeys, Y, Filtjens, J, Taveirne, S, Van Ammel, E, Kerre, T, Matthys, P, Taghon, T, Vandekerckhove, B, Plum, J, Dunay, IR, Diefenbach, A, Leclercq, G.
A Murine Intestinal Intraepithelial NKp46-Negative Innate Lymphoid Cell Population Characterized by Group 1 Properties
Cell Rep 19, 1431-1443, 2017. (Epub 2017 May 16)

Van Cauwenbergh, C, Van Schil, K, Cannoodt, R, Bauwens, M, Van Laethem, T, De Jaegere, S, Steyaert, W, Sante, T, Menten, B, Leroy, BP, Coppieters, F, De Baere, E.
arrEYE: a customized platform for high-resolution copy number analysis of coding and noncoding regions of known and candidate retinal dystrophy genes and retinal noncoding RNAs
Genet Med 19, 457-466, 2017. (Epub 2016 Sep 8)

Van der Borght, K, Scott, CL, Nindl, V, Bouche, A, Martens, L, Sichien, D, Van Moorleghem, J, Vanheerswynghels, M, De Prijck, S, Saeys, Y, Ludewig, B, Gillebert, T, Guilliams, M, Carmeliet, P, Lambrecht, BN.
Myocardial Infarction Primes Autoreactive T Cells through Activation of Dendritic Cells
Cell Rep 18, 3005-3017, 2017. (Epub 2017 Mar 21)

Verstichel, G, Vermijlen, D, Martens, L, Goetgeluk, G, Brouwer, M, Thiault, N, Van Caeneghem, Y, De Munter, S, Weening, K, Bonte, S, Leclercq, G, Taghon, T, Kerre, T, Saeys, Y, Van Dorpe, J, Cheroutre, H, Vandekerckhove, B.
The checkpoint for agonist selection precedes conventional selection in human thymus
Science Immunology 2, eaah4232, 2017. (Epub 2017 Feb 24)

Zuallaert, J, Kim, M, Saeys, Y, De Neve, W.
Interpretable Convolutional Neural Networks for Effective Translation Initiation Site Prediction
2017 Ieee International Conference on Bioinformatics and Biomedicine (Bibm) , 1233-1237, 2017. (Epub Nov 2017)

Aghaeepour, N, Chattopadhyay, P, Chikina, M, Dhaene, T, Van Gassen, S, Kursa, M, Lambrecht, BN, Malek, M, McLachlan, GJ, Qian, Y, Qiu, P, Saeys, Y, Stanton, R, Tong, D, Vens, C, Walkowiak, S, Wang, K, Finak, G, Gottardo, R, et al..
A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes
Cytometry A 89A, 16-21, 2016. (Epub 2015 Oct 8)

Bousquet, J, Anto, JM, Akdis, M, Auffray, C, Keil, T, Momas, I, Postma, D, Valenta, R, Wickman, M, Cambon-Thomsen, A, Haahtela, T, Lambrecht, BN, Lodrup-Carlsen, K, Koppelman, GH, Sunyer, J, Zuberbier, T, et al., Coquet, J, Hammad, H, Schuijs, M, Saeys, Y, et al., Xu, C.
Paving the way of systems biology and precision medicine in allergic diseases: The MeDALL success story
Allergy 71, 1513-1525, 2016. (Epub 2016 Mar 10)

Cannoodt, R, Saelens, W, Saeys, Y.
Computational methods for trajectory inference from single-cell transcriptomics
Eur J Immunol 46, 2496-2506, 2016. (Epub 2016 Sep 28)

Davison, A, McDowell, Gary S, Holden, Jennifer M, Johnson, Harriet F, Koutsovoulos, Georgios D, Liu, MM, Hulpiau, P, Van Roy, F, Wade, Christopher M, Banerjee, R, Yang, F, Chiba, S, Davey, John W, Jackson, Daniel J, Levin, M, Blaxter, Mark L.
Formin Is Associated with Left-Right Asymmetry in the Pond Snail and the Frog
Current Biology 26, 1-7, 2016. (Epub 2016 Mar 7)

Demeestere, D, Dejonckheere, E, Steeland, S, Hulpiau, P, Haustraete, J, Devoogdt, N, Wichert, R, Becker-Pauly, C, Van Wonterghem, E, Dewaele, S, Van Imschoot, G, Aerts, J, Arckens, L, Saeys, Y, Libert, C, Vandenbroucke, RE.
Development and validation of a small single domain antibody that effectively inhibits matrix metalloproteinase 8
Mol Ther 24, 890-902, 2016. (Epub 2016 Jan 18)

Dondelinger, Y, Hulpiau, P, Saeys, Y, Bertrand, MJ, Vandenabeele, P.
An evolutionary perspective on the necroptotic pathway
Trends Cell Biol 26, 721-732, 2016. (Epub 2016 Jun 28)

Folmsbee, SS, Wilcox, DR, Tyberghein, K, De Bleser, P, Tourtellotte, WG, van Hengel, J, van Roy, F, Gottardi, CJ.
alphaT-catenin in restricted brain cell types and its potential connection to autism
J Mol Psychiatry 4, 2, 2016. (Epub 2016 Jun 21)

González, M, Bergmeir, C, Triguero, I, Rodriguez, Y, Benítez, JM.
On the stopping criteria for k-Nearest Neighbor in positive unlabeled time series classification problems
Information Sciences 328, 42-59, 2016. (Epub 2015 Aug 22)

Guilliams, M, Dutertre, CA, Scott, CL, McGovern, N, Sichien, D, Chakarov, S, Van Gassen, S, Chen, J, Poidinger, M, De Prijck, S, Tavernier, SJ, Low, I, et al., Chan, DK, Tan, KK, et al., Saeys, Y, Newell, EW, Lambrecht, BN, et al., Ginhoux, F.
Unsupervised High-Dimensional Analysis Aligns Dendritic Cells across Tissues and Species
Immunity 45, 669-684, 2016. (Epub 2016 Sep 20)

Herrera, F, Ventura, S, Bello, R, Cornelis, C, Zafra, A, Sánchez-Tarragó, D, Vluymans, S.
Multiple Instance Learning: Foundations and Algorithms
Springer , 1-230, 2016. (Epub 2016)

Hulpiau, P, Driege, Y, Staal, J, Beyaert, R.
MALT1 is not alone after all: identification of novel paracaspases
Cell Mol Life Sci 1103-1116, 73, 2016. (Epub 2015 Sep 16)

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