Publications by this IRC author

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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)

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)

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 , in press, 2021. (Epub 2021 May 3)

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)

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)

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)

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)

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)

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 )

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)

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)

Lavaert, M, Liang, KL, Vandamme, N, Park, JE, Roels, J, Kowalczyk, MS, Li, B, Ashenberg, O, Tabaka, M, Dionne, D, Tickle, TL, Slyper, M, Rozenblatt-Rosen, O, Vandekerckhove, B, Leclercq, G, Regev, A, Van Vlierberghe, P, Guilliams, M, Teichmann, SA, et al..
Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes
Immunity 52, 1088-1104, 2020. (Epub 2020 Apr 13)

Park, JE, Botting, RA, Dominguez Conde, C, Popescu, DM, Lavaert, M, Kunz, DJ, Goh, I, Stephenson, E, Ragazzini, R, Tuck, E, Wilbrey-Clark, A, Roberts, K, Kedlian, VR, Ferdinand, JR, He, X, Webb, S, Maunder, D, Vandamme, N, Mahbubani, KT, et al..
A cell atlas of human thymic development defines T cell repertoire formation
Science 367, eaay3224, 2020. (Epub 2020 Feb 21)

Peck, J, Goossens, B, Saeys, Y.
Detecting adversarial manipulation using inductive Venn-ABERS predictors
Neurocomputing 416, 202-217, 2020. (Epub 2020 Apr 10)

Peralta, D, Saeys, Y.
Robust unsupervised dimensionality reduction based on feature clustering for single-cell imaging data
Applied Soft Computing Journal 93, 106421, 2020. (Epub 2020 May 23)

Remmerie, A, Martens, L, Thone, T, Castoldi, A, Seurinck, R, Pavie, B, Roels, J, Vanneste, B, De Prijck, S, Vanhockerhout, M, Binte Abdul Latib, M, Devisscher, L, Hoorens, A, Bonnardel, J, Vandamme, N, Kremer, A, Borghgraef, P, Van Vlierberghe, H, Lippens, S, Pearce, E., Saeys, Y, Scott, CL.
Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver
Immunity 53, 641-657 e14, 2020. (Epub 2020 Aug 26)

Roels, J, Vernaillen, F, Kremer, A, Goncalves, A, Aelterman, J, Luong, HQ, Goossens, B, Philips, W, Lippens, S, Saeys, Y.
An interactive ImageJ plugin for semi-automated image denoising in electron microscopy
Nat Commun 11, 771, 2020. (Epub 2020 Feb 7)

Saeys, Y, Finak, G.
Special Issue on Machine Learning for Single Cell Data
Cytometry A 97, 217-218, 2020. (Epub 2020 Mar 6)

Sanchez-Fernandez, A, Romero, L, Peralta, D, Medina-Perez, M, Saeys, Y, Herrera, F, Tabik, S.
Asynchronous Processing for Latent Fingerprint Identification on Heterogeneous CPU-GPU Systems
IEEE Access 8, 124236–124253, 2020. (Epub 2020 Jun 29)

Todorov, H, Cannoodt, R, Saelens, W, Saeys, Y.
TinGa: fast and flexible trajectory inference with Growing Neural Gas
Bioinformatics 36, i66-i74, 2020. (Epub 2020 Jul 1)

Vandaele, R, Saeys, Y, De Bie, T.
Mining Topological Structure in Graphs through Forest Representations
Journal of Machine Learning Research 21, 1-68, 2020. (Epub Oct 2020)

Van den Berge, K, Roux de Bezieux, H, Street, K, Saelens, W, Cannoodt, R, Saeys, Y, Dudoit, S, Clement, L.
Trajectory-based differential expression analysis for single-cell sequencing data
Nat Commun 11, 1201, 2020. (Epub 2020 Mar 5)

Van de Sande, B, Flerin, C, Davie, K, De Waegeneer, M, Hulselmans, G, Aibar, S, Seurinck, R, Saelens, W, Cannoodt, R, Rouchon, Q, Verbeiren, T, De Maeyer, D, Reumers, J, Saeys, Y, Aerts, S.
A scalable SCENIC workflow for single-cell gene regulatory network analysis
Nat Protoc 15, 2247-2276, 2020. (Epub 2020 Jun 19)

Van Gassen, S, Gaudilliere, B, Angst, MS, Saeys, Y, Aghaeepour, N.
CytoNorm: A Normalization Algorithm for Cytometry Data
Cytometry A , in press, 2020. (Epub 2019 Oct 21)

Verboom, L, Martens, A, Priem, D, Hoste, E, Sze, M, Vikkula, HK, Van Hove, L, Voet, S, Roels, J, Maelfait, J, Bongiovanni, L, de Bruin, A, Scott, CL, Saeys, Y, Pasparakis, M, Bertrand, MJM, van Loo, G.
OTULIN Prevents Liver Inflammation and Hepatocellular Carcinoma by Inhibiting FADD- and RIPK1 Kinase-Mediated Hepatocyte Apoptosis
Cell Rep 30, 2237-2247, 2020. (Epub 2020 Feb 18)

Wendrich, JR, Yang, B, Vandamme, N, Verstaen, K, Smet, W, Van de Velde, C, Minne, M, Wybouw, B, Mor, E, Arents, HE, Nolf, J, Van Duyse, J, Van Isterdael, G, Maere, S, Saeys, Y, De Rybel, B.
Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions
Science 370, eaay4970eaay4970, 2020. (Epub 2020 Sep 17)

Ydens, E, Amann, L, Asselbergh, B, Scott, CL, Martens, L, Sichien, D, Mossad, O, Blank, T, De Prijck, S, Low, D, Masuda, T, Saeys, Y, Timmerman, V, Stumm, R, Ginhoux, F, Prinz, M, Janssens, S, Guilliams, M.
Profiling peripheral nerve macrophages reveals two macrophage subsets with distinct localization, transcriptome and response to injury
Nat Neurosci 23, 676-689, 2020. (Epub 2020 Apr 13)

Cossarizza, A, Chang, HD, Radbruch, A, Acs, A, Adam, D, Adam-Klages, S, Agace, WW, Aghaeepour, N, Akdis, M, Allez, M, Almeida, LN, Alvisi, G, Anderson, G, Andra, I, Annunziato, F, Anselmo, A, Bacher, P, Baldari, CT, Bari, S, et al..
Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)
Eur J Immunol 49, 1457-1973, 2019. (Epub 2019 Oct)

Dubois, H, Sorgeloos, F, Sarvestani, ST, Martens, L, Saeys, Y, Mackenzie, JM, Lamkanfi, M, van Loo, G, Goodfellow, I, Wullaert, A.
Nlrp3 inflammasome activation and Gasdermin D-driven pyroptosis are immunopathogenic upon gastrointestinal norovirus infection
PLoS Pathog 15, e1007709, 2019. (Epub 2019 Apr 24)

Emmaneel, A, Bogaert, DJ, Van Gassen, S, Tavernier, SJ, Dullaers, M, Haerynck, F, Saeys, Y.
A Computational Pipeline for the Diagnosis of CVID Patients
Frontiers in Immunology 10, 2009, 2019. (Epub 2019 Aug 30)

Lippeveld, M, Knill, C, Ladlow, E, Fuller, A, Michaelis, LJ, Saeys, Y, Filby, A, Peralta, D.
Classification of Human White Blood Cells Using Machine Learning for Stain-Free Imaging Flow Cytometry
Cytometry A , in press, 2019. (Epub 2019 Nov 5)

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 16, 1496-1507, 2019. (Epub 2016 Jun 7)

Peralta, D, Saeys, Y.
Distributed, numerically stable distance and covariance computation with MPI for extremely large datasets
2019 IEEE INTERNATIONAL CONGRESS ON BIG DATA (IEEE BIGDATA CONGRESS 2019) , 77-84, 2019. (Epub 2019 Jul)

Roels, J, Hennies, J, Saeys, Y, Philips, W, Kreshuk, A.
Domain Adaptive Segmentation in Volume Electron Microscopy Imaging
2019 Ieee 16th International Symposium on Biomedical Imaging (Isbi 2019) , 1519-1522, 2019. (Epub Oct 2018)

Saelens, W, Cannoodt, R, Todorov, H, Saeys, Y.
A comparison of single-cell trajectory inference methods
Nat Biotechnol 37, 547-554, 2019. (Epub 2019 Apr 1)

Tavernier, SJ, Athanasopoulos, V, Verloo, P, Behrens, G, Staal, J, Bogaert, DJ, Naesens, L, De Bruyne, M, Van Gassen, S, Parthoens, E, Ellyard, J, Cappello, J, Morris, LX, Van Gorp, H, Van Isterdael, G, Saeys, Y, Lamkanfi, M, Schelstraete, P, Dehoorne, J, et al..
A human immune dysregulation syndrome characterized by severe hyperinflammation with a homozygous nonsense Roquin-1 mutation
Nat Commun 10, 4779, 2019. (Epub 2019 oct 21)

Tibbitt, CA, Stark, JM, Martens, L, Ma, J, Mold, JE, Deswarte, K, Oliynyk, G, Feng, X, Lambrecht, BN, De Bleser, P, Nylen, S, Hammad, H, Arsenian Henriksson, M, Saeys, Y, Coquet, JM.
Single-Cell RNA Sequencing of the T Helper Cell Response to House Dust Mites Defines a Distinct Gene Expression Signature in Airway Th2 Cells
Immunity 51, 169-184, 2019. (Epub 2019 Jun 20)

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)

Todorov, H, Saeys, Y.
Computational approaches for high-throughput single-cell data analysis
FEBS J 286, 1451-1467, 2019. (Epub 2018 Jul 30)

Van Hove, H, Martens, L, Scheyltjens, I, De Vlaminck, K, Pombo Antunes, AR, De Prijck, S, Vandamme, N, De Schepper, S, Van Isterdael, G, Scott, CL, Aerts, J, Berx, G, Boeckxstaens, GE, Vandenbroucke, RE, Vereecke, L, Moechars, D, Guilliams, M, Van Ginderachter, JA, Saeys, Y, Movahedi, K.
A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment
Nat Neurosci 22, 1021–1035, 2019. (Epub 2019 May 6)

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)

Vluymans, S, Mac Parthalain, N, Cornelis, C, Saeys, Y.
Weight selection strategies for ordered weighted average based fuzzy rough sets
Information Sciences 501, 155-171, 2019. (Epub 2019 May 29)

Weber, LM, Saelens, W, Cannoodt, R, Soneson, C, Hapfelmeier, A, Gardner, PP, Boulesteix, AL, Saeys, Y, Robinson, MD.
Essential guidelines for computational method benchmarking
Genome Biol 20, 125, 2019. (Epub 2019 Jun 20)

Cambre, I, Gaublomme, D, Burssens, A, Jacques, P, Schryvers, N, De Muynck, A, Meuris, L, Lambrecht, S, Carter, S, de Bleser, P, Saeys, Y, Van Hoorebeke, L, Kollias, G, Mack, M, Simoens, P, Lories, R, Callewaert, N, Schett, G, Elewaut, D.
Mechanical strain determines the site-specific localization of inflammation and tissue damage in arthritis
Nat Commun 9, 4613, 2018. (Epub 2018 Nov 5)

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)