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Items: 11

1.

Essential guidelines for computational method benchmarking.

Weber LM, Saelens W, Cannoodt R, Soneson C, Hapfelmeier A, Gardner PP, Boulesteix AL, Saeys Y, Robinson MD.

Genome Biol. 2019 Jun 20;20(1):125. doi: 10.1186/s13059-019-1738-8. Review.

2.

A comparison of single-cell trajectory inference methods.

Saelens W, Cannoodt R, Todorov H, Saeys Y.

Nat Biotechnol. 2019 May;37(5):547-554. doi: 10.1038/s41587-019-0071-9. Epub 2019 Apr 1.

PMID:
30936559
3.

Network Inference from Single-Cell Transcriptomic Data.

Todorov H, Cannoodt R, Saelens W, Saeys Y.

Methods Mol Biol. 2019;1883:235-249. doi: 10.1007/978-1-4939-8882-2_10.

PMID:
30547403
4.

The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages.

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, Henri S, Pridans C, Hume DA, Lambrecht BN, De Baetselier P, Milling SWF, Van Ginderachter JA, Malissen B, Berx G, Beschin A, Saeys Y, Guilliams M.

Immunity. 2018 Aug 21;49(2):312-325.e5. doi: 10.1016/j.immuni.2018.07.004. Epub 2018 Jul 31.

5.

IncGraph: Incremental graphlet counting for topology optimisation.

Cannoodt R, Ruyssinck J, Ramon J, De Preter K, Saeys Y.

PLoS One. 2018 Apr 26;13(4):e0195997. doi: 10.1371/journal.pone.0195997. eCollection 2018.

6.

A comprehensive evaluation of module detection methods for gene expression data.

Saelens W, Cannoodt R, Saeys Y.

Nat Commun. 2018 Mar 15;9(1):1090. doi: 10.1038/s41467-018-03424-4.

7.

Genomic Amplifications and Distal 6q Loss: Novel Markers for Poor Survival in High-risk Neuroblastoma Patients.

Depuydt P, Boeva V, Hocking TD, Cannoodt R, Ambros IM, Ambros PF, Asgharzadeh S, Attiyeh EF, Combaret V, Defferrari R, Fischer M, Hero B, Hogarty MD, Irwin MS, Koster J, Kreissman S, Ladenstein R, Lapouble E, Laureys G, London WB, Mazzocco K, Nakagawara A, Noguera R, Ohira M, Park JR, Pötschger U, Theissen J, Tonini GP, Valteau-Couanet D, Varesio L, Versteeg R, Speleman F, Maris JM, Schleiermacher G, De Preter K.

J Natl Cancer Inst. 2018 Oct 1;110(10):1084-1093. doi: 10.1093/jnci/djy022.

8.

Early and late effects of pharmacological ALK inhibition on the neuroblastoma transcriptome.

Claeys S, Denecker G, Cannoodt R, Kumps C, Durinck K, Speleman F, De Preter K.

Oncotarget. 2017 Nov 6;8(63):106820-106832. doi: 10.18632/oncotarget.22423. eCollection 2017 Dec 5.

9.

Computational methods for trajectory inference from single-cell transcriptomics.

Cannoodt R, Saelens W, Saeys Y.

Eur J Immunol. 2016 Nov;46(11):2496-2506. doi: 10.1002/eji.201646347. Epub 2016 Oct 19. Review.

10.

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.

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.

Genet Med. 2017 Apr;19(4):457-466. doi: 10.1038/gim.2016.119. Epub 2016 Sep 8.

11.

Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma.

Decock A, Ongenaert M, Cannoodt R, Verniers K, De Wilde B, Laureys G, Van Roy N, Berbegall AP, Bienertova-Vasku J, Bown N, Clément N, Combaret V, Haber M, Hoyoux C, Murray J, Noguera R, Pierron G, Schleiermacher G, Schulte JH, Stallings RL, Tweddle DA; Children’s Cancer and Leukaemia Group (CCLG), De Preter K, Speleman F, Vandesompele J.

Oncotarget. 2016 Jan 12;7(2):1960-72. doi: 10.18632/oncotarget.6477.

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