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Items: 1 to 50 of 74

1.

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.

2.

Computational approaches for high-throughput single-cell data analysis.

Todorov H, Saeys Y.

FEBS J. 2018 Jul 30. doi: 10.1111/febs.14613. [Epub ahead of print] Review.

PMID:
30058136
3.

SpliceRover: Interpretable Convolutional Neural: Networks for Improved Splice Site Prediction.

Zuallaert J, Godin F, Kim M, Soete A, Saeys Y, De Neve W.

Bioinformatics. 2018 Jun 21. doi: 10.1093/bioinformatics/bty497. [Epub ahead of print]

PMID:
29931149
4.

An overview of state-of-the-art image restoration in electron microscopy.

Roels J, Aelterman J, Luong HQ, Lippens S, Pižurica A, Saeys Y, Philips W.

J Microsc. 2018 Sep;271(3):239-254. doi: 10.1111/jmi.12716. Epub 2018 Jun 8. Review.

PMID:
29882967
5.

Ancient Origin of the CARD-Coiled Coil/Bcl10/MALT1-Like Paracaspase Signaling Complex Indicates Unknown Critical Functions.

Staal J, Driege Y, Haegman M, Borghi A, Hulpiau P, Lievens L, Gul IS, Sundararaman S, Gonçalves A, Dhondt I, Pinzón JH, Braeckman BP, Technau U, Saeys Y, van Roy F, Beyaert R.

Front Immunol. 2018 May 24;9:1136. doi: 10.3389/fimmu.2018.01136. eCollection 2018.

6.

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.

7.

GC Content of Early Metazoan Genes and Its Impact on Gene Expression Levels in Mammalian Cell Lines.

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.

Genome Biol Evol. 2018 Mar 1;10(3):909-917. doi: 10.1093/gbe/evy040.

8.

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.

9.

Myeloid cell heterogeneity in cancer: not a single cell alike.

Kiss M, Van Gassen S, Movahedi K, Saeys Y, Laoui D.

Cell Immunol. 2018 Aug;330:188-201. doi: 10.1016/j.cellimm.2018.02.008. Epub 2018 Feb 14. Review.

PMID:
29482836
10.

Nanos genes and their role in development and beyond.

De Keuckelaere E, Hulpiau P, Saeys Y, Berx G, van Roy F.

Cell Mol Life Sci. 2018 Jun;75(11):1929-1946. doi: 10.1007/s00018-018-2766-3. Epub 2018 Feb 3. Review.

PMID:
29397397
11.

Response to Orlova et al. "Science not art: statistically sound methods for identifying subsets in multi-dimensional flow and mass cytometry data sets".

Saeys Y, Van Gassen S, Lambrecht B.

Nat Rev Immunol. 2017 Dec 22;18(1):78. doi: 10.1038/nri.2017.151. No abstract available.

PMID:
29269765
12.

Coordinated Functional Divergence of Genes after Genome Duplication in Arabidopsis thaliana.

De Smet R, Sabaghian E, Li Z, Saeys Y, Van de Peer Y.

Plant Cell. 2017 Nov;29(11):2786-2800. doi: 10.1105/tpc.17.00531. Epub 2017 Oct 25.

13.

TGFβR signalling controls CD103+CD11b+ dendritic cell development in the intestine.

Bain CC, Montgomery J, Scott CL, Kel JM, Girard-Madoux MJH, Martens L, Zangerle-Murray TFP, Ober-Blöbaum J, Lindenbergh-Kortleve D, Samsom JN, Henri S, Lawrence T, Saeys Y, Malissen B, Dalod M, Clausen BE, Mowat AM.

Nat Commun. 2017 Sep 20;8(1):620. doi: 10.1038/s41467-017-00658-6.

14.

Nlrp6- and ASC-Dependent Inflammasomes Do Not Shape the Commensal Gut Microbiota Composition.

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.

Immunity. 2017 Aug 15;47(2):339-348.e4. doi: 10.1016/j.immuni.2017.07.011. Epub 2017 Aug 8.

15.

The checkpoint for agonist selection precedes conventional selection in human thymus.

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.

Sci Immunol. 2017 Feb 24;2(8). pii: eaah4232. doi: 10.1126/sciimmunol.aah4232.

16.

Computational analysis of multimorbidity between asthma, eczema and rhinitis.

Aguilar D, Pinart M, Koppelman GH, Saeys Y, Nawijn MC, Postma DS, Akdis M, Auffray C, Ballereau S, Benet M, García-Aymerich J, González JR, Guerra S, Keil T, Kogevinas M, Lambrecht B, Lemonnier N, Melen E, Sunyer J, Valenta R, Valverde S, Wickman M, Bousquet J, Oliva B, Antó JM.

PLoS One. 2017 Jun 9;12(6):e0179125. doi: 10.1371/journal.pone.0179125. eCollection 2017.

17.

A Murine Intestinal Intraepithelial NKp46-Negative Innate Lymphoid Cell Population Characterized by Group 1 Properties.

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.

Cell Rep. 2017 May 16;19(7):1431-1443. doi: 10.1016/j.celrep.2017.04.068.

18.

ConTra v3: a tool to identify transcription factor binding sites across species, update 2017.

Kreft L, Soete A, Hulpiau P, Botzki A, Saeys Y, De Bleser P.

Nucleic Acids Res. 2017 Jul 3;45(W1):W490-W494. doi: 10.1093/nar/gkx376.

19.

Myocardial Infarction Primes Autoreactive T Cells through Activation of Dendritic Cells.

Van der Borght K, Scott CL, Nindl V, Bouché 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.

Cell Rep. 2017 Mar 21;18(12):3005-3017. doi: 10.1016/j.celrep.2017.02.079.

20.

Bayesian deconvolution of scanning electron microscopy images using point-spread function estimation and non-local regularization.

Roels J, Aelterman J, De Vylder J, Hiep Luong, Saeys Y, Philips W.

Conf Proc IEEE Eng Med Biol Soc. 2016 Aug;2016:443-447. doi: 10.1109/EMBC.2016.7590735.

PMID:
28268367
21.

Evolution and diversity of cadherins and catenins.

Gul IS, Hulpiau P, Saeys Y, van Roy F.

Exp Cell Res. 2017 Sep 1;358(1):3-9. doi: 10.1016/j.yexcr.2017.03.001. Epub 2017 Mar 6. Review.

PMID:
28268172
22.

Mechanisms of the Development of Allergy (MeDALL): Introducing novel concepts in allergy phenotypes.

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, Lodrup Carlsen KC, Koppelman GH, Sunyer J, Zuberbier T, Annesi-Maesano I, Arno A, Bindslev-Jensen C, De Carlo G, Forastiere F, Heinrich J, Kowalski ML, Maier D, Melén E, Smit HA, Standl M, Wright J, Asarnoj A, Benet M, Ballardini N, Garcia-Aymerich J, Gehring U, Guerra S, Hohmann C, Kull I, Lupinek C, Pinart M, Skrindo I, Westman M, Smagghe D, Akdis C, Andersson N, Bachert C, Ballereau S, Ballester F, Basagana X, Bedbrook A, Bergstrom A, von Berg A, Brunekreef B, Burte E, Carlsen KH, Chatzi L, Coquet JM, Curin M, Demoly P, Eller E, Fantini MP, von Hertzen L, Hovland V, Jacquemin B, Just J, Keller T, Kiss R, Kogevinas M, Koletzko S, Lau S, Lehmann I, Lemonnier N, Mäkelä M, Mestres J, Mowinckel P, Nadif R, Nawijn MC, Pellet J, Pin I, Porta D, Rancière F, Rial-Sebbag E, Saeys Y, Schuijs MJ, Siroux V, Tischer CG, Torrent M, Varraso R, Wenzel K, Xu CJ.

J Allergy Clin Immunol. 2017 Feb;139(2):388-399. doi: 10.1016/j.jaci.2016.12.940. Review.

PMID:
28183433
23.

Corrigendum: Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay.

Trypsteen W, Mohammadi P, Van Hecke C, Mestdagh P, Lefever S, Saeys Y, De Bleser P, Vandesompele J, Ciuffi A, Vandekerckhove L, De Spiegelaere W.

Sci Rep. 2017 Jan 24;7:41112. doi: 10.1038/srep41112. No abstract available.

24.

GATA1-Deficient Dendritic Cells Display Impaired CCL21-Dependent Migration toward Lymph Nodes Due to Reduced Levels of Polysialic Acid.

Scheenstra MR, De Cuyper IM, Branco-Madeira F, de Bleser P, Kool M, Meinders M, Hoogenboezem M, Mul E, Wolkers MC, Salerno F, Nota B, Saeys Y, Klarenbeek S, van IJcken WF, Hammad H, Philipsen S, van den Berg TK, Kuijpers TW, Lambrecht BN, Gutiérrez L.

J Immunol. 2016 Dec 1;197(11):4312-4324. Epub 2016 Nov 4.

25.

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.

26.

Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay.

Trypsteen W, Mohammadi P, Van Hecke C, Mestdagh P, Lefever S, Saeys Y, De Bleser P, Vandesompele J, Ciuffi A, Vandekerckhove L, De Spiegelaere W.

Sci Rep. 2016 Oct 26;6:36111. doi: 10.1038/srep36111. Erratum in: Sci Rep. 2017 Jan 24;7:41112.

27.

Unsupervised High-Dimensional Analysis Aligns Dendritic Cells across Tissues and Species.

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, Irac SE, Mattar CN, Sumatoh HR, Low GHL, Chung TJK, Chan DKH, Tan KK, Hon TLK, Fossum E, Bogen B, Choolani M, Chan JKY, Larbi A, Luche H, Henri S, Saeys Y, Newell EW, Lambrecht BN, Malissen B, Ginhoux F.

Immunity. 2016 Sep 20;45(3):669-684. doi: 10.1016/j.immuni.2016.08.015. Epub 2016 Sep 13.

28.

IRF8 Transcription Factor Controls Survival and Function of Terminally Differentiated Conventional and Plasmacytoid Dendritic Cells, Respectively.

Sichien D, Scott CL, Martens L, Vanderkerken M, Van Gassen S, Plantinga M, Joeris T, De Prijck S, Vanhoutte L, Vanheerswynghels M, Van Isterdael G, Toussaint W, Madeira FB, Vergote K, Agace WW, Clausen BE, Hammad H, Dalod M, Saeys Y, Lambrecht BN, Guilliams M.

Immunity. 2016 Sep 20;45(3):626-640. doi: 10.1016/j.immuni.2016.08.013. Epub 2016 Sep 13.

29.

Metazoan evolution of the armadillo repeat superfamily.

Gul IS, Hulpiau P, Saeys Y, van Roy F.

Cell Mol Life Sci. 2017 Feb;74(3):525-541. doi: 10.1007/s00018-016-2319-6. Epub 2016 Aug 6.

PMID:
27497926
30.

An evolutionary perspective on the necroptotic pathway.

Dondelinger Y, Hulpiau P, Saeys Y, Bertrand MJM, Vandenabeele P.

Trends Cell Biol. 2016 Oct;26(10):721-732. doi: 10.1016/j.tcb.2016.06.004. Epub 2016 Jun 28. Review.

PMID:
27368376
31.

Computational flow cytometry: helping to make sense of high-dimensional immunology data.

Saeys Y, Van Gassen S, Lambrecht BN.

Nat Rev Immunol. 2016 Jul;16(7):449-62. doi: 10.1038/nri.2016.56. Epub 2016 Jun 20. Review.

PMID:
27320317
32.

Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph.

Meysman P, Saeys Y, Sabaghian E, Bittremieux W, van de Peer Y, Goethals B, Laukens K.

IEEE/ACM Trans Comput Biol Bioinform. 2016 Jun 7. [Epub ahead of print]

PMID:
27295680
33.

The transcription factor Zeb2 regulates development of conventional and plasmacytoid DCs by repressing Id2.

Scott CL, Soen B, Martens L, Skrypek N, Saelens W, Taminau J, Blancke G, Van Isterdael G, Huylebroeck D, Haigh J, Saeys Y, Guilliams M, Lambrecht BN, Berx G.

J Exp Med. 2016 May 30;213(6):897-911. doi: 10.1084/jem.20151715. Epub 2016 May 16.

34.

Efficient analysis of mouse genome sequences reveal many nonsense variants.

Steeland S, Timmermans S, Van Ryckeghem S, Hulpiau P, Saeys Y, Van Montagu M, Vandenbroucke RE, Libert C.

Proc Natl Acad Sci U S A. 2016 May 17;113(20):5670-5. doi: 10.1073/pnas.1605076113. Epub 2016 May 4.

35.

Yolk Sac Macrophages, Fetal Liver, and Adult Monocytes Can Colonize an Empty Niche and Develop into Functional Tissue-Resident Macrophages.

van de Laar L, Saelens W, De Prijck S, Martens L, Scott CL, Van Isterdael G, Hoffmann E, Beyaert R, Saeys Y, Lambrecht BN, Guilliams M.

Immunity. 2016 Apr 19;44(4):755-68. doi: 10.1016/j.immuni.2016.02.017. Epub 2016 Mar 15.

36.

Paving the way of systems biology and precision medicine in allergic diseases: the MeDALL success story: Mechanisms of the Development of ALLergy; EU FP7-CP-IP; Project No: 261357; 2010-2015.

Bousquet J, Anto JM, Akdis M, Auffray C, Keil T, Momas I, Postma DS, Valenta R, Wickman M, Cambon-Thomsen A, Haahtela T, Lambrecht BN, Lodrup Carlsen KC, Koppelman GH, Sunyer J, Zuberbier T, Annesi-Maesano I, Arno A, Bindslev-Jensen C, De Carlo G, Forastiere F, Heinrich J, Kowalski ML, Maier D, Melén E, Palkonen S, Smit HA, Standl M, Wright J, Asarnoj A, Benet M, Ballardini N, Garcia-Aymerich J, Gehring U, Guerra S, Hohman C, Kull I, Lupinek C, Pinart M, Skrindo I, Westman M, Smagghe D, Akdis C, Albang R, Anastasova V, Anderson N, Bachert C, Ballereau S, Ballester F, Basagana X, Bedbrook A, Bergstrom A, von Berg A, Brunekreef B, Burte E, Carlsen KH, Chatzi L, Coquet JM, Curin M, Demoly P, Eller E, Fantini MP, Gerhard B, Hammad H, von Hertzen L, Hovland V, Jacquemin B, Just J, Keller T, Kerkhof M, Kiss R, Kogevinas M, Koletzko S, Lau S, Lehmann I, Lemonnier N, McEachan R, Mäkelä M, Mestres J, Minina E, Mowinckel P, Nadif R, Nawijn M, Oddie S, Pellet J, Pin I, Porta D, Rancière F, Rial-Sebbag A, Saeys Y, Schuijs MJ, Siroux V, Tischer CG, Torrent M, Varraso R, De Vocht J, Wenger K, Wieser S, Xu C.

Allergy. 2016 Nov;71(11):1513-1525. doi: 10.1111/all.12880. Epub 2016 Aug 23. Review.

37.

Netter: re-ranking gene network inference predictions using structural network properties.

Ruyssinck J, Demeester P, Dhaene T, Saeys Y.

BMC Bioinformatics. 2016 Feb 9;17:76. doi: 10.1186/s12859-016-0913-0.

38.

Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells.

Scott CL, Zheng F, De Baetselier P, Martens L, Saeys Y, De Prijck S, Lippens S, Abels C, Schoonooghe S, Raes G, Devoogdt N, Lambrecht BN, Beschin A, Guilliams M.

Nat Commun. 2016 Jan 27;7:10321. doi: 10.1038/ncomms10321.

39.

Development and Validation of a Small Single-domain Antibody That Effectively Inhibits Matrix Metalloproteinase 8.

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.

Mol Ther. 2016 May;24(5):890-902. doi: 10.1038/mt.2016.2. Epub 2016 Jan 18.

40.

Radiation-induced alternative transcription and splicing events and their applicability to practical biodosimetry.

Macaeva E, Saeys Y, Tabury K, Janssen A, Michaux A, Benotmane MA, De Vos WH, Baatout S, Quintens R.

Sci Rep. 2016 Jan 14;6:19251. doi: 10.1038/srep19251.

41.

An integrated network of Arabidopsis growth regulators and its use for gene prioritization.

Sabaghian E, Drebert Z, Inzé D, Saeys Y.

Sci Rep. 2015 Dec 1;5:17617. doi: 10.1038/srep17617.

42.

A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.

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, Mosmann T, Nolan GP, Scheuermann RH, Brinkman RR.

Cytometry A. 2016 Jan;89(1):16-21. doi: 10.1002/cyto.a.22732. Epub 2015 Oct 8.

43.

FloReMi: Flow density survival regression using minimal feature redundancy.

Van Gassen S, Vens C, Dhaene T, Lambrecht BN, Saeys Y.

Cytometry A. 2016 Jan;89(1):22-9. doi: 10.1002/cyto.a.22734. Epub 2015 Aug 4.

44.

Characterization of genome-wide ordered sequence-tagged Mycobacterium mutant libraries by Cartesian Pooling-Coordinate Sequencing.

Vandewalle K, Festjens N, Plets E, Vuylsteke M, Saeys Y, Callewaert N.

Nat Commun. 2015 May 11;6:7106. doi: 10.1038/ncomms8106.

45.

Phenotyping asthma, rhinitis and eczema in MeDALL population-based birth cohorts: an allergic comorbidity cluster.

Garcia-Aymerich J, Benet M, Saeys Y, Pinart M, Basagaña X, Smit HA, Siroux V, Just J, Momas I, Rancière F, Keil T, Hohmann C, Lau S, Wahn U, Heinrich J, Tischer CG, Fantini MP, Lenzi J, Porta D, Koppelman GH, Postma DS, Berdel D, Koletzko S, Kerkhof M, Gehring U, Wickman M, Melén E, Hallberg J, Bindslev-Jensen C, Eller E, Kull I, Lødrup Carlsen KC, Carlsen KH, Lambrecht BN, Kogevinas M, Sunyer J, Kauffmann F, Bousquet J, Antó JM.

Allergy. 2015 Aug;70(8):973-84. doi: 10.1111/all.12640. Epub 2015 May 20.

PMID:
25932997
46.

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data.

Van Gassen S, Callebaut B, Van Helden MJ, Lambrecht BN, Demeester P, Dhaene T, Saeys Y.

Cytometry A. 2015 Jul;87(7):636-45. doi: 10.1002/cyto.a.22625. Epub 2015 Jan 8.

47.

CATCh, an ensemble classifier for chimera detection in 16S rRNA sequencing studies.

Mysara M, Saeys Y, Leys N, Raes J, Monsieurs P.

Appl Environ Microbiol. 2015 Mar;81(5):1573-84. doi: 10.1128/AEM.02896-14. Epub 2014 Dec 19.

48.

Systematic structural characterization of metabolites in Arabidopsis via candidate substrate-product pair networks.

Morreel K, Saeys Y, Dima O, Lu F, Van de Peer Y, Vanholme R, Ralph J, Vanholme B, Boerjan W.

Plant Cell. 2014 Mar;26(3):929-45. doi: 10.1105/tpc.113.122242. Epub 2014 Mar 31.

49.

NIMEFI: gene regulatory network inference using multiple ensemble feature importance algorithms.

Ruyssinck J, Huynh-Thu VA, Geurts P, Dhaene T, Demeester P, Saeys Y.

PLoS One. 2014 Mar 25;9(3):e92709. doi: 10.1371/journal.pone.0092709. eCollection 2014.

50.

The function of Fcγ receptors in dendritic cells and macrophages.

Guilliams M, Bruhns P, Saeys Y, Hammad H, Lambrecht BN.

Nat Rev Immunol. 2014 Feb;14(2):94-108. doi: 10.1038/nri3582. Epub 2014 Jan 21. Review. Erratum in: Nat Rev Immunol. 2014 May;14(5):349.

PMID:
24445665

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