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Items: 1 to 50 of 75

1.

SPECS: a non-parametric method to identify tissue-specific molecular features for unbalanced sample groups.

Everaert C, Volders PJ, Morlion A, Thas O, Mestdagh P.

BMC Bioinformatics. 2020 Feb 17;21(1):58. doi: 10.1186/s12859-020-3407-z.

2.

SPsimSeq: semi-parametric simulation of bulk and single cell RNA sequencing data.

Assefa AT, Vandesompele J, Thas O.

Bioinformatics. 2020 Feb 17. pii: btaa105. doi: 10.1093/bioinformatics/btaa105. [Epub ahead of print]

PMID:
32065619
3.

Evaluation of a zinc chelate on clinical swine dysentery under field conditions.

Vangroenweghe F, Allais L, Van Driessche E, van Berkel R, Lammers G, Thas O.

Porcine Health Manag. 2020 Jan 16;6:1. doi: 10.1186/s40813-019-0140-y. eCollection 2020.

4.

A unified framework for unconstrained and constrained ordination of microbiome read count data.

Hawinkel S, Kerckhof FM, Bijnens L, Thas O.

PLoS One. 2019 Feb 13;14(2):e0205474. doi: 10.1371/journal.pone.0205474. eCollection 2019.

5.

Clinical diseases in pet black-tailed prairie dogs (Cynomys ludovicianus): a retrospective study in 206 animals.

Thas I, Wagner RA, Thas O.

J Small Anim Pract. 2019 Mar;60(3):153-160. doi: 10.1111/jsap.12974. Epub 2019 Feb 10.

PMID:
30740716
6.

Semiparametric linear transformation models: Effect measures, estimators, and applications.

De Neve J, Thas O, Gerds TA.

Stat Med. 2019 Apr 15;38(8):1484-1501. doi: 10.1002/sim.8078. Epub 2019 Jan 4.

PMID:
30609115
7.

A comprehensive overview of genomic imprinting in breast and its deregulation in cancer.

Goovaerts T, Steyaert S, Vandenbussche CA, Galle J, Thas O, Van Criekinge W, De Meyer T.

Nat Commun. 2018 Oct 8;9(1):4120. doi: 10.1038/s41467-018-06566-7. Review.

8.

High-dimensional prediction of binary outcomes in the presence of between-study heterogeneity.

Mbah C, De Neve J, Thas O.

Stat Methods Med Res. 2019 Sep;28(9):2848-2867. doi: 10.1177/0962280218787544. Epub 2018 Jul 27.

PMID:
30051767
9.

Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data.

Assefa AT, De Paepe K, Everaert C, Mestdagh P, Thas O, Vandesompele J.

Genome Biol. 2018 Jul 24;19(1):96. doi: 10.1186/s13059-018-1466-5.

10.

Confirmation of Mycoplasma hyopneumoniae in a breeding herd through tracheobronchial swab sampling and PCR.

Vangroenweghe FACJ, Willems E, Thas O, Maes DGD.

Vet Rec. 2018 Sep 15;183(10):325. doi: 10.1136/vr.104712. Epub 2018 Jul 14. No abstract available.

PMID:
30007933
11.

On determining the power of digital PCR experiments.

Vynck M, Vandesompele J, Thas O.

Anal Bioanal Chem. 2018 Sep;410(23):5731-5739. doi: 10.1007/s00216-018-1212-6. Epub 2018 Jun 30.

PMID:
29961092
12.

Use of trachea-bronchial swab qPCR testing to confirm Mycoplasma hyopneumoniae seropositivity in an SPF breeding herd.

Vangroenweghe F, Willems E, Malášek J, Thas O, Maes D.

Porcine Health Manag. 2018 Jun 1;4:12. doi: 10.1186/s40813-018-0088-3. eCollection 2018.

13.

Reducing Bias in Digital PCR Quantification Experiments: The Importance of Appropriately Modeling Volume Variability.

Vynck M, Thas O.

Anal Chem. 2018 Jun 5;90(11):6540-6547. doi: 10.1021/acs.analchem.8b00115. Epub 2018 May 21.

PMID:
29739189
14.

Prognostic and Therapeutic Implications of Circulating Androgen Receptor Gene Copy Number in Prostate Cancer Patients Using Droplet Digital Polymerase Chain Reaction.

Buelens S, Claeys T, Dhondt B, Poelaert F, Vynck M, Yigit N, Thas O, Ost P, Vandesompele J, Lumen N, Kumps C.

Clin Genitourin Cancer. 2018 Jun;16(3):197-205.e5. doi: 10.1016/j.clgc.2017.12.008. Epub 2017 Dec 29.

PMID:
29366632
15.

A new approach for modeling patient overall radiosensitivity and predicting multiple toxicity endpoints for breast cancer patients.

Mbah C, De Ruyck K, De Schrijver S, De Sutter C, Schiettecatte K, Monten C, Paelinck L, De Neve W, Thierens H, West C, Amorim G, Thas O, Veldeman L.

Acta Oncol. 2018 May;57(5):604-612. doi: 10.1080/0284186X.2017.1417633. Epub 2018 Jan 4.

PMID:
29299946
16.

Exhaled breath to screen for malignant pleural mesothelioma: a validation study.

Lamote K, Vynck M, Thas O, Van Cleemput J, Nackaerts K, van Meerbeeck JP.

Eur Respir J. 2017 Dec 21;50(6). pii: 1700919. doi: 10.1183/13993003.00919-2017. Print 2017 Dec.

17.

BIGL: Biochemically Intuitive Generalized Loewe null model for prediction of the expected combined effect compatible with partial agonism and antagonism.

Van der Borght K, Tourny A, Bagdziunas R, Thas O, Nazarov M, Turner H, Verbist B, Ceulemans H.

Sci Rep. 2017 Dec 20;7(1):17935. doi: 10.1038/s41598-017-18068-5.

18.

Breath analysis by gas chromatography-mass spectrometry and electronic nose to screen for pleural mesothelioma: a cross-sectional case-control study.

Lamote K, Brinkman P, Vandermeersch L, Vynck M, Sterk PJ, Van Langenhove H, Thas O, Van Cleemput J, Nackaerts K, van Meerbeeck JP.

Oncotarget. 2017 Sep 27;8(53):91593-91602. doi: 10.18632/oncotarget.21335. eCollection 2017 Oct 31.

19.

A broken promise: microbiome differential abundance methods do not control the false discovery rate.

Hawinkel S, Mattiello F, Bijnens L, Thas O.

Brief Bioinform. 2019 Jan 18;20(1):210-221. doi: 10.1093/bib/bbx104.

PMID:
28968702
20.

A unified censored normal regression model for qPCR differential gene expression analysis.

Pipelers P, Clement L, Vynck M, Hellemans J, Vandesompele J, Thas O.

PLoS One. 2017 Aug 17;12(8):e0182832. doi: 10.1371/journal.pone.0182832. eCollection 2017.

21.

Quality control of digital PCR assays and platforms.

Vynck M, Vandesompele J, Thas O.

Anal Bioanal Chem. 2017 Oct;409(25):5919-5931. doi: 10.1007/s00216-017-0538-9. Epub 2017 Aug 10.

PMID:
28799053
22.

Detection of malignant pleural mesothelioma in exhaled breath by multicapillary column/ion mobility spectrometry (MCC/IMS).

Lamote K, Vynck M, Van Cleemput J, Thas O, Nackaerts K, van Meerbeeck JP.

J Breath Res. 2016 Sep 26;10(4):046001. doi: 10.1088/1752-7155/10/4/046001.

PMID:
27669062
23.

Flexible analysis of digital PCR experiments using generalized linear mixed models.

Vynck M, Vandesompele J, Nijs N, Menten B, De Ganck A, Thas O.

Biomol Detect Quantif. 2016 Jun 24;9:1-13. doi: 10.1016/j.bdq.2016.06.001. eCollection 2016 Sep.

24.

Pitfalls in Prediction Modeling for Normal Tissue Toxicity in Radiation Therapy: An Illustration With the Individual Radiation Sensitivity and Mammary Carcinoma Risk Factor Investigation Cohorts.

Mbah C, Thierens H, Thas O, De Neve J, Chang-Claude J, Seibold P, Botma A, West C, De Ruyck K.

Int J Radiat Oncol Biol Phys. 2016 Aug 1;95(5):1466-1476. doi: 10.1016/j.ijrobp.2016.03.034. Epub 2016 Apr 1.

PMID:
27479726
25.

The Future of Digital Polymerase Chain Reaction in Virology.

Vynck M, Trypsteen W, Thas O, Vandekerckhove L, De Spiegelaere W.

Mol Diagn Ther. 2016 Oct;20(5):437-47. doi: 10.1007/s40291-016-0224-1. Review.

PMID:
27351921
26.

A web application for sample size and power calculation in case-control microbiome studies.

Mattiello F, Verbist B, Faust K, Raes J, Shannon WD, Bijnens L, Thas O.

Bioinformatics. 2016 Jul 1;32(13):2038-40. doi: 10.1093/bioinformatics/btw099. Epub 2016 Feb 19.

PMID:
27153704
27.

Constrained Ordination Analysis with Enrichment of Bell-Shaped Response Functions.

Zhang Y, Thas O.

PLoS One. 2016 Apr 21;11(4):e0154079. doi: 10.1371/journal.pone.0154079. eCollection 2016.

28.

Principal bicorrelation analysis: Unraveling associations between three data sources.

Mattiello F, Thas O, Verbist B.

J Biopharm Stat. 2016;26(3):534-51. doi: 10.1080/10543406.2015.1052491. Epub 2015 Jun 22.

PMID:
26098298
29.

ddpcRquant: threshold determination for single channel droplet digital PCR experiments.

Trypsteen W, Vynck M, De Neve J, Bonczkowski P, Kiselinova M, Malatinkova E, Vervisch K, Thas O, Vandekerckhove L, De Spiegelaere W.

Anal Bioanal Chem. 2015 Jul;407(19):5827-34. doi: 10.1007/s00216-015-8773-4. Epub 2015 May 29.

PMID:
26022094
30.

ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering.

Verbist B, Clement L, Reumers J, Thys K, Vapirev A, Talloen W, Wetzels Y, Meys J, Aerssens J, Bijnens L, Thas O.

BMC Bioinformatics. 2015 Feb 22;16:59. doi: 10.1186/s12859-015-0458-7.

31.

Robust regression methods for real-time polymerase chain reaction.

Trypsteen W, De Neve J, Bosman K, Nijhuis M, Thas O, Vandekerckhove L, De Spiegelaere W.

Anal Biochem. 2015 Jul 1;480:34-6. doi: 10.1016/j.ab.2015.04.001. Epub 2015 Apr 8.

PMID:
25862086
32.

Seasonality modifies the effect of a lipid-based nutrient supplement for pregnant rural women on birth length.

Toe LC, Bouckaert KP, De Beuf K, Roberfroid D, Meda N, Thas O, Van Camp J, Kolsteren PW, Huybregts LF.

J Nutr. 2015 Mar;145(3):634-9. doi: 10.3945/jn.114.203448. Epub 2015 Jan 14.

PMID:
25733482
33.

Mining for viral fragments in methylation enriched sequencing data.

Mensaert K, Van Criekinge W, Thas O, Schuuring E, Steenbergen RD, Wisman GB, De Meyer T.

Front Genet. 2015 Feb 4;6:16. doi: 10.3389/fgene.2015.00016. eCollection 2015.

34.

Using transcriptomics to guide lead optimization in drug discovery projects: Lessons learned from the QSTAR project.

Verbist B, Klambauer G, Vervoort L, Talloen W; QSTAR Consortium, Shkedy Z, Thas O, Bender A, Göhlmann HW, Hochreiter S.

Drug Discov Today. 2015 May;20(5):505-13. doi: 10.1016/j.drudis.2014.12.014. Epub 2015 Jan 10.

35.

Increasing the power of the Mann-Whitney test in randomized experiments through flexible covariate adjustment.

Vermeulen K, Thas O, Vansteelandt S.

Stat Med. 2015 Mar 15;34(6):1012-30. doi: 10.1002/sim.6386. Epub 2014 Dec 5.

PMID:
25475954
36.

Comparison of the abiotic preferences of macroinvertebrates in tropical river basins.

Everaert G, De Neve J, Boets P, Dominguez-Granda L, Mereta ST, Ambelu A, Hoang TH, Goethals PL, Thas O.

PLoS One. 2014 Oct 3;9(10):e108898. doi: 10.1371/journal.pone.0108898. eCollection 2014.

37.

VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering.

Verbist BM, Thys K, Reumers J, Wetzels Y, Van der Borght K, Talloen W, Aerssens J, Clement L, Thas O.

Bioinformatics. 2015 Jan 1;31(1):94-101. doi: 10.1093/bioinformatics/btu587. Epub 2014 Aug 31.

PMID:
25178459
38.

unifiedWMWqPCR: the unified Wilcoxon-Mann-Whitney test for analyzing RT-qPCR data in R.

De Neve J, Meys J, Ottoy JP, Clement L, Thas O.

Bioinformatics. 2014 Sep 1;30(17):2494-5. doi: 10.1093/bioinformatics/btu313. Epub 2014 May 2.

PMID:
24794933
39.

The more, the merrier: heterotroph richness stimulates methanotrophic activity.

Ho A, de Roy K, Thas O, De Neve J, Hoefman S, Vandamme P, Heylen K, Boon N.

ISME J. 2014 Sep;8(9):1945-8. doi: 10.1038/ismej.2014.74. Epub 2014 May 2.

40.

Next-generation technologies and data analytical approaches for epigenomics.

Mensaert K, Denil S, Trooskens G, Van Criekinge W, Thas O, De Meyer T.

Environ Mol Mutagen. 2014 Apr;55(3):155-70. doi: 10.1002/em.21841. Epub 2013 Dec 10. Review.

PMID:
24327356
41.

Dissemination and implementation of the ARIA guidelines for allergic rhinitis in general practice.

Van Hoecke H, Vandeplas G, Acke F, Thas O, De Sutter A, Gevaert P, Van Cauwenberge P, Dhooge I.

Int Arch Allergy Immunol. 2014;163(2):106-13. doi: 10.1159/000355953. Epub 2013 Nov 30.

PMID:
24296744
42.

An extension of the Wilcoxon-Mann-Whitney test for analyzing RT-qPCR data.

De Neve J, Thas O, Ottoy JP, Clement L.

Stat Appl Genet Mol Biol. 2013 Jun;12(3):333-46. doi: 10.1515/sagmb-2012-0003.

PMID:
23652635
43.

A predictive model for dysphagia following IMRT for head and neck cancer: introduction of the EMLasso technique.

De Ruyck K, Duprez F, Werbrouck J, Sabbe N, Sofie de L, Boterberg T, Madani I, Thas O, Wilfried de N, Thierens H.

Radiother Oncol. 2013 Jun;107(3):295-9. doi: 10.1016/j.radonc.2013.03.021. Epub 2013 Apr 22.

PMID:
23618501
44.

EMLasso: logistic lasso with missing data.

Sabbe N, Thas O, Ottoy JP.

Stat Med. 2013 Aug 15;32(18):3143-57. doi: 10.1002/sim.5760. Epub 2013 Feb 25.

PMID:
23440969
45.

Environmental conditions and community evenness determine the outcome of biological invasion.

De Roy K, Marzorati M, Negroni A, Thas O, Balloi A, Fava F, Verstraete W, Daffonchio D, Boon N.

Nat Commun. 2013;4:1383. doi: 10.1038/ncomms2392.

46.

Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model.

Van den Abbeele P, Belzer C, Goossens M, Kleerebezem M, De Vos WM, Thas O, De Weirdt R, Kerckhof FM, Van de Wiele T.

ISME J. 2013 May;7(5):949-61. doi: 10.1038/ismej.2012.158. Epub 2012 Dec 13.

47.

Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model.

Beuf KD, Schrijver JD, Thas O, Criekinge WV, Irizarry RA, Clement L.

BMC Bioinformatics. 2012 Nov 15;13:303. doi: 10.1186/1471-2105-13-303.

48.

Analysis of tiling array expression studies with flexible designs in Bioconductor (waveTiling).

De Beuf K, Pipelers P, Andriankaja M, Thas O, Inzé D, Crainiceanu C, Clement L.

BMC Bioinformatics. 2012 Sep 14;13:234. doi: 10.1186/1471-2105-13-234.

49.

Biodiversity of freshwater diatom communities during 1000 years of metal mining, land use, and climate change in central Sweden.

De Laender F, Verschuren D, Bindler R, Thas O, Janssen CR.

Environ Sci Technol. 2012 Aug 21;46(16):9097-105. doi: 10.1021/es3015452. Epub 2012 Aug 10.

PMID:
22827476
50.

The potential for adaptation in a natural Daphnia magna population: broad and narrow-sense heritability of net reproductive rate under Cd stress at two temperatures.

Messiaen M, Janssen CR, Thas O, De Schamphelaere KA.

Ecotoxicology. 2012 Oct;21(7):1899-910. doi: 10.1007/s10646-012-0923-2. Epub 2012 May 22.

PMID:
22614034

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