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Items: 1 to 50 of 91

1.

Transcriptome profiling in blood before and after hepatitis B vaccination shows significant differences in gene expression between responders and non-responders.

Bartholomeus E, De Neuter N, Meysman P, Suls A, Keersmaekers N, Elias G, Jansens H, Hens N, Smits E, Van Tendeloo V, Beutels P, Van Damme P, Ogunjimi B, Laukens K, Mortier G.

Vaccine. 2018 Sep 8. pii: S0264-410X(18)31236-2. doi: 10.1016/j.vaccine.2018.09.001. [Epub ahead of print]

PMID:
30205979
2.

Grasping frequent subgraph mining for bioinformatics applications.

Mrzic A, Meysman P, Bittremieux W, Moris P, Cule B, Goethals B, Laukens K.

BioData Min. 2018 Sep 3;11:20. doi: 10.1186/s13040-018-0181-9. eCollection 2018. Review.

3.

Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing.

Bittremieux W, Meysman P, Noble WS, Laukens K.

J Proteome Res. 2018 Sep 13. doi: 10.1021/acs.jproteome.8b00359. [Epub ahead of print]

PMID:
30184435
4.

In vitro assessment of hepatotoxicity by metabolomics: a review.

Cuykx M, Rodrigues RM, Laukens K, Vanhaecke T, Covaci A.

Arch Toxicol. 2018 Oct;92(10):3007-3029. doi: 10.1007/s00204-018-2286-9. Epub 2018 Aug 25. Review.

PMID:
30155722
5.

Transcriptome profiling of HepG2 cells exposed to the flame retardant 9,10-dihydro-9-oxa-10-phosphaphenanthrene 10-oxide (DOPO).

Krivoshiev BV, Beemster GTS, Sprangers K, Cuypers B, Laukens K, Blust R, Husson SJ.

Toxicol Res (Camb). 2018 Mar 12;7(3):492-502. doi: 10.1039/c8tx00006a. eCollection 2018 May 8.

PMID:
30090599
6.

Author Correction: Multidisciplinary study of the secondary immune response in grandparents re-exposed to chickenpox.

Ogunjimi B, Van den Bergh J, Meysman P, Heynderickx S, Bergs K, Jansens H, Leuridan E, Vorsters A, Goossens H, Laukens K, Cools N, Van Tendeloo V, Hens N, Van Damme P, Smits E, Beutels P.

Sci Rep. 2018 Jul 12;8(1):10824. doi: 10.1038/s41598-018-28930-9.

7.

Memory CD4+ T cell receptor repertoire data mining as a tool for identifying cytomegalovirus serostatus.

De Neuter N, Bartholomeus E, Elias G, Keersmaekers N, Suls A, Jansens H, Smits E, Hens N, Beutels P, Van Damme P, Mortier G, Van Tendeloo V, Laukens K, Meysman P, Ogunjimi B.

Genes Immun. 2018 Jun 15. doi: 10.1038/s41435-018-0035-y. [Epub ahead of print]

PMID:
29904098
8.

Proceedings of the EuBIC developer's meeting 2018.

Willems S, Bouyssié D, Deforce D, Dorfer V, Gorshkov V, Kopczynski D, Laukens K, Locard-Paulet M, Schwämmle V, Uszkoreit J, Valkenborg D, Vaudel M, Bittremieux W.

J Proteomics. 2018 Sep 15;187:25-27. doi: 10.1016/j.jprot.2018.05.015. Epub 2018 Jun 2.

PMID:
29864591
9.

Integrated genomic and metabolomic profiling of ISC1, an emerging Leishmania donovani population in the Indian subcontinent.

Cuypers B, Berg M, Imamura H, Dumetz F, De Muylder G, Domagalska MA, Rijal S, Bhattarai NR, Maes I, Sanders M, Cotton JA, Meysman P, Laukens K, Dujardin JC.

Infect Genet Evol. 2018 Apr 19;62:170-178. doi: 10.1016/j.meegid.2018.04.021. [Epub ahead of print]

10.

speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification.

Beirnaert C, Meysman P, Vu TN, Hermans N, Apers S, Pieters L, Covaci A, Laukens K.

PLoS Comput Biol. 2018 Mar 1;14(3):e1006018. doi: 10.1371/journal.pcbi.1006018. eCollection 2018 Mar.

11.

pBRIT: gene prioritization by correlating functional and phenotypic annotations through integrative data fusion.

Kumar AA, Van Laer L, Alaerts M, Ardeshirdavani A, Moreau Y, Laukens K, Loeys B, Vandeweyer G.

Bioinformatics. 2018 Jul 1;34(13):2254-2262. doi: 10.1093/bioinformatics/bty079.

12.

Increased herpes zoster risk associated with poor HLA-A immediate early 62 protein (IE62) affinity.

Meysman P, De Neuter N, Bartholomeus E, Elias G, Van den Bergh J, Emonds MP, Haasnoot GW, Heynderickx S, Wens J, Michels NR, Lambert J, Lion E, Claas FHJ, Goossens H, Smits E, Van Damme P, Van Tendeloo V, Beutels P, Suls A, Mortier G, Laukens K, Ogunjimi B.

Immunogenetics. 2018 Jun;70(6):363-372. doi: 10.1007/s00251-017-1047-x. Epub 2017 Dec 1.

PMID:
29196796
13.

A tutorial in small molecule identification via electrospray ionization-mass spectrometry: The practical art of structural elucidation.

De Vijlder T, Valkenborg D, Lemière F, Romijn EP, Laukens K, Cuyckens F.

Mass Spectrom Rev. 2018 Sep;37(5):607-629. doi: 10.1002/mas.21551. Epub 2017 Nov 9. Review.

14.

Toxicogenomics of the flame retardant tris (2-butoxyethyl) phosphate in HepG2 cells using RNA-seq.

Krivoshiev BV, Beemster GTS, Sprangers K, Cuypers B, Laukens K, Blust R, Husson SJ.

Toxicol In Vitro. 2018 Feb;46:178-188. doi: 10.1016/j.tiv.2017.10.011. Epub 2017 Oct 9.

PMID:
29024780
15.

Quality control in mass spectrometry-based proteomics.

Bittremieux W, Tabb DL, Impens F, Staes A, Timmerman E, Martens L, Laukens K.

Mass Spectrom Rev. 2018 Sep;37(5):697-711. doi: 10.1002/mas.21544. Epub 2017 Sep 7. Review.

PMID:
28802010
16.

On the feasibility of mining CD8+ T cell receptor patterns underlying immunogenic peptide recognition.

De Neuter N, Bittremieux W, Beirnaert C, Cuypers B, Mrzic A, Moris P, Suls A, Van Tendeloo V, Ogunjimi B, Laukens K, Meysman P.

Immunogenetics. 2018 Mar;70(3):159-168. doi: 10.1007/s00251-017-1023-5. Epub 2017 Aug 4.

PMID:
28779185
17.

A community proposal to integrate proteomics activities in ELIXIR.

Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJR, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, Novak P, Palmblad M, Piovesan D, Pühler A, Schwämmle V, Valkenborg D, van Rijswijk M, Vondrasek J, Eisenacher M, Martens L, Kohlbacher O.

F1000Res. 2017 Jun 13;6. pii: ELIXIR-875. doi: 10.12688/f1000research.11751.1. eCollection 2017.

18.

Multiplexed Spliced-Leader Sequencing: A high-throughput, selective method for RNA-seq in Trypanosomatids.

Cuypers B, Domagalska MA, Meysman P, Muylder G, Vanaerschot M, Imamura H, Dumetz F, Verdonckt TW, Myler PJ, Ramasamy G, Laukens K, Dujardin JC.

Sci Rep. 2017 Jun 16;7(1):3725. doi: 10.1038/s41598-017-03987-0.

19.

InSourcerer: a high-throughput method to search for unknown metabolite modifications by mass spectrometry.

Mrzic A, Lermyte F, Vu TN, Valkenborg D, Laukens K.

Rapid Commun Mass Spectrom. 2017 Sep 15;31(17):1396-1404. doi: 10.1002/rcm.7910.

PMID:
28569011
20.

Genome-Wide SNP Analysis Reveals Distinct Origins of Trypanosoma evansi and Trypanosoma equiperdum.

Cuypers B, Van den Broeck F, Van Reet N, Meehan CJ, Cauchard J, Wilkes JM, Claes F, Goddeeris B, Birhanu H, Dujardin JC, Laukens K, Büscher P, Deborggraeve S.

Genome Biol Evol. 2017 Aug 1;9(8):1990-1997. doi: 10.1093/gbe/evx102.

21.

Multidisciplinary study of the secondary immune response in grandparents re-exposed to chickenpox.

Ogunjimi B, Van den Bergh J, Meysman P, Heynderickx S, Bergs K, Jansens H, Leuridan E, Vorsters A, Goossens H, Laukens K, Cools N, Van Tendeloo V, Hens N, Van Damme P, Smits E, Beutels P.

Sci Rep. 2017 Apr 24;7(1):1077. doi: 10.1038/s41598-017-01024-8. Erratum in: Sci Rep. 2018 Jul 12;8(1):10824.

22.

sfinx: an R package for the elimination of false positives from affinity purification-mass spectrometry datasets.

Titeca K, Meysman P, Laukens K, Martens L, Tavernier J, Eyckerman S.

Bioinformatics. 2017 Jun 15;33(12):1902-1904. doi: 10.1093/bioinformatics/btx076.

PMID:
28186257
23.

Tailored liquid chromatography-mass spectrometry analysis improves the coverage of the intracellular metabolome of HepaRG cells.

Cuykx M, Negreira N, Beirnaert C, Van den Eede N, Rodrigues R, Vanhaecke T, Laukens K, Covaci A.

J Chromatogr A. 2017 Mar 3;1487:168-178. doi: 10.1016/j.chroma.2017.01.050. Epub 2017 Jan 23.

PMID:
28153450
24.

Computational quality control tools for mass spectrometry proteomics.

Bittremieux W, Valkenborg D, Martens L, Laukens K.

Proteomics. 2017 Feb;17(3-4). doi: 10.1002/pmic.201600159. Epub 2016 Oct 17. Review.

PMID:
27549080
25.

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
26.

Practical Approaches for Mining Frequent Patterns in Molecular Datasets.

Naulaerts S, Moens S, Engelen K, Berghe WV, Goethals B, Laukens K, Meysman P.

Bioinform Biol Insights. 2016 May 2;10:37-47. doi: 10.4137/BBI.S38419. eCollection 2016. Review.

27.

Erratum to: Immunological evasion of immediate-early varicella zoster virus proteins.

Meysman P, Fedorov D, Van Tendeloo V, Ogunjimi B, Laukens K.

Immunogenetics. 2016 Jul;68(6-7):487. doi: 10.1007/s00251-016-0912-3. No abstract available.

PMID:
27107763
28.

Apolipoprotein L1 Variant Associated with Increased Susceptibility to Trypanosome Infection.

Cuypers B, Lecordier L, Meehan CJ, Van den Broeck F, Imamura H, Büscher P, Dujardin JC, Laukens K, Schnaufer A, Dewar C, Lewis M, Balmer O, Azurago T, Kyei-Faried S, Ohene SA, Duah B, Homiah P, Mensah EK, Anleah F, Franco JR, Pays E, Deborggraeve S.

MBio. 2016 Apr 12;7(2):e02198-15. doi: 10.1128/mBio.02198-15.

29.

Withaferin A induces heme oxygenase (HO-1) expression in endothelial cells via activation of the Keap1/Nrf2 pathway.

Heyninck K, Sabbe L, Chirumamilla CS, Szarc Vel Szic K, Vander Veken P, Lemmens KJA, Lahtela-Kakkonen M, Naulaerts S, Op de Beeck K, Laukens K, Van Camp G, Weseler AR, Bast A, Haenen GRMM, Haegeman G, Vanden Berghe W.

Biochem Pharmacol. 2016 Jun 1;109:48-61. doi: 10.1016/j.bcp.2016.03.026. Epub 2016 Apr 1.

PMID:
27045103
30.

Designing biomedical proteomics experiments: state-of-the-art and future perspectives.

Maes E, Kelchtermans P, Bittremieux W, De Grave K, Degroeve S, Hooyberghs J, Mertens I, Baggerman G, Ramon J, Laukens K, Martens L, Valkenborg D.

Expert Rev Proteomics. 2016 May;13(5):495-511. doi: 10.1586/14789450.2016.1172967. Epub 2016 Apr 25. Review.

PMID:
27031651
31.

Immunological evasion of immediate-early varicella zoster virus proteins.

Meysman P, Fedorov D, Van Tendeloo V, Ogunjimi B, Laukens K.

Immunogenetics. 2016 Jul;68(6-7):483-486. doi: 10.1007/s00251-016-0911-4. Epub 2016 Mar 29. Erratum in: Immunogenetics. 2016 Jul;68(6-7):487.

PMID:
27020058
32.

Unsupervised Quality Assessment of Mass Spectrometry Proteomics Experiments by Multivariate Quality Control Metrics.

Bittremieux W, Meysman P, Martens L, Valkenborg D, Laukens K.

J Proteome Res. 2016 Apr 1;15(4):1300-7. doi: 10.1021/acs.jproteome.6b00028. Epub 2016 Mar 18.

PMID:
26974716
33.

Protein complex analysis: From raw protein lists to protein interaction networks.

Meysman P, Titeca K, Eyckerman S, Tavernier J, Goethals B, Martens L, Valkenborg D, Laukens K.

Mass Spectrom Rev. 2017 Sep;36(5):600-614. doi: 10.1002/mas.21485. Epub 2015 Dec 28. Review.

PMID:
26709718
34.

SFINX: Straightforward Filtering Index for Affinity Purification-Mass Spectrometry Data Analysis.

Titeca K, Meysman P, Gevaert K, Tavernier J, Laukens K, Martens L, Eyckerman S.

J Proteome Res. 2016 Jan 4;15(1):332-8. doi: 10.1021/acs.jproteome.5b00666. Epub 2015 Dec 17.

PMID:
26616242
35.

COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses.

Moretto M, Sonego P, Dierckxsens N, Brilli M, Bianco L, Ledezma-Tejeida D, Gama-Castro S, Galardini M, Romualdi C, Laukens K, Collado-Vides J, Meysman P, Engelen K.

Nucleic Acids Res. 2016 Jan 4;44(D1):D620-3. doi: 10.1093/nar/gkv1251. Epub 2015 Nov 19.

36.

Open-Source, Platform-Independent Library and Online Scripting Environment for Accessing Thermo Scientific RAW Files.

Kelchtermans P, Silva AS, Argentini A, Staes A, Vandenbussche J, Laukens K, Valkenborg D, Martens L.

J Proteome Res. 2015 Nov 6;14(11):4940-3. doi: 10.1021/acs.jproteome.5b00778. Epub 2015 Oct 29.

PMID:
26477298
37.

Discovery of Spatially Cohesive Itemsets in Three-Dimensional Protein Structures.

Zhou C, Meysman P, Cule B, Laukens K, Goethals B.

IEEE/ACM Trans Comput Biol Bioinform. 2014 Sep-Oct;11(5):814-25. doi: 10.1109/TCBB.2014.2311795.

PMID:
26356855
38.

Metabolomics analysis of the toxicity pathways of triphenyl phosphate in HepaRG cells and comparison to oxidative stress mechanisms caused by acetaminophen.

Van den Eede N, Cuykx M, Rodrigues RM, Laukens K, Neels H, Covaci A, Vanhaecke T.

Toxicol In Vitro. 2015 Dec;29(8):2045-54. doi: 10.1016/j.tiv.2015.08.012. Epub 2015 Aug 28.

PMID:
26318275
39.

iMonDB: Mass Spectrometry Quality Control through Instrument Monitoring.

Bittremieux W, Willems H, Kelchtermans P, Martens L, Laukens K, Valkenborg D.

J Proteome Res. 2015 May 1;14(5):2360-6. doi: 10.1021/acs.jproteome.5b00127. Epub 2015 Apr 2.

PMID:
25798920
40.

Mining the entire Protein DataBank for frequent spatially cohesive amino acid patterns.

Meysman P, Zhou C, Cule B, Goethals B, Laukens K.

BioData Min. 2015 Jan 31;8:4. doi: 10.1186/s13040-015-0038-4. eCollection 2015.

41.

Ectopic microRNA-150-5p transcription sensitizes glucocorticoid therapy response in MM1S multiple myeloma cells but fails to overcome hormone therapy resistance in MM1R cells.

Palagani A, Op de Beeck K, Naulaerts S, Diddens J, Sekhar Chirumamilla C, Van Camp G, Laukens K, Heyninck K, Gerlo S, Mestdagh P, Vandesompele J, Berghe WV.

PLoS One. 2014 Dec 4;9(12):e113842. doi: 10.1371/journal.pone.0113842. eCollection 2014.

42.

A generic approach for "shotgun" analysis of the soluble proteome of plant cell suspension cultures.

De Vijlder T, Valkenborg D, Dewaele D, Remmerie N, Laukens K, Witters E.

J Chromatogr B Analyt Technol Biomed Life Sci. 2015 Jan 1;974:48-56. doi: 10.1016/j.jchromb.2014.10.024. Epub 2014 Oct 27.

PMID:
25463197
43.

Bioinformatics approaches for the functional interpretation of protein lists: from ontology term enrichment to network analysis.

Laukens K, Naulaerts S, Berghe WV.

Proteomics. 2015 Mar;15(5-6):981-96. doi: 10.1002/pmic.201400296. Epub 2015 Feb 20. Review.

PMID:
25430566
44.

Unravelling associations between unassigned mass spectrometry peaks with frequent itemset mining techniques.

Vu TN, Mrzic A, Valkenborg D, Maes E, Lemière F, Goethals B, Laukens K.

Proteome Sci. 2014 Nov 18;12(1):54. doi: 10.1186/s12953-014-0054-1. eCollection 2014.

45.

Towards automated discrimination of lipids versus peptides from full scan mass spectra.

Dittwald P, Nghia VT, Harris GA, Caprioli RM, Van de Plas R, Laukens K, Gambin A, Valkenborg D.

EuPA Open Proteom. 2014 Sep 1;4:87-100.

46.

Varicella-zoster virus-derived major histocompatibility complex class I-restricted peptide affinity is a determining factor in the HLA risk profile for the development of postherpetic neuralgia.

Meysman P, Ogunjimi B, Naulaerts S, Beutels P, Van Tendeloo V, Laukens K.

J Virol. 2015 Jan 15;89(2):962-9. doi: 10.1128/JVI.02500-14. Epub 2014 Oct 29.

47.

Comparative analysis of gene expression: uncovering expression conservation and divergence between Salmonella enterica serovar Typhimurium strains LT2 and 14028S.

Sonego P, Meysman P, Moretto M, Viola R, Laukens K, Cavalieri D, Engelen K.

Methods Mol Biol. 2015;1231:125-35. doi: 10.1007/978-1-4939-1720-4_8.

PMID:
25343862
48.

The radiosensitising effect of gemcitabine and its main metabolite dFdU under low oxygen conditions is in vitro not dependent on functional HIF-1 protein.

Wouters A, Pauwels B, Burrows N, Baay M, Deschoolmeester V, Vu TN, Laukens K, Meijnders P, Van Gestel D, Williams KJ, Van den Weyngaert D, Vermorken JB, Pauwels P, Peeters M, Lardon F.

BMC Cancer. 2014 Aug 16;14:594. doi: 10.1186/1471-2407-14-594.

49.

Efficient reduction of candidate matches in peptide spectrum library searching using the top k most intense peaks.

Vu TN, Bittremieux W, Valkenborg D, Goethals B, Lemière F, Laukens K.

J Proteome Res. 2014 Sep 5;13(9):4175-83. doi: 10.1021/pr401269z. Epub 2014 Jul 24.

PMID:
25004400
50.

jqcML: an open-source java API for mass spectrometry quality control data in the qcML format.

Bittremieux W, Kelchtermans P, Valkenborg D, Martens L, Laukens K.

J Proteome Res. 2014 Jul 3;13(7):3484-7. doi: 10.1021/pr401274z. Epub 2014 Jun 17.

PMID:
24906114

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