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Items: 1 to 50 of 83

1.

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 18. pii: S1567-1348(18)30200-4. doi: 10.1016/j.meegid.2018.04.021. [Epub ahead of print]

PMID:
29679745
2.

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.

3.

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 Feb 14. doi: 10.1093/bioinformatics/bty079. [Epub ahead of print]

PMID:
29452392
4.

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. 2017 Dec 1. doi: 10.1007/s00251-017-1047-x. [Epub ahead of print]

PMID:
29196796
5.

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. 2017 Nov 9. doi: 10.1002/mas.21551. [Epub ahead of print] Review.

PMID:
29120505
6.

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
7.

Quality control in mass spectrometry-based proteomics.

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

Mass Spectrom Rev. 2017 Sep 7. doi: 10.1002/mas.21544. [Epub ahead of print] Review.

PMID:
28802010
8.

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
9.

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.

10.

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.

11.

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
12.

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.

13.

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, Jansen 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.

14.

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
15.

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
16.

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
17.

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
18.

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.

19.

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
20.

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.

21.

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
22.

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
23.

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
24.

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
25.

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
26.

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
27.

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.

28.

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
29.

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
30.

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
31.

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
32.

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.

33.

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.

34.

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
35.

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
36.

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.

37.

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.

38.

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.

39.

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
40.

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.

41.

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
42.

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
43.

Dietary flavanols modulate the transcription of genes associated with cardiovascular pathology without changes in their DNA methylation state.

Milenkovic D, Vanden Berghe W, Boby C, Leroux C, Declerck K, Szarc vel Szic K, Heyninck K, Laukens K, Bizet M, Defrance M, Dedeurwaerder S, Calonne E, Fuks F, Haegeman G, Haenen GR, Bast A, Weseler AR.

PLoS One. 2014 Apr 24;9(4):e95527. doi: 10.1371/journal.pone.0095527. eCollection 2014.

44.

qcML: an exchange format for quality control metrics from mass spectrometry experiments.

Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L.

Mol Cell Proteomics. 2014 Aug;13(8):1905-13. doi: 10.1074/mcp.M113.035907. Epub 2014 Apr 23.

45.

Structural properties of prokaryotic promoter regions correlate with functional features.

Meysman P, Collado-Vides J, Morett E, Viola R, Engelen K, Laukens K.

PLoS One. 2014 Feb 7;9(2):e88717. doi: 10.1371/journal.pone.0088717. eCollection 2014.

46.

The use of the isotopic distribution as a complementary quality metric to assess tandem mass spectra results.

Ghavidel FZ, Mertens I, Baggerman G, Laukens K, Burzykowski T, Valkenborg D.

J Proteomics. 2014 Feb 26;98:150-8. doi: 10.1016/j.jprot.2013.12.013. Epub 2013 Dec 31.

PMID:
24384257
47.

Machine learning applications in proteomics research: how the past can boost the future.

Kelchtermans P, Bittremieux W, De Grave K, Degroeve S, Ramon J, Laukens K, Valkenborg D, Barsnes H, Martens L.

Proteomics. 2014 Mar;14(4-5):353-66. doi: 10.1002/pmic.201300289. Epub 2014 Jan 21. Review.

PMID:
24323524
48.

COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia.

Meysman P, Sonego P, Bianco L, Fu Q, Ledezma-Tejeida D, Gama-Castro S, Liebens V, Michiels J, Laukens K, Marchal K, Collado-Vides J, Engelen K.

Nucleic Acids Res. 2014 Jan;42(Database issue):D649-53. doi: 10.1093/nar/gkt1086. Epub 2013 Nov 8.

49.

A primer to frequent itemset mining for bioinformatics.

Naulaerts S, Meysman P, Bittremieux W, Vu TN, Vanden Berghe W, Goethals B, Laukens K.

Brief Bioinform. 2015 Mar;16(2):216-31. doi: 10.1093/bib/bbt074. Epub 2013 Oct 26. Review.

50.

The role of monocytes in the development of Tuberculosis-associated Immune Reconstitution Inflammatory Syndrome.

Tran HT, Van den Bergh R, Vu TN, Laukens K, Worodria W, Loembé MM, Colebunders R, Kestens L, De Baetselier P, Raes G; TB-IRIS Study Group.

Immunobiology. 2014 Jan;219(1):37-44. doi: 10.1016/j.imbio.2013.07.004. Epub 2013 Jul 25.

PMID:
23958034

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