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Items: 40

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.

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.

5.

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
6.

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]

7.

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.

8.

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
9.

Second ISCB Latin American Student Council Symposium (LA-SCS) 2016.

Monzon AM, Hasenahuer MA, Mancini E, Coimbra N, Cravero F, Cáceres-Molina J, Ramírez-Sarmiento CA, Palopoli N, Meysman P, Parra RG.

F1000Res. 2017 Aug 16;6. pii: ISCB Comm J-1491. doi: 10.12688/f1000research.12321.1. eCollection 2017.

10.

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
11.

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.

12.

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.

13.

Ten simple rules for forming a scientific professional society.

Gaëta BA, De Las Rivas J, Horton P, Meysman P, Mulder N, Romano P, Welch L.

PLoS Comput Biol. 2017 Mar 23;13(3):e1005226. doi: 10.1371/journal.pcbi.1005226. eCollection 2017 Mar. No abstract available.

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.

ISCB-Student Council Narratives: Strategical development of the ISCB-Regional Student Groups in 2016.

Shome S, Meysman P, Parra RG, Monzon AM, Palopoli N, White B, Rahman F, Hassan M, Özkeserli Z, Ashano E, Hughitt VK, Uzair Khan M, Murphy DJ.

F1000Res. 2016 Dec 20;5. pii: ISCB Comm J-2882. doi: 10.12688/f1000research.10420.1. eCollection 2016.

16.

Highlights from the ISCB Student Council Symposia in 2016.

Cuypers B, Jacobsen A, Siranosian B, Schwahn K, Conard AM, Aben N, Hassan M, Fatima N, Hermans SMA, Woghiren M, Meysman P, Rahman F, Jigisha A.

F1000Res. 2016 Dec 15;5. pii: ISCB Comm J-2852. doi: 10.12688/f1000research.10389.1. eCollection 2016.

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.

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
21.

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
22.

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
23.

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
24.

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.

25.

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
26.

Highlights from the Third International Society for Computational Biology (ISCB) European Student Council Symposium 2014.

Francescatto M, Hermans SM, Babaei S, Vicedo E, Borrel A, Meysman P.

BMC Bioinformatics. 2015;16 Suppl 3:A1-9. Epub 2015 Feb 13.

27.

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.

28.

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.

29.

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
30.

Soft skills: an important asset acquired from organizing regional student group activities.

de Ridder J, Meysman P, Oluwagbemi O, Abeel T.

PLoS Comput Biol. 2014 Jul 3;10(7):e1003708. doi: 10.1371/journal.pcbi.1003708. eCollection 2014 Jul.

31.

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.

32.

MAGIC: access portal to a cross-platform gene expression compendium for maize.

Fu Q, Fierro AC, Meysman P, Sanchez-Rodriguez A, Vandepoele K, Marchal K, Engelen K.

Bioinformatics. 2014 May 1;30(9):1316-8. doi: 10.1093/bioinformatics/btt739. Epub 2014 Jan 8.

PMID:
24407224
33.

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.

34.

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.

35.

Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles.

Meysman P, Sánchez-Rodríguez A, Fu Q, Marchal K, Engelen K.

Mol Biol Evol. 2013 Jun;30(6):1302-14. doi: 10.1093/molbev/mst029. Epub 2013 Feb 20.

36.

DNA structural properties in the classification of genomic transcription regulation elements.

Meysman P, Marchal K, Engelen K.

Bioinform Biol Insights. 2012;6:155-68. doi: 10.4137/BBI.S9426. Epub 2012 Jul 2.

37.

Directed module detection in a large-scale expression compendium.

Fu Q, Lemmens K, Sanchez-Rodriguez A, Thijs IM, Meysman P, Sun H, Fierro AC, Engelen K, Marchal K.

Methods Mol Biol. 2012;804:131-65. doi: 10.1007/978-1-61779-361-5_8.

PMID:
22144152
38.

COLOMBOS: access port for cross-platform bacterial expression compendia.

Engelen K, Fu Q, Meysman P, Sánchez-Rodríguez A, De Smet R, Lemmens K, Fierro AC, Marchal K.

PLoS One. 2011;6(7):e20938. doi: 10.1371/journal.pone.0020938. Epub 2011 Jul 14.

39.

Query-based biclustering of gene expression data using Probabilistic Relational Models.

Zhao H, Cloots L, Van den Bulcke T, Wu Y, De Smet R, Storms V, Meysman P, Engelen K, Marchal K.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S37. doi: 10.1186/1471-2105-12-S1-S37.

40.

Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli.

Meysman P, Dang TH, Laukens K, De Smet R, Wu Y, Marchal K, Engelen K.

Nucleic Acids Res. 2011 Jan;39(2):e6. doi: 10.1093/nar/gkq1071. Epub 2010 Nov 4.

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