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Items: 44

1.

mQC: A post-mapping data exploration tool for ribosome profiling.

Verbruggen S, Menschaert G.

Comput Methods Programs Biomed. 2018 Oct 28. pii: S0169-2607(18)30420-6. doi: 10.1016/j.cmpb.2018.10.018. [Epub ahead of print]

PMID:
30401579
2.

Deletion 6q drives T-cell leukemia progression by ribosome modulation.

Gachet S, El-Chaar T, Avran D, Genescà E, Catez F, Quentin S, Delord M, Thérizols G, Briot D, Meunier G, Hernandez L, Pla M, Smits WK, Buijs-Gladdines JGCAM, Van Loocke W, Menschaert G, André-Schmutz I, Taghon T, Van Vlierberghe P, Meijerink JP, Baruchel A, Dombret H, Clappier E, Diaz JJ, Gazin C, de The H, Sigaux F, Soulier J.

Cancer Discov. 2018 Sep 28. pii: CD-17-0831. doi: 10.1158/2159-8290.CD-17-0831. [Epub ahead of print]

PMID:
30266814
3.

Short Open Reading Frames and Their Encoded Peptides.

Rothnagel J, Menschaert G.

Proteomics. 2018 Aug;18(15):e1870117. doi: 10.1002/pmic.201870117. Epub 2018 Jun 26. No abstract available.

PMID:
30134045
4.

Comprehensive Peptide Analysis of Mouse Brain Striatum Identifies Novel sORF-Encoded Polypeptides.

Budamgunta H, Olexiouk V, Luyten W, Schildermans K, Maes E, Boonen K, Menschaert G, Baggerman G.

Proteomics. 2018 May;18(10):e1700218. doi: 10.1002/pmic.201700218. Erratum in: Proteomics. 2018 Aug;18(15):e1870118.

PMID:
29710410
5.

Short Open Reading Frames and Their Encoded Peptides.

Rothnagel J, Menschaert G.

Proteomics. 2018 May;18(10):e1700035. doi: 10.1002/pmic.201700035. No abstract available. Erratum in: Proteomics. 2018 Aug;18(15):e1870117.

PMID:
29691985
6.

Mass spectrometric evidence for neuropeptide-amidating enzymes in Caenorhabditis elegans.

Van Bael S, Watteyne J, Boonen K, De Haes W, Menschaert G, Ringstad N, Horvitz HR, Schoofs L, Husson SJ, Temmerman L.

J Biol Chem. 2018 Apr 20;293(16):6052-6063. doi: 10.1074/jbc.RA117.000731. Epub 2018 Feb 27.

PMID:
29487130
7.

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.

Menschaert G, Wang X, Jones AR, Ghali F, Fenyö D, Olexiouk V, Zhang B, Deutsch EW, Ternent T, Vizcaíno JA.

Genome Biol. 2018 Jan 31;19(1):12. doi: 10.1186/s13059-017-1377-x.

8.

Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini.

Na CH, Barbhuiya MA, Kim MS, Verbruggen S, Eacker SM, Pletnikova O, Troncoso JC, Halushka MK, Menschaert G, Overall CM, Pandey A.

Genome Res. 2018 Jan;28(1):25-36. doi: 10.1101/gr.226050.117. Epub 2017 Nov 21.

9.

An update on sORFs.org: a repository of small ORFs identified by ribosome profiling.

Olexiouk V, Van Criekinge W, Menschaert G.

Nucleic Acids Res. 2018 Jan 4;46(D1):D497-D502. doi: 10.1093/nar/gkx1130.

10.

A Gene Family Coding for Salivary Proteins (SHOT) of the Polyphagous Spider Mite Tetranychus urticae Exhibits Fast Host-Dependent Transcriptional Plasticity.

Jonckheere W, Dermauw W, Khalighi M, Pavlidi N, Reubens W, Baggerman G, Tirry L, Menschaert G, Kant MR, Vanholme B, Van Leeuwen T.

Mol Plant Microbe Interact. 2018 Jan;31(1):112-124. doi: 10.1094/MPMI-06-17-0139-R. Epub 2017 Nov 2.

PMID:
29094648
11.

REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes.

Ndah E, Jonckheere V, Giess A, Valen E, Menschaert G, Van Damme P.

Nucleic Acids Res. 2017 Nov 16;45(20):e168. doi: 10.1093/nar/gkx758.

12.

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR.

J Proteome Res. 2017 Dec 1;16(12):4288-4298. doi: 10.1021/acs.jproteome.7b00370. Epub 2017 Sep 15.

13.

In Search of Lost Small Peptides.

Plaza S, Menschaert G, Payre F.

Annu Rev Cell Dev Biol. 2017 Oct 6;33:391-416. doi: 10.1146/annurev-cellbio-100616-060516. Epub 2017 Jul 31. Review.

PMID:
28759257
14.

proBAMconvert: A Conversion Tool for proBAM/proBed.

Olexiouk V, Menschaert G.

J Proteome Res. 2017 Jul 7;16(7):2639-2644. doi: 10.1021/acs.jproteome.7b00132. Epub 2017 Jun 9.

PMID:
28573858
15.

eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs.

Fijalkowska D, Verbruggen S, Ndah E, Jonckheere V, Menschaert G, Van Damme P.

Nucleic Acids Res. 2017 Jul 27;45(13):7997-8013. doi: 10.1093/nar/gkx469.

16.

Noncoding after All: Biases in Proteomics Data Do Not Explain Observed Absence of lncRNA Translation Products.

Verheggen K, Volders PJ, Mestdagh P, Menschaert G, Van Damme P, Gevaert K, Martens L, Vandesompele J.

J Proteome Res. 2017 Jul 7;16(7):2508-2515. doi: 10.1021/acs.jproteome.7b00085. Epub 2017 Jun 5.

PMID:
28534634
17.

A Role for Human N-alpha Acetyltransferase 30 (Naa30) in Maintaining Mitochondrial Integrity.

Van Damme P, Kalvik TV, Starheim KK, Jonckheere V, Myklebust LM, Menschaert G, Varhaug JE, Gevaert K, Arnesen T.

Mol Cell Proteomics. 2016 Nov;15(11):3361-3372. Epub 2016 Sep 30.

18.

The Salivary Protein Repertoire of the Polyphagous Spider Mite Tetranychus urticae: A Quest for Effectors.

Jonckheere W, Dermauw W, Zhurov V, Wybouw N, Van den Bulcke J, Villarroel CA, Greenhalgh R, Grbić M, Schuurink RC, Tirry L, Baggerman G, Clark RM, Kant MR, Vanholme B, Menschaert G, Van Leeuwen T.

Mol Cell Proteomics. 2016 Dec;15(12):3594-3613. Epub 2016 Oct 4.

19.

Identification of Small Novel Coding Sequences, a Proteogenomics Endeavor.

Olexiouk V, Menschaert G.

Adv Exp Med Biol. 2016;926:49-64. Review.

PMID:
27686805
20.

Fast and Reliable Quantitative Peptidomics with labelpepmatch.

Verdonck R, De Haes W, Cardoen D, Menschaert G, Huhn T, Landuyt B, Baggerman G, Boonen K, Wenseleers T, Schoofs L.

J Proteome Res. 2016 Mar 4;15(3):1080-9. doi: 10.1021/acs.jproteome.5b00845. Epub 2016 Feb 16.

PMID:
26828777
21.

Proteogenomics from a bioinformatics angle: A growing field.

Menschaert G, Fenyö D.

Mass Spectrom Rev. 2017 Sep;36(5):584-599. doi: 10.1002/mas.21483. Epub 2015 Dec 15. Review.

22.

sORFs.org: a repository of small ORFs identified by ribosome profiling.

Olexiouk V, Crappé J, Verbruggen S, Verhegen K, Martens L, Menschaert G.

Nucleic Acids Res. 2016 Jan 4;44(D1):D324-9. doi: 10.1093/nar/gkv1175. Epub 2015 Nov 2.

23.

An update on LNCipedia: a database for annotated human lncRNA sequences.

Volders PJ, Verheggen K, Menschaert G, Vandepoele K, Martens L, Vandesompele J, Mestdagh P.

Nucleic Acids Res. 2015 Apr 30;43(8):4363-4. doi: 10.1093/nar/gkv295. Epub 2015 Mar 31. No abstract available.

24.

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration.

Crappé J, Ndah E, Koch A, Steyaert S, Gawron D, De Keulenaer S, De Meester E, De Meyer T, Van Criekinge W, Van Damme P, Menschaert G.

Nucleic Acids Res. 2015 Mar 11;43(5):e29. doi: 10.1093/nar/gku1283. Epub 2014 Dec 15.

25.

An update on LNCipedia: a database for annotated human lncRNA sequences.

Volders PJ, Verheggen K, Menschaert G, Vandepoele K, Martens L, Vandesompele J, Mestdagh P.

Nucleic Acids Res. 2015 Jan;43(Database issue):D174-80. doi: 10.1093/nar/gku1060. Epub 2014 Nov 5. Erratum in: Nucleic Acids Res. 2015 Apr 30;43(8):4363-4.

26.

A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites.

Koch A, Gawron D, Steyaert S, Ndah E, Crappé J, De Keulenaer S, De Meester E, Ma M, Shen B, Gevaert K, Van Criekinge W, Van Damme P, Menschaert G.

Proteomics. 2014 Dec;14(23-24):2688-98. doi: 10.1002/pmic.201400180. Epub 2014 Oct 2.

27.

N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men.

Van Damme P, Gawron D, Van Criekinge W, Menschaert G.

Mol Cell Proteomics. 2014 May;13(5):1245-61. doi: 10.1074/mcp.M113.036442. Epub 2014 Mar 12.

28.

Colorado potato beetle (Coleoptera) gut transcriptome analysis: expression of RNA interference-related genes.

Swevers L, Huvenne H, Menschaert G, Kontogiannatos D, Kourti A, Pauchet Y, ffrench-Constant R, Smagghe G.

Insect Mol Biol. 2013 Dec;22(6):668-84. doi: 10.1111/imb.12054.

PMID:
24580832
29.

Antigenic peptides: Reviving nuclear translation.

Van Damme P, Menschaert G.

Nat Chem Biol. 2013 Dec;9(12):759-60. doi: 10.1038/nchembio.1394. No abstract available.

PMID:
24231616
30.

Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs.

Crappé J, Van Criekinge W, Trooskens G, Hayakawa E, Luyten W, Baggerman G, Menschaert G.

BMC Genomics. 2013 Sep 23;14:648. doi: 10.1186/1471-2164-14-648.

31.

Improving the identification rate of endogenous peptides using electron transfer dissociation and collision-induced dissociation.

Hayakawa E, Menschaert G, De Bock PJ, Luyten W, Gevaert K, Baggerman G, Schoofs L.

J Proteome Res. 2013 Dec 6;12(12):5410-21. doi: 10.1021/pr400446z. Epub 2013 Oct 3.

PMID:
24032530
32.

PIUS: peptide identification by unbiased search.

Costa EP, Menschaert G, Luyten W, De Grave K, Ramon J.

Bioinformatics. 2013 Aug 1;29(15):1913-4. doi: 10.1093/bioinformatics/btt298. Epub 2013 May 24.

PMID:
23709496
33.

Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.

De Meyer T, Mampaey E, Vlemmix M, Denil S, Trooskens G, Renard JP, De Keulenaer S, Dehan P, Menschaert G, Van Criekinge W.

PLoS One. 2013;8(3):e59068. doi: 10.1371/journal.pone.0059068. Epub 2013 Mar 15.

34.

Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events.

Menschaert G, Van Criekinge W, Notelaers T, Koch A, Crappé J, Gevaert K, Van Damme P.

Mol Cell Proteomics. 2013 Jul;12(7):1780-90. doi: 10.1074/mcp.M113.027540. Epub 2013 Feb 21.

35.

Spectral clustering in peptidomics studies allows homology searching and modification profiling: HomClus, a versatile tool.

Menschaert G, Hayakawa E, Schoofs L, Van Criekinge W, Baggerman G.

J Proteome Res. 2012 May 4;11(5):2774-85. doi: 10.1021/pr201114m. Epub 2012 Mar 30.

PMID:
22409323
36.

Linking mass spectrometric imaging and traditional peptidomics: a validation in the obese mouse model.

Minerva L, Boonen K, Menschaert G, Landuyt B, Baggerman G, Arckens L.

Anal Chem. 2011 Oct 15;83(20):7682-91. doi: 10.1021/ac200888j. Epub 2011 Sep 27.

PMID:
21913672
37.

Diversity in protein glycosylation among insect species.

Vandenborre G, Smagghe G, Ghesquière B, Menschaert G, Nagender Rao R, Gevaert K, Van Damme EJ.

PLoS One. 2011 Feb 23;6(2):e16682. doi: 10.1371/journal.pone.0016682.

38.

Interaction of the tobacco lectin with histone proteins.

Schouppe D, Ghesquière B, Menschaert G, De Vos WH, Bourque S, Trooskens G, Proost P, Gevaert K, Van Damme EJ.

Plant Physiol. 2011 Mar;155(3):1091-102. doi: 10.1104/pp.110.170134. Epub 2011 Jan 11.

39.

Glycosylation signatures in Drosophila: fishing with lectins.

Vandenborre G, Van Damme EJ, Ghesquière B, Menschaert G, Hamshou M, Rao RN, Gevaert K, Smagghe G.

J Proteome Res. 2010 Jun 4;9(6):3235-42. doi: 10.1021/pr1001753.

PMID:
20387871
40.

Peptidomics coming of age: a review of contributions from a bioinformatics angle.

Menschaert G, Vandekerckhove TT, Baggerman G, Schoofs L, Luyten W, Van Criekinge W.

J Proteome Res. 2010 May 7;9(5):2051-61. doi: 10.1021/pr900929m. Review.

PMID:
20377245
41.

A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome.

Menschaert G, Vandekerckhove TT, Baggerman G, Landuyt B, Sweedler JV, Schoofs L, Luyten W, Van Criekinge W.

J Proteome Res. 2010 Feb 5;9(2):990-6. doi: 10.1021/pr900885k.

42.

Spectral clustering in peptidomics studies helps to unravel modification profile of biologically active peptides and enhances peptide identification rate.

Menschaert G, Vandekerckhove TT, Landuyt B, Hayakawa E, Schoofs L, Luyten W, Van Criekinge W.

Proteomics. 2009 Sep;9(18):4381-8. doi: 10.1002/pmic.200900248.

PMID:
19658089
43.

Bioinformatics solutions for MS/MS interpretation tailored to the peptidomics field.

Menschaert G, Vandekerckhove TT, Baggerman G, Landuyt B, Schoofs L, Luyten W, Van Criekinge W.

Commun Agric Appl Biol Sci. 2009;74(4):67-73. No abstract available.

PMID:
20420225
44.

PubMeth: a cancer methylation database combining text-mining and expert annotation.

Ongenaert M, Van Neste L, De Meyer T, Menschaert G, Bekaert S, Van Criekinge W.

Nucleic Acids Res. 2008 Jan;36(Database issue):D842-6. Epub 2007 Oct 11.

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