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Items: 15

1.

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.

2.

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
3.

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
4.

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.

5.

The Human Proteome Organization-Proteomics Standards Initiative Quality Control Working Group: Making Quality Control More Accessible for Biological Mass Spectrometry.

Bittremieux W, Walzer M, Tenzer S, Zhu W, Salek RM, Eisenacher M, Tabb DL.

Anal Chem. 2017 Apr 18;89(8):4474-4479. doi: 10.1021/acs.analchem.6b04310. Epub 2017 Mar 30.

PMID:
28318237
6.

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
7.

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
8.

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
9.

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
10.

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
11.

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
12.

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
13.

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.

14.

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
15.

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.

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