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Items: 16

1.

LNCipedia 5: towards a reference set of human long non-coding RNAs.

Volders PJ, Anckaert J, Verheggen K, Nuytens J, Martens L, Mestdagh P, Vandesompele J.

Nucleic Acids Res. 2019 Jan 8;47(D1):D135-D139. doi: 10.1093/nar/gky1031.

2.

Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.

Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, Martens L, Rodriguez-Navarro S, Moreno-Manzano V, Conesa A.

Genome Res. 2018 Jul;28(7):1096. doi: 10.1101/gr.239137.118. No abstract available.

3.

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.

Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, Martens L, Rodriguez-Navarro S, Moreno-Manzano V, Conesa A.

Genome Res. 2018 Feb 9. doi: 10.1101/gr.222976.117. [Epub ahead of print] Erratum in: Genome Res. 2018 Jul;28(7):1096.

4.

Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows.

Verheggen K, Raeder H, Berven FS, Martens L, Barsnes H, Vaudel M.

Mass Spectrom Rev. 2017 Sep 13. doi: 10.1002/mas.21543. [Epub ahead of print] Review.

PMID:
28902424
5.

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
6.

Unbiased Protein Association Study on the Public Human Proteome Reveals Biological Connections between Co-Occurring Protein Pairs.

Gupta S, Verheggen K, Tavernier J, Martens L.

J Proteome Res. 2017 Jun 2;16(6):2204-2212. doi: 10.1021/acs.jproteome.6b01066. Epub 2017 May 11.

7.

Database Search Engines: Paradigms, Challenges and Solutions.

Verheggen K, Martens L, Berven FS, Barsnes H, Vaudel M.

Adv Exp Med Biol. 2016;919:147-156. Review.

PMID:
27975215
8.

moFF: a robust and automated approach to extract peptide ion intensities.

Argentini A, Goeminne LJ, Verheggen K, Hulstaert N, Staes A, Clement L, Martens L.

Nat Methods. 2016 Nov 29;13(12):964-966. doi: 10.1038/nmeth.4075. No abstract available.

PMID:
27898063
9.

Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics.

Verheggen K, Maddelein D, Hulstaert N, Martens L, Barsnes H, Vaudel M.

J Proteome Res. 2016 Mar 4;15(3):707-12. doi: 10.1021/acs.jproteome.5b00850. Epub 2015 Nov 6.

PMID:
26510693
10.

Exploring the potential of public proteomics data.

Vaudel M, Verheggen K, Csordas A, Raeder H, Berven FS, Martens L, Vizcaíno JA, Barsnes H.

Proteomics. 2016 Jan;16(2):214-25. doi: 10.1002/pmic.201500295. Epub 2015 Dec 15. Review.

11.

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.

12.

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.

13.

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications.

Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L, Joshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, Macnealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S, Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G.

OMICS. 2014 Jan;18(1):10-4. doi: 10.1089/omi.2013.0149.

14.

Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications.

Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L, Joshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, MacNealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S, Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G.

Big Data. 2013 Dec;1(4):196-201. doi: 10.1089/big.2013.0039.

PMID:
27447251
15.

Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory.

Verheggen K, Barsnes H, Martens L.

Proteomics. 2014 Mar;14(4-5):367-77. doi: 10.1002/pmic.201300288. Epub 2013 Nov 27. Review.

PMID:
24285552
16.

Exercise-induced immunosuppression: roles of reactive oxygen species and 5'-AMP-activated protein kinase dephosphorylation within immune cells.

Moir H, Hughes MG, Potter S, Sims C, Butcher LR, Davies NA, Verheggen K, Jones KP, Thomas AW, Webb R.

J Appl Physiol (1985). 2010 May;108(5):1284-92. doi: 10.1152/japplphysiol.00737.2009. Epub 2010 Feb 18.

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