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Items: 19


Towards a standardized bioinformatics infrastructure for N- and O-glycomics.

Rojas-Macias MA, Mariethoz J, Andersson P, Jin C, Venkatakrishnan V, Aoki NP, Shinmachi D, Ashwood C, Madunic K, Zhang T, Miller RL, Horlacher O, Struwe WB, Watanabe Y, Okuda S, Levander F, Kolarich D, Rudd PM, Wuhrer M, Kettner C, Packer NH, Aoki-Kinoshita KF, Lisacek F, Karlsson NG.

Nat Commun. 2019 Jul 22;10(1):3275. doi: 10.1038/s41467-019-11131-x. Review.


A Bioinformatics View of Glycan⁻Virus Interactions.

Le Mercier P, Mariethoz J, Lascano-Maillard J, Bonnardel F, Imberty A, Ricard-Blum S, Lisacek F.

Viruses. 2019 Apr 23;11(4). pii: E374. doi: 10.3390/v11040374. Review.


GlyConnect: Glycoproteomics Goes Visual, Interactive, and Analytical.

Alocci D, Mariethoz J, Gastaldello A, Gasteiger E, Karlsson NG, Kolarich D, Packer NH, Lisacek F.

J Proteome Res. 2019 Feb 1;18(2):664-677. doi: 10.1021/acs.jproteome.8b00766. Epub 2019 Jan 15.


SugarSketcher: Quick and Intuitive Online Glycan Drawing.

Alocci D, Suchánková P, Costa R, Hory N, Mariethoz J, Vařeková RS, Toukach P, Lisacek F.

Molecules. 2018 Dec 5;23(12). pii: E3206. doi: 10.3390/molecules23123206.


UniLectin3D, a database of carbohydrate binding proteins with curated information on 3D structures and interacting ligands.

Bonnardel F, Mariethoz J, Salentin S, Robin X, Schroeder M, Perez S, Lisacek F, Imberty A.

Nucleic Acids Res. 2019 Jan 8;47(D1):D1236-D1244. doi: 10.1093/nar/gky832.


A pipeline to translate glycosaminoglycan sequences into 3D models. Application to the exploration of glycosaminoglycan conformational space.

Clerc O, Mariethoz J, Rivet A, Lisacek F, Pérez S, Ricard-Blum S.

Glycobiology. 2019 Jan 1;29(1):36-44. doi: 10.1093/glycob/cwy084.


Glycomics@ExPASy: Bridging the Gap.

Mariethoz J, Alocci D, Gastaldello A, Horlacher O, Gasteiger E, Rojas-Macias M, Karlsson NG, Packer NH, Lisacek F.

Mol Cell Proteomics. 2018 Nov;17(11):2164-2176. doi: 10.1074/mcp.RA118.000799. Epub 2018 Aug 10.


Understanding the glycome: an interactive view of glycosylation from glycocompositions to glycoepitopes.

Alocci D, Ghraichy M, Barletta E, Gastaldello A, Mariethoz J, Lisacek F.

Glycobiology. 2018 Jun 1;28(6):349-362. doi: 10.1093/glycob/cwy019.


Glycoforest 1.0.

Horlacher O, Jin C, Alocci D, Mariethoz J, Müller M, Karlsson NG, Lisacek F.

Anal Chem. 2017 Oct 17;89(20):10932-10940. doi: 10.1021/acs.analchem.7b02754. Epub 2017 Sep 25.


Navigating the Glycome Space and Connecting the Glycoproteome.

Campbell MP, Peterson RA, Gasteiger E, Mariethoz J, Lisacek F, Packer NH.

Methods Mol Biol. 2017;1558:139-158. doi: 10.1007/978-1-4939-6783-4_7.


Databases and Associated Tools for Glycomics and Glycoproteomics.

Lisacek F, Mariethoz J, Alocci D, Rudd PM, Abrahams JL, Campbell MP, Packer NH, Ståhle J, Widmalm G, Mullen E, Adamczyk B, Rojas-Macias MA, Jin C, Karlsson NG.

Methods Mol Biol. 2017;1503:235-264.


GlycoSiteAlign: Glycosite Alignment Based on Glycan Structure.

Gastaldello A, Alocci D, Baeriswyl JL, Mariethoz J, Lisacek F.

J Proteome Res. 2016 Oct 7;15(10):3916-3928. Epub 2016 Sep 2.


Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search.

Alocci D, Mariethoz J, Horlacher O, Bolleman JT, Campbell MP, Lisacek F.

PLoS One. 2015 Dec 14;10(12):e0144578. doi: 10.1371/journal.pone.0144578. eCollection 2015.


The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

SIB Swiss Institute of Bioinformatics Members.

Nucleic Acids Res. 2016 Jan 4;44(D1):D27-37. doi: 10.1093/nar/gkv1310. Epub 2015 Nov 28.


SugarBindDB, a resource of glycan-mediated host-pathogen interactions.

Mariethoz J, Khatib K, Alocci D, Campbell MP, Karlsson NG, Packer NH, Mullen EH, Lisacek F.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1243-50. doi: 10.1093/nar/gkv1247. Epub 2015 Nov 17.


MzJava: An open source library for mass spectrometry data processing.

Horlacher O, Nikitin F, Alocci D, Mariethoz J, Müller M, Lisacek F.

J Proteomics. 2015 Nov 3;129:63-70. doi: 10.1016/j.jprot.2015.06.013. Epub 2015 Jun 30.


GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination.

Gotz L, Abrahams JL, Mariethoz J, Rudd PM, Karlsson NG, Packer NH, Campbell MP, Lisacek F.

Bioinformatics. 2014 Nov 1;30(21):3131-3. doi: 10.1093/bioinformatics/btu425. Epub 2014 Jul 10.


Toolboxes for a standardised and systematic study of glycans.

Campbell MP, Ranzinger R, Lütteke T, Mariethoz J, Hayes CA, Zhang J, Akune Y, Aoki-Kinoshita KF, Damerell D, Carta G, York WS, Haslam SM, Narimatsu H, Rudd PM, Karlsson NG, Packer NH, Lisacek F.

BMC Bioinformatics. 2014;15 Suppl 1:S9. doi: 10.1186/1471-2105-15-S1-S9. Epub 2014 Jan 10.


UniCarbKB: building a knowledge platform for glycoproteomics.

Campbell MP, Peterson R, Mariethoz J, Gasteiger E, Akune Y, Aoki-Kinoshita KF, Lisacek F, Packer NH.

Nucleic Acids Res. 2014 Jan;42(Database issue):D215-21. doi: 10.1093/nar/gkt1128. Epub 2013 Nov 13.

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