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Items: 19

1.

Reactome from a WikiPathways Perspective.

Bohler A, Wu G, Kutmon M, Pradhana LA, Coort SL, Hanspers K, Haw R, Pico AR, Evelo CT.

PLoS Comput Biol. 2016 May 20;12(5):e1004941. doi: 10.1371/journal.pcbi.1004941. eCollection 2016 May.

2.

WikiPathways: capturing the full diversity of pathway knowledge.

Kutmon M, Riutta A, Nunes N, Hanspers K, Willighagen EL, Bohler A, Mélius J, Waagmeester A, Sinha SR, Miller R, Coort SL, Cirillo E, Smeets B, Evelo CT, Pico AR.

Nucleic Acids Res. 2016 Jan 4;44(D1):D488-94. doi: 10.1093/nar/gkv1024. Epub 2015 Oct 19.

3.

NOA: a cytoscape plugin for network ontology analysis.

Zhang C, Wang J, Hanspers K, Xu D, Chen L, Pico AR.

Bioinformatics. 2013 Aug 15;29(16):2066-7. doi: 10.1093/bioinformatics/btt334. Epub 2013 Jun 7.

4.

GO-Elite: a flexible solution for pathway and ontology over-representation.

Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, Conklin BR, Pico AR, Salomonis N.

Bioinformatics. 2012 Aug 15;28(16):2209-10. doi: 10.1093/bioinformatics/bts366. Epub 2012 Jun 27.

5.

Mosaic: making biological sense of complex networks.

Zhang C, Hanspers K, Kuchinsky A, Salomonis N, Xu D, Pico AR.

Bioinformatics. 2012 Jul 15;28(14):1943-4. doi: 10.1093/bioinformatics/bts278. Epub 2012 May 9.

6.

WikiPathways: building research communities on biological pathways.

Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo CT, Pico AR.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1301-7. doi: 10.1093/nar/gkr1074. Epub 2011 Nov 16.

7.

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services.

van Iersel MP, Pico AR, Kelder T, Gao J, Ho I, Hanspers K, Conklin BR, Evelo CT.

BMC Bioinformatics. 2010 Jan 4;11:5. doi: 10.1186/1471-2105-11-5.

8.

Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors.

Salomonis N, Nelson B, Vranizan K, Pico AR, Hanspers K, Kuchinsky A, Ta L, Mercola M, Conklin BR.

PLoS Comput Biol. 2009 Nov;5(11):e1000553. doi: 10.1371/journal.pcbi.1000553. Epub 2009 Nov 6.

9.

Mining biological pathways using WikiPathways web services.

Kelder T, Pico AR, Hanspers K, van Iersel MP, Evelo C, Conklin BR.

PLoS One. 2009 Jul 30;4(7):e6447. doi: 10.1371/journal.pone.0006447.

10.

Presenting and exploring biological pathways with PathVisio.

van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, Conklin BR, Evelo C.

BMC Bioinformatics. 2008 Sep 25;9:399. doi: 10.1186/1471-2105-9-399.

11.

WikiPathways: pathway editing for the people.

Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C.

PLoS Biol. 2008 Jul 22;6(7):e184. doi: 10.1371/journal.pbio.0060184. No abstract available.

12.

Integration of biological networks and gene expression data using Cytoscape.

Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD.

Nat Protoc. 2007;2(10):2366-82.

13.

Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells.

Nord AS, Vranizan K, Tingley W, Zambon AC, Hanspers K, Fong LG, Hu Y, Bacchetti P, Ferrin TE, Babbitt PC, Doniger SW, Skarnes WC, Young SG, Conklin BR.

PLoS One. 2007 Jul 18;2(7):e617.

14.

GenMAPP 2: new features and resources for pathway analysis.

Salomonis N, Hanspers K, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Stuart J, Conklin BR, Pico AR.

BMC Bioinformatics. 2007 Jun 24;8:217.

15.

A system-based approach to interpret dose- and time-dependent microarray data: quantitative integration of gene ontology analysis for risk assessment.

Yu X, Griffith WC, Hanspers K, Dillman JF 3rd, Ong H, Vredevoogd MA, Faustman EM.

Toxicol Sci. 2006 Aug;92(2):560-77. Epub 2006 Apr 6.

16.

Increased DNA microarray hybridization specificity using sscDNA targets.

Barker CS, Griffin C, Dolganov GM, Hanspers K, Yang JY, Erle DJ.

BMC Genomics. 2005 Apr 22;6:57.

17.

Gene expression profiles during human CD4+ T cell differentiation.

Lee MS, Hanspers K, Barker CS, Korn AP, McCune JM.

Int Immunol. 2004 Aug;16(8):1109-24. Epub 2004 Jun 21.

18.

Spotted long oligonucleotide arrays for human gene expression analysis.

Barczak A, Rodriguez MW, Hanspers K, Koth LL, Tai YC, Bolstad BM, Speed TP, Erle DJ.

Genome Res. 2003 Jul;13(7):1775-85. Epub 2003 Jun 12.

19.

Treatment with sulfatide or its precursor, galactosylceramide, prevents diabetes in NOD mice.

Buschard K, Hanspers K, Fredman P, Reich EP.

Autoimmunity. 2001;34(1):9-17.

PMID:
11681495
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