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Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.

Waagmeester A, Kutmon M, Riutta A, Miller R, Willighagen EL, Evelo CT, Pico AR.

PLoS Comput Biol. 2016 Jun 23;12(6):e1004989. doi: 10.1371/journal.pcbi.1004989. eCollection 2016 Jun.


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.


Longer genotypically-estimated leukocyte telomere length is associated with increased adult glioma risk.

Walsh KM, Codd V, Rice T, Nelson CP, Smirnov IV, McCoy LS, Hansen HM, Elhauge E, Ojha J, Francis SS, Madsen NR, Bracci PM, Pico AR, Molinaro AM, Tihan T, Berger MS, Chang SM, Prados MD, Jenkins RB, Wiemels JL; ENGAGE Consortium Telomere Group., Samani NJ, Wiencke JK, Wrensch MR.

Oncotarget. 2015 Dec 15;6(40):42468-77. doi: 10.18632/oncotarget.6468.


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.


From scientific discovery to cures: bright stars within a galaxy.

Williams RS, Lotia S, Holloway AK, Pico AR.

Cell. 2015 Sep 24;163(1):21-3. doi: 10.1016/j.cell.2015.09.007.


Glioma Groups Based on 1p/19q, IDH, and TERT Promoter Mutations in Tumors.

Eckel-Passow JE, Lachance DH, Molinaro AM, Walsh KM, Decker PA, Sicotte H, Pekmezci M, Rice T, Kosel ML, Smirnov IV, Sarkar G, Caron AA, Kollmeyer TM, Praska CE, Chada AR, Halder C, Hansen HM, McCoy LS, Bracci PM, Marshall R, Zheng S, Reis GF, Pico AR, O'Neill BP, Buckner JC, Giannini C, Huse JT, Perry A, Tihan T, Berger MS, Chang SM, Prados MD, Wiemels J, Wiencke JK, Wrensch MR, Jenkins RB.

N Engl J Med. 2015 Jun 25;372(26):2499-508. doi: 10.1056/NEJMoa1407279. Epub 2015 Jun 10.


PathVisio 3: an extendable pathway analysis toolbox.

Kutmon M, van Iersel MP, Bohler A, Kelder T, Nunes N, Pico AR, Evelo CT.

PLoS Comput Biol. 2015 Feb 23;11(2):e1004085. doi: 10.1371/journal.pcbi.1004085. eCollection 2015 Feb.


The Cytoscape app article collection.

Pico AR, Bader GD, Demchak B, Guitart Pla O, Hull T, Longabaugh W, Lopes C, Lotia S, Molenaar P, Montojo J, Morris JH, Ono K, Schwikowski B, Welker D, Ideker T.

F1000Res. 2014 Jul 1;3:138. doi: 10.12688/f1000research.4642.1. eCollection 2014.


CyAnimator: Simple Animations of Cytoscape Networks.

Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE.

Version 2. F1000Res. 2015 Aug 5 [revised 2015 Jan 1];4:482. doi: 10.12688/f1000research.6852.2.


setsApp for Cytoscape: Set operations for Cytoscape Nodes and Edges.

Morris JH, Lotia S, Wu A, Doncheva NT, Albrecht M, Pico AR, Ferrin TE.

Version 2. F1000Res. 2014 Jul 1 [revised 2015 Jan 1];3:149. doi: 10.12688/f1000research.4392.2.


enhancedGraphics: a Cytoscape app for enhanced node graphics.

Morris JH, Kuchinsky A, Ferrin TE, Pico AR.

F1000Res. 2014 Jul 1;3:147. doi: 10.12688/f1000research.4460.1. eCollection 2014.


Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions.

Morris JH, Knudsen GM, Verschueren E, Johnson JR, Cimermancic P, Greninger AL, Pico AR.

Nat Protoc. 2014 Nov;9(11):2539-54. doi: 10.1038/nprot.2014.164. Epub 2014 Oct 2.


WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization.

Kutmon M, Lotia S, Evelo CT, Pico AR.

Version 2. F1000Res. 2014 Jul 1 [revised 2014 Jan 1];3:152. doi: 10.12688/f1000research.4254.2.


Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk.

Walsh KM, Codd V, Smirnov IV, Rice T, Decker PA, Hansen HM, Kollmeyer T, Kosel ML, Molinaro AM, McCoy LS, Bracci PM, Cabriga BS, Pekmezci M, Zheng S, Wiemels JL, Pico AR, Tihan T, Berger MS, Chang SM, Prados MD, Lachance DH, O'Neill BP, Sicotte H, Eckel-Passow JE; ENGAGE Consortium Telomere Group, van der Harst P, Wiencke JK, Samani NJ, Jenkins RB, Wrensch MR.

Nat Genet. 2014 Jul;46(7):731-5. doi: 10.1038/ng.3004. Epub 2014 Jun 8.


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.


Genetic variants in telomerase-related genes are associated with an older age at diagnosis in glioma patients: evidence for distinct pathways of gliomagenesis.

Walsh KM, Rice T, Decker PA, Kosel ML, Kollmeyer T, Hansen HM, Zheng S, McCoy LS, Bracci PM, Anderson E, Hsuang G, Wiemels JL, Pico AR, Smirnov I, Molinaro AM, Tihan T, Berger MS, Chang SM, Prados MD, Lachance DH, Sicotte H, Eckel-Passow JE, Wiencke JK, Jenkins RB, Wrensch MR.

Neuro Oncol. 2013 Aug;15(8):1041-7. doi: 10.1093/neuonc/not051. Epub 2013 Jun 3.


Cytoscape app store.

Lotia S, Montojo J, Dong Y, Bader GD, Pico AR.

Bioinformatics. 2013 May 15;29(10):1350-1. doi: 10.1093/bioinformatics/btt138. Epub 2013 Apr 16.


Inherited variant on chromosome 11q23 increases susceptibility to IDH-mutated but not IDH-normal gliomas regardless of grade or histology.

Rice T, Zheng S, Decker PA, Walsh KM, Bracci P, Xiao Y, McCoy LS, Smirnov I, Patoka JS, Hansen HM, Hsuang G, Wiemels JL, Tihan T, Pico AR, Prados MD, Chang SM, Berger MS, Caron A, Fink S, Kollmeyer T, Rynearson A, Voss J, Kosel ML, Fridley BL, Lachance DH, Eckel-Passow JE, Sicotte H, O'Neill BP, Giannini C, Wiencke JK, Jenkins RB, Wrensch MR.

Neuro Oncol. 2013 May;15(5):535-41. doi: 10.1093/neuonc/nos324. Epub 2013 Jan 29.


Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies.

Walsh KM, Anderson E, Hansen HM, Decker PA, Kosel ML, Kollmeyer T, Rice T, Zheng S, Xiao Y, Chang JS, McCoy LS, Bracci PM, Wiemels JL, Pico AR, Smirnov I, Lachance DH, Sicotte H, Eckel-Passow JE, Wiencke JK, Jenkins RB, Wrensch MR.

Genet Epidemiol. 2013 Feb;37(2):222-8. doi: 10.1002/gepi.21707. Epub 2012 Dec 31.


A travel guide to Cytoscape plugins.

Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T.

Nat Methods. 2012 Nov;9(11):1069-76. doi: 10.1038/nmeth.2212. Epub 2012 Nov 6.

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