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    Alex Pico, PhD

    TitleStaff Research Scientist II
    SchoolUCSF School of Medicine
    DepartmentNeurological Surgery

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       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Morris JH, Knudsen GM, Verschueren E, Johnson JR, Cimermancic P, Greninger AL, Pico AR. Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc. 2014 Nov; 9(11):2539-54.
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      2. Morris JH, Kuchinsky A, Ferrin TE, Pico AR. enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Res. 2014; 3:147.
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      3. Kutmon M, Lotia S, Evelo CT, Pico AR. WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization. F1000Res. 2014; 3:152.
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      4. 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. Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk. Nat Genet. 2014 Jun 8.
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      5. Zhang C, Wang J, Hanspers K, Xu D, Chen L, Pico AR. NOA: a cytoscape plugin for network ontology analysis. Bioinformatics. 2013 Aug 15; 29(16):2066-7.
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      6. 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. Genetic variants in telomerase-related genes are associated with an older age at diagnosis in glioma patients: evidence for distinct pathways of gliomagenesis. Neuro Oncol. 2013 Aug; 15(8):1041-7.
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      7. Lotia S, Montojo J, Dong Y, Bader GD, Pico AR. Cytoscape app store. Bioinformatics. 2013 May 15; 29(10):1350-1.
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      8. 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. Inherited variant on chromosome 11q23 increases susceptibility to IDH-mutated but not IDH-normal gliomas regardless of grade or histology. Neuro Oncol. 2013 May; 15(5):535-41.
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      9. 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. Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies. Genet Epidemiol. 2013 Feb; 37(2):222-8.
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      10. Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. A travel guide to Cytoscape plugins. Nat Methods. 2012 Nov; 9(11):1069-76.
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      11. Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, Bruneau BG. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 2012 Sep 28; 151(1):206-20.
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      12. Jenkins RB, Xiao Y, Sicotte H, Decker PA, Kollmeyer TM, Hansen HM, Kosel ML, Zheng S, Walsh KM, Rice T, Bracci P, McCoy LS, Smirnov I, Patoka JS, Hsuang G, Wiemels JL, Tihan T, Pico AR, Prados MD, Chang SM, Berger MS, Caron AA, Fink SR, Halder C, Rynearson AL, Fridley BL, Buckner JC, O'Neill BP, Giannini C, Lachance DH, Wiencke JK, Eckel-Passow JE, Wrensch MR. A low-frequency variant at 8q24.21 is strongly associated with risk of oligodendroglial tumors and astrocytomas with IDH1 or IDH2 mutation. Nat Genet. 2012 Oct; 44(10):1122-5.
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      13. Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, Conklin BR, Pico AR, Salomonis N. GO-Elite: a flexible solution for pathway and ontology over-representation. Bioinformatics. 2012 Aug 15; 28(16):2209-10.
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      14. Zhang C, Hanspers K, Kuchinsky A, Salomonis N, Xu D, Pico AR. Mosaic: making biological sense of complex networks. Bioinformatics. 2012 Jul 15; 28(14):1943-4.
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      15. Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo CT, Pico AR. WikiPathways: building research communities on biological pathways. Nucleic Acids Res. 2012 Jan; 40(Database issue):D1301-7.
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      16. Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD. The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010 Sep; 28(9):935-42.
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      17. Kelder T, Conklin BR, Evelo CT, Pico AR. Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. PLoS Biol. 2010; 8(8).
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      18. Yuan P, Leonetti MD, Pico AR, Hsiung Y, MacKinnon R. Structure of the human BK channel Ca2+-activation apparatus at 3.0 A resolution. Science. 2010 Jul 9; 329(5988):182-6.
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      19. Salomonis N, Schlieve CR, Pereira L, Wahlquist C, Colas A, Zambon AC, Vranizan K, Spindler MJ, Pico AR, Cline MS, Clark TA, Williams A, Blume JE, Samal E, Mercola M, Merrill BJ, Conklin BR. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proc Natl Acad Sci U S A. 2010 Jun 8; 107(23):10514-9.
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      20. van Iersel MP, Pico AR, Kelder T, Gao J, Ho I, Hanspers K, Conklin BR, Evelo CT. The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinformatics. 2010; 11:5.
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      21. Salomonis N, Nelson B, Vranizan K, Pico AR, Hanspers K, Kuchinsky A, Ta L, Mercola M, Conklin BR. Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. PLoS Comput Biol. 2009 Nov; 5(11):e1000553.
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      22. Kelder T, Pico AR, Hanspers K, van Iersel MP, Evelo C, Conklin BR. Mining biological pathways using WikiPathways web services. PLoS One. 2009; 4(7):e6447.
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      23. Wrensch M, Jenkins RB, Chang JS, Yeh RF, Xiao Y, Decker PA, Ballman KV, Berger M, Buckner JC, Chang S, Giannini C, Halder C, Kollmeyer TM, Kosel ML, LaChance DH, McCoy L, O'Neill BP, Patoka J, Pico AR, Prados M, Quesenberry C, Rice T, Rynearson AL, Smirnov I, Tihan T, Wiemels J, Yang P, Wiencke JK. Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. Nat Genet. 2009 Aug; 41(8):905-8.
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      24. Pico AR, Smirnov IV, Chang JS, Yeh RF, Wiemels JL, Wiencke JK, Tihan T, Conklin BR, Wrensch M. SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system. Nucleic Acids Res. 2009 Jan; 37(Database issue):D803-9.
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      25. van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, Conklin BR, Evelo C. Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics. 2008; 9:399.
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      26. Adriaens ME, Jaillard M, Waagmeester A, Coort SL, Pico AR, Evelo CT. The public road to high-quality curated biological pathways. Drug Discov Today. 2008 Oct; 13(19-20):856-62.
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      27. Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22; 6(7):e184.
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      28. Hu JC, Aramayo R, Bolser D, Conway T, Elsik CG, Gribskov M, Kelder T, Kihara D, Knight TF, Pico AR, Siegele DA, Wanner BL, Welch RD. The emerging world of wikis. Science. 2008 Jun 6; 320(5881):1289-90.
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      29. Chang JS, Yeh RF, Wiencke JK, Wiemels JL, Smirnov I, Pico AR, Tihan T, Patoka J, Miike R, Sison JD, Rice T, Wrensch MR. Pathway analysis of single-nucleotide polymorphisms potentially associated with glioblastoma multiforme susceptibility using random forests. Cancer Epidemiol Biomarkers Prev. 2008 Jun; 17(6):1368-73.
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      30. Salomonis N, Hanspers K, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Stuart J, Conklin BR, Pico AR. GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics. 2007; 8:217.
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      31. 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. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2007; 2(10):2366-82.
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      32. Pico AR. RCK domain model of calcium activation in BK channels. 2003.
      33. Jiang Y, Pico A, Cadene M, Chait BT, MacKinnon R. Structure of the RCK domain from the E. coli K+ channel and demonstration of its presence in the human BK channel. Neuron. 2001 Mar; 29(3):593-601.
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      34. Schindler T, Sicheri F, Pico A, Gazit A, Levitzki A, Kuriyan J. Crystal structure of Hck in complex with a Src family-selective tyrosine kinase inhibitor. Mol Cell. 1999 May; 3(5):639-48.
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      35. Brent A Field, Alexander R Pico, Richard T Marrocco. Neurocomputing. Local cortical injections of glutamate and noradrenaline alter high-frequency (245 Hz) neuronal activity in rat cortex. 1999; 26-27:123-130.
      36. LaFevre-Bernt M, Sicheri F, Pico A, Porter M, Kuriyan J, Miller WT. Intramolecular regulatory interactions in the Src family kinase Hck probed by mutagenesis of a conserved tryptophan residue. J Biol Chem. 1998 Nov 27; 273(48):32129-34.
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      37. A R Pico, C S Houk, T J R Weakley, C J Page. A new strontium-copper ethylene glycol complex : synthesis and structure of [Sr(C2H6O2)5] [Cu(C2H4O2)2].C2H6O2. Inorganica Chimica Acta. 1997; (258):155-160.
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