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Alex Pico, PhD

TitleStaff Research Scientist II
SchoolUCSF School of Medicine
DepartmentGladstone Institutes
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    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. Shah R, Murthy V, Pacold M, Danielson K, Tanriverdi K, Larson MG, Hanspers K, Pico A, Mick E, Reis J, de Ferranti S, Freinkman E, Levy D, Hoffmann U, Osganian S, Das S, Freedman JE. Extracellular RNAs Are Associated With Insulin Resistance and Metabolic Phenotypes. Diabetes Care. 2017 Apr; 40(4):546-553. PMID: 28183786.
      View in: PubMed
    2. Shah R, Pico A, Freedman JE. Translational Epidemiology: Entering a Brave New World of Team Science. Circ Res. 2016 Oct 28; 119(10):1060-1062. PMID: 27789584.
      View in: PubMed
    3. Waagmeester A, Kutmon M, Riutta A, Miller R, Willighagen EL, Evelo CT, Pico A. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PLoS Comput Biol. 2016 Jun; 12(6):e1004989. PMID: 27336457; PMCID: PMC4918977.
    4. Bohler A, Wu G, Kutmon M, Pradhana LA, Coort SL, Hanspers K, Haw R, Pico A, Evelo CT. Reactome from a WikiPathways Perspective. PLoS Comput Biol. 2016 05; 12(5):e1004941. PMID: 27203685; PMCID: PMC4874630.
    5. 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 A, Molinaro AM, Tihan T, Berger MS, Chang SM, Prados MD, Jenkins RB, Wiemels JL, Telomere Group EC, Samani NJ, Wiencke JK, Wrensch MR. Longer genotypically-estimated leukocyte telomere length is associated with increased adult glioma risk. Oncotarget. 2015 Dec 15; 6(40):42468-77. PMID: 26646793; PMCID: PMC4767445.
    6. 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 A. WikiPathways: capturing the full diversity of pathway knowledge. Nucleic Acids Res. 2016 Jan 04; 44(D1):D488-94. PMID: 26481357; PMCID: PMC4702772.
    7. Williams RS, Lotia S, Holloway AK, Pico A. From scientific discovery to cures: bright stars within a galaxy. Cell. 2015 Sep 24; 163(1):21-3. PMID: 26406364.
      View in: PubMed
    8. Subramanian SL, Kitchen RR, Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A. Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. J Extracell Vesicles. 2015; 4:27497. PMID: 26320941; PMCID: PMC4553261.
    9. Morris JH, Vijay D, Federowicz S, Pico A, Ferrin TE. CyAnimator: Simple Animations of Cytoscape Networks. F1000Res. 2015; 4:482. PMID: 26937268; PMCID: PMC4752027.
    10. Nersisyan L, Johnson G, Riel-Mehan M, Pico A, Arakelyan A. PSFC: a Pathway Signal Flow Calculator App for Cytoscape. F1000Res. 2015; 4:480. PMID: 26834984; PMCID: PMC4706054.
    11. 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 A, 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. Glioma Groups Based on 1p/19q, IDH, and TERT Promoter Mutations in Tumors. N Engl J Med. 2015 Jun 25; 372(26):2499-508. PMID: 26061753; PMCID: PMC4489704.
    12. Kutmon M, van Iersel MP, Bohler A, Kelder T, Nunes N, Pico A, Evelo CT. PathVisio 3: an extendable pathway analysis toolbox. PLoS Comput Biol. 2015 Feb; 11(2):e1004085. PMID: 25706687; PMCID: PMC4338111.
    13. Morris JH, Knudsen GM, Verschueren E, Johnson JR, Cimermancic P, Greninger AL, Pico A. Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc. 2014 Nov; 9(11):2539-54. PMID: 25275790; PMCID: PMC4332878.
    14. Morris JH, Kuchinsky A, Ferrin TE, Pico A. enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Res. 2014; 3:147. PMID: 25285206; PMCID: PMC4176421.
    15. Pico A, 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. The Cytoscape app article collection. F1000Res. 2014; 3:138. PMID: 25580224; PMCID: PMC4288400.
    16. Kutmon M, Lotia S, Evelo CT, Pico A. WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization. F1000Res. 2014; 3:152. PMID: 25254103.
      View in: PubMed
    17. Morris JH, Wu A, Doncheva NT, Albrecht M, Ferrin TE. setsApp for Cytoscape: Set operations for Cytoscape Nodes and Edges. F1000Res. 2014; 3:149. PMID: 25352980.
      View in: PubMed
    18. 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 A, Tihan T, Berger MS, Chang SM, Prados MD, Lachance DH, O'Neill BP, Sicotte H, Eckel-Passow JE, van der Harst P, Wiencke JK, Samani NJ, Jenkins RB, Wrensch MR. Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk. Nat Genet. 2014 Jul; 46(7):731-5. PMID: 24908248; PMCID: PMC4074274.
    19. Zhang C, Wang J, Hanspers K, Xu D, Chen L, Pico A. NOA: a cytoscape plugin for network ontology analysis. Bioinformatics. 2013 Aug 15; 29(16):2066-7. PMID: 23749961; PMCID: PMC3722524.
    20. 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 A, 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. PMID: 23733245; PMCID: PMC3714154.
    21. Lotia S, Montojo J, Dong Y, Bader GD, Pico A. Cytoscape app store. Bioinformatics. 2013 May 15; 29(10):1350-1. PMID: 23595664; PMCID: PMC3654709.
    22. 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 A, 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. PMID: 23361564; PMCID: PMC3635511.
    23. 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 A, 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. PMID: 23280628; PMCID: PMC3670948.
    24. Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico A, Bader GD, Ideker T. A travel guide to Cytoscape plugins. Nat Methods. 2012 Nov; 9(11):1069-76. PMID: 23132118; PMCID: PMC3649846.
    25. Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico A, 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. PMID: 22981692; PMCID: PMC3462286.
    26. 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 A, 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. PMID: 22922872; PMCID: PMC3600846.
    27. Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, Conklin BR, Pico A, Salomonis N. GO-Elite: a flexible solution for pathway and ontology over-representation. Bioinformatics. 2012 Aug 15; 28(16):2209-10. PMID: 22743224; PMCID: PMC3413395.
    28. Zhang C, Hanspers K, Kuchinsky A, Salomonis N, Xu D, Pico A. Mosaic: making biological sense of complex networks. Bioinformatics. 2012 Jul 15; 28(14):1943-4. PMID: 22576176; PMCID: PMC3389769.
    29. Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo CT, Pico A. WikiPathways: building research communities on biological pathways. Nucleic Acids Res. 2012 Jan; 40(Database issue):D1301-7. PMID: 22096230; PMCID: PMC3245032.
    30. 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. PMID: 20829833; PMCID: PMC3001121.
    31. Kelder T, Conklin BR, Evelo CT, Pico A. Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. PLoS Biol. 2010 Aug 31; 8(8). PMID: 20824171; PMCID: PMC2930872.
    32. Yuan P, Leonetti MD, Pico A, Hsiung Y, MacKinnon R. Structure of the human BK channel Ca2+-activation apparatus at 3.0 A resolution. Science. 2010 Jul 09; 329(5988):182-6. PMID: 20508092; PMCID: PMC3022345.
    33. Salomonis N, Schlieve CR, Pereira L, Wahlquist C, Colas A, Zambon AC, Vranizan K, Spindler MJ, Pico A, 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 08; 107(23):10514-9. PMID: 20498046; PMCID: PMC2890851.
    34. van Iersel MP, Pico A, 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 Jan 04; 11:5. PMID: 20047655; PMCID: PMC2824678.
    35. Salomonis N, Nelson B, Vranizan K, Pico A, 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. PMID: 19893621; PMCID: PMC2764345.
    36. Kelder T, Pico A, Hanspers K, van Iersel MP, Evelo C, Conklin BR. Mining biological pathways using WikiPathways web services. PLoS One. 2009 Jul 30; 4(7):e6447. PMID: 19649250; PMCID: PMC2714472.
    37. 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 A, 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. PMID: 19578366; PMCID: PMC2923561.
    38. Pico A, 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. PMID: 18984625; PMCID: PMC2686434.
    39. van Iersel MP, Kelder T, Pico A, Hanspers K, Coort S, Conklin BR, Evelo C. Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics. 2008 Sep 25; 9:399. PMID: 18817533; PMCID: PMC2569944.
    40. Adriaens ME, Jaillard M, Waagmeester A, Coort SL, Pico A, Evelo CT. The public road to high-quality curated biological pathways. Drug Discov Today. 2008 Oct; 13(19-20):856-62. PMID: 18652912; PMCID: PMC3646620.
    41. Pico A, 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. PMID: 18651794; PMCID: PMC2475545.
    42. Hu JC, Aramayo R, Bolser D, Conway T, Elsik CG, Gribskov M, Kelder T, Kihara D, Knight TF, Pico A, Siegele DA, Wanner BL, Welch RD. The emerging world of wikis. Science. 2008 Jun 06; 320(5881):1289-90. PMID: 18535227.
      View in: PubMed
    43. Chang JS, Yeh RF, Wiencke JK, Wiemels JL, Smirnov I, Pico A, 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. PMID: 18559551.
      View in: PubMed
    44. Salomonis N, Hanspers K, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Stuart J, Conklin BR, Pico A. GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics. 2007 Jun 24; 8:217. PMID: 17588266; PMCID: PMC1924866.
    45. 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 A, 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. PMID: 17947979; PMCID: PMC3685583.
    46. Pico A . RCK domain model of calcium activation in BK channels. 2003.
    47. 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. PMID: 11301020.
      View in: PubMed
    48. 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. PMID: 10360180.
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    49. 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.
    50. 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. PMID: 9822689.
      View in: PubMed
    51. 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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