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Alexander R. Pico, Ph.D. - Publications

Affiliations: 
Bioinformatics Gladstone Institutes 
Area:
Ion channels, structural biology, network biology, bioinformatics, pathways
Website:
http://gladstoneinstitutes.org/scientist/pico
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52 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Odom GJ, Ban Y, Colaprico A, Liu L, Silva TC, Sun X, Pico AR, Zhang B, Wang L, Chen X. PathwayPCA: an R/Bioconductor Package for Pathway Based Integrative Analysis of Multi-Omics Data. Proteomics. e1900409. PMID 32430990 DOI: 10.1002/Pmic.201900409  0.392
2020 Waagmeester A, Stupp G, Burgstaller-Muehlbacher S, Good BM, Griffith M, Griffith OL, Hanspers K, Hermjakob H, Hudson TS, Hybiske K, Keating SM, Manske M, Mayers M, Mietchen D, Mitraka E, ... Pico AR, et al. Wikidata as a knowledge graph for the life sciences. Elife. 9. PMID 32180547 DOI: 10.7554/Elife.52614  0.314
2020 Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, ... ... Pico AR, et al. Proteogenomic Characterization of Endometrial Carcinoma. Cell. PMID 32059776 DOI: 10.1016/J.Cell.2020.01.026  0.331
2019 Gustavsen JA, Pai S, Isserlin R, Demchak B, Pico AR. RCy3: Network biology using Cytoscape from within R. F1000research. 8: 1774. PMID 31819800 DOI: 10.12688/F1000Research.20887.3  0.301
2019 Murillo OD, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson AR, Srinivasan S, Chung A, Laurent CD, Kitchen RR, Galeev T, Warrell J, Diao JA, Welsh JA, ... ... Pico AR, et al. exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids. Cell. 177: 463-477.e15. PMID 30951672 DOI: 10.1016/J.Cell.2019.02.018  0.33
2018 Treister A, Pico AR. Identifier Mapping in Cytoscape: . F1000research. 7: 725. PMID 30079244 DOI: 10.12688/F1000Research.14807.2  0.314
2018 Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T. The Cytoscape Automation app article collection. F1000research. 7: 800. PMID 29983926 DOI: 10.12688/F1000Research.15355.1  0.322
2017 Keserci S, Livingston E, Wan L, Pico AR, Chacko G. Research synergy and drug development: Bright stars in neighboring constellations. Heliyon. 3: e00442. PMID 29264408 DOI: 10.1016/J.Heliyon.2017.E00442  0.301
2017 Slenter DN, Kutmon M, Hanspers K, Riutta A, Windsor J, Nunes N, Mélius J, Cirillo E, Coort SL, Digles D, Ehrhart F, Giesbertz P, Kalafati M, Martens M, Miller R, ... ... Pico AR, et al. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. Nucleic Acids Research. PMID 29136241 DOI: 10.1093/Nar/Gkx1064  0.409
2017 Daily K, Ho Sui SJ, Schriml LM, Dexheimer PJ, Salomonis N, Schroll R, Bush S, Keddache M, Mayhew C, Lotia S, Perumal TM, Dang K, Pantano L, Pico AR, Grassman E, et al. Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives. Scientific Data. 4: 170030. PMID 28350385 DOI: 10.1038/Sdata.2017.30  0.566
2016 Waagmeester A, Kutmon M, Riutta A, Miller R, Willighagen EL, Evelo CT, Pico AR. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. Plos Computational Biology. 12: e1004989. PMID 27336457 DOI: 10.1371/Journal.Pcbi.1004989  0.385
2016 Bohler A, Wu G, Kutmon M, Pradhana LA, Coort SL, Hanspers K, Haw R, Pico AR, Evelo CT. Reactome from a WikiPathways Perspective. Plos Computational Biology. 12: e1004941. PMID 27203685 DOI: 10.1371/Journal.Pcbi.1004941  0.419
2016 Kutmon M, Riutta A, Hanspers K, Bohler A, Pico A, Evelo C. WikiPathways allows curation, visualization and analysis of biological pathways F1000research. 5. DOI: 10.7490/F1000Research.1112575.1  0.324
2015 Nersisyan L, Johnson G, Riel-Mehan M, Pico A, Arakelyan A. PSFC: a Pathway Signal Flow Calculator App for Cytoscape. F1000research. 4: 480. PMID 26834984 DOI: 10.12688/F1000Research.6706.1  0.338
2015 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. WikiPathways: capturing the full diversity of pathway knowledge. Nucleic Acids Research. PMID 26481357 DOI: 10.1093/Nar/Gkv1024  0.415
2015 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. Journal of Extracellular Vesicles. 4: 27497. PMID 26320941 DOI: 10.3402/Jev.V4.27497  0.341
2015 Kutmon M, van Iersel MP, Bohler A, Kelder T, Nunes N, Pico AR, Evelo CT. PathVisio 3: an extendable pathway analysis toolbox. Plos Computational Biology. 11: e1004085. PMID 25706687 DOI: 10.1371/Journal.Pcbi.1004085  0.391
2014 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. The Cytoscape app article collection. F1000research. 3: 138. PMID 25580224 DOI: 10.12688/F1000Research.4642.1  0.321
2014 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. Nature Protocols. 9: 2539-54. PMID 25275790 DOI: 10.1038/Nprot.2014.164  0.31
2014 Kutmon M, Lotia S, Evelo CT, Pico AR. WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization. F1000research. 3: 152. PMID 25254103 DOI: 10.12688/F1000Research.4254.2  0.39
2013 Zhang C, Wang J, Hanspers K, Xu D, Chen L, Pico AR. NOA: a cytoscape plugin for network ontology analysis. Bioinformatics (Oxford, England). 29: 2066-7. PMID 23749961 DOI: 10.1093/Bioinformatics/Btt334  0.309
2013 Lotia S, Montojo J, Dong Y, Bader GD, Pico AR. Cytoscape app store. Bioinformatics (Oxford, England). 29: 1350-1. PMID 23595664 DOI: 10.1093/Bioinformatics/Btt138  0.307
2013 Bohler A, Kutmon M, Iersel MPv, Kelder T, Hanspers K, Pico AR, Evelo CT. PathVisio 3: new features for pathway analysis and visualization F1000research. 4. DOI: 10.7490/F1000Research.1093983.1  0.304
2012 Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. A travel guide to Cytoscape plugins. Nature Methods. 9: 1069-76. PMID 23132118 DOI: 10.1038/Nmeth.2212  0.319
2012 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, et al. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 151: 206-20. PMID 22981692 DOI: 10.1016/J.Cell.2012.07.035  0.3
2012 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 (Oxford, England). 28: 2209-10. PMID 22743224 DOI: 10.1093/Bioinformatics/Bts366  0.693
2012 Zhang C, Hanspers K, Kuchinsky A, Salomonis N, Xu D, Pico AR. Mosaic: making biological sense of complex networks. Bioinformatics (Oxford, England). 28: 1943-4. PMID 22576176 DOI: 10.1093/Bioinformatics/Bts278  0.579
2012 Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo CT, Pico AR. WikiPathways: building research communities on biological pathways. Nucleic Acids Research. 40: D1301-7. PMID 22096230 DOI: 10.1093/Nar/Gkr1074  0.607
2012 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, ... ... Pico A, et al. The BioPAX community standard for pathway data sharing (Nature Biotechnology (2010) 28, (935-942)) Nature Biotechnology. 30: 365. DOI: 10.1038/Nbt0412-365C  0.314
2010 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, ... ... Pico A, et al. The BioPAX community standard for pathway data sharing. Nature Biotechnology. 28: 935-42. PMID 20829833 DOI: 10.1038/Nbt.1666  0.413
2010 Kelder T, Conklin BR, Evelo CT, Pico AR. Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. Plos Biology. 8. PMID 20824171 DOI: 10.1371/Journal.Pbio.1000472  0.589
2010 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 (New York, N.Y.). 329: 182-6. PMID 20508092 DOI: 10.1126/Science.1190414  0.46
2010 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, et al. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proceedings of the National Academy of Sciences of the United States of America. 107: 10514-9. PMID 20498046 DOI: 10.1073/Pnas.0912260107  0.719
2010 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. 11: 5. PMID 20047655 DOI: 10.1186/1471-2105-11-5  0.55
2010 Pico A. WikiPathways: Community Curation of Biological Pathways Nature Precedings. 5: 1-1. DOI: 10.1038/Npre.2010.5359.1  0.393
2010 Iersel MPv, Pico AR, Kelder T, Gao J, Ho I, Hanspers K, Conklin BR, Evelo CTA. BridgeDb: standardized access to gene, protein and metabolite identifier mapping services Nature Precedings. DOI: 10.1038/Npre.2010.5023.1  0.552
2010 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, ... ... Pico A, et al. Erratum: Corrigendum: The BioPAX community standard for pathway data sharing Nature Biotechnology. 28: 1308-1308. DOI: 10.1038/Nbt1210-1308C  0.314
2009 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 Computational Biology. 5: e1000553. PMID 19893621 DOI: 10.1371/Journal.Pcbi.1000553  0.674
2009 Kelder T, Pico AR, Hanspers K, van Iersel MP, Evelo C, Conklin BR. Mining biological pathways using WikiPathways web services. Plos One. 4: e6447. PMID 19649250 DOI: 10.1371/Journal.Pone.0006447  0.566
2009 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 Research. 37: D803-9. PMID 18984625 DOI: 10.1093/Nar/Gkn756  0.572
2008 van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, Conklin BR, Evelo C. Presenting and exploring biological pathways with PathVisio. Bmc Bioinformatics. 9: 399. PMID 18817533 DOI: 10.1186/1471-2105-9-399  0.61
2008 Adriaens ME, Jaillard M, Waagmeester A, Coort SL, Pico AR, Evelo CT. The public road to high-quality curated biological pathways. Drug Discovery Today. 13: 856-62. PMID 18652912 DOI: 10.1016/J.Drudis.2008.06.013  0.401
2008 Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. Plos Biology. 6: e184. PMID 18651794 DOI: 10.1371/Journal.Pbio.0060184  0.589
2008 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 Epidemiology, Biomarkers & Prevention : a Publication of the American Association For Cancer Research, Cosponsored by the American Society of Preventive Oncology. 17: 1368-73. PMID 18559551 DOI: 10.1158/1055-9965.Epi-07-2830  0.327
2008 Hanspers K, Pico AR, Salomonis N, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Conklin BR. An Introduction to Pathway Analysis with GenMAPP Nci Nature Pathway Interaction Database. DOI: 10.1038/Pid.2008.1  0.684
2007 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, ... ... Pico AR, et al. Integration of biological networks and gene expression data using Cytoscape. Nature Protocols. 2: 2366-82. PMID 17947979 DOI: 10.1038/Nprot.2007.324  0.576
2007 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. 8: 217. PMID 17588266 DOI: 10.1186/1471-2105-8-217  0.712
2001 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. 29: 593-601. PMID 11301020 DOI: 10.1016/S0896-6273(01)00236-7  0.644
1999 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 Molecular Cell. 3: 639-648. PMID 10360180 DOI: 10.1016/S1097-2765(00)80357-3  0.485
1999 Lafevre-Bernt M, Sicheri F, Pico A, Porter M, Kuriyan J, Todd Miller W. Intramolecular regulatory interactions in the Src family kinase Hck probed by mutagenesis of a conserved tryptophan residue Journal of Biological Chemistry. 273: 32129-32134. PMID 9822689 DOI: 10.1074/Jbc.273.48.32129  0.481
1997 Babcock AJ, Pico AR, Page CJ. Sol-gel synthesis of the strontium-copper oxycarbonate superconductors Sr2CuO2(CO3)1-x(BO3)x Materials Research Society Symposium - Proceedings. 453: 59-64. DOI: 10.1557/Proc-453-59  0.538
1997 Pico AR, Houk CS, Weakley TJR, Page CJ. A new strontium-copper ethylene glycol complex: Synthesis and structure of [Sr(C2H6O2)5] [Cu(C2H4O2)2] · C2H6O2 Inorganica Chimica Acta. 258: 155-160. DOI: 10.1016/S0020-1693(96)05494-1  0.537
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