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Alexander R. Pico, Ph.D. - Publications

Bioinformatics Gladstone Institutes 
Ion channels, structural biology, network biology, bioinformatics, pathways

62 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
2021 Huang C, Chen L, Savage SR, Eguez RV, Dou Y, Li Y, da Veiga Leprevost F, Jaehnig EJ, Lei JT, Wen B, Schnaubelt M, Krug K, Song X, Cieślik M, Chang HY, ... ... Pico AR, et al. Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma. Cancer Cell. PMID 33417831 DOI: 10.1016/j.ccell.2020.12.007  0.4
2020 Martens M, Ammar A, Riutta A, Waagmeester A, Slenter DN, Hanspers K, A Miller R, Digles D, Lopes EN, Ehrhart F, Dupuis LJ, Winckers LA, Coort SL, Willighagen EL, Evelo CT, ... Pico AR, et al. WikiPathways: connecting communities. Nucleic Acids Research. PMID 33211851 DOI: 10.1093/nar/gkaa1024  0.76
2020 Hanspers K, Riutta A, Summer-Kutmon M, Pico AR. Pathway information extracted from 25 years of pathway figures. Genome Biology. 21: 273. PMID 33168034 DOI: 10.1186/s13059-020-02181-2  0.76
2020 Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, et al. Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Scientific Data. 7: 247. PMID 32678106 DOI: 10.1038/S41597-020-00589-W  0.56
2020 Mendiola AS, Ryu JK, Bardehle S, Meyer-Franke A, Ang KK, Wilson C, Baeten KM, Hanspers K, Merlini M, Thomas S, Petersen MA, Williams A, Thomas R, Rafalski VA, Meza-Acevedo R, ... ... Pico AR, et al. Author Correction: Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation. Nature Immunology. PMID 32661365 DOI: 10.1038/S41590-020-0754-X  0.76
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  0.4
2020 Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, et al. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Scientific Data. 7: 136. PMID 32371892 DOI: 10.1038/S41597-020-0477-8  0.56
2020 Mendiola AS, Ryu JK, Bardehle S, Meyer-Franke A, Ang KK, Wilson C, Baeten KM, Hanspers K, Merlini M, Thomas S, Petersen MA, Williams A, Thomas R, Rafalski VA, Meza-Acevedo R, ... ... Pico AR, et al. Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation. Nature Immunology. PMID 32284594 DOI: 10.1038/S41590-020-0654-0  0.76
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  0.76
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  0.4
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  0.76
2018 Ryu JK, Rafalski VA, Meyer-Franke A, Adams RA, Poda SB, Rios Coronado PE, Pedersen LØ, Menon V, Baeten KM, Sikorski SL, Bedard C, Hanspers K, Bardehle S, Mendiola AS, Davalos D, ... ... Pico AR, et al. Fibrin-targeting immunotherapy protects against neuroinflammation and neurodegeneration. Nature Immunology. PMID 30323343 DOI: 10.1038/S41590-018-0232-X  0.76
2018 Shah R, Ziegler O, Yeri A, Liu X, Murthy V, Rabideau D, Xiao CY, Hanspers K, Belcher A, Tackett M, Rosenzweig A, Pico AR, Januzzi JL, Das S. MicroRNAs Associated With Reverse Left Ventricular Remodeling in Humans Identify Pathways of Heart Failure Progression. Circulation. Heart Failure. 11: e004278. PMID 29438982 DOI: 10.1161/Circheartfailure.117.004278  0.76
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  0.76
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  0.52
2017 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, et al. Extracellular RNAs Are Associated With Insulin Resistance and Metabolic Phenotypes. Diabetes Care. PMID 28183786 DOI: 10.2337/Dc16-1354  0.76
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  0.56
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  0.76
2015 Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE. CyAnimator: Simple Animations of Cytoscape Networks. F1000research. 4: 482. PMID 26937268 DOI: 10.12688/F1000Research.6852.2  0.76
2015 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, et al. Longer genotypically-estimated leukocyte telomere length is associated with increased adult glioma risk. Oncotarget. PMID 26646793 DOI: 10.18632/Oncotarget.6468  0.76
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  0.76
2015 Williams RS, Lotia S, Holloway AK, Pico AR. From Scientific Discovery to Cures: Bright Stars within a Galaxy. Cell. 163: 21-3. PMID 26406364 DOI: 10.1016/J.Cell.2015.09.007  0.76
2015 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, ... ... Pico AR, et al. Glioma Groups Based on 1p/19q, IDH, and TERT Promoter Mutations in Tumors. The New England Journal of Medicine. 372: 2499-508. PMID 26061753 DOI: 10.1056/Nejmoa1407279  0.76
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  0.76
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  0.76
2014 Morris JH, Kuchinsky A, Ferrin TE, Pico AR. enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000research. 3: 147. PMID 25285206 DOI: 10.12688/F1000Research.4460.1  0.76
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  0.76
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  0.76
2014 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, et al. Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk. Nature Genetics. 46: 731-5. PMID 24908248 DOI: 10.1038/Ng.3004  0.76
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  0.76
2013 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, et al. Genetic variants in telomerase-related genes are associated with an older age at diagnosis in glioma patients: evidence for distinct pathways of gliomagenesis. Neuro-Oncology. 15: 1041-7. PMID 23733245 DOI: 10.1093/Neuonc/Not051  0.76
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  0.76
2013 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, et al. Inherited variant on chromosome 11q23 increases susceptibility to IDH-mutated but not IDH-normal gliomas regardless of grade or histology. Neuro-Oncology. 15: 535-41. PMID 23361564 DOI: 10.1093/Neuonc/Nos324  0.76
2013 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, et al. Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies. Genetic Epidemiology. 37: 222-8. PMID 23280628 DOI: 10.1002/Gepi.21707  0.76
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  0.76
2012 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, ... ... Pico AR, et al. A low-frequency variant at 8q24.21 is strongly associated with risk of oligodendroglial tumors and astrocytomas with IDH1 or IDH2 mutation. Nature Genetics. 44: 1122-5. PMID 22922872 DOI: 10.1038/Ng.2388  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
2009 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, ... ... Pico AR, et al. Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. Nature Genetics. 41: 905-8. PMID 19578366 DOI: 10.1038/Ng.408  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
2008 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 (New York, N.Y.). 320: 1289-90. PMID 18535227 DOI: 10.1126/Science.320.5881.1289B  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
1999 Field BA, Pico AR, Marrocco RT. Local cortical injections of glutamate and noradrenaline alter high-frequency (245 Hz) neuronal activity in rat cortex Neurocomputing. 26: 123-130. DOI: 10.1016/S0925-2312(99)00069-7  0.76
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  0.76
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  0.76
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