Alex Pico, PhD

Publications

• COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff-Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Willighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R, COVID-19 Disease Map Community. Mol Syst Biol. 2021 Dec; 17(12):e10851.
• SARS-CoV-2 spike protein induces abnormal inflammatory blood clots neutralized by fibrin immunotherapy. Ryu JK, Sozmen EG, Dixit K, Montano M, Matsui Y, Liu Y, Helmy E, Deerinck TJ, Yan Z, Schuck R, Acevedo RM, Spencer CM, Thomas R, Pico AR, Zamvil SS, Lynch KL, Ellisman MH, Greene WC, Akassoglou K. bioRxiv. 2021 Oct 13.
• COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R, COVID-19 Disease Map Community. Mol Syst Biol. 2021 10; 17(10):e10387.
• Introducing R as a smart version of calculators enables beginners to explore it on their own. Choudhary K, Pico AR. F1000Res. 2021; 10:859.
• Ten simple rules for creating reusable pathway models for computational analysis and visualization. Hanspers K, Kutmon M, Coort SL, Digles D, Dupuis LJ, Ehrhart F, Hu F, Lopes EN, Martens M, Pham N, Shin W, Slenter DN, Waagmeester A, Willighagen EL, Winckers LA, Evelo CT, Pico AR. PLoS Comput Biol. 2021 08; 17(8):e1009226.
• scNetViz: from single cells to networks using Cytoscape. Choudhary K, Meng EC, Diaz-Mejia JJ, Bader GD, Pico AR, Morris JH. F1000Res. 2021; 10.
• WikiPathways: connecting communities. 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, Kutmon M. Nucleic Acids Res. 2021 01 08; 49(D1):D613-D621.
• Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma. 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, Cieslik M, Chang HY, Wyczalkowski MA, Li K, Colaprico A, Li QK, Clark DJ, Hu Y, Cao L, Pan J, Wang Y, Cho KC, Shi Z, Liao Y, Jiang W, Anurag M, Ji J, Yoo S, Zhou DC, Liang WW, Wendl M, Vats P, Carr SA, Mani DR, Zhang Z, Qian J, Chen XS, Pico AR, Wang P, Chinnaiyan AM, Ketchum KA, Kinsinger CR, Robles AI, An E, Hiltke T, Mesri M, Thiagarajan M, Weaver AM, Sikora AG, Lubinski J, Wierzbicka M, Wiznerowicz M, Satpathy S, Gillette MA, Miles G, Ellis MJ, Omenn GS, Rodriguez H, Boja ES, Dhanasekaran SM, Ding L, Nesvizhskii AI, El-Naggar AK, Chan DW, Zhang H, Zhang B, Clinical Proteomic Tumor Analysis Consortium. Cancer Cell. 2021 03 08; 39(3):361-379.e16.
• Shared Mechanisms Govern HIV Transcriptional Suppression in Circulating CD103+ and Gut CD4+ T Cells. Yukl SA, Khan S, Chen TH, Trapecar M, Wu F, Xie G, Telwatte S, Fulop D, Pico AR, Laird GM, Ritter KD, Jones NG, Lu CM, Siliciano RF, Roan NR, Milush JM, Somsouk M, Deeks SG, Hunt PW, Sanjabi S. J Virol. 2020 12 22; 95(2).
• The Dynamic Platelet Transcriptome in Obesity and Weight Loss. Ezzaty Mirhashemi M, Shah RV, Kitchen RR, Rong J, Spahillari A, Pico AR, Vitseva O, Levy D, Demarco D, Shah S, Iafrati MD, Larson MG, Tanriverdi K, Freedman JE. Arterioscler Thromb Vasc Biol. 2021 02; 41(2):854-864.
• Pathway information extracted from 25 years of pathway figures. Hanspers K, Riutta A, Summer-Kutmon M, Pico AR. Genome Biol. 2020 11 09; 21(1):273.
• Mir-30d Regulates Cardiac Remodeling by Intracellular and Paracrine Signaling. Li J, Salvador AM, Li G, Valkov N, Ziegler O, Yeri A, Yang Xiao C, Meechoovet B, Alsop E, Rodosthenous RS, Kundu P, Huan T, Levy D, Tigges J, Pico AR, Ghiran I, Silverman MG, Meng X, Kitchen R, Xu J, Van Keuren-Jensen K, Shah R, Xiao J, Das S. Circ Res. 2021 01 08; 128(1):e1-e23.
• Comprehensive Metabolic Phenotyping Refines Cardiovascular Risk in Young Adults. Murthy VL, Reis JP, Pico AR, Kitchen R, Lima JAC, Lloyd-Jones D, Allen NB, Carnethon M, Lewis GD, Nayor M, Vasan RS, Freedman JE, Clish CB, Shah RV. Circulation. 2020 12; 142(22):2110-2127.
• Molecular Signature of Multisystem Cardiometabolic Stress and Its Association With Prognosis. Murthy VL, Yu B, Wang W, Zhang X, Alkis T, Pico AR, Yeri A, Bhupathiraju SN, Bressler J, Ballantyne CM, Freedman JE, Ordovas J, Boerwinkle E, Tucker KL, Shah R. JAMA Cardiol. 2020 10 01; 5(10):1144-1153.
• Metabolic Architecture of Acute Exercise Response in Middle-Aged Adults in the Community. Nayor M, Shah RV, Miller PE, Blodgett JB, Tanguay M, Pico AR, Murthy VL, Malhotra R, Houstis NE, Deik A, Pierce KA, Bullock K, Dailey L, Velagaleti RS, Moore SA, Ho JE, Baggish AL, Clish CB, Larson MG, Vasan RS, Lewis GD. Circulation. 2020 11 17; 142(20):1905-1924.
• Author Correction: Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation. 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, Tognatta R, Yan Z, Pfaff SJ, Machado MR, Bedard C, Coronado PER, Jiang X, Wang J, Pleiss MA, Green AJ, Zamvil SS, Pico AR, Bruneau BG, Arkin MR, Akassoglou K. Nat Immunol. 2020 Sep; 21(9):1135.
• Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. 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, Barillot E, Dopazo J, Orta-Resendiz A, Messina F, Valencia A, Funahashi A, Kitano H, Auffray C, Balling R, Schneider R. Sci Data. 2020 07 17; 7(1):247.
• PathwayPCA: an R/Bioconductor Package for Pathway Based Integrative Analysis of Multi-Omics Data. Odom GJ, Ban Y, Colaprico A, Liu L, Silva TC, Sun X, Pico AR, Zhang B, Wang L, Chen X. Proteomics. 2020 11; 20(21-22):e1900409.
• COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. 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, Barillot E, Dopazo J, Orta-Resendiz A, Messina F, Valencia A, Funahashi A, Kitano H, Auffray C, Balling R, Schneider R. Sci Data. 2020 05 05; 7(1):136.
• Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation. 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, Tognatta R, Yan Z, Pfaff SJ, Machado MR, Bedard C, Rios Coronado PE, Jiang X, Wang J, Pleiss MA, Green AJ, Zamvil SS, Pico AR, Bruneau BG, Arkin MR, Akassoglou K. Nat Immunol. 2020 05; 21(5):513-524.
• Wikidata as a knowledge graph for the life sciences. 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, Putman T, Riutta A, Queralt-Rosinach N, Schriml LM, Shafee T, Slenter D, Stephan R, Thornton K, Tsueng G, Tu R, Ul-Hasan S, Willighagen E, Wu C, Su AI. Elife. 2020 03 17; 9.
• Proteogenomic Characterization of Endometrial Carcinoma. 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, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czekanski A, Jedryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD, Ding L, Zhang B, Liu T, Fenyö D, Clinical Proteomic Tumor Analysis Consortium. Cell. 2020 02 20; 180(4):729-748.e26.
• Circulating miRNAs and Risk of Sudden Death in Patients With Coronary Heart Disease. Silverman MG, Yeri A, Moorthy MV, Camacho Garcia F, Chatterjee NA, Glinge CSA, Tfelt-Hansen J, Salvador AM, Pico AR, Shah R, Albert CM, Das S. JACC Clin Electrophysiol. 2020 01; 6(1):70-79.
• RCy3: Network biology using Cytoscape from within R. Gustavsen JA, Pai S, Isserlin R, Demchak B, Pico AR. F1000Res. 2019; 8:1774.
• Cytoscape Automation: empowering workflow-based network analysis. Otasek D, Morris JH, Bouças J, Pico AR, Demchak B. Genome Biol. 2019 09 02; 20(1):185.
• exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids. 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, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah RV, Yeri A, Jenkins LM, Ahsen ME, Cordon-Cardo C, Dogra N, Gifford SM, Smith JT, Stolovitzky G, Tewari AK, Wunsch BH, Yadav KK, Danielson KM, Filant J, Moeller C, Nejad P, Paul A, Simonson B, Wong DK, Zhang X, Balaj L, Gandhi R, Sood AK, Alexander RP, Wang L, Wu C, Wong DTW, Galas DJ, Van Keuren-Jensen K, Patel T, Jones JC, Das S, Cheung KH, Pico AR, Su AI, Raffai RL, Laurent LC, Roth ME, Gerstein MB, Milosavljevic A. Cell. 2019 04 04; 177(2):463-477.e15.
• Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data. Diaz-Mejia JJ, Meng EC, Pico AR, MacParland SA, Ketela T, Pugh TJ, Bader GD, Morris JH. F1000Res. 2019; 8.
• Proteins Altered by Surgical Weight Loss Highlight Biomarkers of Insulin Resistance in the Community. Shah RV, Hwang SJ, Yeri A, Tanriverdi K, Pico AR, Yao C, Murthy V, Ho J, Vitseva O, Demarco D, Shah S, Iafrati MD, Levy D, Freedman JE. Arterioscler Thromb Vasc Biol. 2019 01; 39(1):107-115.
• Proteomic analysis of heart failure hospitalization among patients with chronic kidney disease: The Heart and Soul Study. Dubin RF, Whooley M, Pico A, Ganz P, Schiller NB, Meyer C. PLoS One. 2018; 13(12):e0208042.
• Fibrin-targeting immunotherapy protects against neuroinflammation and neurodegeneration. 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, Machado MR, Chan JP, Plastira I, Petersen MA, Pfaff SJ, Ang KK, Hallenbeck KK, Syme C, Hakozaki H, Ellisman MH, Swanson RA, Zamvil SS, Arkin MR, Zorn SH, Pico AR, Mucke L, Freedman SB, Stavenhagen JB, Nelson RB, Akassoglou K. Nat Immunol. 2018 11; 19(11):1212-1223.
• Associations of Circulating Extracellular RNAs With Myocardial Remodeling and Heart Failure. Shah RV, Rong J, Larson MG, Yeri A, Ziegler O, Tanriverdi K, Murthy V, Liu X, Xiao C, Pico AR, Huan T, Levy D, Lewis GD, Rosenzweig A, Vasan RS, Das S, Freedman JE. JAMA Cardiol. 2018 09 01; 3(9):871-876.
• The Cytoscape Automation app article collection. 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. F1000Res. 2018; 7:800.
• Identifier Mapping in Cytoscape. Treister A, Pico AR. F1000Res. 2018; 7:725.
• MicroRNAs Associated With Reverse Left Ventricular Remodeling in Humans Identify Pathways of Heart Failure Progression. 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. Circ Heart Fail. 2018 02; 11(2):e004278.
• WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. 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, Nishida K, Rieswijk L, Waagmeester A, Eijssen LMT, Evelo CT, Pico AR, Willighagen EL. Nucleic Acids Res. 2018 01 04; 46(D1):D661-D667.
• Research synergy and drug development: Bright stars in neighboring constellations. Keserci S, Livingston E, Wan L, Pico AR, Chacko G. Heliyon. 2017 Nov; 3(11):e00442.
• Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives. 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, Nordling D, Hide W, Hatzopoulos AK, Malik P, Cancelas JA, Lutzko C, Aronow BJ, Omberg L. Sci Data. 2017 03 28; 4:170030.
• Extracellular RNAs Are Associated With Insulin Resistance and Metabolic Phenotypes. 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. Diabetes Care. 2017 Apr; 40(4):546-553.
• Translational Epidemiology: Entering a Brave New World of Team Science. Shah R, Pico AR, Freedman JE. Circ Res. 2016 10 28; 119(10):1060-1062.
• 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 06; 12(6):e1004989.
• 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 05; 12(5):e1004941.
• 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.
• 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 04; 44(D1):D488-94.
• 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.
• Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. 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. J Extracell Vesicles. 2015; 4:27497.
• CyAnimator: Simple Animations of Cytoscape Networks. Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE. F1000Res. 2015; 4:482.
• PSFC: a Pathway Signal Flow Calculator App for Cytoscape. Nersisyan L, Johnson G, Riel-Mehan M, Pico A, Arakelyan A. F1000Res. 2015; 4:480.
• 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.
• 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; 11(2):e1004085.
• 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.
• 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; 3:138.
• WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization. Kutmon M, Lotia S, Evelo CT, Pico AR. F1000Res. 2014; 3:152.
• enhancedGraphics: a Cytoscape app for enhanced node graphics. Morris JH, Kuchinsky A, Ferrin TE, Pico AR. F1000Res. 2014; 3:147.
• setsApp for Cytoscape: Set operations for Cytoscape Nodes and Edges. Morris JH, Lotia S, Wu A, Doncheva NT, Albrecht M, Pico AR, Ferrin TE. F1000Res. 2014; 3:149.
• 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.
• 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.
• 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.
• Cytoscape app store. Lotia S, Montojo J, Dong Y, Bader GD, Pico AR. Bioinformatics. 2013 May 15; 29(10):1350-1.
• 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.
• 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.
• 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.
• Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. 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. Cell. 2012 Sep 28; 151(1):206-20.
• A low-frequency variant at 8q24.21 is strongly associated with risk of oligodendroglial tumors and astrocytomas with IDH1 or IDH2 mutation. 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. Nat Genet. 2012 Oct; 44(10):1122-5.
• GO-Elite: a flexible solution for pathway and ontology over-representation. Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, Conklin BR, Pico AR, Salomonis N. Bioinformatics. 2012 Aug 15; 28(16):2209-10.
• Mosaic: making biological sense of complex networks. Zhang C, Hanspers K, Kuchinsky A, Salomonis N, Xu D, Pico AR. Bioinformatics. 2012 Jul 15; 28(14):1943-4.
• WikiPathways: building research communities on biological pathways. Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo CT, Pico AR. Nucleic Acids Res. 2012 Jan; 40(Database issue):D1301-7.
• The BioPAX community standard for pathway data sharing. 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. Nat Biotechnol. 2010 Sep; 28(9):935-42.
• Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. Kelder T, Conklin BR, Evelo CT, Pico AR. PLoS Biol. 2010 Aug 31; 8(8).
• Structure of the human BK channel Ca2+-activation apparatus at 3.0 A resolution. Yuan P, Leonetti MD, Pico AR, Hsiung Y, MacKinnon R. Science. 2010 Jul 09; 329(5988):182-6.
• Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. 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. Proc Natl Acad Sci U S A. 2010 Jun 08; 107(23):10514-9.
• The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. van Iersel MP, Pico AR, Kelder T, Gao J, Ho I, Hanspers K, Conklin BR, Evelo CT. BMC Bioinformatics. 2010 Jan 04; 11:5.
• Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. Salomonis N, Nelson B, Vranizan K, Pico AR, Hanspers K, Kuchinsky A, Ta L, Mercola M, Conklin BR. PLoS Comput Biol. 2009 Nov; 5(11):e1000553.
• Mining biological pathways using WikiPathways web services. Kelder T, Pico AR, Hanspers K, van Iersel MP, Evelo C, Conklin BR. PLoS One. 2009 Jul 30; 4(7):e6447.
• Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. 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. Nat Genet. 2009 Aug; 41(8):905-8.
• SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system. Pico AR, Smirnov IV, Chang JS, Yeh RF, Wiemels JL, Wiencke JK, Tihan T, Conklin BR, Wrensch M. Nucleic Acids Res. 2009 Jan; 37(Database issue):D803-9.
• Presenting and exploring biological pathways with PathVisio. van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, Conklin BR, Evelo C. BMC Bioinformatics. 2008 Sep 25; 9:399.
• The public road to high-quality curated biological pathways. Adriaens ME, Jaillard M, Waagmeester A, Coort SL, Pico AR, Evelo CT. Drug Discov Today. 2008 Oct; 13(19-20):856-62.
• WikiPathways: pathway editing for the people. Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. PLoS Biol. 2008 Jul 22; 6(7):e184.
• The emerging world of wikis. 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. Science. 2008 Jun 06; 320(5881):1289-90.
• Pathway analysis of single-nucleotide polymorphisms potentially associated with glioblastoma multiforme susceptibility using random forests. Chang JS, Yeh RF, Wiencke JK, Wiemels JL, Smirnov I, Pico AR, Tihan T, Patoka J, Miike R, Sison JD, Rice T, Wrensch MR. Cancer Epidemiol Biomarkers Prev. 2008 Jun; 17(6):1368-73.
• GenMAPP 2: new features and resources for pathway analysis. Salomonis N, Hanspers K, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Stuart J, Conklin BR, Pico AR. BMC Bioinformatics. 2007 Jun 24; 8:217.
• Integration of biological networks and gene expression data using Cytoscape. 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. Nat Protoc. 2007; 2(10):2366-82.
• RCK domain model of calcium activation in BK channels Pico AR. . 2003.
• Neurocomputing Brent A Field, Alexander R Pico, Richard T Marrocco. . Local cortical injections of glutamate and noradrenaline alter high-frequency (245 Hz) neuronal activity in rat cortex. 1999; 26-27:123-130.
• A new strontium-copper ethylene glycol complex : synthesis and structure of [Sr(C2H6O2)5] [Cu(C2H4O2)2].C2H6O2 A R Pico, C S Houk, T J R Weakley, C J Page. . Inorganica Chimica Acta. 1997; (258):155-160.

More Publications