Alex Pico, PhD

Title(s)Core Dir / Res Investigator, Business Service Ctr
SchoolChancellor/EVC/FAS
Phone--
ORCID ORCID Icon0000-0001-5706-2163 Additional info
vCardDownload vCard

    Collapse Overview 
    Collapse Overview
    As the Bioinformatics Core Director and Research Investigator at Gladstone Institutes in affiliation with UCSF, Dr. Pico's expertise lies in data mining, information storage and retrieval, and the development of computational tools for biomedical research. Through his work, he has authored various research publications on topics such as drug repurposing, multiomic profiling, and the construction of massive knowledge graphs of biomedical information. His contributions to projects like the COVID-19 Disease Map and WikiPathways have facilitated the sharing of valuable research insights across scientific communities. By leveraging programming languages and smart tools like R, Dr. Pico strives to empower researchers and explore the vast potential of biomedical data for precision medicine and scientific discovery.

    Collapse Featured Content 
    Collapse Twitter

    Collapse Bibliographic 
    Collapse 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. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. WikiPathways 2024: next generation pathway database. Nucleic Acids Res. 2024 Jan 05; 52(D1):D679-D689. Agrawal A, Balci H, Hanspers K, Coort SL, Martens M, Slenter DN, Ehrhart F, Digles D, Waagmeester A, Wassink I, Abbassi-Daloii T, Lopes EN, Iyer A, Acosta JM, Willighagen LG, Nishida K, Riutta A, Basaric H, Evelo CT, Willighagen EL, Kutmon M, Pico AR. PMID: 37941138; PMCID: PMC10767877.
      View in: PubMed   Mentions: 1     Fields:    
    2. In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response. Sci Adv. 2023 Dec 08; 9(49):eadj4884. Chen X, Haribowo AG, Baik AH, Fossati A, Stevenson E, Chen YR, Reyes NS, Peng T, Matthay MA, Traglia M, Pico AR, Jarosz DF, Buchwalter A, Ghaemmaghami S, Swaney DL, Jain IH. PMID: 38064566; PMCID: PMC10708181.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    3. Using published pathway figures in enrichment analysis and machine learning. BMC Genomics. 2023 Nov 25; 24(1):713. Shin MG, Pico AR. PMID: 38007419; PMCID: PMC10676589.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    4. BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs. Bioinformatics. 2023 Sep 02; 39(9). Callaghan J, Xu CH, Xin J, Cano MA, Riutta A, Zhou E, Juneja R, Yao Y, Narayan M, Hanspers K, Agrawal A, Pico AR, Wu C, Su AI. PMID: 37707514.
      View in: PubMed   Mentions:    Fields:    
    5. Using Published Pathway Figures in Enrichment Analysis and Machine Learning. bioRxiv. 2023 Jul 12. Shin MG, Pico A. PMID: 37461614; PMCID: PMC10350053.
      View in: PubMed   Mentions:
    6. Drugst.One - A plug-and-play solution for online systems medicine and network-based drug repurposing. ArXiv. 2023 Jul 04. Maier A, Hartung M, Abovsky M, Adamowicz K, Bader GD, Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Helmy M, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, List M, Lobentanzer S, Loscalzo J, Malod-Dognin N, Manz Q, Matschinske J, Mee M, Oubounyt M, Pico AR, Pillich RT, Poschenrieder JM, Pratt D, Pržulj N, Sadegh S, Saez-Rodriguez J, Sarkar S, Shaked G, Shamir R, Trummer N, Turhan U, Wang R, Zolotareva O, Baumbach J. PMID: 37332567; PMCID: PMC10274948.
      View in: PubMed   Mentions:
    7. Defining blood-induced microglia functions in neurodegeneration through multiomic profiling. Nat Immunol. 2023 07; 24(7):1173-1187. Mendiola AS, Yan Z, Dixit K, Johnson JR, Bouhaddou M, Meyer-Franke A, Shin MG, Yong Y, Agrawal A, MacDonald E, Muthukumar G, Pearce C, Arun N, Cabriga B, Meza-Acevedo R, Alzamora MDPS, Zamvil SS, Pico AR, Ryu JK, Krogan NJ, Akassoglou K. PMID: 37291385; PMCID: PMC10307624.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    8. BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs. ArXiv. 2023 Apr 18. Callaghan J, Xu CH, Xin J, Cano MA, Riutta A, Zhou E, Juneja R, Yao Y, Narayan M, Hanspers K, Agrawal A, Pico AR, Wu C, Su AI. PMID: 37131885; PMCID: PMC10153288.
      View in: PubMed   Mentions:
    9. NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange. Bioinformatics. 2023 03 01; 39(3). Pillich RT, Chen J, Churas C, Fong D, Gyori BM, Ideker T, Karis K, Liu SN, Ono K, Pico A, Pratt D. PMID: 36882166; PMCID: PMC10023220.
      View in: PubMed   Mentions: 4     Fields:    
    10. The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information. Bioinformatics. 2023 02 03; 39(2). Morris JH, Soman K, Akbas RE, Zhou X, Smith B, Meng EC, Huang CC, Cerono G, Schenk G, Rizk-Jackson A, Harroud A, Sanders L, Costes SV, Bharat K, Chakraborty A, Pico AR, Mardirossian T, Keiser M, Tang A, Hardi J, Shi Y, Musen M, Israni S, Huang S, Rose PW, Nelson CA, Baranzini SE. PMID: 36759942; PMCID: PMC9940622.
      View in: PubMed   Mentions: 12     Fields:    
    11. COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. 2021 Dec; 17(12):e10851. 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. PMID: 34939300; PMCID: PMC8696085.
      View in: PubMed   Mentions: 9     Fields:    
    12. SARS-CoV-2 spike protein induces abnormal inflammatory blood clots neutralized by fibrin immunotherapy. bioRxiv. 2021 Oct 13. 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. PMID: 34671772; PMCID: PMC8528086.
      View in: PubMed   Mentions: 1  
    13. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. 2021 10; 17(10):e10387. 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. PMID: 34664389; PMCID: PMC8524328.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCells
    14. Introducing R as a smart version of calculators enables beginners to explore it on their own. F1000Res. 2021; 10:859. Choudhary K, Pico AR. PMID: 35399224; PMCID: PMC8976183.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    15. Ten simple rules for creating reusable pathway models for computational analysis and visualization. PLoS Comput Biol. 2021 08; 17(8):e1009226. 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. PMID: 34411100; PMCID: PMC8375987.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimals
    16. scNetViz: from single cells to networks using Cytoscape. F1000Res. 2021; 10. Choudhary K, Meng EC, Diaz-Mejia JJ, Bader GD, Pico AR, Morris JH. PMID: 34912541; PMCID: PMC8593621.
      View in: PubMed   Mentions:    Fields:    
    17. WikiPathways: connecting communities. Nucleic Acids Res. 2021 01 08; 49(D1):D613-D621. 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. PMID: 33211851; PMCID: PMC7779061.
      View in: PubMed   Mentions: 319     Fields:    Translation:Humans
    18. Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma. Cancer Cell. 2021 03 08; 39(3):361-379.e16. 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. PMID: 33417831; PMCID: PMC7946781.
      View in: PubMed   Mentions: 124     Fields:    Translation:Humans
    19. Shared Mechanisms Govern HIV Transcriptional Suppression in Circulating CD103+ and Gut CD4+ T Cells. J Virol. 2020 12 22; 95(2). 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. PMID: 33115867; PMCID: PMC7944458.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    20. The Dynamic Platelet Transcriptome in Obesity and Weight Loss. Arterioscler Thromb Vasc Biol. 2021 02; 41(2):854-864. 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. PMID: 33297754; PMCID: PMC8105277.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    21. Pathway information extracted from 25 years of pathway figures. Genome Biol. 2020 11 09; 21(1):273. Hanspers K, Riutta A, Summer-Kutmon M, Pico AR. PMID: 33168034; PMCID: PMC7649569.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    22. Mir-30d Regulates Cardiac Remodeling by Intracellular and Paracrine Signaling. Circ Res. 2021 01 08; 128(1):e1-e23. 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. PMID: 33092465; PMCID: PMC7790887.
      View in: PubMed   Mentions: 51     Fields:    Translation:AnimalsCells
    23. Comprehensive Metabolic Phenotyping Refines Cardiovascular Risk in Young Adults. Circulation. 2020 12; 142(22):2110-2127. 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. PMID: 33073606; PMCID: PMC7880553.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    24. Molecular Signature of Multisystem Cardiometabolic Stress and Its Association With Prognosis. JAMA Cardiol. 2020 10 01; 5(10):1144-1153. 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. PMID: 32717046; PMCID: PMC7376474.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    25. Metabolic Architecture of Acute Exercise Response in Middle-Aged Adults in the Community. Circulation. 2020 11 17; 142(20):1905-1924. 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. PMID: 32927962; PMCID: PMC8049528.
      View in: PubMed   Mentions: 34     Fields:    Translation:Humans
    26. Author Correction: Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation. Nat Immunol. 2020 Sep; 21(9):1135. 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. PMID: 32661365.
      View in: PubMed   Mentions: 2     Fields:    
    27. Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Sci Data. 2020 07 17; 7(1):247. 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. PMID: 32678106; PMCID: PMC7366451.
      View in: PubMed   Mentions: 1     Fields:    
    28. PathwayPCA: an R/Bioconductor Package for Pathway Based Integrative Analysis of Multi-Omics Data. Proteomics. 2020 11; 20(21-22):e1900409. Odom GJ, Ban Y, Colaprico A, Liu L, Silva TC, Sun X, Pico AR, Zhang B, Wang L, Chen X. PMID: 32430990; PMCID: PMC7677175.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    29. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Sci Data. 2020 05 05; 7(1):136. 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. PMID: 32371892; PMCID: PMC7200764.
      View in: PubMed   Mentions: 66     Fields:    Translation:HumansCellsPHPublic Health
    30. Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation. Nat Immunol. 2020 05; 21(5):513-524. 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. PMID: 32284594; PMCID: PMC7523413.
      View in: PubMed   Mentions: 69     Fields:    Translation:HumansAnimalsCells
    31. Wikidata as a knowledge graph for the life sciences. Elife. 2020 03 17; 9. 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. PMID: 32180547; PMCID: PMC7077981.
      View in: PubMed   Mentions: 35     Fields:    Translation:Humans
    32. Proteogenomic Characterization of Endometrial Carcinoma. Cell. 2020 02 20; 180(4):729-748.e26. 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. PMID: 32059776; PMCID: PMC7233456.
      View in: PubMed   Mentions: 175     Fields:    Translation:HumansAnimalsCells
    33. Circulating miRNAs and Risk of Sudden Death in Patients With Coronary Heart Disease. JACC Clin Electrophysiol. 2020 01; 6(1):70-79. 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. PMID: 31971908; PMCID: PMC6981228.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    34. RCy3: Network biology using Cytoscape from within R. F1000Res. 2019; 8:1774. Gustavsen JA, Pai S, Isserlin R, Demchak B, Pico AR. PMID: 31819800; PMCID: PMC6880260.
      View in: PubMed   Mentions: 77     Fields:    
    35. Cytoscape Automation: empowering workflow-based network analysis. Genome Biol. 2019 09 02; 20(1):185. Otasek D, Morris JH, Bouças J, Pico AR, Demchak B. PMID: 31477170; PMCID: PMC6717989.
      View in: PubMed   Mentions: 479     Fields:    
    36. exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids. Cell. 2019 04 04; 177(2):463-477.e15. 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. PMID: 30951672; PMCID: PMC6616370.
      View in: PubMed   Mentions: 140     Fields:    Translation:HumansCells
    37. Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data. F1000Res. 2019; 8. Diaz-Mejia JJ, Meng EC, Pico AR, MacParland SA, Ketela T, Pugh TJ, Bader GD, Morris JH. PMID: 31508207; PMCID: PMC6720041.
      View in: PubMed   Mentions: 36     Fields:    
    38. Proteins Altered by Surgical Weight Loss Highlight Biomarkers of Insulin Resistance in the Community. Arterioscler Thromb Vasc Biol. 2019 01; 39(1):107-115. 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. PMID: 30580566; PMCID: PMC6309981.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    39. Proteomic analysis of heart failure hospitalization among patients with chronic kidney disease: The Heart and Soul Study. PLoS One. 2018; 13(12):e0208042. Dubin RF, Whooley M, Pico A, Ganz P, Schiller NB, Meyer C. PMID: 30557359; PMCID: PMC6296511.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    40. Fibrin-targeting immunotherapy protects against neuroinflammation and neurodegeneration. Nat Immunol. 2018 11; 19(11):1212-1223. 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. PMID: 30323343; PMCID: PMC6317891.
      View in: PubMed   Mentions: 90     Fields:    Translation:HumansAnimals
    41. Associations of Circulating Extracellular RNAs With Myocardial Remodeling and Heart Failure. JAMA Cardiol. 2018 09 01; 3(9):871-876. 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. PMID: 30090932; PMCID: PMC6233646.
      View in: PubMed   Mentions: 20     Fields:    Translation:Humans
    42. The Cytoscape Automation app article collection. F1000Res. 2018; 7:800. 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. PMID: 29983926; PMCID: PMC6013757.
      View in: PubMed   Mentions: 10     Fields:    
    43. Identifier Mapping in Cytoscape: idmapper. F1000Res. 2018; 7:725. Treister A, Pico AR. PMID: 30079244; PMCID: PMC6053696.
      View in: PubMed   Mentions: 7     Fields:    
    44. MicroRNAs Associated With Reverse Left Ventricular Remodeling in Humans Identify Pathways of Heart Failure Progression. Circ Heart Fail. 2018 02; 11(2):e004278. 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. PMID: 29438982; PMCID: PMC5813824.
      View in: PubMed   Mentions: 21     Fields:    Translation:Humans
    45. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. Nucleic Acids Res. 2018 01 04; 46(D1):D661-D667. 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. PMID: 29136241; PMCID: PMC5753270.
      View in: PubMed   Mentions: 413     Fields:    Translation:HumansAnimals
    46. Research synergy and drug development: Bright stars in neighboring constellations. Heliyon. 2017 Nov; 3(11):e00442. Keserci S, Livingston E, Wan L, Pico AR, Chacko G. PMID: 29264408; PMCID: PMC5727381.
      View in: PubMed   Mentions: 3  
    47. Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives. Sci Data. 2017 03 28; 4:170030. 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. PMID: 28350385; PMCID: PMC5369318.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansAnimalsCells
    48. Extracellular RNAs Are Associated With Insulin Resistance and Metabolic Phenotypes. Diabetes Care. 2017 Apr; 40(4):546-553. 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. PMID: 28183786; PMCID: PMC5360281.
      View in: PubMed   Mentions: 40     Fields:    Translation:Humans
    49. Translational Epidemiology: Entering a Brave New World of Team Science. Circ Res. 2016 10 28; 119(10):1060-1062. Shah R, Pico AR, Freedman JE. PMID: 27789584; PMCID: PMC5123762.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    50. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PLoS Comput Biol. 2016 06; 12(6):e1004989. Waagmeester A, Kutmon M, Riutta A, Miller R, Willighagen EL, Evelo CT, Pico AR. PMID: 27336457; PMCID: PMC4918977.
      View in: PubMed   Mentions: 16     Fields:    Translation:Humans
    51. Reactome from a WikiPathways Perspective. PLoS Comput Biol. 2016 05; 12(5):e1004941. Bohler A, Wu G, Kutmon M, Pradhana LA, Coort SL, Hanspers K, Haw R, Pico AR, Evelo CT. PMID: 27203685; PMCID: PMC4874630.
      View in: PubMed   Mentions: 18     Fields:    Translation:Humans
    52. Longer genotypically-estimated leukocyte telomere length is associated with increased adult glioma risk. Oncotarget. 2015 Dec 15; 6(40):42468-77. 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, Wiemels JL, ENGAGE Consortium Telomere Group, Samani NJ, Wiencke JK, Wrensch MR. PMID: 26646793; PMCID: PMC4767445.
      View in: PubMed   Mentions: 64     Fields:    Translation:HumansCells
    53. WikiPathways: capturing the full diversity of pathway knowledge. Nucleic Acids Res. 2016 Jan 04; 44(D1):D488-94. 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. PMID: 26481357; PMCID: PMC4702772.
      View in: PubMed   Mentions: 216     Fields:    Translation:Humans
    54. From scientific discovery to cures: bright stars within a galaxy. Cell. 2015 Sep 24; 163(1):21-3. Williams RS, Lotia S, Holloway AK, Pico AR. PMID: 26406364.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimals
    55. Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. J Extracell Vesicles. 2015; 4:27497. 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. PMID: 26320941; PMCID: PMC4553261.
      View in: PubMed   Mentions: 31     Fields:    
    56. PSFC: a Pathway Signal Flow Calculator App for Cytoscape. F1000Res. 2015; 4:480. Nersisyan L, Johnson G, Riel-Mehan M, Pico A, Arakelyan A. PMID: 26834984; PMCID: PMC4706054.
      View in: PubMed   Mentions: 10     Fields:    
    57. CyAnimator: Simple Animations of Cytoscape Networks. F1000Res. 2015; 4:482. Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE. PMID: 26937268.
      View in: PubMed   Mentions: 6     Fields:    
    58. Glioma Groups Based on 1p/19q, IDH, and TERT Promoter Mutations in Tumors. N Engl J Med. 2015 Jun 25; 372(26):2499-508. 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, Wiemels J, Wiencke JK, Wrensch MR, Jenkins RB. PMID: 26061753; PMCID: PMC4489704.
      View in: PubMed   Mentions: 956     Fields:    Translation:HumansCells
    59. PathVisio 3: an extendable pathway analysis toolbox. PLoS Comput Biol. 2015 Feb; 11(2):e1004085. Kutmon M, van Iersel MP, Bohler A, Kelder T, Nunes N, Pico AR, Evelo CT. PMID: 25706687; PMCID: PMC4338111.
      View in: PubMed   Mentions: 199     Fields:    Translation:HumansAnimalsCells
    60. Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc. 2014 Nov; 9(11):2539-54. Morris JH, Knudsen GM, Verschueren E, Johnson JR, Cimermancic P, Greninger AL, Pico AR. PMID: 25275790; PMCID: PMC4332878.
      View in: PubMed   Mentions: 85     Fields:    
    61. enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Res. 2014; 3:147. Morris JH, Kuchinsky A, Ferrin TE, Pico AR. PMID: 25285206; PMCID: PMC4176421.
      View in: PubMed   Mentions: 25     Fields:    
    62. The Cytoscape app article collection. F1000Res. 2014; 3:138. 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. PMID: 25580224; PMCID: PMC4288400.
      View in: PubMed   Mentions: 7     Fields:    
    63. WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization. F1000Res. 2014; 3:152. Kutmon M, Lotia S, Evelo CT, Pico AR. PMID: 25254103; PMCID: PMC4168754.
      View in: PubMed   Mentions: 35     Fields:    
    64. setsApp: Set operations for Cytoscape Nodes and Edges. F1000Res. 2014; 3:149. Morris JH, Wu A, Doncheva NT, Albrecht M, Ferrin TE. PMID: 25352980; PMCID: PMC4207244.
      View in: PubMed   Mentions: 7     Fields:    
    65. Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk. Nat Genet. 2014 Jul; 46(7):731-5. 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, 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. PMID: 24908248; PMCID: PMC4074274.
      View in: PubMed   Mentions: 103     Fields:    Translation:HumansCells
    66. NOA: a cytoscape plugin for network ontology analysis. Bioinformatics. 2013 Aug 15; 29(16):2066-7. Zhang C, Wang J, Hanspers K, Xu D, Chen L, Pico AR. PMID: 23749961; PMCID: PMC3722524.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    67. 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. 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. PMID: 23733245; PMCID: PMC3714154.
      View in: PubMed   Mentions: 29     Fields:    Translation:Humans
    68. Cytoscape app store. Bioinformatics. 2013 May 15; 29(10):1350-1. Lotia S, Montojo J, Dong Y, Bader GD, Pico AR. PMID: 23595664; PMCID: PMC3654709.
      View in: PubMed   Mentions: 75     Fields:    
    69. 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. 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. PMID: 23361564; PMCID: PMC3635511.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    70. 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. 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. PMID: 23280628; PMCID: PMC3670948.
      View in: PubMed   Mentions: 26     Fields:    Translation:Humans
    71. A travel guide to Cytoscape plugins. Nat Methods. 2012 Nov; 9(11):1069-76. Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. PMID: 23132118; PMCID: PMC3649846.
      View in: PubMed   Mentions: 709     Fields:    
    72. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 2012 Sep 28; 151(1):206-20. 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. PMID: 22981692; PMCID: PMC3462286.
      View in: PubMed   Mentions: 356     Fields:    Translation:HumansAnimalsCells
    73. 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. 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. PMID: 22922872; PMCID: PMC3600846.
      View in: PubMed   Mentions: 80     Fields:    Translation:HumansCells
    74. GO-Elite: a flexible solution for pathway and ontology over-representation. Bioinformatics. 2012 Aug 15; 28(16):2209-10. Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, Conklin BR, Pico AR, Salomonis N. PMID: 22743224; PMCID: PMC3413395.
      View in: PubMed   Mentions: 155     Fields:    
    75. Mosaic: making biological sense of complex networks. Bioinformatics. 2012 Jul 15; 28(14):1943-4. Zhang C, Hanspers K, Kuchinsky A, Salomonis N, Xu D, Pico AR. PMID: 22576176; PMCID: PMC3389769.
      View in: PubMed   Mentions: 18     Fields:    
    76. WikiPathways: building research communities on biological pathways. Nucleic Acids Res. 2012 Jan; 40(Database issue):D1301-7. Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo CT, Pico AR. PMID: 22096230; PMCID: PMC3245032.
      View in: PubMed   Mentions: 258     Fields:    
    77. The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010 Sep; 28(9):935-42. 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. PMID: 20829833; PMCID: PMC3001121.
      View in: PubMed   Mentions: 336     Fields:    Translation:Cells
    78. Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. PLoS Biol. 2010 Aug 31; 8(8). Kelder T, Conklin BR, Evelo CT, Pico AR. PMID: 20824171; PMCID: PMC2930872.
      View in: PubMed   Mentions: 20     Fields:    Translation:Humans
    79. Structure of the human BK channel Ca2+-activation apparatus at 3.0 A resolution. Science. 2010 Jul 09; 329(5988):182-6. Yuan P, Leonetti MD, Pico AR, Hsiung Y, MacKinnon R. PMID: 20508092; PMCID: PMC3022345.
      View in: PubMed   Mentions: 173     Fields:    Translation:HumansCells
    80. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proc Natl Acad Sci U S A. 2010 Jun 08; 107(23):10514-9. 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. PMID: 20498046; PMCID: PMC2890851.
      View in: PubMed   Mentions: 136     Fields:    Translation:HumansAnimalsCells
    81. The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinformatics. 2010 Jan 04; 11:5. van Iersel MP, Pico AR, Kelder T, Gao J, Ho I, Hanspers K, Conklin BR, Evelo CT. PMID: 20047655; PMCID: PMC2824678.
      View in: PubMed   Mentions: 73     Fields:    
    82. Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. PLoS Comput Biol. 2009 Nov; 5(11):e1000553. Salomonis N, Nelson B, Vranizan K, Pico AR, Hanspers K, Kuchinsky A, Ta L, Mercola M, Conklin BR. PMID: 19893621; PMCID: PMC2764345.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansCells
    83. Mining biological pathways using WikiPathways web services. PLoS One. 2009 Jul 30; 4(7):e6447. Kelder T, Pico AR, Hanspers K, van Iersel MP, Evelo C, Conklin BR. PMID: 19649250; PMCID: PMC2714472.
      View in: PubMed   Mentions: 67     Fields:    
    84. Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. Nat Genet. 2009 Aug; 41(8):905-8. 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. PMID: 19578366; PMCID: PMC2923561.
      View in: PubMed   Mentions: 304     Fields:    Translation:HumansCells
    85. SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system. Nucleic Acids Res. 2009 Jan; 37(Database issue):D803-9. Pico AR, Smirnov IV, Chang JS, Yeh RF, Wiemels JL, Wiemels JL, Wiencke JK, Tihan T, Conklin BR, Wrensch M. PMID: 18984625; PMCID: PMC2686434.
      View in: PubMed   Mentions: 16     Fields:    Translation:Humans
    86. Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics. 2008 Sep 25; 9:399. van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, Conklin BR, Evelo C. PMID: 18817533; PMCID: PMC2569944.
      View in: PubMed   Mentions: 174     Fields:    Translation:Cells
    87. The public road to high-quality curated biological pathways. Drug Discov Today. 2008 Oct; 13(19-20):856-62. Adriaens ME, Jaillard M, Waagmeester A, Coort SL, Pico AR, Evelo CT. PMID: 18652912; PMCID: PMC3646620.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansAnimals
    88. WikiPathways: pathway editing for the people. PLoS Biol. 2008 Jul 22; 6(7):e184. Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. PMID: 18651794; PMCID: PMC2475545.
      View in: PubMed   Mentions: 296     Fields:    Translation:Cells
    89. The emerging world of wikis. Science. 2008 Jun 06; 320(5881):1289-90. 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. PMID: 18535227.
      View in: PubMed   Mentions: 13     Fields:    
    90. 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. Chang JS, Yeh RF, Wiencke JK, Wiemels JL, Wiemels JL, Smirnov I, Pico AR, Tihan T, Patoka J, Miike R, Sison JD, Rice T, Wrensch MR. PMID: 18559551; PMCID: PMC6986563.
      View in: PubMed   Mentions: 52     Fields:    Translation:Humans
    91. GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics. 2007 Jun 24; 8:217. Salomonis N, Hanspers K, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Stuart J, Conklin BR, Pico AR. PMID: 17588266; PMCID: PMC1924866.
      View in: PubMed   Mentions: 120     Fields:    Translation:Cells
    92. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2007; 2(10):2366-82. 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. PMID: 17947979; PMCID: PMC3685583.
      View in: PubMed   Mentions: 1245     Fields:    
    93. RCK domain model of calcium activation in BK channels. 2003. Pico AR. View Publication.
    94. Neurocomputing. Local cortical injections of glutamate and noradrenaline alter high-frequency (245 Hz) neuronal activity in rat cortex. 1999; 26-27:123-130. Brent A Field, Alexander R Pico, Richard T Marrocco. View Publication.
    95. 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. A R Pico, C S Houk, T J R Weakley, C J Page. View Publication.
    With one click, see people who:

    Mentor Faculty

    Run Clinical Trials

    Work in Global Health Equity

    Offer Student Projects

    See more options in the Advanced Search tab

    Alex's Networks
    Concepts (339)
    Derived automatically from this person's publications.
    Explore
    _
    Co-Authors (72)
    People in Profiles who have published with this person.
    Explore
    _
    Similar People (60)
    People who share similar concepts with this person.
    Explore
    _
    Same Department
    Search Department
    _

    UCSF Profiles is managed by the UCSF Clinical and Translational Science Institute (CTSI), part of the Clinical and Translational Science Award program funded by the National Center for Advancing Translational Sciences (Grant Number UL1 TR000004) at the National Institutes of Health (NIH).

    We use cookies to operate our website. We also use cookies to analyze our site’s performance and improve your experience on our site. For more information about how we use cookies, please see our Website Terms of Use. This site is running Profiles RNS version UCSF-v3.1.0-3-g1ef1264b on PROFILES-PWEB04.

    Copyright © The Regents of the University of California.