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Alexander R. Pico
Researcher at Gladstone Institutes
Publications - 114
Citations - 16466
Alexander R. Pico is an academic researcher from Gladstone Institutes. The author has contributed to research in topics: WikiPathways : Pathways for the people & Glioma. The author has an hindex of 40, co-authored 108 publications receiving 12916 citations. Previous affiliations of Alexander R. Pico include University of Toronto & Maastricht University.
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Journal ArticleDOI
Integration of biological networks and gene expression data using Cytoscape
Melissa S. Cline,Michael E. Smoot,Ethan Cerami,Allan Kuchinsky,Nerius Landys,Christopher T. Workman,Rowan H. Christmas,Iliana Avila-Campilo,Iliana Avila-Campilo,Michael L. Creech,Benjamin Gross,Kristina Hanspers,Ruth Isserlin,Ryan Kelley,Sarah Killcoyne,Samad Lotia,Steven Maere,John H. Morris,Keiichiro Ono,Vuk Pavlovic,Alexander R. Pico,Aditya Vailaya,Peng-Liang Wang,Annette M. Adler,Bruce R. Conklin,Leroy Hood,Martin Kuiper,Chris Sander,Ilya Schmulevich,Benno Schwikowski,Guy J. Warner,Trey Ideker,Gary D. Bader +32 more
TL;DR: This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest.
Journal ArticleDOI
Glioma Groups Based on 1p/19q, IDH, and TERT Promoter Mutations in Tumors
Jeanette E. Eckel-Passow,Daniel H. Lachance,Annette M. Molinaro,Kyle M. Walsh,Paul A. Decker,Hugues Sicotte,Melike Pekmezci,Terri Rice,Matt L. Kosel,Ivan Smirnov,Gobinda Sarkar,Alissa Caron,Thomas M. Kollmeyer,Corinne Praska,Anisha R. Chada,Chandralekha Halder,Helen M. Hansen,Lucie McCoy,Paige M. Bracci,Roxanne Marshall,Shichun Zheng,Gerald F. Reis,Alexander R. Pico,Brian P. O'Neill,Jan C. Buckner,Caterina Giannini,Jason T. Huse,Arie Perry,Tarik Tihan,Mitchell S. Berger,Susan M. Chang,Michael D. Prados,Joseph L. Wiemels,John K. Wiencke,Margaret Wrensch,Robert B. Jenkins +35 more
TL;DR: The five glioma molecular groups had different ages at onset, overall survival, and associations with germline variants, which implies that they are characterized by distinct mechanisms of pathogenesis.
Journal ArticleDOI
A travel guide to Cytoscape plugins
Rintaro Saito,Michael E. Smoot,Keiichiro Ono,Johannes Ruscheinski,Peng-Liang Wang,Samad Lotia,Alexander R. Pico,Gary D. Bader,Trey Ideker +8 more
TL;DR: A travel guide to the world of plugins, covering the 152 publicly available plugins for Cytoscape 2.5–2.8 and ongoing efforts to distribute, organize and maintain the quality of the collection.
Journal ArticleDOI
Cytoscape Automation: empowering workflow-based network analysis.
TL;DR: Cytoscape Automation (CA), which marries CyToscape to highly productive workflow systems, for example, Python/R in Jupyter/RStudio, is described, which exposes over 270 Cytoscapes core functions and 34 apps as REST-callable functions with standardized JSON interfaces backed by Swagger documentation.
Journal ArticleDOI
WikiPathways : a multifaceted pathway database bridging metabolomics to other omics research
Denise Slenter,Martina Kutmon,Kristina Hanspers,Anders Riutta,Jacob Windsor,Nuno Nunes,Jonathan Mélius,Elisa Cirillo,Susan L. Coort,Daniela Digles,Friederike Ehrhart,Pieter Giesbertz,Marianthi Kalafati,Marvin Martens,Ryan A. Miller,Kozo Nishida,Linda Rieswijk,Andra Waagmeester,Lars M. T. Eijssen,Lars M. T. Eijssen,Chris T. Evelo,Alexander R. Pico,Egon Willighagen +22 more
TL;DR: There is a doubling of the number of annotated metabolite nodes in WikiPathways and an OpenAPI documentation of the authors' web services and the FAIR annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data.