Literature DB >> 29092927

The Cancer Genomics Cloud: Collaborative, Reproducible, and Democratized-A New Paradigm in Large-Scale Computational Research.

Jessica W Lau1, Erik Lehnert1, Anurag Sethi1, Raunaq Malhotra1, Gaurav Kaushik1, Zeynep Onder1, Nick Groves-Kirkby1, Aleksandar Mihajlovic1, Jack DiGiovanna1, Mladen Srdic1, Dragan Bajcic1, Jelena Radenkovic1, Vladimir Mladenovic1, Damir Krstanovic1, Vladan Arsenijevic1, Djordje Klisic1, Milan Mitrovic1, Igor Bogicevic1, Deniz Kural1, Brandi Davis-Dusenbery.   

Abstract

The Seven Bridges Cancer Genomics Cloud (CGC; www.cancergenomicscloud.org) enables researchers to rapidly access and collaborate on massive public cancer genomic datasets, including The Cancer Genome Atlas. It provides secure on-demand access to data, analysis tools, and computing resources. Researchers from diverse backgrounds can easily visualize, query, and explore cancer genomic datasets visually or programmatically. Data of interest can be immediately analyzed in the cloud using more than 200 preinstalled, curated bioinformatics tools and workflows. Researchers can also extend the functionality of the platform by adding their own data and tools via an intuitive software development kit. By colocalizing these resources in the cloud, the CGC enables scalable, reproducible analyses. Researchers worldwide can use the CGC to investigate key questions in cancer genomics. Cancer Res; 77(21); e3-6. ©2017 AACR. ©2017 American Association for Cancer Research.

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Year:  2017        PMID: 29092927      PMCID: PMC5832960          DOI: 10.1158/0008-5472.CAN-17-0387

Source DB:  PubMed          Journal:  Cancer Res        ISSN: 0008-5472            Impact factor:   12.701


  10 in total

1.  Data analysis: Create a cloud commons.

Authors:  Lincoln D Stein; Bartha M Knoppers; Peter Campbell; Gad Getz; Jan O Korbel
Journal:  Nature       Date:  2015-07-09       Impact factor: 49.962

2.  The increasing dominance of teams in production of knowledge.

Authors:  Stefan Wuchty; Benjamin F Jones; Brian Uzzi
Journal:  Science       Date:  2007-04-12       Impact factor: 47.728

3.  The future of cancer genomics.

Authors: 
Journal:  Nat Med       Date:  2015-02       Impact factor: 53.440

4.  RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS.

Authors:  Gaurav Kaushik; Sinisa Ivkovic; Janko Simonovic; Nebojsa Tijanic; Brandi Davis-Dusenbery; Deniz Kural
Journal:  Pac Symp Biocomput       Date:  2017

5.  Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1.

Authors:  Roel G W Verhaak; Katherine A Hoadley; Elizabeth Purdom; Victoria Wang; Yuan Qi; Matthew D Wilkerson; C Ryan Miller; Li Ding; Todd Golub; Jill P Mesirov; Gabriele Alexe; Michael Lawrence; Michael O'Kelly; Pablo Tamayo; Barbara A Weir; Stacey Gabriel; Wendy Winckler; Supriya Gupta; Lakshmi Jakkula; Heidi S Feiler; J Graeme Hodgson; C David James; Jann N Sarkaria; Cameron Brennan; Ari Kahn; Paul T Spellman; Richard K Wilson; Terence P Speed; Joe W Gray; Matthew Meyerson; Gad Getz; Charles M Perou; D Neil Hayes
Journal:  Cancer Cell       Date:  2010-01-19       Impact factor: 31.743

6.  Mammary Tumor-Associated RNAs Impact Tumor Cell Proliferation, Invasion, and Migration.

Authors:  Sarah D Diermeier; Kung-Chi Chang; Susan M Freier; Junyan Song; Osama El Demerdash; Alexander Krasnitz; Frank Rigo; C Frank Bennett; David L Spector
Journal:  Cell Rep       Date:  2016-09-27       Impact factor: 9.423

7.  The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.

Authors:  Jordi Barretina; Giordano Caponigro; Nicolas Stransky; Kavitha Venkatesan; Adam A Margolin; Sungjoon Kim; Christopher J Wilson; Joseph Lehár; Gregory V Kryukov; Dmitriy Sonkin; Anupama Reddy; Manway Liu; Lauren Murray; Michael F Berger; John E Monahan; Paula Morais; Jodi Meltzer; Adam Korejwa; Judit Jané-Valbuena; Felipa A Mapa; Joseph Thibault; Eva Bric-Furlong; Pichai Raman; Aaron Shipway; Ingo H Engels; Jill Cheng; Guoying K Yu; Jianjun Yu; Peter Aspesi; Melanie de Silva; Kalpana Jagtap; Michael D Jones; Li Wang; Charles Hatton; Emanuele Palescandolo; Supriya Gupta; Scott Mahan; Carrie Sougnez; Robert C Onofrio; Ted Liefeld; Laura MacConaill; Wendy Winckler; Michael Reich; Nanxin Li; Jill P Mesirov; Stacey B Gabriel; Gad Getz; Kristin Ardlie; Vivien Chan; Vic E Myer; Barbara L Weber; Jeff Porter; Markus Warmuth; Peter Finan; Jennifer L Harris; Matthew Meyerson; Todd R Golub; Michael P Morrissey; William R Sellers; Robert Schlegel; Levi A Garraway
Journal:  Nature       Date:  2012-03-28       Impact factor: 49.962

8.  Integrated genomic and molecular characterization of cervical cancer.

Authors: 
Journal:  Nature       Date:  2017-01-23       Impact factor: 49.962

9.  Making sense of replications.

Authors:  Brian A Nosek; Timothy M Errington
Journal:  Elife       Date:  2017-01-19       Impact factor: 8.140

10.  An open investigation of the reproducibility of cancer biology research.

Authors:  Timothy M Errington; Elizabeth Iorns; William Gunn; Fraser Elisabeth Tan; Joelle Lomax; Brian A Nosek
Journal:  Elife       Date:  2014-12-10       Impact factor: 8.140

  10 in total
  43 in total

Review 1.  Progress Toward Cancer Data Ecosystems.

Authors:  Robert L Grossman
Journal:  Cancer J       Date:  2018 May/Jun       Impact factor: 3.360

2.  Cancer Informatics for Cancer Centers (CI4CC): Building a Community Focused on Sharing Ideas and Best Practices to Improve Cancer Care and Patient Outcomes.

Authors:  Jill S Barnholtz-Sloan; Dana E Rollison; Amrita Basu; Alexander D Borowsky; Alex Bui; Jack DiGiovanna; Montserrat Garcia-Closas; Jeanine M Genkinger; Travis Gerke; Marta Induni; James V Lacey; Lisa Mirel; Jennifer B Permuth; Joel Saltz; Elizabeth A Shenkman; Cornelia M Ulrich; W Jim Zheng; Sorena Nadaf; Warren A Kibbe
Journal:  JCO Clin Cancer Inform       Date:  2020-02

3.  The Germline Variants rs61757955 and rs34988193 Are Predictive of Survival in Lower Grade Glioma Patients.

Authors:  Ajay Chatrath; Manjari Kiran; Pankaj Kumar; Aakrosh Ratan; Anindya Dutta
Journal:  Mol Cancer Res       Date:  2019-01-16       Impact factor: 5.852

4.  Nebula: ultra-efficient mapping-free structural variant genotyper.

Authors:  Parsoa Khorsand; Fereydoun Hormozdiari
Journal:  Nucleic Acids Res       Date:  2021-05-07       Impact factor: 16.971

5.  Systematic Establishment of Robustness and Standards in Patient-Derived Xenograft Experiments and Analysis.

Authors:  Yvonne A Evrard; Anuj Srivastava; Jelena Randjelovic; James H Doroshow; Dennis A Dean; Jeffrey S Morris; Jeffrey H Chuang
Journal:  Cancer Res       Date:  2020-03-09       Impact factor: 12.701

6.  Novel, abundant Drosha isoforms are deficient in miRNA processing in cancer cells.

Authors:  Lisheng Dai; Lillian Hallmark; Xavier Bofill De Ros; Howard Crouch; Sean Chen; Tony Shi; Acong Yang; Chuanjiang Lian; Yongmei Zhao; Bao Tran; Shuo Gu
Journal:  RNA Biol       Date:  2020-08-30       Impact factor: 4.652

7.  QuagmiR: a cloud-based application for isomiR big data analytics.

Authors:  Xavier Bofill-De Ros; Kevin Chen; Susanna Chen; Nikola Tesic; Dusan Randjelovic; Nikola Skundric; Svetozar Nesic; Vojislav Varjacic; Elizabeth H Williams; Raunaq Malhotra; Minjie Jiang; Shuo Gu
Journal:  Bioinformatics       Date:  2019-05-01       Impact factor: 6.937

8.  Building Containerized Workflows Using the BioDepot-Workflow-Builder.

Authors:  Ling-Hong Hung; Jiaming Hu; Trevor Meiss; Alyssa Ingersoll; Wes Lloyd; Daniel Kristiyanto; Yuguang Xiong; Eric Sobie; Ka Yee Yeung
Journal:  Cell Syst       Date:  2019-09-11       Impact factor: 10.304

9.  Microbiome analyses of blood and tissues suggest cancer diagnostic approach.

Authors:  Gregory D Poore; Evguenia Kopylova; Qiyun Zhu; Carolina Carpenter; Serena Fraraccio; Stephen Wandro; Tomasz Kosciolek; Stefan Janssen; Jessica Metcalf; Se Jin Song; Jad Kanbar; Sandrine Miller-Montgomery; Robert Heaton; Rana Mckay; Sandip Pravin Patel; Austin D Swafford; Rob Knight
Journal:  Nature       Date:  2020-03-11       Impact factor: 49.962

10.  NCI Imaging Data Commons.

Authors:  Andrey Fedorov; William J R Longabaugh; David Pot; David A Clunie; Steve Pieper; Hugo J W L Aerts; André Homeyer; Rob Lewis; Afshin Akbarzadeh; Dennis Bontempi; William Clifford; Markus D Herrmann; Henning Höfener; Igor Octaviano; Chad Osborne; Suzanne Paquette; James Petts; Davide Punzo; Madelyn Reyes; Daniela P Schacherer; Mi Tian; George White; Erik Ziegler; Ilya Shmulevich; Todd Pihl; Ulrike Wagner; Keyvan Farahani; Ron Kikinis
Journal:  Cancer Res       Date:  2021-06-15       Impact factor: 12.701

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