Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.

Literature DB >> 29092941

NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.

Dexter Pratt¹, Jing Chen², Rudolf Pillich², Vladimir Rynkov², Aaron Gary², Barry Demchak², Trey Ideker^2,3.

Abstract

We present NDEx 2.0, the latest release of the Network Data Exchange (NDEx) online data commons (www.ndexbio.org) and the ways in which it can be used to (i) improve the quality and abundance of biological networks relevant to the cancer research community; (ii) provide a medium for collaboration involving networks; and (iii) facilitate the review and dissemination of networks. We describe innovations addressing the challenges of an online data commons: scalability, data integration, data standardization, control of content and format by authors, and decentralized mechanisms for review. The practical use of NDEx is presented in the context of a novel strategy to foster network-oriented communities of interest in cancer research by adapting methods from academic publishing and social media. Cancer Res; 77(21); e58-61. ©2017 AACR. ©2017 American Association for Cancer Research.

Entities: Disease

Mesh：

Year: 2017 PMID： 29092941 PMCID： PMC5679399 DOI： 10.1158/0008-5472.CAN-17-0606

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

6 in total

1. Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Authors: Paul Shannon; Andrew Markiel; Owen Ozier; Nitin S Baliga; Jonathan T Wang; Daniel Ramage; Nada Amin; Benno Schwikowski; Trey Ideker
Journal: Genome Res Date: 2003-11 Impact factor: 9.043

2. DARPA's Big Mechanism program.

Authors: Paul R Cohen
Journal: Phys Biol Date: 2015-07-16 Impact factor: 2.583

3. NDEx: A Community Resource for Sharing and Publishing of Biological Networks.

Authors: Rudolf T Pillich; Jing Chen; Vladimir Rynkov; David Welker; Dexter Pratt
Journal: Methods Mol Biol Date: 2017

4. NDEx, the Network Data Exchange.

Authors: Dexter Pratt; Jing Chen; David Welker; Ricardo Rivas; Rudolf Pillich; Vladimir Rynkov; Keiichiro Ono; Carol Miello; Lyndon Hicks; Sandor Szalma; Aleksandar Stojmirovic; Radu Dobrin; Michael Braxenthaler; Jan Kuentzer; Barry Demchak; Trey Ideker
Journal: Cell Syst Date: 2015-10-28 Impact factor: 10.304

Review 5. The cancer cell map initiative: defining the hallmark networks of cancer.

Authors: Nevan J Krogan; Scott Lippman; David A Agard; Alan Ashworth; Trey Ideker
Journal: Mol Cell Date: 2015-05-21 Impact factor: 17.970

6. CRAVAT: cancer-related analysis of variants toolkit.

Authors: Christopher Douville; Hannah Carter; Rick Kim; Noushin Niknafs; Mark Diekhans; Peter D Stenson; David N Cooper; Michael Ryan; Rachel Karchin
Journal: Bioinformatics Date: 2013-01-16 Impact factor: 6.937

6 in total

23 in total

1. Informatics Tools for Cancer Research and Care: Bridging the Gap Between Innovation and Implementation.

Authors: Jeremy L Warner; Juli D Klemm
Journal: JCO Clin Cancer Inform Date: 2020-09

2. Interpretation of cancer mutations using a multiscale map of protein systems.

Authors: Fan Zheng; Marcus R Kelly; Dana J Ramms; Marissa L Heintschel; Kai Tao; Beril Tutuncuoglu; John J Lee; Keiichiro Ono; Helene Foussard; Michael Chen; Kari A Herrington; Erica Silva; Sophie N Liu; Jing Chen; Christopher Churas; Nicholas Wilson; Anton Kratz; Rudolf T Pillich; Devin N Patel; Jisoo Park; Brent Kuenzi; Michael K Yu; Katherine Licon; Dexter Pratt; Jason F Kreisberg; Minkyu Kim; Danielle L Swaney; Xiaolin Nan; Stephanie I Fraley; J Silvio Gutkind; Nevan J Krogan; Trey Ideker
Journal: Science Date: 2021-10-01 Impact factor: 63.714

3. Proteogenomic Network Analysis of Context-Specific KRAS Signaling in Mouse-to-Human Cross-Species Translation.

Authors: Douglas K Brubaker; Joao A Paulo; Shikha Sheth; Emily J Poulin; Olesja Popow; Brian A Joughin; Samantha Dale Strasser; Alina Starchenko; Steven P Gygi; Douglas A Lauffenburger; Kevin M Haigis
Journal: Cell Syst Date: 2019-09-11 Impact factor: 10.304

NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.

1. Cytoscape: a software environment for integrated models of biomolecular interaction networks.

2. DARPA's Big Mechanism program.

3. NDEx: A Community Resource for Sharing and Publishing of Biological Networks.

4. NDEx, the Network Data Exchange.

Review 5. The cancer cell map initiative: defining the hallmark networks of cancer.

6. CRAVAT: cancer-related analysis of variants toolkit.

1. Informatics Tools for Cancer Research and Care: Bridging the Gap Between Innovation and Implementation.

2. Interpretation of cancer mutations using a multiscale map of protein systems.

3. Proteogenomic Network Analysis of Context-Specific KRAS Signaling in Mouse-to-Human Cross-Species Translation.

Review 4. Multi-omics integration in biomedical research - A metabolomics-centric review.

5. Genomic Correlates of DNA Damage in Breast Cancer Subtypes.

6. Classifying tumors by supervised network propagation.

7. Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases.

8. Pathway information extracted from 25 years of pathway figures.

9. Voltage-Dependent Anion Channels Influence Cytotoxicity of ME-344, a Therapeutic Isoflavone.

10. Consensus transcriptional regulatory networks of coronavirus-infected human cells.