Literature DB >> 33247935

An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries.

Braja Gopal Patra1, Babak Soltanalizadeh2, Nan Deng2, Leqing Wu2, Vahed Maroufy2, Canglin Wu3, W Jim Zheng4, Kirk Roberts4, Hulin Wu2,4, Ashraf Yaseen2.   

Abstract

The exponential growth of genomic/genetic data in the era of Big Data demands new solutions for making these data findable, accessible, interoperable and reusable. In this article, we present a web-based platform named Gene Expression Time-Course Research (GETc) Platform that enables the discovery and visualization of time-course gene expression data and analytical results from the NIH/NCBI-sponsored Gene Expression Omnibus (GEO). The analytical results are produced from an analytic pipeline based on the ordinary differential equation model. Furthermore, in order to extract scientific insights from these results and disseminate the scientific findings, close and efficient collaborations between domain-specific experts from biomedical and scientific fields and data scientists is required. Therefore, GETc provides several recommendation functions and tools to facilitate effective collaborations. GETc platform is a very useful tool for researchers from the biomedical genomics community to present and communicate large numbers of analysis results from GEO. It is generalizable and broadly applicable across different biomedical research areas. GETc is a user-friendly and efficient web-based platform freely accessible at http://genestudy.org/.
© The Author(s) 2020. Published by Oxford University Press.

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Year:  2020        PMID: 33247935      PMCID: PMC7698665          DOI: 10.1093/database/baaa074

Source DB:  PubMed          Journal:  Database (Oxford)        ISSN: 1758-0463            Impact factor:   4.462


  27 in total

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2.  A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data.

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Journal:  Bioinformatics       Date:  2004-08-12       Impact factor: 6.937

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Authors:  Dina Demner-Fushman; Willie J Rogers; Alan R Aronson
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5.  NCBI GEO: archive for functional genomics data sets--update.

Authors:  Tanya Barrett; Stephen E Wilhite; Pierre Ledoux; Carlos Evangelista; Irene F Kim; Maxim Tomashevsky; Kimberly A Marshall; Katherine H Phillippy; Patti M Sherman; Michelle Holko; Andrey Yefanov; Hyeseung Lee; Naigong Zhang; Cynthia L Robertson; Nadezhda Serova; Sean Davis; Alexandra Soboleva
Journal:  Nucleic Acids Res       Date:  2012-11-27       Impact factor: 16.971

6.  PubMed related articles: a probabilistic topic-based model for content similarity.

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Journal:  BMC Bioinformatics       Date:  2007-10-30       Impact factor: 3.169

7.  Modeling genome-wide dynamic regulatory network in mouse lungs with influenza infection using high-dimensional ordinary differential equations.

Authors:  Shuang Wu; Zhi-Ping Liu; Xing Qiu; Hulin Wu
Journal:  PLoS One       Date:  2014-05-06       Impact factor: 3.240

8.  A collaborative approach for research paper recommender system.

Authors:  Khalid Haruna; Maizatul Akmar Ismail; Damiasih Damiasih; Joko Sutopo; Tutut Herawan
Journal:  PLoS One       Date:  2017-10-05       Impact factor: 3.240

9.  DataMed - an open source discovery index for finding biomedical datasets.

Authors:  Xiaoling Chen; Anupama E Gururaj; Burak Ozyurt; Ruiling Liu; Ergin Soysal; Trevor Cohen; Firat Tiryaki; Yueling Li; Nansu Zong; Min Jiang; Deevakar Rogith; Mandana Salimi; Hyeon-Eui Kim; Philippe Rocca-Serra; Alejandra Gonzalez-Beltran; Claudiu Farcas; Todd Johnson; Ron Margolis; George Alter; Susanna-Assunta Sansone; Ian M Fore; Lucila Ohno-Machado; Jeffrey S Grethe; Hua Xu
Journal:  J Am Med Inform Assoc       Date:  2018-03-01       Impact factor: 4.497

10.  Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis.

Authors:  Guocai Chen; Juan Camilo Ramírez; Nan Deng; Xing Qiu; Canglin Wu; W Jim Zheng; Hulin Wu
Journal:  Database (Oxford)       Date:  2019-01-01       Impact factor: 3.451

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