Literature DB >> 27773806

Using Big Data to Discover Diagnostics and Therapeutics for Gastrointestinal and Liver Diseases.

Benjamin Wooden1, Nicolas Goossens2, Yujin Hoshida3, Scott L Friedman1.   

Abstract

Technologies such as genome sequencing, gene expression profiling, proteomic and metabolomic analyses, electronic medical records, and patient-reported health information have produced large amounts of data from various populations, cell types, and disorders (big data). However, these data must be integrated and analyzed if they are to produce models or concepts about physiological function or mechanisms of pathogenesis. Many of these data are available to the public, allowing researchers anywhere to search for markers of specific biological processes or therapeutic targets for specific diseases or patient types. We review recent advances in the fields of computational and systems biology and highlight opportunities for researchers to use big data sets in the fields of gastroenterology and hepatology to complement traditional means of diagnostic and therapeutic discovery.
Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Big Data; Drug Repurposing; Precision Medicine; Translational Bioinformatics

Mesh:

Substances:

Year:  2016        PMID: 27773806      PMCID: PMC5193106          DOI: 10.1053/j.gastro.2016.09.065

Source DB:  PubMed          Journal:  Gastroenterology        ISSN: 0016-5085            Impact factor:   33.883


  126 in total

1.  A vision for the future of genomics research.

Authors:  Francis S Collins; Eric D Green; Alan E Guttmacher; Mark S Guyer
Journal:  Nature       Date:  2003-04-14       Impact factor: 49.962

2.  Towards building a disease-phenotype knowledge base: extracting disease-manifestation relationship from literature.

Authors:  Rong Xu; Li Li; Quanqiu Wang
Journal:  Bioinformatics       Date:  2013-07-04       Impact factor: 6.937

3.  Bring on the biomarkers.

Authors:  George Poste
Journal:  Nature       Date:  2011-01-13       Impact factor: 49.962

Review 4.  A survey of current trends in computational drug repositioning.

Authors:  Jiao Li; Si Zheng; Bin Chen; Atul J Butte; S Joshua Swamidass; Zhiyong Lu
Journal:  Brief Bioinform       Date:  2015-03-31       Impact factor: 11.622

Review 5.  Computational drug repositioning: from data to therapeutics.

Authors:  M R Hurle; L Yang; Q Xie; D K Rajpal; P Sanseau; P Agarwal
Journal:  Clin Pharmacol Ther       Date:  2013-01-15       Impact factor: 6.875

6.  Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets.

Authors:  Silpa Suthram; Joel T Dudley; Annie P Chiang; Rong Chen; Trevor J Hastie; Atul J Butte
Journal:  PLoS Comput Biol       Date:  2010-02-05       Impact factor: 4.475

Review 7.  Global Epidemiology of Nonalcoholic Fatty Liver Disease and Perspectives on US Minority Populations.

Authors:  Zaki A Sherif; Armana Saeed; Shima Ghavimi; Seyed-Mehdi Nouraie; Adeyinka O Laiyemo; Hassan Brim; Hassan Ashktorab
Journal:  Dig Dis Sci       Date:  2016-04-01       Impact factor: 3.199

Review 8.  High-Dimensional Statistical Learning: Roots, Justifications, and Potential Machineries.

Authors:  Amin Zollanvari
Journal:  Cancer Inform       Date:  2016-04-12

9.  Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy.

Authors:  Jinyan Du; Paula Bernasconi; Karl R Clauser; D R Mani; Stephen P Finn; Rameen Beroukhim; Melissa Burns; Bina Julian; Xiao P Peng; Haley Hieronymus; Rebecca L Maglathlin; Timothy A Lewis; Linda M Liau; Phioanh Nghiemphu; Ingo K Mellinghoff; David N Louis; Massimo Loda; Steven A Carr; Andrew L Kung; Todd R Golub
Journal:  Nat Biotechnol       Date:  2008-12-21       Impact factor: 54.908

10.  DrugComboRanker: drug combination discovery based on target network analysis.

Authors:  Lei Huang; Fuhai Li; Jianting Sheng; Xiaofeng Xia; Jinwen Ma; Ming Zhan; Stephen T C Wong
Journal:  Bioinformatics       Date:  2014-06-15       Impact factor: 6.937

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  18 in total

1.  GIDB: a knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal cancer.

Authors:  Ying Wang; Yueqian Wang; Shuangkuai Wang; Yuantao Tong; Ling Jin; Hui Zong; Rongbin Zheng; Jinxuan Yang; Zeyu Zhang; En Ouyang; Mengyan Zhou; Xiaoyan Zhang
Journal:  Database (Oxford)       Date:  2019-01-01       Impact factor: 3.451

2.  Random gene sets in predicting survival of patients with hepatocellular carcinoma.

Authors:  Timo Itzel; Rainer Spang; Thorsten Maass; Stefan Munker; Stephanie Roessler; Matthias P Ebert; Hans J Schlitt; Wolfgang Herr; Matthias Evert; Andreas Teufel
Journal:  J Mol Med (Berl)       Date:  2019-04-17       Impact factor: 4.599

Review 3.  Big data in systemic sclerosis: Great potential for the future.

Authors:  Mislav Radic; Tracy M Frech
Journal:  J Scleroderma Relat Disord       Date:  2020-07-06

Review 4.  Quantifying the progression of non-alcoholic fatty liver disease in human biomimetic liver microphysiology systems with fluorescent protein biosensors.

Authors:  Manush Saydmohammed; Anupma Jha; Vineet Mahajan; Dillon Gavlock; Tong Ying Shun; Richard DeBiasio; Daniel Lefever; Xiang Li; Celeste Reese; Erin E Kershaw; Vijay Yechoor; Jaideep Behari; Alejandro Soto-Gutierrez; Larry Vernetti; Andrew Stern; Albert Gough; Mark T Miedel; D Lansing Taylor
Journal:  Exp Biol Med (Maywood)       Date:  2021-05-06

Review 5.  Omics-derived hepatocellular carcinoma risk biomarkers for precision care of chronic liver diseases.

Authors:  Naoto Fujiwara; Tongqi Qian; Bhuvaneswari Koneru; Yujin Hoshida
Journal:  Hepatol Res       Date:  2020-05-15       Impact factor: 4.942

Review 6.  Upper Respiratory Symptoms, Gut Health and Mucosal Immunity in Athletes.

Authors:  Candice Colbey; Amanda J Cox; David B Pyne; Ping Zhang; Allan W Cripps; Nicholas P West
Journal:  Sports Med       Date:  2018-03       Impact factor: 11.136

Review 7.  Big Data's Role in Precision Public Health.

Authors:  Shawn Dolley
Journal:  Front Public Health       Date:  2018-03-07

Review 8.  Translational Aspects of Diet and Non-Alcoholic Fatty Liver Disease.

Authors:  Nicolas Goossens; François R Jornayvaz
Journal:  Nutrients       Date:  2017-09-28       Impact factor: 5.717

Review 9.  Harnessing big 'omics' data and AI for drug discovery in hepatocellular carcinoma.

Authors:  Bin Chen; Lana Garmire; Diego F Calvisi; Mei-Sze Chua; Robin K Kelley; Xin Chen
Journal:  Nat Rev Gastroenterol Hepatol       Date:  2020-01-03       Impact factor: 46.802

10.  Transcriptome-based repurposing of apigenin as a potential anti-fibrotic agent targeting hepatic stellate cells.

Authors:  Daniel F Hicks; Nicolas Goossens; Ana Blas-García; Takuma Tsuchida; Benjamin Wooden; Michael C Wallace; Natalia Nieto; Abigale Lade; Benjamin Redhead; Arthur I Cederbaum; Joel T Dudley; Bryan C Fuchs; Youngmin A Lee; Yujin Hoshida; Scott L Friedman
Journal:  Sci Rep       Date:  2017-03-03       Impact factor: 4.996

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