Literature DB >> 31286058

Use of big data in drug development for precision medicine: an update.

Tongqi Qian1, Shijia Zhu2, Yujin Hoshida2.   

Abstract

INTRODUCTION: Big-data-driven drug development resources and methodologies have been evolving with ever-expanding data from large-scale biological experiments, clinical trials, and medical records from participants in data collection initiatives. The enrichment of biological- and clinical-context-specific large-scale data has enabled computational inference more relevant to real-world biomedical research, particularly identification of therapeutic targets and drugs for specific diseases and clinical scenarios. AREAS COVERED: Here we overview recent progresses made in the fields: new big-data-driven approach to therapeutic target discovery, candidate drug prioritization, inference of clinical toxicity, and machine-learning methods in drug discovery. EXPERT OPINION: In the near future, much larger volumes and complex datasets for precision medicine will be generated, e.g., individual and longitudinal multi-omic, and direct-to-consumer datasets. Closer collaborations between experts with different backgrounds would also be required to better translate analytic results into prognosis and treatment in the clinical practice. Meanwhile, cloud computing with protected patient privacy would become more routine analytic practice to fill the gaps within data integration along with the advent of big-data. To conclude, integration of multitudes of data generated for each individual along with techniques tailored for big-data analytics may eventually enable us to achieve precision medicine.

Entities:  

Keywords:  Big data; drug development; high-throughput screen; in silico drug discovery; machine learning; precision medicine

Year:  2019        PMID: 31286058      PMCID: PMC6613936          DOI: 10.1080/23808993.2019.1617632

Source DB:  PubMed          Journal:  Expert Rev Precis Med Drug Dev        ISSN: 2380-8993


  106 in total

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2.  The ENCODE (ENCyclopedia Of DNA Elements) Project.

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Journal:  Science       Date:  2004-10-22       Impact factor: 47.728

3.  A fast learning algorithm for deep belief nets.

Authors:  Geoffrey E Hinton; Simon Osindero; Yee-Whye Teh
Journal:  Neural Comput       Date:  2006-07       Impact factor: 2.026

4.  The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.

Authors:  Justin Lamb; Emily D Crawford; David Peck; Joshua W Modell; Irene C Blat; Matthew J Wrobel; Jim Lerner; Jean-Philippe Brunet; Aravind Subramanian; Kenneth N Ross; Michael Reich; Haley Hieronymus; Guo Wei; Scott A Armstrong; Stephen J Haggarty; Paul A Clemons; Ru Wei; Steven A Carr; Eric S Lander; Todd R Golub
Journal:  Science       Date:  2006-09-29       Impact factor: 47.728

5.  The human disease network.

Authors:  Kwang-Il Goh; Michael E Cusick; David Valle; Barton Childs; Marc Vidal; Albert-László Barabási
Journal:  Proc Natl Acad Sci U S A       Date:  2007-05-14       Impact factor: 11.205

6.  ACToR--Aggregated Computational Toxicology Resource.

Authors:  Richard Judson; Ann Richard; David Dix; Keith Houck; Fathi Elloumi; Matthew Martin; Tommy Cathey; Thomas R Transue; Richard Spencer; Maritja Wolf
Journal:  Toxicol Appl Pharmacol       Date:  2008-07-11       Impact factor: 4.219

7.  Gene expression profiling predicts clinical outcome of breast cancer.

Authors:  Laura J van 't Veer; Hongyue Dai; Marc J van de Vijver; Yudong D He; Augustinus A M Hart; Mao Mao; Hans L Peterse; Karin van der Kooy; Matthew J Marton; Anke T Witteveen; George J Schreiber; Ron M Kerkhoven; Chris Roberts; Peter S Linsley; René Bernards; Stephen H Friend
Journal:  Nature       Date:  2002-01-31       Impact factor: 49.962

8.  Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators.

Authors:  Haley Hieronymus; Justin Lamb; Kenneth N Ross; Xiao P Peng; Cristina Clement; Anna Rodina; Maria Nieto; Jinyan Du; Kimberly Stegmaier; Srilakshmi M Raj; Katherine N Maloney; Jon Clardy; William C Hahn; Gabriela Chiosis; Todd R Golub
Journal:  Cancer Cell       Date:  2006-09-28       Impact factor: 31.743

9.  A gene-expression signature as a predictor of survival in breast cancer.

Authors:  Marc J van de Vijver; Yudong D He; Laura J van't Veer; Hongyue Dai; Augustinus A M Hart; Dorien W Voskuil; George J Schreiber; Johannes L Peterse; Chris Roberts; Matthew J Marton; Mark Parrish; Douwe Atsma; Anke Witteveen; Annuska Glas; Leonie Delahaye; Tony van der Velde; Harry Bartelink; Sjoerd Rodenhuis; Emiel T Rutgers; Stephen H Friend; René Bernards
Journal:  N Engl J Med       Date:  2002-12-19       Impact factor: 91.245

10.  Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.

Authors:  Sekar Kathiresan; Olle Melander; Candace Guiducci; Aarti Surti; Noël P Burtt; Mark J Rieder; Gregory M Cooper; Charlotta Roos; Benjamin F Voight; Aki S Havulinna; Björn Wahlstrand; Thomas Hedner; Dolores Corella; E Shyong Tai; Jose M Ordovas; Göran Berglund; Erkki Vartiainen; Pekka Jousilahti; Bo Hedblad; Marja-Riitta Taskinen; Christopher Newton-Cheh; Veikko Salomaa; Leena Peltonen; Leif Groop; David M Altshuler; Marju Orho-Melander
Journal:  Nat Genet       Date:  2008-01-13       Impact factor: 38.330

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  13 in total

1.  A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19.

Authors:  Alzbeta Tuerkova; Barbara Zdrazil
Journal:  J Cheminform       Date:  2020-11-25       Impact factor: 5.514

2.  A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19.

Authors:  Alzbeta Tuerkova; Barbara Zdrazil
Journal:  J Cheminform       Date:  2020-11-25       Impact factor: 5.514

3.  Identification and Development of Therapeutics for COVID-19.

Authors:  Halie M Rando; Nils Wellhausen; Soumita Ghosh; Alexandra J Lee; Anna Ada Dattoli; Fengling Hu; James Brian Byrd; Diane N Rafizadeh; Ronan Lordan; Yanjun Qi; Yuchen Sun; Christian Brueffer; Jeffrey M Field; Marouen Ben Guebila; Nafisa M Jadavji; Ashwin N Skelly; Bharath Ramsundar; Jinhui Wang; Rishi Raj Goel; YoSon Park; Simina M Boca; Anthony Gitter; Casey S Greene
Journal:  mSystems       Date:  2021-11-02       Impact factor: 6.496

Review 4.  Open Data Revolution in Clinical Research: Opportunities and Challenges.

Authors:  Mohamed H Shahin; Sanchita Bhattacharya; Diego Silva; Sarah Kim; Jackson Burton; Jagdeep Podichetty; Klaus Romero; Daniela J Conrado
Journal:  Clin Transl Sci       Date:  2020-03-10       Impact factor: 4.689

5.  Genome-wide investigation of gene-cancer associations for the prediction of novel therapeutic targets in oncology.

Authors:  Adrián Bazaga; Dan Leggate; Hendrik Weisser
Journal:  Sci Rep       Date:  2020-07-01       Impact factor: 4.379

Review 6.  Precision Medicine in Interventional Cardiology.

Authors:  Thijmen W Hokken; Joana M Ribeiro; Peter P De Jaegere; Nicolas M Van Mieghem
Journal:  Interv Cardiol       Date:  2020-04-23

7.  A System Biology-Based Approach for Designing Combination Therapy in Cancer Precision Medicine.

Authors:  S H Sabzpoushan
Journal:  Biomed Res Int       Date:  2020-08-26       Impact factor: 3.411

Review 8.  Genome-based therapeutic interventions for β-type hemoglobinopathies.

Authors:  Kariofyllis Karamperis; Maria T Tsoumpeli; Fotios Kounelis; Maria Koromina; Christina Mitropoulou; Catia Moutinho; George P Patrinos
Journal:  Hum Genomics       Date:  2021-06-05       Impact factor: 4.639

9.  Evolving scenario of big data and Artificial Intelligence (AI) in drug discovery.

Authors:  Manish Kumar Tripathi; Abhigyan Nath; Tej P Singh; A S Ethayathulla; Punit Kaur
Journal:  Mol Divers       Date:  2021-06-23       Impact factor: 3.364

10.  BioDWH2: an automated graph-based data warehouse and mapping tool.

Authors:  Marcel Friedrichs
Journal:  J Integr Bioinform       Date:  2021-02-22
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