Literature DB >> 29304189

Metabolomics technology and bioinformatics for precision medicine.

Rajeev K Azad, Vladimir Shulaev.   

Abstract

Precision medicine is rapidly emerging as a strategy to tailor medical treatment to a small group or even individual patients based on their genetics, environment and lifestyle. Precision medicine relies heavily on developments in systems biology and omics disciplines, including metabolomics. Combination of metabolomics with sophisticated bioinformatics analysis and mathematical modeling has an extreme power to provide a metabolic snapshot of the patient over the course of disease and treatment or classifying patients into subpopulations and subgroups requiring individual medical treatment. Although a powerful approach, metabolomics have certain limitations in technology and bioinformatics. We will review various aspects of metabolomics technology and bioinformatics, from data generation, bioinformatics analysis, data fusion and mathematical modeling to data management, in the context of precision medicine.
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Entities:  

Keywords:  GC-MS; LC-MS; NMR; bioinformatics; mass spectrometry; metabolite profiling; metabolomics; precision medicine

Year:  2019        PMID: 29304189      PMCID: PMC6954408          DOI: 10.1093/bib/bbx170

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   11.622


  279 in total

Review 1.  From sample treatment to biomarker discovery: A tutorial for untargeted metabolomics based on GC-(EI)-Q-MS.

Authors:  Annalaura Mastrangelo; Alessia Ferrarini; Fernanda Rey-Stolle; Antonia García; Coral Barbas
Journal:  Anal Chim Acta       Date:  2015-10-23       Impact factor: 6.558

2.  MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions.

Authors:  Seunghak Lee; Fereydoun Hormozdiari; Can Alkan; Michael Brudno
Journal:  Nat Methods       Date:  2009-05-31       Impact factor: 28.547

3.  Rapid evaporative ionization mass spectrometry for high-throughput screening in food analysis: The case of boar taint.

Authors:  Kaat Verplanken; Sara Stead; Renata Jandova; Christof Van Poucke; Jan Claereboudt; Julie Vanden Bussche; Sarah De Saeger; Zoltan Takats; Jella Wauters; Lynn Vanhaecke
Journal:  Talanta       Date:  2017-03-21       Impact factor: 6.057

4.  Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth.

Authors:  Menachem Fromer; Jennifer L Moran; Kimberly Chambert; Eric Banks; Sarah E Bergen; Douglas M Ruderfer; Robert E Handsaker; Steven A McCarroll; Michael C O'Donovan; Michael J Owen; George Kirov; Patrick F Sullivan; Christina M Hultman; Pamela Sklar; Shaun M Purcell
Journal:  Am J Hum Genet       Date:  2012-10-05       Impact factor: 11.025

Review 5.  Pharmacometabonomics in humans: a new tool for personalized medicine.

Authors:  Jeremy R Everett
Journal:  Pharmacogenomics       Date:  2015-05-01       Impact factor: 2.533

6.  In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project's reference genome database.

Authors:  Calum J Walsh; Caitriona M Guinane; Colin Hill; R Paul Ross; Paul W O'Toole; Paul D Cotter
Journal:  BMC Microbiol       Date:  2015-09-16       Impact factor: 3.605

7.  Fecal metabolomics in pediatric spondyloarthritis implicate decreased metabolic diversity and altered tryptophan metabolism as pathogenic factors.

Authors:  M L Stoll; R Kumar; E J Lefkowitz; R Q Cron; C D Morrow; S Barnes
Journal:  Genes Immun       Date:  2016-10-27       Impact factor: 2.676

8.  Non-invasive urinary metabolomic profiling discriminates prostate cancer from benign prostatic hyperplasia.

Authors:  Clara Pérez-Rambla; Leonor Puchades-Carrasco; María García-Flores; José Rubio-Briones; José Antonio López-Guerrero; Antonio Pineda-Lucena
Journal:  Metabolomics       Date:  2017-03-09       Impact factor: 4.290

Review 9.  Metabolomics and Its Application to Acute Lung Diseases.

Authors:  Kathleen A Stringer; Ryan T McKay; Alla Karnovsky; Bernadette Quémerais; Paige Lacy
Journal:  Front Immunol       Date:  2016-02-29       Impact factor: 7.561

10.  PubChem Substance and Compound databases.

Authors:  Sunghwan Kim; Paul A Thiessen; Evan E Bolton; Jie Chen; Gang Fu; Asta Gindulyte; Lianyi Han; Jane He; Siqian He; Benjamin A Shoemaker; Jiyao Wang; Bo Yu; Jian Zhang; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2015-09-22       Impact factor: 16.971

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  17 in total

1.  Oncogenic ACSM1 in prostate cancer is through metabolic and extracellular matrix-receptor interaction signaling pathways.

Authors:  Yongchen Guo; Chunna Ren; Wentao Huang; Wancai Yang; Yonghua Bao
Journal:  Am J Cancer Res       Date:  2022-04-15       Impact factor: 5.942

2.  Predicting response to lisinopril in treating hypertension: a pilot study.

Authors:  Brandon J Sonn; Jessica L Saben; Glenn McWilliams; Shelby K Shelton; Hania K Flaten; Angelo D'Alessandro; Andrew A Monte
Journal:  Metabolomics       Date:  2019-10-03       Impact factor: 4.290

Review 3.  Precision medicine: Concept and tools.

Authors:  Nardeep Naithani; Sharmila Sinha; Pratibha Misra; Biju Vasudevan; Rajesh Sahu
Journal:  Med J Armed Forces India       Date:  2021-07-03

4.  Exploring the Interdisciplinary Nature of Precision Medicine:Network Analysis and Visualization.

Authors:  Xin Xu; Jiming Hu; Xiaoguang Lyu; He Huang; Xingyu Cheng
Journal:  JMIR Med Inform       Date:  2021-01-11

5.  Foodomics: Analytical Opportunities and Challenges.

Authors:  Alberto Valdés; Gerardo Álvarez-Rivera; Bárbara Socas-Rodríguez; Miguel Herrero; Elena Ibáñez; Alejandro Cifuentes
Journal:  Anal Chem       Date:  2021-11-23       Impact factor: 6.986

6.  SPME-LC/MS-based serum metabolomic phenotyping for distinguishing ovarian cancer histologic subtypes: a pilot study.

Authors:  Mariola Olkowicz; Hernando Rosales-Solano; Vathany Kulasingam; Janusz Pawliszyn
Journal:  Sci Rep       Date:  2021-11-17       Impact factor: 4.379

7.  Ontogeny Related Changes in the Pediatric Liver Metabolome.

Authors:  Christopher M Wilson; Qian Li; Roger Gaedigk; Charlie Bi; Saskia N de Wildt; J Steven Leeder; Brooke L Fridley
Journal:  Front Pediatr       Date:  2020-09-29       Impact factor: 3.418

8.  Targeted 1H NMR metabolomics and immunological phenotyping of human fresh blood and serum samples discriminate between healthy individuals and inflammatory bowel disease patients treated with anti-TNF.

Authors:  Sara Notararigo; Manuel Martín-Pastor; Juan E Viñuela-Roldán; Adriano Quiroga; J Enrique Dominguez-Munoz; Manuel Barreiro-de Acosta
Journal:  J Mol Med (Berl)       Date:  2021-05-21       Impact factor: 4.599

Review 9.  Prospects and challenges of cancer systems medicine: from genes to disease networks.

Authors:  Mohammad Reza Karimi; Amir Hossein Karimi; Shamsozoha Abolmaali; Mehdi Sadeghi; Ulf Schmitz
Journal:  Brief Bioinform       Date:  2022-01-17       Impact factor: 11.622

Review 10.  Metabolomics in Autoimmune Diseases: Focus on Rheumatoid Arthritis, Systemic Lupus Erythematous, and Multiple Sclerosis.

Authors:  Naeun Yoon; Ah-Kyung Jang; Yerim Seo; Byung Hwa Jung
Journal:  Metabolites       Date:  2021-11-29
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