Literature DB >> 25798291

Personal genomes, quantitative dynamic omics and personalized medicine.

George I Mias1, Michael Snyder1.   

Abstract

The rapid technological developments following the Human Genome Project have made possible the availability of personalized genomes. As the focus now shifts from characterizing genomes to making personalized disease associations, in combination with the availability of other omics technologies, the next big push will be not only to obtain a personalized genome, but to quantitatively follow other omics. This will include transcriptomes, proteomes, metabolomes, antibodyomes, and new emerging technologies, enabling the profiling of thousands of molecular components in individuals. Furthermore, omics profiling performed longitudinally can probe the temporal patterns associated with both molecular changes and associated physiological health and disease states. Such data necessitates the development of computational methodology to not only handle and descriptively assess such data, but also construct quantitative biological models. Here we describe the availability of personal genomes and developing omics technologies that can be brought together for personalized implementations and how these novel integrated approaches may effectively provide a precise personalized medicine that focuses on not only characterization and treatment but ultimately the prevention of disease.

Entities:  

Year:  2013        PMID: 25798291      PMCID: PMC4366006          DOI: 10.1007/s40484-013-0005-3

Source DB:  PubMed          Journal:  Quant Biol        ISSN: 2095-4689


  265 in total

1.  Printing proteins as microarrays for high-throughput function determination.

Authors:  G MacBeath; S L Schreiber
Journal:  Science       Date:  2000-09-08       Impact factor: 47.728

2.  Multidimensional identification of tissue biomarkers of gastric cancer.

Authors:  Tiannan Guo; Lingling Fan; Wai Har Ng; Yi Zhu; Mengfatt Ho; Wei Keat Wan; Kiat Hon Lim; Whee Sze Ong; Sze Sing Lee; Shiang Huang; Oi Lian Kon; Siu Kwan Sze
Journal:  J Proteome Res       Date:  2012-05-07       Impact factor: 4.466

3.  B cells promote insulin resistance through modulation of T cells and production of pathogenic IgG antibodies.

Authors:  Daniel A Winer; Shawn Winer; Lei Shen; Persis P Wadia; Jason Yantha; Geoffrey Paltser; Hubert Tsui; Ping Wu; Matthew G Davidson; Michael N Alonso; Hwei X Leong; Alec Glassford; Maria Caimol; Justin A Kenkel; Thomas F Tedder; Tracey McLaughlin; David B Miklos; H-Michael Dosch; Edgar G Engleman
Journal:  Nat Med       Date:  2011-04-17       Impact factor: 53.440

Review 4.  Interplay between lipids and branched-chain amino acids in development of insulin resistance.

Authors:  Christopher B Newgard
Journal:  Cell Metab       Date:  2012-05-02       Impact factor: 27.287

5.  NGSQC: cross-platform quality analysis pipeline for deep sequencing data.

Authors:  Manhong Dai; Robert C Thompson; Christopher Maher; Rafael Contreras-Galindo; Mark H Kaplan; David M Markovitz; Gil Omenn; Fan Meng
Journal:  BMC Genomics       Date:  2010-12-02       Impact factor: 3.969

6.  Cytoscape 2.8: new features for data integration and network visualization.

Authors:  Michael E Smoot; Keiichiro Ono; Johannes Ruscheinski; Peng-Liang Wang; Trey Ideker
Journal:  Bioinformatics       Date:  2010-12-12       Impact factor: 6.937

7.  Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations.

Authors:  Michał J Okoniewski; Crispin J Miller
Journal:  BMC Bioinformatics       Date:  2006-06-02       Impact factor: 3.169

8.  Functional peptide microarrays for specific and sensitive antibody diagnostics.

Authors:  Heiko Andresen; Carsten Grötzinger; Kim Zarse; Oliver J Kreuzer; Eva Ehrentreich-Förster; Frank F Bier
Journal:  Proteomics       Date:  2006-03       Impact factor: 3.984

9.  Fast and accurate short read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2009-05-18       Impact factor: 6.937

10.  DELLY: structural variant discovery by integrated paired-end and split-read analysis.

Authors:  Tobias Rausch; Thomas Zichner; Andreas Schlattl; Adrian M Stütz; Vladimir Benes; Jan O Korbel
Journal:  Bioinformatics       Date:  2012-09-15       Impact factor: 6.937

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  13 in total

1.  Longitudinal personal DNA methylome dynamics in a human with a chronic condition.

Authors:  Rui Chen; Lin Xia; Kailing Tu; Meixue Duan; Kimberly Kukurba; Jennifer Li-Pook-Than; Dan Xie; Michael Snyder
Journal:  Nat Med       Date:  2018-11-05       Impact factor: 53.440

2.  Toward more transparent and reproducible omics studies through a common metadata checklist and data publications.

Authors:  Eugene Kolker; Vural Özdemir; Lennart Martens; William Hancock; Gordon Anderson; Nathaniel Anderson; Sukru Aynacioglu; Ancha Baranova; Shawn R Campagna; Rui Chen; John Choiniere; Stephen P Dearth; Wu-Chun Feng; Lynnette Ferguson; Geoffrey Fox; Dmitrij Frishman; Robert Grossman; Allison Heath; Roger Higdon; Mara H Hutz; Imre Janko; Lihua Jiang; Sanjay Joshi; Alexander Kel; Joseph W Kemnitz; Isaac S Kohane; Natali Kolker; Doron Lancet; Elaine Lee; Weizhong Li; Andrey Lisitsa; Adrian Llerena; Courtney Macnealy-Koch; Jean-Claude Marshall; Paola Masuzzo; Amanda May; George Mias; Matthew Monroe; Elizabeth Montague; Sean Mooney; Alexey Nesvizhskii; Santosh Noronha; Gilbert Omenn; Harsha Rajasimha; Preveen Ramamoorthy; Jerry Sheehan; Larry Smarr; Charles V Smith; Todd Smith; Michael Snyder; Srikanth Rapole; Sanjeeva Srivastava; Larissa Stanberry; Elizabeth Stewart; Stefano Toppo; Peter Uetz; Kenneth Verheggen; Brynn H Voy; Louise Warnich; Steven W Wilhelm; Gregory Yandl
Journal:  OMICS       Date:  2014-01

Review 3.  Precision medicine in diabetes: an opportunity for clinical translation.

Authors:  Jordi Merino; Jose C Florez
Journal:  Ann N Y Acad Sci       Date:  2018-01       Impact factor: 5.691

4.  Use of the "Exposome" in the Practice of Epidemiology: A Primer on -Omic Technologies.

Authors:  D Gayle DeBord; Tania Carreón; Thomas J Lentz; Paul J Middendorf; Mark D Hoover; Paul A Schulte
Journal:  Am J Epidemiol       Date:  2016-08-15       Impact factor: 4.897

5.  Whole-exome sequencing identifies tetratricopeptide repeat domain 7A (TTC7A) mutations for combined immunodeficiency with intestinal atresias.

Authors:  Rui Chen; Silvia Giliani; Gaetana Lanzi; George I Mias; Silvia Lonardi; Kerry Dobbs; John Manis; Hogune Im; Jennifer E Gallagher; Douglas H Phanstiel; Ghia Euskirchen; Philippe Lacroute; Keith Bettinger; Daniele Moratto; Katja Weinacht; Davide Montin; Eleonora Gallo; Giovanna Mangili; Fulvio Porta; Lucia D Notarangelo; Stefania Pedretti; Waleed Al-Herz; Wasmi Alfahdli; Anne Marie Comeau; Russell S Traister; Sung-Yun Pai; Graziella Carella; Fabio Facchetti; Kari C Nadeau; Michael Snyder; Luigi D Notarangelo
Journal:  J Allergy Clin Immunol       Date:  2013-07-04       Impact factor: 14.290

6.  BioDB extractor: customized data extraction system for commonly used bioinformatics databases.

Authors:  Rajiv Karbhal; Sangeeta Sawant; Urmila Kulkarni-Kale
Journal:  BioData Min       Date:  2015-10-28       Impact factor: 2.522

7.  Integrative analysis of longitudinal metabolomics data from a personal multi-omics profile.

Authors:  Larissa Stanberry; George I Mias; Winston Haynes; Roger Higdon; Michael Snyder; Eugene Kolker
Journal:  Metabolites       Date:  2013-09-03

8.  Computational cancer biology: education is a natural key to many locks.

Authors:  Frank Emmert-Streib; Shu-Dong Zhang; Peter Hamilton
Journal:  BMC Cancer       Date:  2015-01-15       Impact factor: 4.430

9.  A systematic study on drug-response associated genes using baseline gene expressions of the Cancer Cell Line Encyclopedia.

Authors:  Xiaoming Liu; Jiasheng Yang; Yi Zhang; Yun Fang; Fayou Wang; Jun Wang; Xiaoqi Zheng; Jialiang Yang
Journal:  Sci Rep       Date:  2016-03-10       Impact factor: 4.379

10.  Metabolome progression during early gut microbial colonization of gnotobiotic mice.

Authors:  Angela Marcobal; Tahir Yusufaly; Steven Higginbottom; Michael Snyder; Justin L Sonnenburg; George I Mias
Journal:  Sci Rep       Date:  2015-06-29       Impact factor: 4.996

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