Literature DB >> 30149217

Turning omics data into therapeutic insights.

Amanda Kedaigle1, Ernest Fraenkel2.   

Abstract

Omics technologies have made it easier and cheaper to evaluate thousands of biological molecules at once. These advances have led to novel therapies approved for use in the clinic, elucidated the mechanisms behind disease-associated mutations, led to increased accuracy in disease subtyping and personalized medicine, and revealed novel uses and treatment regimes for existing drugs through drug repurposing and pharmacology studies. In this review, we summarize some of these milestones and discuss the potential of integrative analyses that combine multiple data types for further advances.
Copyright © 2018 Elsevier Ltd. All rights reserved.

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Year:  2018        PMID: 30149217      PMCID: PMC6204089          DOI: 10.1016/j.coph.2018.08.006

Source DB:  PubMed          Journal:  Curr Opin Pharmacol        ISSN: 1471-4892            Impact factor:   5.547


  57 in total

1.  Molecular signatures database (MSigDB) 3.0.

Authors:  Arthur Liberzon; Aravind Subramanian; Reid Pinchback; Helga Thorvaldsdóttir; Pablo Tamayo; Jill P Mesirov
Journal:  Bioinformatics       Date:  2011-05-05       Impact factor: 6.937

Review 2.  Microbiome at the Frontier of Personalized Medicine.

Authors:  Purna C Kashyap; Nicholas Chia; Heidi Nelson; Eran Segal; Eran Elinav
Journal:  Mayo Clin Proc       Date:  2017-12       Impact factor: 7.616

3.  Revealing disease-associated pathways by network integration of untargeted metabolomics.

Authors:  Leila Pirhaji; Pamela Milani; Mathias Leidl; Timothy Curran; Julian Avila-Pacheco; Clary B Clish; Forest M White; Alan Saghatelian; Ernest Fraenkel
Journal:  Nat Methods       Date:  2016-08-01       Impact factor: 28.547

4.  An integrated genomic analysis of human glioblastoma multiforme.

Authors:  D Williams Parsons; Siân Jones; Xiaosong Zhang; Jimmy Cheng-Ho Lin; Rebecca J Leary; Philipp Angenendt; Parminder Mankoo; Hannah Carter; I-Mei Siu; Gary L Gallia; Alessandro Olivi; Roger McLendon; B Ahmed Rasheed; Stephen Keir; Tatiana Nikolskaya; Yuri Nikolsky; Dana A Busam; Hanna Tekleab; Luis A Diaz; James Hartigan; Doug R Smith; Robert L Strausberg; Suely Kazue Nagahashi Marie; Sueli Mieko Oba Shinjo; Hai Yan; Gregory J Riggins; Darell D Bigner; Rachel Karchin; Nick Papadopoulos; Giovanni Parmigiani; Bert Vogelstein; Victor E Velculescu; Kenneth W Kinzler
Journal:  Science       Date:  2008-09-04       Impact factor: 47.728

5.  A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.

Authors:  Aravind Subramanian; Rajiv Narayan; Steven M Corsello; David D Peck; Ted E Natoli; Xiaodong Lu; Joshua Gould; John F Davis; Andrew A Tubelli; Jacob K Asiedu; David L Lahr; Jodi E Hirschman; Zihan Liu; Melanie Donahue; Bina Julian; Mariya Khan; David Wadden; Ian C Smith; Daniel Lam; Arthur Liberzon; Courtney Toder; Mukta Bagul; Marek Orzechowski; Oana M Enache; Federica Piccioni; Sarah A Johnson; Nicholas J Lyons; Alice H Berger; Alykhan F Shamji; Angela N Brooks; Anita Vrcic; Corey Flynn; Jacqueline Rosains; David Y Takeda; Roger Hu; Desiree Davison; Justin Lamb; Kristin Ardlie; Larson Hogstrom; Peyton Greenside; Nathanael S Gray; Paul A Clemons; Serena Silver; Xiaoyun Wu; Wen-Ning Zhao; Willis Read-Button; Xiaohua Wu; Stephen J Haggarty; Lucienne V Ronco; Jesse S Boehm; Stuart L Schreiber; John G Doench; Joshua A Bittker; David E Root; Bang Wong; Todd R Golub
Journal:  Cell       Date:  2017-11-30       Impact factor: 41.582

6.  Personal omics profiling reveals dynamic molecular and medical phenotypes.

Authors:  Rui Chen; George I Mias; Jennifer Li-Pook-Than; Lihua Jiang; Hugo Y K Lam; Rong Chen; Elana Miriami; Konrad J Karczewski; Manoj Hariharan; Frederick E Dewey; Yong Cheng; Michael J Clark; Hogune Im; Lukas Habegger; Suganthi Balasubramanian; Maeve O'Huallachain; Joel T Dudley; Sara Hillenmeyer; Rajini Haraksingh; Donald Sharon; Ghia Euskirchen; Phil Lacroute; Keith Bettinger; Alan P Boyle; Maya Kasowski; Fabian Grubert; Scott Seki; Marco Garcia; Michelle Whirl-Carrillo; Mercedes Gallardo; Maria A Blasco; Peter L Greenberg; Phyllis Snyder; Teri E Klein; Russ B Altman; Atul J Butte; Euan A Ashley; Mark Gerstein; Kari C Nadeau; Hua Tang; Michael Snyder
Journal:  Cell       Date:  2012-03-16       Impact factor: 41.582

7.  IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype.

Authors:  Sevin Turcan; Daniel Rohle; Anuj Goenka; Logan A Walsh; Fang Fang; Emrullah Yilmaz; Carl Campos; Armida W M Fabius; Chao Lu; Patrick S Ward; Craig B Thompson; Andrew Kaufman; Olga Guryanova; Ross Levine; Adriana Heguy; Agnes Viale; Luc G T Morris; Jason T Huse; Ingo K Mellinghoff; Timothy A Chan
Journal:  Nature       Date:  2012-02-15       Impact factor: 69.504

Review 8.  Multi-omics approaches to disease.

Authors:  Yehudit Hasin; Marcus Seldin; Aldons Lusis
Journal:  Genome Biol       Date:  2017-05-05       Impact factor: 13.583

9.  Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package.

Authors:  Nurcan Tuncbag; Sara J C Gosline; Amanda Kedaigle; Anthony R Soltis; Anthony Gitter; Ernest Fraenkel
Journal:  PLoS Comput Biol       Date:  2016-04-20       Impact factor: 4.475

Review 10.  More Is Better: Recent Progress in Multi-Omics Data Integration Methods.

Authors:  Sijia Huang; Kumardeep Chaudhary; Lana X Garmire
Journal:  Front Genet       Date:  2017-06-16       Impact factor: 4.599

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  5 in total

Review 1.  Phosphoproteomics: a valuable tool for uncovering molecular signaling in cancer cells.

Authors:  Jacqueline S Gerritsen; Forest M White
Journal:  Expert Rev Proteomics       Date:  2021-09-16       Impact factor: 4.250

2.  The comparison of miRNAs that respond to anti-breast cancer drugs and usnic acid for the treatment of breast cancer.

Authors:  Demet Cansaran-Duman; Ümmügülsüm Tanman; Sevcan Yangın; Orhan Atakol
Journal:  Cytotechnology       Date:  2020-10-30       Impact factor: 2.058

Review 3.  Proteome-Scale Mapping of Perturbed Proteostasis in Living Cells.

Authors:  Isabel Lam; Erinc Hallacli; Vikram Khurana
Journal:  Cold Spring Harb Perspect Biol       Date:  2020-02-03       Impact factor: 10.005

4.  A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules.

Authors:  Natasha L Patel-Murray; Miriam Adam; Nhan Huynh; Brook T Wassie; Pamela Milani; Ernest Fraenkel
Journal:  Sci Rep       Date:  2020-01-22       Impact factor: 4.379

Review 5.  Epigenetic Studies of Chinese Herbal Medicine: Pleiotropic Role of DNA Methylation.

Authors:  Wenqian Guo; Han Ma; Chong-Zhi Wang; Jin-Yi Wan; Haiqiang Yao; Chun-Su Yuan
Journal:  Front Pharmacol       Date:  2021-12-07       Impact factor: 5.810

  5 in total

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