Literature DB >> 22144616

Improving validation practices in "omics" research.

John P A Ioannidis1, Muin J Khoury.   

Abstract

"Omics" research poses acute challenges regarding how to enhance validation practices and eventually the utility of this rich information. Several strategies may be useful, including routine replication, public data and protocol availability, funding incentives, reproducibility rewards or penalties, and targeted repeatability checks.

Entities:  

Mesh：

Year:  2011        PMID： 22144616      PMCID： PMC5624327          DOI： 10.1126/science.1211811

Source DB:  PubMed          Journal:  Science        ISSN： 0036-8075            Impact factor:   47.728


  19 in total

1.  Disclose all data in publications.

Authors:  Keith Baggerly
Journal:  Nature       Date:  2010-09-23       Impact factor: 49.962

2.  Repeatability of published microarray gene expression analyses.

Authors:  John P A Ioannidis; David B Allison; Catherine A Ball; Issa Coulibaly; Xiangqin Cui; Aedín C Culhane; Mario Falchi; Cesare Furlanello; Laurence Game; Giuseppe Jurman; Jon Mangion; Tapan Mehta; Michael Nitzberg; Grier P Page; Enrico Petretto; Vera van Noort
Journal:  Nat Genet       Date:  2008-01-28       Impact factor: 38.330

3.  Comparative analysis to guide quality improvements in proteomics.

Authors:  Matthias Mann
Journal:  Nat Methods       Date:  2009-10       Impact factor: 28.547

4.  An empirical assessment of validation practices for molecular classifiers.

Authors:  Peter J Castaldi; Issa J Dahabreh; John P A Ioannidis
Journal:  Brief Bioinform       Date:  2011-02-07       Impact factor: 11.622

Review 5.  Biomarker studies: a call for a comprehensive biomarker study registry.

Authors:  Fabrice Andre; Lisa M McShane; Stefan Michiels; David F Ransohoff; Douglas G Altman; Jorge S Reis-Filho; Daniel F Hayes; Lajos Pusztai
Journal:  Nat Rev Clin Oncol       Date:  2011-03       Impact factor: 66.675

Review 6.  Development of the 21-gene assay and its application in clinical practice and clinical trials.

Authors:  Joseph A Sparano; Soonmyung Paik
Journal:  J Clin Oncol       Date:  2008-02-10       Impact factor: 44.544

7.  The Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Initiative: methods of the EGAPP Working Group.

Authors:  Steven M Teutsch; Linda A Bradley; Glenn E Palomaki; James E Haddow; Margaret Piper; Ned Calonge; W David Dotson; Michael P Douglas; Alfred O Berg
Journal:  Genet Med       Date:  2009-01       Impact factor: 8.822

8.  Public availability of published research data in high-impact journals.

Authors:  Alawi A Alsheikh-Ali; Waqas Qureshi; Mouaz H Al-Mallah; John P A Ioannidis
Journal:  PLoS One       Date:  2011-09-07       Impact factor: 3.240

9.  A HUPO test sample study reveals common problems in mass spectrometry-based proteomics.

Authors:  Alexander W Bell; Eric W Deutsch; Catherine E Au; Robert E Kearney; Ron Beavis; Salvatore Sechi; Tommy Nilsson; John J M Bergeron
Journal:  Nat Methods       Date:  2009-06       Impact factor: 28.547

10.  Why most published research findings are false.

Authors:  John P A Ioannidis
Journal:  PLoS Med       Date:  2005-08-30       Impact factor: 11.613
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  75 in total

1.  Research priorities. Shining light into black boxes.

Authors:  A Morin; J Urban; P D Adams; I Foster; A Sali; D Baker; P Sliz
Journal:  Science       Date:  2012-04-13       Impact factor: 47.728

2.  Irreproducible experimental results: causes, (mis)interpretations, and consequences.

Authors:  Joseph Loscalzo
Journal:  Circulation       Date:  2012-03-13       Impact factor: 29.690

3.  A call for bioimaging software usability.

Authors:  Anne E Carpenter; Lee Kamentsky; Kevin W Eliceiri
Journal:  Nat Methods       Date:  2012-06-28       Impact factor: 28.547

4.  A population approach to precision medicine.

Authors:  Muin J Khoury; Marta L Gwinn; Russell E Glasgow; Barnett S Kramer
Journal:  Am J Prev Med       Date:  2012-06       Impact factor: 5.043

5.  Standard Proteoforms and Their Complexes for Native Mass Spectrometry.

Authors:  Luis F Schachner; Ashley N Ives; John P McGee; Rafael D Melani; Jared O Kafader; Philip D Compton; Steven M Patrie; Neil L Kelleher
Journal:  J Am Soc Mass Spectrom       Date:  2019-04-08       Impact factor: 3.109

6.  Predictive genetic testing, risk communication, and risk perception: an international expert meeting in Berlin, Germany.

Authors:  Eva Fisher; Steffi Achilles; Holger Tönnies
Journal:  J Community Genet       Date:  2013-12-10

Review 7.  Considerations when processing and interpreting genomics data of the placenta.

Authors:  Chaini Konwar; Giulia Del Gobbo; Victor Yuan; Wendy P Robinson
Journal:  Placenta       Date:  2019-01-07       Impact factor: 3.481

Review 8.  High-throughput gene expression and mutation profiling: current methods and future perspectives.

Authors:  Thomas Karn
Journal:  Breast Care (Basel)       Date:  2013-12       Impact factor: 2.860

9.  Gender Interacts with Opioid Receptor Polymorphism A118G and Serotonin Receptor Polymorphism -1438 A/G on Speed-Dating Success.

Authors:  Karen Wu; Chuansheng Chen; Robert K Moyzis; Ellen Greenberger; Zhaoxia Yu
Journal:  Hum Nat       Date:  2016-09

Review 10.  Opportunities and challenges for selected emerging technologies in cancer epidemiology: mitochondrial, epigenomic, metabolomic, and telomerase profiling.

Authors:  Mukesh Verma; Muin J Khoury; John P A Ioannidis
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2012-12-14       Impact factor: 4.254
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