Efficiency through analysis

Apr 28, 2011
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The May Editorial in Nature Methods discusses how the overall efficiency of research can be improved by comparative analysis of research method and tool performance.

Although such analysis studies aren’t considered as ‘sexy’ as basic exploratory research, the benefits for and gratitude from the community can be profound. Large well-funded laboratories are more likely to have the resources to perform such analyses and should not discount the advantages to performing such studies and publishing the results.

Nature Methods has published several such analysis studies in the past. A (probably incomplete) selection is listed below. We will strive to publish even more in the future. Our ‘Analysis’ article type is actually dedicated to these kinds of studies. We encourage communities and labs to both contribute such analyses and suggest methodological areas that would benefit from them. The selection below may provide some inspiration.

2005
Multiple-laboratory comparison of microarray platforms
doi:10.1038/nmeth756
Independence and reproducibility across microarry platforms
doi:10.1038/nmeth757
Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations
doi:10.1038/nmeth785

2006
A guide to choosing fluorescent proteins
doi:10.1038/nmeth819

2007
Reproducible isolation of distinct, overlapping segments of the phosphoproteome
doi:10.1038/nmeth1005
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
doi:10.1038/nmeth1043

2008
Cyclic nucleotide analogs as probes of signaling pathways
doi:10.1038/nmeth0408-277

2009
Cost-effective strategies for completing the interactome
doi:10.1038/nmeth.1283
A HUPO test sample study reveals common problems in mass spectrometry-based proteomics
doi:10.1038/nmeth.1333

2010
Comprehensive comparative analysis of strand-specific RNA sequencing methods
doi:10.1038/nmeth.1491
Microbial community resemblance methods differ in their ability to detect biologically relevant patterns
doi:10.1038/nmeth.1499
Validation of two ribosomal RNA removal methods for microbial metatranscriptomics
doi:10.1038/nmeth.1507

2011
Chemically defined conditions for human iPSC derivation and culture
doi:10.1038/nmeth.1593
Two-photon absorption properties of fluorescent proteins
doi:10.1038/nmeth.1596

Daniel Evanko

Editor, Springer Nature

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