Nature Methods | Methagora

Efficiency through analysis

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

Cost-effective strategies for completing the interactome

doi:10.1038/nmeth.1283

Cyclic nucleotide analogs as probes of signaling pathways

doi:10.1038/nmeth0408-277

2009

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

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