Method of the Year 2009

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• • Biotechnology
  • Cell biology
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  • Protein biochemistry
  • Proteomics
  • Stem cells
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  • Systems biology

In 2007 we chose Next Generation Sequencing.
In 2008 we chose Super-resolution Imaging.

Now it is time for you, our readers, to help us choose the Method of the Year 2009. Just sign in using your free nature.com registration and vote on our Methods to Watch from previous years or a paper that a visitor has recommended.

Alternatively, you can recommend a paper that represents a method you believe came into its own in 2009 and will have a wide-ranging impact on biology. This paper can be any recently published paper from this year or past years published in any journal. Just provide a link to the paper or other online description of the method and vote away!

Want more information or want to comment? Read the editorial or go to our blog methagora and comment.

• Systems biology

  • • 21+ votes

      2- votes

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  • Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

    • 
      Original article citation: Cell 138," 795 - 806, (2009).

    • Categories: Proteomics, Genetics and genomics, and Systems biology
    • Recommended by : Herman Altenried on 11/05/2009 02:42AM GMT
      
      The publication shows that by using MRM based targeted proteomics an unsurpassed sensitivity, reproducibility and throughput in proteomics experiments is achieved. This is the first glimpse into the future of proteomics!!
    • Comment on this subject: 0 comments made

  • • 9+ votes

      6- votes

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  • Global identification of yeast chromosome interactions using Genome conformation capture

    • 
      Original article citation: Fungal Genetics and Biology 46," 879 - 886, (2009).

    • Categories: Cell biology, Biotechnology, Genetics and genomics, and Systems biology
    • Recommended by : Cliff Dawson on 10/23/2009 01:06AM GMT
      
      Genome conformation capture (GCC) is a powerful method to uncover inter- and intra- chromosomal interactions that underlie genome architecture, in any cell, under any condition. This method utilises next-generation sequencing, and is the first described method of its type, with the Hi-C (Lieberman-Aiden et al) method following shortly after. Analyses reveal exciting prospects for cell biology.
    • Comment on this subject: 0 comments made

  • • 12+ votes

      7- votes

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  • A 3D digital atlas of C. elegans and its application to single-cell analyses

    • 
      Original article citation: Nat Meth 6," 667 - 672, (2009).

    • Categories: Biotechnology, Genetics and genomics, Systems biology, and Cell biology
    • Recommended by : Hanchuan Peng on 09/09/2009 02:45AM GMT
      
      Isn't it a cool thing to be able to target individual cells uniquely and unambiguously?
    • Comment on this subject: 2 comments made

  • • 2+ votes

      9- votes

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  • Universal sample preparation method for proteome analysis

    • 
      Original article citation: Nat Meth 6," 359 - 362, (2009).

    • Categories: Proteomics, Biotechnology, Protein biochemistry, and Systems biology
    • Recommended by : Peter Nollert on 08/24/2009 11:54PM GMT
      
      1. the filter-aided sample preparation method impacts the 'forgotten half' of proteomics: membrane proteins & their complexes 2. the method described is *very* simple: SDS & urea reagent and a MWCO filter; no new tools required at all
    • Comment on this subject: 1 comment made

  • • 8+ votes

      5- votes

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  • Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans

    • 
      Original article citation: Nature 460," 762 - 765, (2009).

    • Categories: Proteomics, Systems biology, and Cell biology
    • Recommended by the Editor: Veronique Kiermer on 08/14/2009 03:33PM GMT
      
      Aebersold and colleagues achieve absolute quantification of protein concentration at the proteome level (83% of the mass spec-detectable proteome) for a microbe of moderate complexity (3,600+ predicted ORFs based on the genomic sequence). That's a feat! And it is very elegant as they use a clever combination of approaches. Proteotypic peptides-based absolute measurements for a subset of 'anchor' proteins provide calibration points to translate relative abundance measurements, obtained by spectral counting, into absolute quantitative values for the rest of the proteins. And they show it works by verifying with cryo-electron tomography. This technology allows the comparison of absolute abundance of different proteins across different samples (as opposed to typical mass spec approaches in which you compare relative abundance of proteins across samples, using one as reference to infer how the others compare). In my opinion, this is a big step forward and it opens up a lot of possibilities for using mass spec in systems biology.
    • Comment on this subject: 0 comments made

  • • 1+ votes

      12- votes

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  • A meta-network of -omics

    • 
      Original article citation: Nat Meth 5," 25 - 25, (2008).

    • Categories: Systems biology, Genetics and genomics, Cell biology, and Proteomics
    • Recommended by the Editor: Nicole Rusk on 07/28/2009 04:36PM GMT
      
      In 2007 we called for a network that would link databases in the biosciences in our Methods to Watch section. We envisaged a scenario in which a wealth of information on, for example, genome, epigenome, transcriptome, proteome, and glycome would be easily accessible to a researcher and aid in the scientific discovery process. Is there still a need for such a meta-network or are scientists satisfied with the current network of databases?
    • Comment on this subject: 0 comments made

  • • 1+ votes

      12- votes

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  • Experimental micro-matchmaking

    • 
      Original article citation: Nat Meth 6," 36 - 36, (2009).

    • Categories: Cell biology, Genetics and genomics, and Systems biology
    • Recommended by the Editor: Nicole Rusk on 07/28/2009 04:24PM GMT
      
      How close are we to a reliable high-throughput experimental validation for computationally predicted microRNA targets?
    • Comment on this subject: 0 comments made

  • • 8+ votes

      4- votes

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  • Imaging through automation

    • 
      Original article citation: Nat Meth 6," 34 - 34, (2009).

    • Categories: Imaging, Systems biology, Cell biology, and Microbiology
    • Recommended by the Editor: Daniel Evanko on 07/23/2009 04:23PM GMT
      
      Microscopists are developing methods that allow computers to take control of nearly all steps of imaging and analysis. Last year we suggested that the capabilities provided by these methods for conducting experiments that are effectively impossible by manual observation make them a method to watch. Have these methods proven their potential sufficiently to be chosen as Method of the Year or do they still have a ways to go?
    • Comment on this subject: 0 comments made

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