Method of the Year 2009

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• • Biotechnology
  • Cell biology
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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.

• Cell biology

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  • Direct RNA sequencing

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      Original article citation: Nature 461," 814 - 818, (2009).

    • Categories: Others, Genetics and genomics, Cell biology, and Synthetic biology
    • Recommended by : Bekir Ulker on 11/03/2009 06:10PM GMT
      
      Direct RNA sequencing without converting RNA to cDNA, a long desired method now on the edge of being readily available to scientists. This method eliminates the biases, complexity and errors introduced by nucleic acid amplification and requires minute amounts of starting RNA material. This method would lead to major surprises and discoveries in RNA processing as well as various RNA species that organisms might have and the biological roles.
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  • • 9+ votes

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  • Global identification of yeast chromosome interactions using Genome conformation capture

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      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

  • • 20+ votes

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  • Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

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      Original article citation: Science 326," 289 - 293, (2009).

    • Categories: Cell biology and Genetics and genomics
    • Recommended by : David Galas on 10/21/2009 03:43PM GMT
      
      The added power of this modified method to lay out the 3D arrangement of the chromosomes of the genome in the nucleus is a major advance. we had some information before this, but now we can look at the full arrangement, in any cells, underany conditions. Very clever technique coupled with beautiful computational analysis.
    • Comment on this subject: 0 comments made

  • • 12+ votes

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

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      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

  • • 8+ votes

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

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      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.
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  • • 3+ votes

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  • The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

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      Original article citation: Science 320," 1344 - 1349, (2008).

    • Categories: Genetics and genomics and Cell biology
    • Recommended by the Editor: Nicole Rusk on 08/14/2009 12:23AM GMT
      
      Though followed within a few weeks by independent groups from the Sanger institute, Cal Tech and University of Queensland this was the first paper describing RNA-seq and thus the first to show the power of second generation sequencing for transcriptome analysis.
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  • • 7+ votes

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  • PreTect method: Multiplex real-time mRNA detection

    • Tor Molden
      Original article citation: Journal of Virological Methods 142," 204 , (2007).

    • Categories: Biotechnology, Cell biology, Others, and Microbiology
    • Recommended by : Frank Karlsen on 08/12/2009 10:54AM GMT
      
      This method can amplify and detect up to 6 mRNA hotspots selected by microarray or other methods in any routine diagnostic setting. The method has been demonstrated to find cervical pre-cancer directly with very high clinical sensitivity and specificity by amplification and detection of 6 different oncogene markers at the same time. The method has been demonstrated in 18 international per-review articles. The method is in use in 20 countries around the world. The method was already demonstrated to be used for cervical cancer screening in 2003. Since than it has been demonstrated to be functional i more than 200 000 clinical samples. The method is ideal for routine diagnostics of 6 different mRNA from any bacteria, virus, parasite or cell in the same sample. The PreTect method can be used on any fluorescence reader only including adaptable software. The PreTect method has been demonstrated to work in sample that is collected in methanol based media for up to one month in room temperature. The PreTect method is independent of the length of the mRNA and can only amplify mRNA and not double stranded DNA. The PreTect method has bee demonstrated to only amplify mRNA in a mixture of purified RNA and DNA.
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  • • 1+ votes

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  • A meta-network of -omics

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      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?
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  • Experimental micro-matchmaking

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      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

  • • 9+ votes

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  • Top-down mass spectrometry

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      Original article citation: Nat Meth 5," 24 - 24, (2008).

    • Categories: Proteomics, Biotechnology, Protein biochemistry, and Cell biology
    • Recommended by the Editor: Allison Doerr on 07/27/2009 01:57PM GMT
      
      Top-down mass spectrometry was selected as a Method to Watch at the end of 2007. This tool is particularly useful for analyzing protein post-translational modifications, but it is not yet a high-throughput method. Have we seen the developments needed to drive its limits?
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