Nature Methods is 5 years old!

It’s hard to believe that five years have gone by since Veronique Kiermer, Nicole Rusk and myself saw the first issue of Nature Methods go out the door. In some ways it doesn’t feel like it was that long ago while in others it feels like much, much longer. But it has certainly been a rewarding and stimulating five years and we are thrilled with the success that Nature Methods has enjoyed.

To help celebrate, Veronique asked a local pastry shop run her friend called “”https://www.howsweetitispastry.com">How Sweet It Is" to bake a cake using the cover image of our inaugural issue. It turned out spectacularly and tasted just as good. I’m hoping to convince Veronique to post a blog entry describing the undertaking with accompanying pictures.

While our readers won’t be able to taste the cake, they can see a picture of it in its full glory (minus a slice) on the cover of the October issue. Below, I have pasted an image of the October 2009 cover next to an image of our October 2004 cover so you can see how well the artisans recreated our first cover.

oct_covers

Our readers can however, enjoy a special selection of content in our special anniversary issue. Science Historians Angela Creager and Hannah Landecker provide fascinating Historical Commentaries on the roles methods have played in 20th Century biological science. We are also indebted to Steven Shapin for his help in pointing us to these two people, without whom the issue wouldn’t be as special as it is.

Of course we must also thank the practicing scientists who wrote the scientific commentaries on a selection of methodological topics that have appeared in Nature Methods over its first five years. While we would have liked to include more topics, this limited selection illustrates quite well how Nature Methods has participated in conveying important methodological developments to our readers. For a full description of the special commentaries in the issue please see the editorial.

Finally, we would like to thank all our authors, reviewers and readers for their support over the years. We hope everyone enjoys this special issue and we look forward to another five years of communicating methodological advances.

Voting for the Method of the Year now even easier

To help prevent automated spamming of the Method of the Year voting we require that anyone wishing to vote be a registered user of nature.com . Unfortunately, the regular nature.com registration required answering quite a few questions and it is quite likely that some people would rather not bother.

We have now done away with all the questions. All you need to do is provide a username and password and you can immediately log in and begin voting. We hope this will encourage more people to participate and vote for their choice of Method of the Year.

Methods papers from the recent literature

We hope you’ve had a chance to check out our selection of Research Highlights in the September issue. In addition, you might find the following list of methods papers from the last few months to be intriguing.

Noninvasive optical imaging of apoptosis by caspase-targeted activity-based probes

Nature Medicine 15, 967 – 973 (2009)

Determination of protein structural flexibility by microsecond force spectroscopy

Nature Nanotechnology 4, 514 – 517 (2009)

Development of GFP-based biosensors possessing the binding properties of antibodies

PNAS 106, 11895 – 11900 (2009)

Quantification of the yeast transcriptome by single-molecule sequencing

Nature Biotechnology 27, 652 – 658 (2009)

Partial sequencing of a single DNA molecule with a scanning tunnelling microscope

Nature Nanotechnology 4, 518 – 522 (2009)

Virtual taphonomy using synchrotron tomographic microscopy reveals cryptic features and internal structure of modern and fossil plants

PNAS 106, 12013 – 12018 (2009)

Top downloads for August ’09

A paper describing a potential new pipeline for structural genomics based on small angle X-ray scattering was far and away the most popular paper of the August issue. It will be very interesting to see what kind of impact it has on the field. While it may not provide high-resolution structures like x-ray crystalography, it is certainly faster and has a higher success rate, both of which are critical parameters for high-throughput pipelines. A paper from Helicos describing new terminator nucleotides for single-molecule next-generation sequencing (or should this be 2nd or 3rd generation?) made it to the #5 spot.

Top 7 research papers published in the August issue

1. Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

2. Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human

3. Mass spectrometry of membrane transporters reveals subunit stoichiometry and interactions

4. SHOREmap: simultaneous mapping and mutation identification by deep sequencing

5. Virtual terminator nucleotides for next-generation DNA sequencing

6. Global discovery of adaptive mutations

7. Metabolic network analysis integrated with transcript verification for sequenced genomes

The top five spots in the ten most popular papers published prior to our August issue and downloaded during August are unchanged since last month. We have a surprise appearance of an old and slightly controversial paper at position #6. This appearance appears to be the result of their publication of a follow-up paper in PNAS at the beginning of August. Squeaking in at #9 and #10 are two papers from the July issue. The top downloaded paper in July was also close behind but didn’t quite make it.

Top 10 research papers published prior to the August issue

1. Mapping and quantifying mammalian transcriptomes by RNA-Seq

2. mRNA-Seq whole-transcriptome analysis of a single cell

3. Universal sample preparation method for proteome analysis

4. Stem cell transcriptome profiling via massive-scale mRNA sequencing

5. Isolation of human iPS cells using EOS lentiviral vectors to select for pluripotency

6. The development of a bioengineered organ germ method

7. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

8. Stable knockdown of microRNA : in vivo: by lentiviral vectors

9. In vivo fluorescence imaging with high-resolution microlenses

10. Mapping the structure and conformational movements of proteins with transition metal ion FRET

Next-generation naming

What wasn’t to like when people started talking about ‘next-generation’ sequencing? It sounds so cutting edge and futuristic. But now what?

‘Next-next-generation’ and the inevitable ‘next-next-next-generation’ bring back memories of MAPKK and MAPKKK except that those had intrinsic meaning to them that were obvious to the reader; thus, they worked.

Recently, people have started using the terms ‘second generation’ to refer to the 454, Illumina and SOLiD sequencing platforms and ‘third generation’ to refer to the Helicos and PacBio platforms. Nanopore-based platforms may also qualify for the ‘third generation’ moniker.

But while the acronym NGS was readily adopted by people to refer to next-generation sequencing, SGS and 2GS just haven’t seen the same kind of uptake in the community as acronyms for second-generation sequencing. For some reason they just aren’t as visually satisfying. Eventually, I think one of these will be picked up and popularized. While neither may be beautiful (if that can be said for any acronym), either of them would be infinitely better than NNGS and, heaven forbid, NNNGS.