Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators
PNAS 106, 15651 - 15656 (2009)

The yeast Wsc1 cell surface sensor behaves like a nanospring in vivo
Nature Chemical Biology 5, 857 - 862 (2009)

Genetic address book for retinal cell types
Nature Neuroscience 12, 1197 - 1204 (2009)

Protein quantification across hundreds of experimental conditions
PNAS 106, 15544 - 15548 (2009)

Biocompatible Functionalized Polyglycerol Microgels with Cell Penetrating Properties
Angewandte Chemie International Edition 48, 7540 - 7545 (2009)

Single-molecule sequencing of an individual human genome
Nature Biotechnology 27, 847 - 850 (2009)

Cell-selective metabolic labeling of proteins
Nature Chemical Biology 5, 715 - 717 (2009)

Generation of Functional Eyes from Pluripotent Cells
PLoS Biology 7, e1000174 (2009)

RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data
Bioinformatics 25, 2615 - 2616 (2009)

Targeted capture and massively parallel sequencing of 12 human exomes
Nature 461, 272 - 276 (2009)

Sensitive digital quantification of DNA methylation in clinical samples
Nature Biotechnology 27, 858 - 863 (2009)

Is knowledge about ones genome power or is it toxic information we need to be protected from?

The recent rise in companies providing direct to consumer (DTC) genetic tests has prompted a closer look at the potential societal impact of these services. Responses in different countries vary from restrictive to liberal.

Are specific laws regulating DTC genetic test needed? Should all DTC tests be treated equally before the law of should there be a distinction between tests that screen for a particular variant or mutation with a proven association to disease and tests that do genome wide screens? Should a distinction be made between tests with proven clinical utility that could lead to medical intervention vs tests that provide non-actionable information.

In the editorial in the November issue of Nature Methods we look at this topic and put forth the idea that the onus is also on the consumer to educate themselves about the kind of information these tests offer.

Ideally consumers who receive test information will have access to professionals to discuss these data. However, a shortage of genetic counselors and physicians trained in genomic medicine may make this difficult at present. Should medical schools rethink their curricula?

Is privacy of genetic information sufficiently safeguarded?

Not all DTC genetic tests are done for medical reasons, should ancestry testing be exempt from any regulation?

We are interested to hear the views of our readers on this topic.

To help celebrate, Veronique asked a local pastry shop run her friend called "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.

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.

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.

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 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-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.

In 2006 Mitchell Sogin presented the concept of a rare biosphere, low-abundance microbial populations that have persisted over large evolutionary time scales. Sogin described it as a ‘potentially inexhaustible reservoir of genomic innovation’ which lets microbial communities recover from environmental assault and allows them to adapt to changed circumstances.

How do scientists determine microbial diversity? Sequence reads covering the hypervariable regions of 16S rRNA genes are often used for classification. These ‘pyrotags’ (named thus since they are obtained on Roche’s 454 sequencer) can be classified by matching them against a rRNA sequence database.

The challenge is that for most microbial species the 16S rRNA gene is not known. An alternative is shotgun sequencing and grouping of reads into operational taxonomic units; i.e. a cluster of sequences with a defined difference to a neighboring cluster — commonly a sequence difference of 3% is required at the species level, 5% at the genus level.

But with predictions of an ever larger rare biosphere voices of caution are starting to be heard saying that its size is overestimated. Is everything that is classified as a new and rare species indeed real, or simply a sequencing error?

Most recently we featured an error correction program in our own pages that addressed this issue; and a note of caution by Phil Hugenholtz and colleagues about ‘Wrinkles in the rare biosphere’ just appeared in "Early View" in Environmental Microbiology.

How well founded are the concerns of an artificially inflated rare biosphere? Are current estimates of the rare biosphere really 10-fold too high? If so, what are the consequences — does it mean that the rare biosphere is far less important than assumed? Is it not such an inexhaustible reservoir after all but just background noise?

We understand that these are very controversial issues and we would love to hear from you.

However, this increase pales in comparison to recent and continuing advances in the throughput of DNA sequencing technology that have resulted in an astonishing increase in the production of DNA sequence by biologists. This is certainly true in the field of metagenomics which involves shotgun sequencing of the genomes (or transcriptomes) of all the organisms in an environmental sample. Biologists are adopting this technology at an rate that was completely unanticipated by most people in the field. This is creating a situation where comprehensive analysis of the resulting sequences, whose analysis is far more complex than for single-genome sequence, is becoming computationally intractable with existing resources and pipelines. The Joint Genome Institute's call for large scale (Terabase) "Grand Challenge” metagenomic projects highlights the scale of datasets that people are now discussing.

The editorial in the September issue of Nature Methods discusses this situation and calls for concerted efforts to ameliorate the metagenome-analysis gridlock that appears imminent. The recently formed M5 (metagenomics, metadata, metaanalysis, multiscale-models and metainfrastructure) Consortium will be proposing a promising solution, the 'M5 Platform', later this year. We hope these efforts will find support and be successful at ensuring this deluge of valuable data is analyzed efficiently and productively.

We often receive comments from our print subscribers that their copy of Nature Methods tends to get pilferred from their mailbox or desk but we certainly never expected to witness a theft of this scale. We are doubtful that demand for the journal is such that a black market has developed for copies at cut-rate prices but it is humorous to imagine what the culprits response was when they opened the boxes.

Top 8 research papers published in the July issue
1. Quantitative analysis of gene expression in a single cell by qPCR
2. Mapping the structure and conformational movements of proteins with transition metal ion FRET
3. Limitations and possibilities of small RNA digital gene expression profiling
4. Enabling IMAC purification of low abundance recombinant proteins from E. coli lysates
5. In vivo fluorescence imaging with high-resolution microlenses
6. Protein interaction platforms: visualization of interacting proteins in yeast
7. Agouti C57BL/6N embryonic stem cells for mouse genetic resources
8. Reaching the protein folding speed limit with large, sub-microsecond pressure jumps

There has been very little movement in the ten most popular papers published prior to our July issue and downloaded during July. The exception is the appearance of the HUPO test sample paper from June appearing at #7. The papers below this have changed but mostly because a large number of papers have very similar download numbers and they shuffle around from month to month.

Top 10 research papers published prior to the July 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. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
7. A HUPO test sample study reveals common problems in mass spectrometry–based proteomics
8. Generation of transgene-free induced pluripotent mouse stem cells by the piggyBac transposon
9. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
10. A versatile tool for conditional gene expression and knockdown

Proteomic analysis of S-nitrosylation and denitrosylation by resin-assisted capture
Nature Biotechnology 27, 557-559 (2009)

Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing
Science 324, 1210-1213 (2009)

Validated germline-competent embryonic stem cell lines from nonobese diabetic mice
Nature Medicine 15, 814-818 (2009)

Unfolding Individual Als5p Adhesion Proteins on Live Cells
ACS Nano, 3, 1677-1682 (2009)

Development of aliphatic biodegradable photoluminescent polymers
PNAS 106, 10086-10091 (2009)

Directing cell motions on micropatterned ratchets
Nature Physics 5, 606-612 (2009)

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding
Genome Research, published online 22 June 2009

Twin-spot MARCM to reveal the developmental origin and identity of neurons
Nature Neuroscience 12, 947-953 (2009)

The establishment of gene silencing at single-cell resolution
Nature Genetics 41, 800-806 (2009)

DNA relaxation dynamics as a probe for the intracellular environment
PNAS 106, 9250-9255 (2009)

Interactive exploration of chemical space with Scaffold Hunter
Nature Chemical Biology 5, 581-583 (2009)

Bioactivity-guided mapping and navigation of chemical space
Nature Chemical Biology 5, 585 - 592 (2009)

Last year we invited our readers to help us in the selection of the Method of the Year 2008 by nominating and voting for their choice. While participation was good, it wasn't high enough to have much impact on our choice. This year we are starting voting a month earlier and are hopeful that the level of participation will be substantially higher.

We also want to clarify that we are not asking people to nominate and vote for papers published in Nature Methods. Although anyone who wants to nominate a Nature Methods paper is welcome to do so, we hope that readers will consider the broader universe of biological research methods.

It is quite likely that our choice will not be a method represented by a single paper but rather a class of methods like next-generation sequencing or super-resolution imaging. But readers are welcome to pick a single paper that represents a broader methodological advance they want to nominate and explain their choice to other readers.

We have already seeded the voting with our Methods to Watch from the last two years. Maybe one of them will now be ready to be declared Method of the Year.

As always, we welcome your feedback and encourage you to vote for the method you think deserves to be declared the Method of the Year 2009 and encourage your colleagues to do so as well. Just go to http://www.nature.com/nmeth/votemoy2009 and start voting!

As part of our standard material sharing policy, Nature Methods generally requires that authors provide a useable software program implementing any new algorithm that is integral to a method they're reporting. But we have never said anything about naming the software.

It recently came to our attention that there are a number of factors that act to discourage authors of new algorithms from naming a software implementation of their algorithm. As discussed in the editorial, this can lead to difficulties later on and in many cases providing a name for the software has benefits that outweigh the potential hazards. Read the editorial and then let us know what you think.

Top 5 research papers published in the June issue
1. Predicting microRNA targets and functions: traps for the unwary
2. Automated unrestricted multigene recombineering for multiprotein complex production
3. A HUPO test sample study reveals common problems in mass spectrometry–based proteomics
4. Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster
5. High-throughput ethomics in large groups of Drosophila

There has been quite a reshuffling of the ten most popular papers published prior to our June issue and downloaded during June. Part of this movement may be due to the fact that beginning this month I have decided to use the number of successfully downloaded PDFs rather than combined PDF and HTML views but I think most of the explanation is the high quality of the papers published in our May issue which have displaced some of the older papers.

Top 10 research papers published prior to the June 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. Isolation of human iPS cells using EOS lentiviral vectors to select for pluripotency
5. Super-resolution video microscopy of live cells by structured illumination
6. Generation of transgene-free induced pluripotent mouse stem cells by the piggyBac transposon
7. Stem cell transcriptome profiling via massive-scale mRNA sequencing
8. Genetically encoded fluorescent indicator for intracellular hydrogen peroxide
9. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
10. Enzymatic assembly of DNA molecules up to several hundred kilobases