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- 1From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedSean A McKinney, Christopher S Murphy, Kristin L Hazelwood, Michael W Davidson & Loren L Looger Nat. Methods 6, 131-133 (2009). In the version of the supplementary information file originally posted online, the...
- 2From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedLast month I wrote about color blindness and ways to make information accessible to individuals with color vision deficiencies. I would like to continue by considering graphical alternatives to color that could improve...
- 3From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedTo fully exploit the potential of high-throughput transcript sequencing (RNA-seq), analysis algorithms are essential. Grabherr et al. now add Trinity, a de novo assembler, to the toolbox. First, the Inchworm module...
- 4From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedFrom the mid-1980s through the mid-1990s, Greg Wilson worked in high-performance scientific computing in Edinburgh, UK. His job was to help physicists migrate their homemade software onto massively parallel...
- 5From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedGenome-wide profiling of transcription factors based on massive parallel sequencing of immunoprecipitated chromatin (ChIP-seq) requires nanogram amounts of DNA. Here we describe a high-fidelity, single-tube linear DNA...
- 6From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedPhenotypic screens of a complex in vivo structure predict function for essential genes in the worm. The power of a forward genetic screen is that it picks out, from all the possible genes in a genome, those that are...
- 7From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedA combination of techniques is used to measure and model RNA dynamics in dendritic cells. Almost nothing in biology is simple. Making a molecule such as mRNA, for instance, involves a dynamic interplay of several...
- 8From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedWe designed a real-time computer vision system, the Multi-Worm Tracker (MWT), which can simultaneously quantify the behavior of dozens of Caenorhabditis elegans on a Petri plate at video rates. We examined three...
- 9From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedMonya Baker Nat. Methods 8, 293-297 (2011); published online 30 March 2011; corrected after print 6 April 2011. In the version of this article initially published, a reference was incomplete. The error has been...
- 10From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedYou have just developed and characterized a new method that you think researchers will find interesting and valuable. As you are writing a paper, you decide, 'Let's give the method a clever acronym, so people will...
- 11From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedHigh-throughput sequencing of nucleic acids has evolved over the last decade as a powerful new strategy for investigations into disease and disease-causing organisms, as evidenced by the number of commercial platforms...
- 12From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedCross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with...
- 13From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedHeterogeneity in cell populations poses a major obstacle to understanding complex biological processes. Here we present a microfluidic platform containing thousands of nanoliter-scale chambers suitable for live-cell...
- 14From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedIn science, logical steps can lead to surprising places. When outlining his research interests, Xiaoliang Sunney Xie splits his laboratory pursuits in three: dynamics of gene expression in living cells, single-molecule...
- 15From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedTwo complementary methods facilitate genome-wide enrichment of hydroxymethylated DNA. In 2009, Anjana Rao and her team from Harvard Medical School characterized an enzyme responsible for producing a modified DNA...
- 16From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedTo the Editor: Fluorescent proteins are known to display in certain cases an on-off blinking and switching behavior (1). We could not yet find a report investigating the impact of this phenomenon on superresolution...
- 17From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedA single-molecule pull-down method provides a simple way for biologists to examine their favorite protein at the single-molecule level. Intracellular signaling depends on specific dynamic physical interactions...
- 18From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedApplying pulsed excitation together with time-gated detection improves the fluorescence on-off contrast in continuous-wave stimulated emission depletion (cW-STED) microscopy, thus revealing finer details in fixed and...
- 19From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedKrieger et al. describe cysteine shotgun mass spectrometry, a method to map how cysteines are exposed in proteins in cells by mechanical, thermal or drug-based stress. Exposed cysteine residues are labeled with...
- 20From: Nature Methods. (Vol. 8, Issue 7) Peer-ReviewedTo quantitatively understand chemosensory behaviors, it is desirable to present many animals with repeatable, well-defined chemical stimuli. To that end, we describe a microfluidic system to analyze Caenorhabditis...