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Editorial

Private funding for science p537

doi:10.1038/nmeth.3923

With federal funding for life science becoming increasingly competitive in the United States, it would be a mistake, particularly for young investigators, not to carefully consider money from private sources.


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This Month

The Author File: Vladislav Verkhusha p539

Vivien Marx

doi:10.1038/nmeth.3905

A new near-infrared optogenetic system and science as a family business.


Points of Significance: Logistic regression pp541 - 542

Jake Lever, Martin Krzywinski & Naomi Altman

doi:10.1038/nmeth.3904

Regression can be used on categorical responses to estimate probabilities and to classify.


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Research Highlights

Watching translation of single mRNAs in cells p543

Four studies describe methods to image the dynamics of translation at the single-transcript level in real time in living cells, with exciting results.

Miniature magnetic force probes pp544 - 545

Magnetoplasmonic nanoparticles can manipulate cell surface receptors with single-molecule precision to clarify the effects of force application and receptor clustering.

Topographical transcriptomes pp544 - 545

Three experimental methods generate global maps of in vivo RNA interactions.

Arrival of the Argonautes p546

An Argonaute protein enables precision genome editing in mammalian cells.

Capturing transcription factors in the wild p549

An assay that snares transcription factors with genomic DNA fragments reveals how genetic and epigenetic factors shape binding behavior.

Methods in Brief

Tools in Brief

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Technology Feature

Plants: a tool box of cell-based assays pp551 - 554

Vivien Marx

doi:10.1038/nmeth.3900

Cell-based assays are less routine for plant biologists than for researchers who work with animal or human cells, but that is changing.


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News and Views

Genotyping tumor clones from single-cell data pp555 - 556

Nicholas E Navin & Ken Chen

doi:10.1038/nmeth.3903

A new statistical approach mitigates technical errors in single-cell DNA sequencing data to advance the study of tumor evolution and diversity.

See also: Brief Communication by Roth et al.


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Analysis

Quantitative assessment of fluorescent proteins pp557 - 562

Paula J Cranfill, Brittney R Sell, Michelle A Baird, John R Allen, Zeno Lavagnino, H Martijn de Gruiter, Gert-Jan Kremers, Michael W Davidson, Alessandro Ustione & David W Piston

doi:10.1038/nmeth.3891

This Analysis provides a head-to-head comparison of >40 monomeric fluorescent proteins in terms of photophysical properties, photostability and performance in fusions to help users choose the best-performing tools.


Comparison of Cas9 activators in multiple species pp563 - 567

Alejandro Chavez, Marcelle Tuttle, Benjamin W Pruitt, Ben Ewen-Campen, Raj Chari, Dmitry Ter-Ovanesyan, Sabina J Haque, Ryan J Cecchi, Emma J K Kowal, Joanna Buchthal, Benjamin E Housden, Norbert Perrimon, James J Collins & George Church

doi:10.1038/nmeth.3871

A comparison of seven dCas9-based transcriptional activators shows that VPR, SAM, and Suntag perform best in cell lines from a variety of organisms.


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Brief Communications

Flyception: imaging brain activity in freely walking fruit flies pp569 - 572

Dhruv Grover, Takeo Katsuki & Ralph J Greenspan

doi:10.1038/nmeth.3866

Flyception is a tracking and imaging system that enables the monitoring of brain activity in freely walking fruit flies, making the analysis of calcium dynamics possible in studies of neural mechanisms such as those that underlie social behaviors.


Clonal genotype and population structure inference from single-cell tumor sequencing pp573 - 576

Andrew Roth, Andrew McPherson, Emma Laks, Justina Biele, Damian Yap, Adrian Wan, Maia A Smith, Cydney B Nielsen, Jessica N McAlpine, Samuel Aparicio, Alexandre Bouchard-Côté & Sohrab P Shah

doi:10.1038/nmeth.3867

The open-source Single Cell Genotyper software addresses common artifacts in single-cell sequencing data in order to robustly infer clonal genotypes, enabling the study of tumor heterogeneity and evolution.

See also: News and Views by Navin & Chen


Data-driven hypothesis weighting increases detection power in genome-scale multiple testing pp577 - 580

Nikolaos Ignatiadis, Bernd Klaus, Judith B Zaugg & Wolfgang Huber

doi:10.1038/nmeth.3885

For multiple hypothesis testing in genomics and other large-scale data analyses, the independent hypothesis weighting (IHW) approach uses data-driven P-value weight assignment to improve power while controlling the false discovery rate.


DADA2: High-resolution sample inference from Illumina amplicon data pp581 - 583

Benjamin J Callahan, Paul J McMurdie, Michael J Rosen, Andrew W Han, Amy Jo A Johnson & Susan P Holmes

doi:10.1038/nmeth.3869

DADA2 is an open-source software package that denoises and removes sequencing errors from Illumina amplicon sequence data to distinguish microbial sample sequences differing by as little as a single nucleotide.


Quantitative detection of low-abundance somatic structural variants in normal cells by high-throughput sequencing pp584 - 586

Wilber Quispe-Tintaya, Tatyana Gorbacheva, Moonsook Lee, Sergei Makhortov, Vasily N Popov, Jan Vijg & Alexander Y Maslov

doi:10.1038/nmeth.3893

Structural Variant Search, a combination of a chimera-free library preparation and a non-consensus-based SV-calling algorithm, enables the quantitative detection of rare somatic variants.


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Articles

A hybrid approach for de novo human genome sequence assembly and phasing pp587 - 590

Yulia Mostovoy, Michal Levy-Sakin, Jessica Lam, Ernest T Lam, Alex R Hastie, Patrick Marks, Joyce Lee, Catherine Chu, Chin Lin, Željko Džakula, Han Cao, Stephen A Schlebusch, Kristina Giorda, Michael Schnall-Levin, Jeffrey D Wall & Pui-Yan Kwok

doi:10.1038/nmeth.3865

The combination of short-read sequence data, synthetic long reads and physical genome mapping allows for a phased de novo assembly of human genomes.


A bacterial phytochrome-based optogenetic system controllable with near-infrared light pp591 - 597

Andrii A Kaberniuk, Anton A Shemetov & Vladislav V Verkhusha

doi:10.1038/nmeth.3864

Optogenetic tools such as a BphP1–PpsR2 pair can be harnessed to exert spatiotemporal control over signaling pathways or transcriptional events. The BphP1–PpsR2 system is activated by near-infrared light, making it suitable for in vivo applications.


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