Volume 15 Issue 1, January 2018

Editorial

Method of the Year 2017: Organoids

The ability to prod stem cells into three-dimensional tissue models makes for a powerful way to study human biology. But these exciting tools are still works in progress.

Focus:

Method of the Year 2017
Editorial 03 Jan 2018
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This Month

Kasper Lage

Scoring genes in light of their 'friends', and a naval approach to science.

Vivien Marx
This Month 03 Jan 2018
Machine learning: supervised methods

Supervised learning algorithms extract general principles from observed examples guided by a specific prediction objective.

Danilo Bzdok
Martin Krzywinski
Naomi Altman
This Month 03 Jan 2018

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Correspondence

A profusion of confusion in NGS methods naming

James Hadfield
Jacques Retief
Correspondence 03 Jan 2018
motifStack for the analysis of transcription factor binding site evolution

Jianhong Ou
Scot A Wolfe
Lihua Julie Zhu
Correspondence 03 Jan 2018

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Research Highlights

It takes two to trans-Tango

Trans-Tango allows trans-synaptic mapping of presynaptic and postsynaptic partners in Drosophila.

Nina Vogt
Research Highlights 03 Jan 2018
Reflecting on light sheets

Reflective coverslips can improve spatiotemporal resolution and collection efficiency in diSPIM light-sheet fluorescence microscopy.

Christian Schnell
Research Highlights 03 Jan 2018
Sequencing DNA, no mistake

Building redundancy into fluorogenic sequencing makes for error-free DNA sequence reads.

Tal Nawy
Research Highlights 03 Jan 2018
High-resolution mapping of R loops

Two novel techniques refine genome-wide mapping of R loops.

Vesna Todorovic
Research Highlights 03 Jan 2018

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Methods in Brief

A shortcut to high-dimensional data

Methods in Brief 03 Jan 2018
Nascent proteome labeling in vivo

Methods in Brief 03 Jan 2018
Pooled screens expand to new phenotypes

Methods in Brief 03 Jan 2018
False discovery rate estimation for metabolomics

Methods in Brief 03 Jan 2018

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Tools in Brief

Electrophysiology at a massive scale

Tools in Brief 03 Jan 2018
Annotating full-length long noncoding RNAs

Tools in Brief 03 Jan 2018
Imaging 3D enzyme dynamics in 2D

Tools in Brief 03 Jan 2018
Fast curve fitting on a graphics processing unit

Tools in Brief 03 Jan 2018

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Research Highlights

Depleting endogenous proteins

Using antibodies to target specific proteins for rapid degradation is a versatile approach for studying the function of endogenous proteins.

Ada Yee
Research Highlights 03 Jan 2018

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News Feature

Organoids: the body builders

Michael Eisenstein

Focus:

Method of the Year 2017
News Feature 03 Jan 2018

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Primer

Organoids

A brief overview of stem cell-derived organoids: how they are made and what the challenges are.

Natalie de Souza

Focus:

Method of the Year 2017
Primer 03 Jan 2018

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Commentary

Imaging organoids: a bright future ahead

Anne C Rios
Hans Clevers

Collections:

Method of the Year 2017

Stem cells from development to the clinic
Commentary 03 Jan 2018
Organoids required! A new path to understanding human brain development and disease

Paola Arlotta

Collections:

Method of the Year 2017

Stem cells from development to the clinic
Commentary 03 Jan 2018

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Method to Watch

Spatial transcriptomics

It will soon be commonplace to localize gene expression in tissues.

Tal Nawy

Focus:

Method of the Year 2017
Method to Watch 03 Jan 2018
Structure via super-resolution

Fluorescence nanoscopy is extending its reach into structural biology.

Natalie de Souza

Focus:

Method of the Year 2017
Method to Watch 03 Jan 2018
Towards a dynamic 3D genome

Sequencing and imaging bring unique aspects to genome architecture.

Nicole Rusk

Focus:

Method of the Year 2017
Method to Watch 03 Jan 2018
Transformative electrophysiology

Increases in throughput push electrophysiology into a new era.

Nina Vogt

Focus:

Method of the Year 2017
Method to Watch 03 Jan 2018
Mass spectrometry imaging takes off

Recent advances in mass spectrometry imaging enable label-free molecular mapping in single cells and in 3D.

Allison Doerr

Focus:

Method of the Year 2017
Method to Watch 03 Jan 2018
Tracing cellular descent

Sophisticated barcoding approaches are transforming cell lineaging.

Tal Nawy

Focus:

Method of the Year 2017
Method to Watch 03 Jan 2018
The new XFELs

New X-ray free-electron (XFEL) facilities will broaden access to this technology, facilitate methods development, and push boundaries in structural biology.

Allison Doerr

Focus:

Method of the Year 2017
Method to Watch 03 Jan 2018
Machine learning in neuroscience

In the era of big data, neuroscience can profit from deep-learning approaches.

Nina Vogt

Focus:

Method of the Year 2017
Method to Watch 03 Jan 2018

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Technology Feature

Chemical biology: fats as research subjects

Fats add structure, they signal, they interact. In the lab, lipids are tough to work with but worth the challenge.

Vivien Marx

Collection:

NatureTech
Technology Feature 03 Jan 2018

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Resource

Multicolor quantitative confocal imaging cytometry

This resource paper describes the steps involved in carrying out quantitative multicolour imaging in tissue. It is applied to cleared mouse bone and plots the spatial distribution of specific cell populations within the marrow.

Daniel L Coutu
Konstantinos D Kokkaliaris
Timm Schroeder
Resource 13 Nov 2017
Systematic characterization of maturation time of fluorescent proteins in living cells

This work characterizes the maturation kinetics of 50 cyan to far-red fluorescent proteins and provides evidence that proteins that mature faster than their brighter but slower counterparts are more useful for quantitative evaluation of fast processes.

Enrique Balleza
J Mark Kim
Philippe Cluzel
Resource 20 Nov 2017

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Brief Communication

Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics

An integrated cheminformatics workflow aids the functional and structural annotation of unknown metabolites found across multiple biological systems.

Zijuan Lai
Hiroshi Tsugawa
Oliver Fiehn
Brief Communication 27 Nov 2017
Programmable full-adder computations in communicating three-dimensional cell cultures

Designer cells executing rationally assembled genetic programs that can process input signals with programmable logic are combined in a 3D cell culture that performs three-input, two-output full-adder computations.

David Ausländer
Simon Ausländer
Martin Fussenegger
Brief Communication 04 Dec 2017

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Article

NetSig: network-based discovery from cancer genomes

NetSig is a network-based statistic that identifies cancer driver genes with high accuracy and can be combined with gene-based statistical tests; results are validated with a large-scale in vivo tumorigenesis assay.

Heiko Horn
Michael S Lawrence
Kasper Lage
Article 04 Dec 2017
PDB-wide identification of biological assemblies from conserved quaternary structure geometry

Monomeric and homo-oligomeric protein quaternary structure states are predicted on a PDB-wide scale using a method that approaches the accuracy of manual annotation.

Sucharita Dey
David W Ritchie
Emmanuel D Levy
Article 20 Nov 2017
A permanent window for the murine lung enables high-resolution imaging of cancer metastasis

The window for high-resolution imaging of the lung (WHRIL) enables longitudinal imaging of the same region of murine lung tissue over a period of weeks, and this enables the visualization of spontaneous cancer metastasis from the earliest stages.

David Entenberg
Sonia Voiculescu
John Condeelis
Article 27 Nov 2017
An improved MS2 system for accurate reporting of the mRNA life cycle

An improved MS2-tagging system for live-cell RNA imaging allows faithful monitoring of the mRNA life cycle, overcoming degradation artifacts associated with previous versions and having implications regarding mRNA regulation in yeast.

Evelina Tutucci
Maria Vera
Robert H Singer
Article 13 Nov 2017

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Volume 15 Issue 1, January 2018

Editorial

This Month

Correspondence

Research Highlights

Methods in Brief

Tools in Brief

Research Highlights

News Feature

Primer

Commentary

Method to Watch

Technology Feature

Resource

Brief Communication

Article

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