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Nature Methods Contents: January 2018, Volume 15 No 1 pp 1 - 89

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Nature Methods
TABLE OF CONTENTS

January 2018 Volume 15, Issue 1

Special Feature
Editorial
This Month
Correspondence
Research Highlights
News Feature
Primer
Commentaries
Methods to Watch
Technology Feature
Resources
Brief Communications
Articles
 

 
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Special Feature

Top
Method of the Year 2016
 
We've chosen organoids as Method of the Year 2017, for their immense potential as tools to study human biology in health and disease. A News Feature gives a flavor of the exciting applications of these 3D constructs, and a Primer provides a short overview for newcomers to the field. Two expert Commentaries consider these tools from different angles: how cutting-edge imaging is synergizing with organoid culture to deepen our view into many biological systems, and how pluripotent stem cell-derived constructs can be used to model the human brain. As in the past, we've also chosen eight 'methods to watch' for the future.

Editorial

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Special Feature: Method of the Year 2017
Method of the Year 2017: Organoids   p1
doi:10.1038/nmeth.4575
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.
 

This Month

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The Author File: Kasper Lage   p3
Vivien Marx
doi:10.1038/nmeth.4539
Scoring genes in light of their 'friends', and a naval approach to science.
 

Points of significance: Machine learning: supervised methods   pp5 - 6
Danilo Bzdok, Martin Krzywinski and Naomi Altman
doi:10.1038/nmeth.4551
Supervised learning algorithms extract general principles from observed examples guided by a specific prediction objective.
 

Correspondence

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A profusion of confusion in NGS methods naming   pp7 - 8
James Hadfield and Jacques Retief
doi:10.1038/nmeth.4558
 

motifStack for the analysis of transcription factor binding site evolution   pp8 - 9
Jianhong Ou, Scot A Wolfe, Michael H Brodsky and Lihua Julie Zhu
doi:10.1038/nmeth.4555
 

Research Highlights

Top

It takes two to trans-Tango
Trans-Tango allows trans-synaptic mapping of presynaptic and postsynaptic partners in Drosophila.

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

Sequencing DNA, no mistake
Building redundancy into fluorogenic sequencing makes for error-free DNA sequence reads.

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

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

Methods in Brief

Top

A shortcut to high-dimensional data | Nascent proteome labeling in vivo | Pooled screens expand to new phenotypes | False discovery rate estimation for metabolomics

Tools in Brief

Top

Electrophysiology at a massive scale | Annotating full-length long noncoding RNAs | Imaging 3D enzyme dynamics in 2D | Fast curve fitting on a graphics processing unit

Methods
JOBS of the week
Postdoctoral Researcher
Leibniz Institute for Natural Product Research and Infection Biology
Postdoctoral Research Scientist
Columbia University Medical Center - Department of Obstetrics and Gynecology
Preclinical Research Assistant
Imanova Limited
Staff Scientist
Carnegie Institution for Science, Dept. Geophysical Laboratory
Data Scientist in Biostatistics / Bioinformatics
Oklahoma Medical Research Foundation (OMRF)
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Methods
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SMART 2018 : Scientific Methods in Academic Research and Teaching
07.06.18
Bacau, Romania
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News Feature

Top

Special Feature: Method of the Year 2017
Organoids: the body builders   pp19 - 22
Michael Eisenstein
doi:10.1038/nmeth.4538
 

Primer

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Special Feature: Method of the Year 2017
Organoids   p23
Natalie de Souza
doi:10.1038/nmeth.4576
A brief overview of stem cell-derived organoids: how they are made and what the challenges are.
 

Commentaries

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Special Feature: Method of the Year 2017
Imaging organoids: a bright future ahead   pp24 - 26
Anne C Rios and Hans Clevers
doi:10.1038/nmeth.4537
 

Special Feature: Method of the Year 2017
Organoids required! A new path to understanding human brain development and disease   pp27 - 29
Paola Arlotta
doi:10.1038/nmeth.4557
 

Methods to Watch

Top

Special Feature: Method of the Year 2017
Spatial transcriptomics   p30
Tal Nawy
doi:10.1038/nmeth.4542
It will soon be commonplace to localize gene expression in tissues.
 

Special Feature: Method of the Year 2017
Structure via super-resolution   p30
Natalie de Souza
doi:10.1038/nmeth.4543
Fluorescence nanoscopy is extending its reach into structural biology.
 

Special Feature: Method of the Year 2017
Towards a dynamic 3D genome   p31
Nicole Rusk
doi:10.1038/nmeth.4544
Sequencing and imaging bring unique aspects to genome architecture.
 

Special Feature: Method of the Year 2017
Transformative electrophysiology   p31
Nina Vogt
doi:10.1038/nmeth.4545
Increases in throughput push electrophysiology into a new era.
 

Special Feature: Method of the Year 2017
Mass spectrometry imaging takes off   p32
Allison Doerr
doi:10.1038/nmeth.4546
Recent advances in mass spectrometry imaging enable label-free molecular mapping in single cells and in 3D.
 

Special Feature: Method of the Year 2017
Tracing cellular descent   p32
Tal Nawy
doi:10.1038/nmeth.4547
Sophisticated barcoding approaches are transforming cell lineaging.
 

Special Feature: Method of the Year 2017
The new XFELs   p33
Allison Doerr
doi:10.1038/nmeth.4548
New X-ray free-electron (XFEL) facilities will broaden access to this technology, facilitate methods development, and push boundaries in structural biology.
 

Special Feature: Method of the Year 2017
Machine learning in neuroscience   p33
Nina Vogt
doi:10.1038/nmeth.4549
In the era of big data, neuroscience can profit from deep-learning approaches.
 

Technology Feature

Top

Chemical biology: fats as research subjects   pp35 - 38
Vivien Marx
doi:10.1038/nmeth.4550
Fats add structure, they signal, they interact. In the lab, lipids are tough to work with but worth the challenge.
 

Resources

Top

Multicolor quantitative confocal imaging cytometry   pp39 - 46
Daniel L Coutu, Konstantinos D Kokkaliaris, Leo Kunz and Timm Schroeder
doi:10.1038/nmeth.4503
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.
 

Systematic characterization of maturation time of fluorescent proteins in living cells   pp47 - 51
Enrique Balleza, J Mark Kim and Philippe Cluzel
doi:10.1038/nmeth.4509
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.
 

Brief Communications

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Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics   pp53 - 56
Zijuan Lai, Hiroshi Tsugawa, Gert Wohlgemuth, Sajjan Mehta, Matthew Mueller et al.
doi:10.1038/nmeth.4512
An integrated cheminformatics workflow aids the functional and structural annotation of unknown metabolites found across multiple biological systems.
 

Programmable full-adder computations in communicating three-dimensional cell cultures   pp57 - 60
David Ausl√§nder, Simon Ausl√§nder, Xavier Pierrat, Leon Hellmann, Leila Rachid et al.
doi:10.1038/nmeth.4505
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.
 

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Articles

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NetSig: network-based discovery from cancer genomes   pp61 - 66
Heiko Horn, Michael S Lawrence, Candace R Chouinard, Yashaswi Shrestha, Jessica Xin Hu et al.
doi:10.1038/nmeth.4514
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.
 

PDB-wide identification of biological assemblies from conserved quaternary structure geometry   pp67 - 72
Sucharita Dey, David W Ritchie and Emmanuel D Levy
doi:10.1038/nmeth.4510
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.
 

A permanent window for the murine lung enables high-resolution imaging of cancer metastasis   pp73 - 80
David Entenberg, Sonia Voiculescu, Peng Guo, Lucia Borriello, Yarong Wang et al.
doi:10.1038/nmeth.4511
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.
 

An improved MS2 system for accurate reporting of the mRNA life cycle   pp81 - 89
Evelina Tutucci, Maria Vera, Jeetayu Biswas, Jennifer Garcia, Roy Parker et al.
doi:10.1038/nmeth.4502
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.
 

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