Monday, December 3, 2018

Nature Methods Contents: December 2018, Volume 15 No 12

Nature Methods


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TABLE OF CONTENTS

December 2018 Volume 15, Issue 12

Editorial
This Month
Correspondence
Comment
Research Highlights
Technology Feature
News & Views
Perspectives
Review Articles
Brief Communications
Articles
Amendments & Corrections

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Editorial

Challenges for cryo-EM    p985
doi:10.1038/s41592-018-0256-z

Changes at Nature Methods    p985
doi:10.1038/s41592-018-0257-y

This Month

Olga Troyanskaya    p987
Vivien Marx
doi:10.1038/s41592-018-0226-5

Correspondence

Impact of optical aberrations on axial position determination by photometry    pp989 - 990
Rasmus Ø. Thorsen, Christiaan N. Hulleman, Mathias Hammer, David Grünwald, Sjoerd Stallinga et al.
doi:10.1038/s41592-018-0227-4

Reply to 'Impact of optical aberrations on axial position determination by photometry'    pp990 - 992
Christian Franke & Sebastian van de Linde
doi:10.1038/s41592-018-0228-3

CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data    pp992 - 993
Jonathan Y. Hsu, Charles P. Fulco, Mitchel A. Cole, Matthew C. Canver, Danilo Pellin et al.
doi:10.1038/s41592-018-0225-6

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Comment

Comparing phenotypic variation between inbred and outbred mice    pp994 - 996
Alexander H. Tuttle, Vivek M. Philip, Elissa J. Chesler & Jeffrey S. Mogil
doi:10.1038/s41592-018-0224-7

Research Highlights

Next-generation peptide sequencing    p997
Lei Tang
doi:10.1038/s41592-018-0240-7

Mapping mouse development    p998
Rita Strack
doi:10.1038/s41592-018-0241-6

Recording transcriptional activity    p999
Nicole Rusk
doi:10.1038/s41592-018-0242-5

Sequence meets space    p1000
Tal Nawy
doi:10.1038/s41592-018-0243-4

The UK Biobank    p1001
Nicole Rusk
doi:10.1038/s41592-018-0245-2

Split proteins by design    p1001
Rita Strack
doi:10.1038/s41592-018-0246-1

Cell portrait of a mouse    p1001
Tal Nawy
doi:10.1038/s41592-018-0247-0

Enhanced antibody validation    p1001
Allison Doerr
doi:10.1038/s41592-018-0248-z

Partial ordered polypeptides    p1002
Lei Tang
doi:10.1038/s41592-018-0249-y

Protein-based cell barcodes    p1002
Tal Nawy
doi:10.1038/s41592-018-0250-5

A nonhuman primate imaging resource    p1002
Rita Strack
doi:10.1038/s41592-018-0251-4

A methionine modification method    p1002
Allison Doerr
doi:10.1038/s41592-018-0252-3

Expanding the optogenetics toolkit    p1003
Kate Gao
doi:10.1038/s41592-018-0244-3

Methods
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Technology Feature

Specialty probes give super-res imaging that special blink    pp1005 - 1008
Vivien Marx
doi:10.1038/s41592-018-0231-8

News & Views

Bayesian deep learning for single-cell analysis    pp1009 - 1010
Gregory P. Way & Casey S. Greene
doi:10.1038/s41592-018-0230-9

Perspectives

Faster, sharper, and deeper: structured illumination microscopy for biological imaging    pp1011 - 1019
Yicong Wu & Hari Shroff
doi:10.1038/s41592-018-0211-z

A Perspective on super-resolution structured illumination microscopy reviews advances in these methods and focuses on matching user needs in terms of imaging speed, sample depth, and desired resolution with the appropriate instrumentation.

Review Articles

Acoustic tweezers for the life sciences    pp1021 - 1028
Adem Ozcelik, Joseph Rufo, Feng Guo, Yuyang Gu, Peng Li et al.
doi:10.1038/s41592-018-0222-9

This review discusses and contrasts different acoustic-tweezer technologies and their applications in biology.

Brief Communications

Nanobody immunostaining for correlated light and electron microscopy with preservation of ultrastructure    pp1029 - 1032
Tao Fang, Xiaotang Lu, Daniel Berger, Christina Gmeiner, Julia Cho et al.
doi:10.1038/s41592-018-0177-x

NATIVE is a correlative light and electron microscopy approach that is based on nanobody-mediated immunohistochemistry. The approach does not require harsh permeabilization and preserves ultrastructure well.

Cell-type-specific and projection-specific brain-wide reconstruction of single neurons    pp1033 - 1036
Rui Lin, Ruiyu Wang, Jing Yuan, Qiru Feng, Youtong Zhou et al.
doi:10.1038/s41592-018-0184-y

An AAV-based platform achieves sparse yet bright labeling of neurons with cell-type specificity. This technology will facilitate the reconstruction of neurons in the mouse brain.

Closed-loop all-optical interrogation of neural circuits in vivo    pp1037 - 1040
Zihui Zhang, Lloyd E. Russell, Adam M. Packer, Oliver M. Gauld & Michael Häusser
doi:10.1038/s41592-018-0183-z

A closed-loop all-optical strategy allows manipulation of neurons on the basis of their ongoing activity and can be used to clamp neuronal activity to a preset level, boost sensory-evoked activity or yoke together the activity of trigger and target neurons.

Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples    pp1041 - 1044
Yuan Gao & Hongzhe Li
doi:10.1038/s41592-018-0182-0

DEMIC uses contigs and coverage data to compare growth rates between bacterial samples.

Efficient scarless genome editing in human pluripotent stem cells    pp1045 - 1047
Kazuya Ikeda, Nobuko Uchida, Toshinobu Nishimura, Joseph White, Renata M. Martin et al.
doi:10.1038/s41592-018-0212-y

The combination of positive and negative selection strategies, paired with the use of shRNAs to avoid random integration, allows efficient and scarless CRISPR-based homologous recombination.

Articles

Interpretation of an individual functional genomics experiment guided by massive public data    pp1049 - 1052
Young-suk Lee, Aaron K. Wong, Alicja Tadych, Boris M. Hartmann, Christopher Y. Park et al.
doi:10.1038/s41592-018-0218-5

YETI puts individual -omics experiments in the context of public genomics data by creating an integrated dataset-specific functional network, thus allowing more thorough interpretation of the data.

Deep generative modeling for single-cell transcriptomics    pp1053 - 1058
Romain Lopez, Jeffrey Regier, Michael B. Cole, Michael I. Jordan & Nir Yosef
doi:10.1038/s41592-018-0229-2

scVI is a ready-to-use generative deep learning tool for large-scale single-cell RNA-seq data that enables raw data processing and a wide range of rapid and accurate downstream analyses.

Identification of differentially methylated cell types in epigenome-wide association studies    pp1059 - 1066
Shijie C. Zheng, Charles E. Breeze, Stephan Beck & Andrew E. Teschendorff
doi:10.1038/s41592-018-0213-x

CellDMC finds cell type–specific differential methylation in mixtures of cells, including epithelial tissues, and scenarios in which methylation changes in opposite directions in different cell types.

Found In Translation: a machine learning model for mouse-to-human inference    pp1067 - 1073
Rachelly Normand, Wenfei Du, Mayan Briller, Renaud Gaujoux, Elina Starosvetsky et al.
doi:10.1038/s41592-018-0214-9

The machine learning approach FIT leverages public mouse and human expression data to improve the translation of mouse model results to analogous human disease.

Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments    pp1074 - 1082
Daniel Benhalevy, Dimitrios G. Anastasakis & Markus Hafner
doi:10.1038/s41592-018-0220-y

Proximity-CLIP, a method that combines proximity-based protein biotinylation and UV crosslinking, profiles RNAs and ribonucleoproteins in any cellular compartment.

A particle-filter framework for robust cryo-EM 3D reconstruction    pp1083 - 1089
Mingxu Hu, Hongkun Yu, Kai Gu, Zhao Wang, Huabin Ruan et al.
doi:10.1038/s41592-018-0223-8

A particle-filter algorithm for single-particle cryo-electron microscopy, implemented in a tool called THUNDER, provides high-dimensional parameter estimation, improving the obtainable resolution for several protein structures.

Content-aware image restoration: pushing the limits of fluorescence microscopy    pp1090 - 1097
Martin Weigert, Uwe Schmidt, Tobias Boothe, Andreas Müller, Alexandr Dibrov et al.
doi:10.1038/s41592-018-0216-7

Content-aware image restoration (CARE) uses deep learning to improve microscopy images. CARE bypasses the trade-offs between imaging speed, resolution, and maximal light exposure that limit fluorescence imaging to enable discovery.

An explant technique for high-resolution imaging and manipulation of mycobacterial granulomas    pp1098 - 1107
Mark R. Cronan, Molly A. Matty, Allison F. Rosenberg, Landry Blanc, Charlie J. Pyle et al.
doi:10.1038/s41592-018-0215-8

An ex vivo 3D culture model of mycobacterial granulomas recapitulates the in vivo physiology of these structures and enables longitudinal imaging studies. The platform allows genetic and pharmacological manipulation of this key structure.

Fast, in vivo voltage imaging using a red fluorescent indicator    pp1108 - 1116
Madhuvanthi Kannan, Ganesh Vasan, Cheng Huang, Simon Haziza, Jin Zhong Li et al.
doi:10.1038/s41592-018-0188-7

VARNAM is a red-shifted genetically encoded voltage sensor based on the Ace opsin. It is applied in Drosophila, mouse brain slices and behaving mice. It can be readily combined with blue-light-sensitive tools for dual-color applications.

Brain-wide circuit interrogation at the cellular level guided by online analysis of neuronal function    pp1117 - 1125
Nikita Vladimirov, Chen Wang, Burkhard Höckendorf, Avinash Pujala, Masashi Tanimoto et al.
doi:10.1038/s41592-018-0221-x

Imaging of neuronal activity across the whole zebrafish brain in combination with online analysis allows for manipulating neuronal activity according to function. This approach is used to ablate or activate neurons in fictively swimming zebrafish larvae.

Amendments & Corrections

Author Correction: Comprehensive comparative analysis of 5′-end RNA-sequencing methods    p1126
Xian Adiconis, Adam L. Haber, Sean K. Simmons, Ami Levy Moonshine, Zhe Ji et al.
doi:10.1038/s41592-018-0237-2

Publisher Correction: Transparent Danionella translucida as a genetically tractable vertebrate brain model    p1126
Lisanne Schulze, Jörg Henninger, Mykola Kadobianskyi, Thomas Chaigne, Ana Isabel Faustino et al.
doi:10.1038/s41592-018-0217-6

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