Nature Search

Dose-efficient cryo-electron microscopy for thick samples using tilt- corrected scanning transmission electron microscopy

Tilt-corrected bright-field scanning transmission electron microscopy offers enhanced cryogenic electron microscopy contrast and substantial improvement in dose efficiency for thick samples such as bacterial cells and large organelles, while still being able to perform single-particle analysis.

Yue Yu
Katherine A. Spoth
Lena F. Kourkoutis
ResearchOpen Access23 Sept 2025
Nature Methods

Volume: 22, P: 2138-2148
Whole-brain 3D mapping of human neural transplant innervation

Transplantation of cells into the central nervous system has developed into a major avenue for replacing neurons lost to neurodegenerative disease. Here the authors develop an approach combining viral-based transynaptic tracing labeling and whole brain imaging to trace synaptic innervation of human neurons transplanted into a mouse background.

Jonas Doerr
Martin Karl Schwarz
Oliver Brüstle
ResearchOpen Access19 Jan 2017
Nature Communications

Volume: 8, P: 1-7
Extreme weather event attribution predicts climate policy support across the world

Literature produced inconsistent findings regarding the links between extreme weather events and climate policy support across regions, populations and events. This global study offers a holistic assessment of these relationships and highlights the role of subjective attribution.

Viktoria Cologna
Simona Meiler
Amber Zenklusen
ResearchOpen Access01 Jul 2025
Nature Climate Change

Volume: 15, P: 725-735
A realistic phantom dataset for benchmarking cryo-ET data annotation

A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarking.

Ariana Peck
Yue Yu
Mohammadreza Paraan
ResearchOpen Access26 Aug 2025
Nature Methods

Volume: 22, P: 1819-1823
A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features

Single-nucleus and single-cell RNA sequencing plus spatial profiling with four methods of core biopsies from 60 patients with metastatic breast cancer reveal patient-specific gene expression programs of breast cancer metastases that are maintained across time, site of metastasis and spatial profiling method, with spatial phenotypes correlating with microenvironmental features.

Johanna Klughammer
Daniel L. Abravanel
Nikhil Wagle
ResearchOpen Access30 Oct 2024
Nature Medicine

Volume: 30, P: 3236-3249
A draft human pangenome reference

An initial draft of the human pangenome is presented and made publicly available by the Human Pangenome Reference Consortium; the draft contains 94 de novo haplotype assemblies from 47 ancestrally diverse individuals.

Wen-Wei Liao
Mobin Asri
Benedict Paten
ResearchOpen Access10 May 2023
Nature

Volume: 617, P: 312-324
Disparities in air pollution attributable mortality in the US population by race/ethnicity and sociodemographic factors

Disparities in mortality attributable to PM_2.5 air pollution was more pronounced by race/ethnicity than other sociodemographic factors such as education, rurality and social vulnerability index, according to population estimates using US Census data.

Pascal Geldsetzer
Daniel Fridljand
Tarik Benmarhnia
Research01 Jul 2024
Nature Medicine

Volume: 30, P: 2821-2829
DNA methylation signature of chronic low-grade inflammation and its role in cardio-respiratory diseases

Chronic inflammation, marked by C-reactive protein, has been associated with changes in methylation, but the causal relationship is unclear. Here, the authors perform a Epigenome-wide association meta-analysis for C-reactive protein levels and find that these methylation changes are likely the consequence of inflammation and could contribute to disease.

Matthias Wielscher
Pooja R. Mandaviya
Marjo-Riitta Järvelin
ResearchOpen Access03 May 2022
Nature Communications

Volume: 13, P: 1-14
Small molecules enable highly efficient neuronal conversion of human fibroblasts

To increase the efficiency of direct neuronal conversion of postnatal human fibroblasts, the authors combine two-factor neuronal programming with small molecules. This method increases the yield and purity of functional neuron-like cells by more than 15-fold.

Julia Ladewig
Jerome Mertens
Oliver Brüstle
Research08 Apr 2012
Nature Methods

Volume: 9, P: 575-578
Recombination between heterologous human acrocentric chromosomes

Comparisons within the human pangenome establish that homologous regions on short arms of heterologous human acrocentric chromosomes actively recombine, leading to the high rate of Robertsonian translocation breakpoints in these regions.

Andrea Guarracino
Silvia Buonaiuto
Erik Garrison
ResearchOpen Access10 May 2023
Nature

Volume: 617, P: 335-343
Pangenome graph construction from genome alignments with Minigraph-Cactus

Constructing genome graphs directly from genome assemblies overcomes single-reference bias.

Glenn Hickey
Jean Monlong
Benedict Paten
Research10 May 2023
Nature Biotechnology

Volume: 42, P: 663-673
One-step nanoscale expansion microscopy reveals individual protein shapes

Combining expansion microscopy with super-resolution radial fluctuations captures the morphology of single proteins.

Ali H. Shaib
Abed Alrahman Chouaib
Silvio O. Rizzoli
ResearchOpen Access09 Oct 2024
Nature Biotechnology

Volume: 43, P: 1539-1547
Increased mutation and gene conversion within human segmental duplications

A study comparing the pattern of single-nucleotide variation between unique and duplicated regions of the human genome shows that mutation rate and interlocus gene conversion are elevated in duplicated regions.

Mitchell R. Vollger
Philip C. Dishuck
Evan E. Eichler
ResearchOpen Access10 May 2023
Nature

Volume: 617, P: 325-334
Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu

An approach combining cryo-electron microscopy and mass spectrometry analysis of protein complexes enriched directly from cells enables structure determination of unknown complexes at atomic resolution.

Chi-Min Ho
Xiaorun Li
Z. Hong Zhou
Research25 Nov 2019
Nature Methods

Volume: 17, P: 79-85
Illuminating the multidimensional contributions of small-scale fisheries

A study aimed at revealing the role of small-scale fisheries in sustainable development shows they provide at least 40% of the global fishing catch and affect the livelihoods of 1 in 12 people in the world, among other important contributions.

Xavier Basurto
Nicolas L. Gutierrez
Shakuntala H. Thilsted
ResearchOpen Access15 Jan 2025
Nature

Volume: 637, P: 875-884
Thermophoretic trap for single amyloid fibril and protein aggregation studies

A thermophoretic trapping approach enables users to observe the behavior of single amyloid fibrils in solution for hours without any immobilization.

Martin Fränzl
Tobias Thalheim
Frank Cichos
Research24 Jun 2019
Nature Methods

Volume: 16, P: 611-614
Microsecond time-resolved X-ray scattering by utilizing MHz repetition rate at second-generation XFELs

The MHz repetition rates available at second-generation X-ray free-electron lasers enable the collection of microsecond time-resolved X-ray scattering data with exceptionally low noise, providing insights into protein structural dynamics.

Patrick E. Konold
Leonardo Monrroy
Sebastian Westenhoff
ResearchOpen Access05 Jul 2024
Nature Methods

Volume: 21, P: 1608-1611
449 VASOPRESSIN (VP) RELEASE IN FETAL NEWBORN AND ADULT SHEEP INDUCED BY HYPOXIA: CORRELATION WITH β-ENDORPHIN IMMUNOACTIVITY (-EP) & PaO2

Raymond I Stark
Salha A Daniel
L Stanley James
Research01 Apr 1981
Pediatric Research

Volume: 15, P: 515
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

A multi-laboratory study in the form of a community challenge assesses the quality of models that can be produced from cryo-EM maps using different software tools, the reproducibility of models generated by different users and the performance of metrics used for model validation.

Catherine L. Lawson
Andriy Kryshtafovych
Wah Chiu
ResearchOpen Access04 Feb 2021
Nature Methods

Volume: 18, P: 156-164
Hydroclimate volatility on a warming Earth

Rapid transitions between extreme wet and extreme dry conditions — ‘hydroclimate whiplash’ — have marked environmental and societal impacts. This Review outlines observed and projected changes in hydroclimate whiplash, suggesting that subseasonal and interannual volatility will increase markedly with ongoing warming.

Daniel L. Swain
Andreas F. Prein
Danielle Touma
Reviews09 Jan 2025
Nature Reviews Earth & Environment

Volume: 6, P: 35-50
Excitation-induced ataxin-3 aggregation in neurons from patients with Machado–Joseph disease

Human neurons derived from induced pluripotent stem cells permit the study of aberrant protein processing and aggregation in Machado–Joseph disease.

Philipp Koch
Peter Breuer
Oliver Brüstle
Research23 Nov 2011
Nature

Volume: 480, P: 543-546
A genetically encoded near-infrared fluorescent calcium ion indicator

NIR-GECO1, the first near-infrared genetically encoded calcium ion (Ca²⁺) indicator, enables improved Ca²⁺ imaging in conjunction with blue-light-activated optogenetic tools and multiplexed imaging in cell cultures and tissue slices.

Yong Qian
Kiryl D. Piatkevich
Robert E. Campbell
Research21 Jan 2019
Nature Methods

Volume: 16, P: 171-174
ReDU: a framework to find and reanalyze public mass spectrometry data

Repository-scale reanalysis of public mass spectrometry-based metabolomics data is facilitated by the Reanalysis of Data User (ReDU) interface, a system that uses consistent formatting and controlled vocabularies for metadata capture.

Alan K. Jarmusch
Mingxun Wang
Pieter C. Dorrestein
Research17 Aug 2020
Nature Methods

Volume: 17, P: 901-904
Lactobacillus plantarum attenuates anxiety-related behavior and protects against stress-induced dysbiosis in adult zebrafish

Daniel J. Davis
Holly M. Doerr
Elizabeth C. Bryda
ResearchOpen Access19 Sept 2016
Scientific Reports

Volume: 6, P: 1-11
Glutamatergic synaptic integration of locomotion speed via septoentorhinal projections

The authors describe a glutamatergic septoentorhinal pathway that provides running-speed-correlated input to MEC layer 2/3. The speed signal is integrated by several MEC cell classes and converted into speed-dependent output. This speed circuit may be important for the spatial computations of MEC neurons.

Daniel Justus
Dennis Dalügge
Stefan Remy
Research28 Nov 2016
Nature Neuroscience

Volume: 20, P: 16-19
Best practices and benchmarks for intact protein analysis for top-down mass spectrometry

The Consortium for Top-Down Proteomics presents a decision-tree-based guide to sample preparation and analysis protocols for researchers performing top-down mass-spectrometry-based analysis of intact proteins.

Daniel P. Donnelly
Catherine M. Rawlins
Jeffrey N. Agar
ReviewsOpen Access27 Jun 2019
Nature Methods

Volume: 16, P: 587-594
Macromolecular modeling and design in Rosetta: recent methods and frameworks

This Perspective reviews tools developed over the past five years in the macromolecular modeling, docking and design software Rosetta.

Julia Koehler Leman
Brian D. Weitzner
Richard Bonneau
Reviews01 Jun 2020
Nature Methods

Volume: 17, P: 665-680

Search

Dose-efficient cryo-electron microscopy for thick samples using tilt- corrected scanning transmission electron microscopy

Whole-brain 3D mapping of human neural transplant innervation

Extreme weather event attribution predicts climate policy support across the world

A realistic phantom dataset for benchmarking cryo-ET data annotation

A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features

A draft human pangenome reference

Disparities in air pollution attributable mortality in the US population by race/ethnicity and sociodemographic factors

DNA methylation signature of chronic low-grade inflammation and its role in cardio-respiratory diseases

Small molecules enable highly efficient neuronal conversion of human fibroblasts

Recombination between heterologous human acrocentric chromosomes

Pangenome graph construction from genome alignments with Minigraph-Cactus

One-step nanoscale expansion microscopy reveals individual protein shapes

Increased mutation and gene conversion within human segmental duplications

Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu

Illuminating the multidimensional contributions of small-scale fisheries

Thermophoretic trap for single amyloid fibril and protein aggregation studies

Microsecond time-resolved X-ray scattering by utilizing MHz repetition rate at second-generation XFELs

449 VASOPRESSIN (VP) RELEASE IN FETAL NEWBORN AND ADULT SHEEP INDUCED BY HYPOXIA: CORRELATION WITH β-ENDORPHIN IMMUNOACTIVITY (-EP) & PaO2

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

Hydroclimate volatility on a warming Earth

Excitation-induced ataxin-3 aggregation in neurons from patients with Machado–Joseph disease

A genetically encoded near-infrared fluorescent calcium ion indicator

ReDU: a framework to find and reanalyze public mass spectrometry data

Lactobacillus plantarum attenuates anxiety-related behavior and protects against stress-induced dysbiosis in adult zebrafish

Glutamatergic synaptic integration of locomotion speed via septoentorhinal projections

Best practices and benchmarks for intact protein analysis for top-down mass spectrometry

Macromolecular modeling and design in Rosetta: recent methods and frameworks

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