@naturemethods profile picture
Nature Methods @naturemethods

Nature Methods publishes cutting-edge methods, tools, analyses, resources, reviews, news and commentary, supporting life sciences research. Tweets by editors.

Joined March 2011
  • Tweets 5,733
  • Following 1,086
  • Followers 154,994
1,857 Photos and videos
An Analysis evaluated the effect of pretraining dataset size and diversity on the performance of single-cell foundation models. @AlanDenAdel @nfusi @SriRaghavanMD @avapamini @peterswinter @lorin_crawford nature.com/articles/s41592-0…

Evaluating the role of pretraining dataset size and diversity on single-cell foundation model...

Nature Methods - The performance of single-cell foundation models is dependent on many factors. This study assesses the effect of the pretraining dataset’s size and diversity, revealing...

nature.com
1
3
11
2,470
Read the associated Research Briefing here: nature.com/articles/s41592-0…

Scaling up training dataset size for transcriptomic AI models is much pain with little gain

Nature Methods - The advantages of training foundation models for single-cell datasets on large (tens of millions of cells) datasets have not been systematically tested. We evaluated the role of...

nature.com
5
1,160
Nature Methods@naturemethods
Jun 15
A lightweight head-mounted multiplane microscope allows simultaneous imaging of 1800 neurons in freely moving mice, sampled over weeks. nature.com/articles/s41592-0…
13
49
4,688
m6A-ARTR-DBiT offers a spatial assay to profile the distribution of m6A across the transcriptome in intact tissue sections. nature.com/articles/s41592-0…

Spatially resolved m6A profiling using m6A-ARTR-DBiT

Nature Methods - m6A-ARTR-DBiT offers a spatial assay to profile the distribution of N6-methyladenosine (m6A) across the transcriptome in intact tissue sections.

nature.com
1
7
27
4,232
And read the associated News & Views here: nature.com/articles/s41592-0…

Spatial epitranscriptomics: from Cinderella to queen

Nature Methods - The m6A-ARTR-DBiT technique allows the spatial profiling of m6A mRNA modifications.

nature.com
2
2
2,397
Nature Methods@naturemethods
Jun 15
OrthoFinder v3: a tool for phylogenetic orthology inference with boosted accuracy and scalability for massive datasets. @Steve__Kelly @dr_belcher @David__Emms nature.com/articles/s41592-0…

OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability

Nature Methods - The updated OrthoFinder v3 software boosts accuracy and scalability in phylogenetic orthology inference with massive and diverse datasets.

nature.com
6
26
3,207
We are very excited to bring back our popular Points of View column, written by @helenajambor! Check out her first column in our July issue about the usage of color scales in scientific figures. nature.com/articles/s41592-0…
1
1
5
1,587
Also read this month's Editorial which (re)introduces the Points of View. nature.com/articles/s41592-0…

Points of View, anew

Nature Methods - This month, we reintroduce the Points of View column, with updated practical advice for visualizing scientific data.

nature.com
2
4
1,176
Nature Methods@naturemethods
Jun 12
Our June issue is live! 🎉 nature.com/nmeth/volumes/23/… On the cover, an absolutely gorgeous image of neurites and mitochondria in a brain organoid, captured using the MOSAIC microscope. Paper here: nature.com/articles/s41592-0…
10
31
2,947
Nature Methods@naturemethods
Jun 11
A Perspective discusses the use of external validation using independent datasets for improving human neuroimaging studies. @DScheinost nature.com/articles/s41592-0…

External validation improves generalizability, replicability and reproducibility in predictive...

Nature Methods - This Perspective promotes the use of external validation using independent datasets for human neuroimaging studies.

nature.com
2
7
2,388
Nature Methods@naturemethods
Jun 11
A Perspective discusses challenges in macromolecular ensemble prediction and the methodological advances that are needed. @stephanie_mul nature.com/articles/s41592-0…

From possibility to precision in macromolecular ensemble prediction

Nature Methods - This Perspective discusses current challenges in macromolecular ensemble prediction and the infrastructure and methodological advances needed to overcome these barriers.

nature.com
5
22
3,608
Chromatix: a standardized framework for developing, sharing and reusing wave-optics simulations. @diptodipdeb @srinituraga @HHMIJanelia nature.com/articles/s41592-0…
1
4
18
3,096
And read the associated Research Briefing here: nature.com/articles/s41592-0…

A fast open-source wave optics simulator

Nature Methods - We built an open-source library of wave optics models — Chromatix — that enables optics simulations to be scaled efficiently on modern computing hardware. Chromatix...

nature.com
1
3
982
Nature Methods@naturemethods
Jun 11
A Perspective provides minimum community standards and best-practice guidelines for hydroxyl radical protein footprinting-mass spectrometry. nature.com/articles/s41592-0…
2
13
2,670
Nature Methods@naturemethods
Jun 11
SAGE-net: a scalable, efficient sequence-to-function modeling framework for personal genome analysis. nature.com/articles/s41592-0…

A scalable approach to investigating sequence-to-function predictions from personal genomes

Nature Methods - Modeling the effect of DNA sequence variation on phenotypes such as gene expression faces unique challenges when deciphering inter-individual variation. This study presents a...

nature.com
9
48
5,563
Nature Methods@naturemethods
Jun 11
Brightness demixing: a method for simultaneously detecting different fluorophores in single-molecule localization microscopy based on brightness. @S_LevequeFort @LE_Laurent_ nature.com/articles/s41592-0…
6
20
1,941
Neuropixels Opto probes combine high-density recording sites with optical waveguide-based light emission sites to simultaneously record neuronal activity and optogenetic stimulation. nature.com/articles/s41592-0…

Neuropixels Opto: combining high-resolution electrophysiology and optogenetics

Nature Methods - Neuropixels Opto probes combine high-density recording sites with optical waveguide-based light emission sites for simultaneous recording of neuronal activity and optogenetic...

nature.com
1
4
14
3,584
Read the associated Research Briefing here: nature.com/articles/s41592-0…

Reading and writing neural activity with Neuropixels Opto probes

Nature Methods - High-density electrophysiology devices allow neuroscientists to observe spikes from large populations of neurons, and optogenetics allows them to drive or suppress those spikes. We...

nature.com
2
5
2,153
Nature Methods@naturemethods
Jun 4
TADShop: a study benchmarking 43 computational methods for identifying topologically associating domains. nature.com/articles/s41592-0…
7
41
3,978
A correlative workflow combining cryo-EM and focused ion beam secondary ion mass spectrometry enables subcellular chemical mapping. nature.com/articles/s41592-0…

Subcellular chemical mapping using correlated cryogenic electron and mass spectrometry imaging

Nature Methods - A correlative workflow combining cryo-EM and focused ion beam secondary ion mass spectrometry (FIB-SIMS) facilitates subcellular chemical analysis with high spatial resolution.

nature.com
1
7
14
3,142
Read the News & Views highlighting this work, here: nature.com/articles/s41592-0…

Adding chemical identity to cryo-electron microscopy

Nature Methods - A correlative workflow combining cryo-electron microscopy and cryo-electron tomography with secondary ion mass spectrometry generates spatially registered chemical maps from the...

nature.com
1
4
2,097
Load more