Outlook |
Featured
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Technology Feature |
So … you’ve been hacked
Research institutions are under siege from cybercriminals and other digital assailants. How do you make sure you don’t let them in?
- Michael Brooks
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Technology Feature |
No installation required: how WebAssembly is changing scientific computing
Enabling code execution in the web browser, the multilanguage tool is powerful but complicated.
- Jeffrey M. Perkel
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News Explainer |
AI-generated images and video are here: how could they shape research?
Scientists are already using image-generating models to jazz up papers and presentations. But some say these tools could harm research.
- Carissa Wong
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Technology Feature |
Five tips for digitizing handwritten data
Need to digitize field notes or historical documents? Researchers share their best practices.
- Alla Katsnelson
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Career Column |
Structural biology for researchers with low vision
Scientists seek to analyse biomolecules at the highest level of resolution. We developed and adapted assistive technologies to help those who are blind to do the same.
- Olivia Shaw
- , Cynthia Yurkovich
- & Jodi Hadden-Perilla
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News Explainer |
How journals are fighting back against a wave of questionable images
Publishers are deploying AI-based tools to detect suspicious images, but generative AI threatens their efforts.
- Nicola Jones
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Editorial |
Cyberattacks on knowledge institutions are increasing: what can be done?
For months, ransomware attacks have debilitated research at the British Library in London and Berlin’s natural history museum. They show how vulnerable scientific and educational institutions are to this kind of crime.
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News |
AI beats human sleuth at finding problematic images in research papers
An algorithm that takes just seconds to scan a paper for duplicated images racks up more suspicious images than a person.
- Anil Oza
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News |
Can AI predict who will win a Nobel Prize?
With a few modifications, ChatGPT-like models could enhance the art of identifying future laureates.
- Gemma Conroy
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Career Column |
How my broken elbow made the ableism of computer programming personal
Amy Ko’s accident gave her an insight into the degree to which her discipline caters mainly to non-disabled people, reinspiring her to invent more accessible programming languages.
- Amy Ko
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Article
| Open Access
Clustering predicted structures at the scale of the known protein universe
The novel Foldseek clustering algorithm defines 2.30 million clusters of AlphaFold structures, identifying remote structural similarity of human immune-related proteins in prokaryotic species.
- Inigo Barrio-Hernandez
- , Jingi Yeo
- & Martin Steinegger
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Article
| Open Access
Identifying attacks in the Russia–Ukraine conflict using seismic array data
Analysis of seismic waves caused by explosions in northern Ukraine recorded by a local network in 2022 demonstrated the ability to automatically identify individual attacks during the Russia–Ukraine conflict in close to real time.
- Ben D. E. Dando
- , Bettina P. Goertz-Allmann
- & Alexander Liashchuk
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Article
| Open Access
Faster sorting algorithms discovered using deep reinforcement learning
Artificial intelligence goes beyond the current state of the art by discovering unknown, faster sorting algorithms as a single-player game using a deep reinforcement learning agent. These algorithms are now used in the standard C++ sort library.
- Daniel J. Mankowitz
- , Andrea Michi
- & David Silver
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Technology Feature |
The sleight-of-hand trick that can simplify scientific computing
Computational environments and the tools to manage them can help researchers to deliver code that is reproducible, documented and shareable.
- Jeffrey M. Perkel
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News Explainer |
Moon mission failure: why is it so hard to pull off a lunar landing?
The ispace lander’s failed touchdown highlights the challenges Moon landings pose, especially for private companies.
- Alexandra Witze
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Nature Video |
The driving test for driverless cars
A virtual world filled with bad AI drivers can be used to test autonomous vehicles.
- Shamini Bundell
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Technology Feature |
‘Spell-checker for statistics’ reduces errors in the psychology literature
Developed to detect statistical errors, statcheck reduces mistakes in reported P values by up to 4.5-fold.
- Dalmeet Singh Chawla
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Technology Feature |
Hunting for the best bioscience software tool? Check this database
A data set funded by the Chan Zuckerberg Initiative shows how research software and tools are used across disciplines — and helps developers gain credit for their work.
- Matthew Hutson
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News Explainer |
Should I join Mastodon? A scientists’ guide to Twitter’s rival
The open-source platform has added nearly half a million users in little more than a week — but should scientists make the leap? We examine the pros and cons.
- Chris Stokel-Walker
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Correspondence |
Nigeria’s energy policy needs state-of-the-art modelling tools
- Qazeem Opeyemi Ogunlowo
- , Wook Ho Na
- & Hyun Woo Lee
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Technology Feature |
Poor English skills? New AIs help researchers to write better
Machine-learning tools can correct grammar and advise on the style and tone of presentations — but they must be used with caution.
- Alla Katsnelson
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Article
| Open Access
Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape
A new phylogenomic method is developed that can detect recombinations in virus lineages in pandemic-scale datasets.
- Yatish Turakhia
- , Bryan Thornlow
- & Russell Corbett-Detig
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Article
| Open Access
Spatially resolved clonal copy number alterations in benign and malignant tissue
Copy number variations inferred from spatial transcriptomics data in benign and malignant tissue reveal clonal architecture at the organ-wide level.
- Andrew Erickson
- , Mengxiao He
- & Joakim Lundeberg
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Article |
Transcriptome variation in human tissues revealed by long-read sequencing
To understand the contribution of variants to transcript expression regulation, long-read transcriptome data are generated from the GTEx resource, and a new software package to perform allele-specific analysis is developed.
- Dafni A. Glinos
- , Garrett Garborcauskas
- & Beryl B. Cummings
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Technology Feature |
Six tips for better spreadsheets
Microsoft Excel and Google Sheets are powerful and widely used. But there’s a right way and a wrong way to use them, data scientists say.
- Jeffrey M. Perkel
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Technology Feature |
Ex-Google chief’s venture aims to save neglected science software
Schmidt Futures is creating the US$40-million Virtual Institute of Scientific Software to fund the maintenance of researcher-written code.
- David Matthews
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Technology Feature |
Need web data? Here’s how to harvest them
Webscraping is a useful tool for gathering data from public websites, but researchers must develop some fundamental software skills to use it.
- Michael Eisenstein
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Career Q&A |
Why science needs more research software engineers
Ten years after their profession got its name, research software engineers seek to swell their ranks.
- Chris Woolston
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Perspective |
Transitioning organizations to post-quantum cryptography
Standards and recommendations for transitioning organizations to quantum-secure cryptographic protocols are outlined, including a discussion of transition timelines and the leading strategies to protect systems against quantum attacks.
- David Joseph
- , Rafael Misoczki
- & Royal Hansen
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Technology Feature |
In pursuit of data immortality
Data sharing can save important scientific work from extinction, but only if researchers take care to ensure that resources are easy to find and reuse.
- Michael Eisenstein
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News Explainer |
Where is Russia’s cyberwar? Researchers decipher its strategy
Many analysts expected an unprecedented level of cyberattacks when Russia invaded Ukraine — which so far haven’t materialized.
- Elizabeth Gibney
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Technology Feature |
Cut the tyranny of copy-and-paste with these coding tools
‘Executable manuscripts’ insert results directly into documents, eliminating common mistakes.
- Jeffrey M. Perkel
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Technology Feature |
How to fix your scientific coding errors
Software bugs are frustrating. Adopting some simple strategies can help you to avoid them, and fix them when they occur.
- Jeffrey M. Perkel
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Technology Feature |
Terra takes the pain out of ‘omics’ computing in the cloud
The web-based tool allows scalable, user-friendly computation across multiple data sets
- Jeffrey M. Perkel
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News |
Journals adopt AI to spot duplicated images in manuscripts
A few publishers are using automated software to catch flaws in submitted papers.
- Richard Van Noorden
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Technology Feature |
How remouldable computer hardware is speeding up science
Field-programmable gate arrays can speed up applications ranging from genomic alignment to deep learning.
- Jeffrey M. Perkel
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Article |
Using DNA sequencing data to quantify T cell fraction and therapy response
A robust, cost-effective technique based on whole-exome sequencing data can be used to characterize immune infiltrates, relate the extent of these infiltrates to somatic changes in tumours, and enables prediction of tumour responses to immune checkpoint inhibition therapy.
- Robert Bentham
- , Kevin Litchfield
- & Nicholas McGranahan
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Technology Feature |
Drowning in the literature? These smart software tools can help
Search engines that highlight key papers are keeping scientists up to date.
- David Matthews
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News |
Autocorrect errors in Excel still creating genomics headache
Despite geneticists being warned about spreadsheet problems, 30% of published papers contain mangled gene names in supplementary data.
- Dyani Lewis
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Outlook |
Accelerating the diagnosis of epilepsy with computer modelling
The start-up Neuronostics is using the brain waves of large numbers of people to assess an individual’s risk of seizure disorders more quickly and accurately.
- Eric Bender
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Technology Feature |
Old-school computing: when your lab PC is ancient
Maintaining outdated PCs can be a matter of necessity — and a labour of love.
- Anna Nowogrodzki
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Technology Feature |
Reactive, reproducible, collaborative: computational notebooks evolve
A new breed of notebooks is taking data visualization and collaborative functionality to the next level, with spreadsheet simplicity.
- Jeffrey M. Perkel
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Technology Feature |
AI spots cell structures that humans can’t
Models can predict the location of cell structures from light-microscopy images alone, without the need for harmful fluorescence labelling.
- Amber Dance
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Technology Feature |
Five reasons why researchers should learn to love the command line
The text interface is intimidating, but can save researchers from mundane computing tasks. Just be sure you know what you’re doing.
- Jeffrey M. Perkel
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News Feature |
Ten computer codes that transformed science
From Fortran to arXiv.org, these advances in programming and platforms sent biology, climate science and physics into warp speed.
- Jeffrey M. Perkel
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Technology Feature |
Sharper signals: how machine learning is cleaning up microscopy images
Computers trained to reduce the noise in micrographs can now tackle fresh data by themselves.
- Amber Dance
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Technology Feature |
Why scientists are turning to Rust
Despite having a steep learning curve, the programming language offers speed and safety.
- Jeffrey M. Perkel
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News |
tl;dr: this AI sums up research papers in a sentence
Search engine’s tool for summarizing studies promises easier skim-reading.
- Jeffrey M. Perkel
- & Richard Van Noorden
AI’s keen diagnostic eye