Volume 21 Issue 11, November 2024

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fill="#666" fill-rule="evenodd" transform="matrix(0 -1 1 0 0 10)"/> </svg> </li><li class="c-breadcrumbs__item" id="breadcrumb4" itemprop="itemListElement" itemscope itemtype="https://schema.org/ListItem"> <span itemprop="name">issue 11</span><meta itemprop="position" content="5"></li> </ol> </div> </nav> </div> <div id="content"> <div class="u-container u-mb-32" data-component="article-container"> <main> <div class="u-display-flex u-align-items-center u-justify-content-space-between u-flex-wrap u-mb-16"> <h1 class="u-h2 u-mb-0 u-mr-8" data-container-type="title">Volume 21 Issue 11, November 2024</h1> <nav class="u-hide-print" data-track-component="issue navigation" aria-label="issue navigation" role="navigation"> <ul class="c-pagination app-pagination-borderless"> <li class="c-pagination__item"> <a href="/nmeth/volumes/21/issues/10" class="c-pagination__link" data-track="click" data-track-action="previous link" data-track-label="link"> <svg class="u-flex-static u-mr-8 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class="app-volumes-cover__copy" data-test="issue-description"> <div> <h2 class="u-h3">Microscopic art</h2> <p data-promo-text data-promo-text-threshold="560">An image of a section of small intestine from a mouse won fourth place in the Nikon Small World 2024 Photomicrography competition.</p> <p data-promo-text data-promo-text-threshold="560">See <a href="https://doi.org/10.1038/s41592-024-02531-z">Editorial</a></p> <p class="app-volumes-cover__image-copy-text" data-test="issue-image-credit" data-credit="Image: Amy Engevik, Medical University of South Carolina. Cover design: Thomas Phillips">Image: Amy Engevik, Medical University of South Carolina. Cover design: Thomas Phillips</p> </div> </div> <div class="app-volumes-cover__image"> <img src="https://media.springernature.com/w440/springer-static/cover-hires/journal/41592/21/11" alt="Volume 21 Issue 11" data-test="issue-cover-image"/> <p class="u-mt-16 u-mb-0"> <a href="/nmeth/subscribe" class="u-button u-button--primary u-button--full-width" data-test="issue-page-subscribe-button" data-track="click" data-track-action="subscribe" data-track-category="nature-issue-page" data-track-label="button">Subscribe</a> </p> </div> </div> <div class="l-with-sidebar__sidebar" style="--with-sidebar--basis: 385px;" data-test="issue-toc-container"> <aside class="u-full-height app-toc u-pa-16" aria-label="Issue navigation" class="hide-print"> <div data-container-type="issue-reading-companion"> <div class="clear cleared" data-component=reading-companion-placeholder> <div data-component=reading-companion-sticky> <nav id="toc"> <div data-component="reading-companion-sections"> <h1 class="app-toc__title">Table of Contents</h1> <ol class="u-list-reset u-mb-0" data-component="reading-companion-section-items"> <li class="app-toc__item" data-section="0"> <a href="#Editorial" data-id="Editorial" data-track="click" data-track-action="section anchor" data-track-category="reading companion" data-track-label="link:Editorial" class="u-display-block u-pt-8 u-pb-8">Editorial</a> </li> <li class="app-toc__item" data-section="1"> <a href="#ThisMonth" data-id="ThisMonth" data-track="click" data-track-action="section anchor" data-track-category="reading companion" data-track-label="link:This Month" class="u-display-block u-pt-8 u-pb-8">This Month</a> </li> <li class="app-toc__item" data-section="2"> <a href="#Correspondence" data-id="Correspondence" data-track="click" data-track-action="section anchor" data-track-category="reading companion" data-track-label="link:Correspondence" class="u-display-block u-pt-8 u-pb-8">Correspondence</a> </li> <li class="app-toc__item" data-section="3"> <a href="#ResearchHighlights" data-id="ResearchHighlights" data-track="click" data-track-action="section anchor" data-track-category="reading companion" data-track-label="link:Research Highlights" class="u-display-block u-pt-8 u-pb-8">Research Highlights</a> </li> <li class="app-toc__item" data-section="4"> <a href="#TechnologyFeature" data-id="TechnologyFeature" data-track="click" data-track-action="section anchor" data-track-category="reading companion" data-track-label="link:Technology Feature" class="u-display-block u-pt-8 u-pb-8">Technology Feature</a> </li> <li class="app-toc__item" data-section="5"> <a href="#NewsandViews" data-id="NewsandViews" data-track="click" data-track-action="section anchor" data-track-category="reading companion" data-track-label="link:News & Views" class="u-display-block u-pt-8 u-pb-8">News & Views</a> </li> <li class="app-toc__item" data-section="6"> <a href="#ResearchBriefings" data-id="ResearchBriefings" data-track="click" data-track-action="section anchor" data-track-category="reading companion" data-track-label="link:Research Briefings" class="u-display-block u-pt-8 u-pb-8">Research Briefings</a> </li> <li class="app-toc__item" data-section="7"> <a href="#ReviewArticles" data-id="ReviewArticles" data-track="click" data-track-action="section anchor" data-track-category="reading companion" data-track-label="link:Review Articles" class="u-display-block u-pt-8 u-pb-8">Review Articles</a> </li> <li class="app-toc__item" data-section="8"> <a href="#BriefCommunications" data-id="BriefCommunications" data-track="click" data-track-action="section anchor" data-track-category="reading companion" data-track-label="link:Brief Communications" class="u-display-block u-pt-8 u-pb-8">Brief Communications</a> </li> <li class="app-toc__item" data-section="9"> <a href="#Articles" data-id="Articles" data-track="click" data-track-action="section anchor" data-track-category="reading companion" data-track-label="link:Articles" class="u-display-block u-pt-8 u-pb-8">Articles</a> </li> <li class="app-toc__item" data-section="10"> <a href="#Analysis" data-id="Analysis" data-track="click" data-track-action="section anchor" data-track-category="reading companion" data-track-label="link:Analysis" class="u-display-block u-pt-8 u-pb-8">Analysis</a> </li> </ol> </div> </nav> </div> </div> </div> </aside> </div> </div> <div data-track-component="issue section list"> <section id="Editorial" aria-labelledby="Editorial" class="u-mb-48 u-mt-48" data-container-type=issue-section-list data-track-component="issue section list"> <div class="c-section-heading" data-test="title"> <h2>Editorial</h2> </div> <ul class="app-article-list-row"> <li class="app-article-list-row__item" data-test="issue-page-article-0-0"> <div class="u-full-height"> <div class="app-article-list-row__mpu"> <article class="u-full-height c-card c-card--flush c-card--major" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02531-z" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Microscopic art</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>With a pictorial Editorial this month, we celebrate the beauty of microscopy images.</p> </div> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Editorial</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-11-07" itemprop="datePublished">07 Nov 2024</time> </div> </article> <div class="c-ad c-ad--300x250" data-test="issue-page-mpu-ad"> <div class="c-ad__inner"> <div id="div-gpt-ad-right-2" class="div-gpt-ad medium-rectangle c-ad c-ad--300x250 advert js-ad hide-print grade-c-hide" data-ad-type="right" data-test="right-ad" data-pa11y-ignore data-gpt data-gpt-unitpath="/285/nmeth.nature.com/issue" data-gpt-sizes="300x250" data-gpt-targeting="pos=right;artid=/nmeth/volumes/21/issues/11;path=/nmeth/volumes/21/issues/11" > <noscript> <a href="//pubads.g.doubleclick.net/gampad/jump?iu=/285/nmeth.nature.com/issue&sz=300x250&c=-1263711401&t=pos%3Dright%26artid%3D/nmeth/volumes/21/issues/11"> <img data-test="gpt-advert-fallback-img" src="//pubads.g.doubleclick.net/gampad/ad?iu=/285/nmeth.nature.com/issue&sz=300x250&c=-1263711401&t=pos%3Dright%26artid%3D/nmeth/volumes/21/issues/11" alt="Advertisement" width="300" height="250"/> </a> </noscript> </div> <p class="c-ad__label u-mb-0 u-mt-8">Advertisement</p> </div> </div> </div> </div> </li> </ul> <a href="#toc">Top of page ⤴</a></section> <section id="ThisMonth" aria-labelledby="ThisMonth" class="u-mb-48 u-mt-48" data-container-type=issue-section-list data-track-component="issue section list"> <div class="c-section-heading" data-test="title"> <h2>This Month</h2> </div> <ul class="app-article-list-row"> <li class="app-article-list-row__item" data-test="issue-page-article-1-0"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02490-5" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Scientists who marry scientists</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>When spouses are both scientists, they mix the typical research career decisions with some marriage-related ones.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Vivien Marx</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">This Month</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-15" itemprop="datePublished">15 Oct 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-1-1"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02485-2" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">The bearded dragon <i>Pogona vitticeps</i></a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>The Australian bearded dragon is so called for its distinctive ‘beard’ of spiky scales that can darken and expand during social and defensive displays. This lizard has become a reptilian model system to study the evolution, function and dynamics of neurons and neural circuits (including during sleep) in the amniote brain.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Lorenz A. Fenk</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Felix Baier</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Gilles Laurent</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">This Month</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-11-07" itemprop="datePublished">07 Nov 2024</time> </div> </article> </div> </li> </ul> <div class="u-hide" data-has-native="true"></div><a href="#toc">Top of page ⤴</a></section> <section id="Correspondence" aria-labelledby="Correspondence" class="u-mb-48 u-mt-48" data-container-type=issue-section-list data-track-component="issue section list"> <div class="c-section-heading" data-test="title"> <h2>Correspondence</h2> </div> <ul class="app-article-list-row"> <li class="app-article-list-row__item" data-test="issue-page-article-2-0"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02413-4" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Navigate: an open-source platform for smart light-sheet microscopy</a> </h3> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Zach Marin</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Xiaoding Wang</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Kevin M. Dean</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Correspondence</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-09-11" itemprop="datePublished">11 Sept 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-2-1"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02428-x" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Making fluorescence-based integrative structures and associated kinetic information accessible</a> </h3> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Christian A. Hanke</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">John D. Westbrook</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Brinda Vallat</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Correspondence</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-09-30" itemprop="datePublished">30 Sept 2024</time> </div> </article> </div> </li> </ul> <a href="#toc">Top of page ⤴</a></section> <section id="ResearchHighlights" aria-labelledby="ResearchHighlights" class="u-mb-48 u-mt-48" data-container-type=issue-section-list data-track-component="issue section list"> <div class="c-section-heading" data-test="title"> <h2>Research Highlights</h2> </div> <ul class="app-article-list-row"> <li class="app-article-list-row__item" data-test="issue-page-article-3-0"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02508-y" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">A leap for mesoscale imaging</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>A computational mesoscale microscope offers large-scale volumetric imaging of intravital dynamics with cellular resolution.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Rita Strack</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Research Highlight</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-11-07" itemprop="datePublished">07 Nov 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-3-1"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02509-x" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Multi-pass nanopore for single-molecule protein sequencing</a> </h3> <ul data-test="author-list" class="c-author-list c-author-list--compact u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Arunima Singh</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Research Highlight</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-11-07" itemprop="datePublished">07 Nov 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-3-2"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02510-4" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Fallopian tube assembloids</a> </h3> <ul data-test="author-list" class="c-author-list c-author-list--compact u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Madhura Mukhopadhyay</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Research Highlight</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-11-07" itemprop="datePublished">07 Nov 2024</time> </div> </article> </div> </li> </ul> <a href="#toc">Top of page ⤴</a></section> <section id="TechnologyFeature" aria-labelledby="TechnologyFeature" class="u-mb-48 u-mt-48" data-container-type=issue-section-list data-track-component="issue section list"> <div class="c-section-heading" data-test="title"> <h2>Technology Feature</h2> </div> <ul class="app-article-list-row"> <li class="app-article-list-row__item" data-test="issue-page-article-4-0"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02489-y" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Pushing the limits of MRI brain imaging</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>A new generation of increasingly powerful magnets is dramatically extending the resolution, speed and analytical capabilities of magnetic resonance imaging for brain research.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Michael Eisenstein</span></li> </ul> <div> <p class="u-mr-8 u-display-inline">Collection: </p> <ul class="u-list-reset u-display-inline"> <li class="c-pill"> <a href="/collections/fxvqrpnlcq" data-track="click" data-track-action="view collection" data-track-label="link">NatureTech</a> </li> </ul> </div> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Technology Feature</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-11-07" itemprop="datePublished">07 Nov 2024</time> </div> </article> </div> </li> </ul> <div class="u-hide" data-has-native="true"></div><a href="#toc">Top of page ⤴</a></section> <section id="NewsandViews" aria-labelledby="NewsandViews" class="u-mb-48 u-mt-48" data-container-type=issue-section-list data-track-component="issue section list"> <div class="c-section-heading" data-test="title"> <h2>News & Views</h2> </div> <ul class="app-article-list-row"> <li class="app-article-list-row__item" data-test="issue-page-article-5-0"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02402-7" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Constructing and personalizing population pangenome graphs</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>Pangenome graphs signify a new frontier in genome representation. Recent advances in constructing and personalizing them mark progress in this area.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Rayan Chikhi</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Yoann Dufresne</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Paul Medvedev</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">News & Views</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-21" itemprop="datePublished">21 Oct 2024</time> </div> </article> </div> </li> </ul> <a href="#toc">Top of page ⤴</a></section> <section id="ResearchBriefings" aria-labelledby="ResearchBriefings" class="u-mb-48 u-mt-48" data-container-type=issue-section-list data-track-component="issue section list"> <div class="c-section-heading" data-test="title"> <h2>Research Briefings</h2> </div> <ul class="app-article-list-row"> <li class="app-article-list-row__item" data-test="issue-page-article-6-0"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02473-6" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Ultra-high-field MRI for fast imaging of the human brain at mesoscale resolution</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>Very high-resolution images of the human brain obtained in vivo in a few minutes with MRI at an ultra-high magnetic field of 11.7 T reveal exquisite details. Biological and behavioral tests confirm the safety of the method, opening the door for human brain exploration at mesoscale resolution.</p> </div> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Research Briefing</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-17" itemprop="datePublished">17 Oct 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-6-1"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02466-5" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">A method for quantitative and base-resolution sequencing of pseudouridine</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>Quantitative and sensitive methods for the detection of pseudouridine (Ψ) have been lacking. Now, a method termed 2-bromoacrylamide-assisted cyclization sequencing (BACS) has been developed that enables the accurate quantification of Ψ stoichiometry, precise identification of Ψ positions and robust detection of densely modified Ψ sites.</p> </div> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Research Briefing</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-09-30" itemprop="datePublished">30 Sept 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-6-2"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02460-x" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Expanding the genome editing toolbox with designer CRISPR–Cas-like transposons</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>Similarly to CRISPR–Cas systems, TnpB proteins from bacterial transposons can be employed as RNA-guided endonucleases for genome editing. By combining rational protein design and machine learning, ISDra2 TnpB variants with enhanced editing efficiency and a broader targeting range were developed, along with a prediction tool to design effective guiding RNAs.</p> </div> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Research Briefing</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-09-23" itemprop="datePublished">23 Sept 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-6-3"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02461-w" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Measuring multiple intracellular biochemical properties of proteins with next-generation sequencing</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>We developed LABEL-seq, a platform that enables measurement of protein properties and functions at scale by leveraging the intracellular self-assembly of an RNA-binding domain (RBD) and protein-encoding RNA barcode. Enrichment of RBD–protein fusions, followed by high-throughput sequencing of the co-enriched barcodes, enables the profiling of protein abundance, activity, interactions and druggability at scale.</p> </div> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Research Briefing</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-21" itemprop="datePublished">21 Oct 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-6-4"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02465-6" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">SCUBA-D: a freshly trained diffusion model generates high-quality protein structures</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>The accuracy of SCUBA-D, a protein backbone structure diffusion model trained independently and orthogonally to existing protein structure prediction networks, is confirmed by the X-ray structures of 16 designed proteins and a protein complex, and by experimental validation of designed heme-binding proteins and Ras-binding proteins.</p> </div> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Research Briefing</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-28" itemprop="datePublished">28 Oct 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-6-5"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02459-4" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Mapping voltage activity in a live mouse brain in 3D using confocal light field microscopy</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>Voltage imaging, a promising technique for directly recording neuronal activity, faces barriers to broad application due to current limitations in compatible imaging modalities. Our team introduces an advanced confocal light field microscopy method enabling high-throughput, rapid and low-noise 3D voltage imaging in awake mice.</p> </div> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Research Briefing</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-08" itemprop="datePublished">08 Oct 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-6-6"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02435-y" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Exoskeleton empowers large-scale neural recordings in freely roaming mice</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>A robotic neural recording system can sense the intended motion of the mouse that it is connected to, and it moves with the animal as it explores physical spaces. The robot can support recording interfaces that are much heavier and larger than mice and provide new capabilities for brain-wide recordings in locomoting mice.</p> </div> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Research Briefing</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-07" itemprop="datePublished">07 Oct 2024</time> </div> </article> </div> </li> </ul> <a href="#toc">Top of page ⤴</a></section> <section id="ReviewArticles" aria-labelledby="ReviewArticles" class="u-mb-48 u-mt-48" data-container-type=issue-section-list data-track-component="issue section list"> <div class="c-section-heading" data-test="title"> <h2>Review Articles</h2> </div> <ul class="app-article-list-row"> <li class="app-article-list-row__item" data-test="issue-page-article-7-0"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02396-2" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Controlling the sound of light: photoswitching optoacoustic imaging</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>This Review describes how photoswitchable probes and associated hardware innovations are poised to transform optoacoustic imaging in life sciences research.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Andre C. Stiel</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Vasilis Ntziachristos</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Review Article</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-09-25" itemprop="datePublished">25 Sept 2024</time> </div> </article> </div> </li> </ul> <a href="#toc">Top of page ⤴</a></section> <section id="BriefCommunications" aria-labelledby="BriefCommunications" class="u-mb-48 u-mt-48" data-container-type=issue-section-list data-track-component="issue section list"> <div class="c-section-heading" data-test="title"> <h2>Brief Communications</h2> </div> <ul class="app-article-list-row"> <li class="app-article-list-row__item" data-test="issue-page-article-8-0"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02430-3" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Building pangenome graphs</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>PGGB is a modular framework for efficiently building unbiased pangenome graphs, supporting diverse downstream analyses.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Erik Garrison</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Andrea Guarracino</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Pjotr Prins</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Brief Communication</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-21" itemprop="datePublished">21 Oct 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-8-1"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02472-7" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">In vivo imaging of the human brain with the Iseult 11.7-T MRI scanner</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>In a technological tour de force, a whole-body 11.7-T MRI scanner has been developed. Here images of the human brain are presented while safety for the imaged human volunteers has been ascertained.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Nicolas Boulant</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Franck Mauconduit</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Denis Le Bihan</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Brief Communication</span> </span> <span class="c-meta__item c-meta__item--block-at-lg" itemprop="openAccess" data-test="open-access"><span class="u-color-open-access">Open Access</span></span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-17" itemprop="datePublished">17 Oct 2024</time> </div> </article> </div> </li> </ul> <a href="#toc">Top of page ⤴</a></section> <section id="Articles" aria-labelledby="Articles" class="u-mb-48 u-mt-48" data-container-type=issue-section-list data-track-component="issue section list"> <div class="c-section-heading" data-test="title"> <h2>Articles</h2> </div> <ul class="app-article-list-row"> <li class="app-article-list-row__item" data-test="issue-page-article-9-0"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02407-2" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Personalized pangenome references</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>This work introduces a <i>k</i>-mer-based approach to customizing a pangenome reference, making it more relevant to a new sample of interest. This method enhances the accuracy of genotyping small variants and large structural variants.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Jouni Sirén</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Parsa Eskandar</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Benedict Paten</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Article</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-09-11" itemprop="datePublished">11 Sept 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-9-1"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02439-8" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Absolute quantitative and base-resolution sequencing reveals comprehensive landscape of pseudouridine across the human transcriptome</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>This study introduces a chemical method, BACS, that generates Ψ-to-C mutation signatures, allowing for sequencing and quantification of Ψ at single-base resolution.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Haiqi Xu</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Linzhen Kong</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Chun-Xiao Song</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Article</span> </span> <span class="c-meta__item c-meta__item--block-at-lg" itemprop="openAccess" data-test="open-access"><span class="u-color-open-access">Open Access</span></span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-09-30" itemprop="datePublished">30 Sept 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-9-2"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02424-1" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>This work presents Strainy, a long-read metagenome assembler that allows the identification of strain distributions and mutational patterns in environmental metagenomes.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Ekaterina Kazantseva</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Ataberk Donmez</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Mikhail Kolmogorov</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Article</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-09-26" itemprop="datePublished">26 Sept 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-9-3"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02453-w" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">scNanoSeq-CUT&Tag: a single-cell long-read CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>This work presents scNanoSeq-CUT&Tag, using long-read sequencing to profile histone modifications and DNA-binding proteins at the single-cell level.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Qingqing Li</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Yuqing Guo</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Fuchou Tang</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Article</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-07" itemprop="datePublished">07 Oct 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-9-4"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02457-6" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Multiomic characterization of RNA microenvironments by oligonucleotide-mediated proximity-interactome mapping</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>Oligonucleotide-mediated proximity-interactome MAPping (O-MAP) enables precise multiomic characterization of biomolecular interaction networks at target RNAs. Distinct O-MAP workflows reveal RNA-adjacent proteins, transcripts and genomic loci.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Ashley F. Tsue</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Evan E. Kania</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">David M. Shechner</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Article</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-28" itemprop="datePublished">28 Oct 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-9-5"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02463-8" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Interpretable spatially aware dimension reduction of spatial transcriptomics with STAMP</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>Spatial Transcriptomics Analysis with topic Modeling to uncover spatial Patterns (STAMP) is a versatile and scalable method for dimension reduction in spatially resolved transcriptomics that enables discovery of biologically relevant tissue domains.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Chengwei Zhong</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Kok Siong Ang</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Jinmiao Chen</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Article</span> </span> <span class="c-meta__item c-meta__item--block-at-lg" itemprop="openAccess" data-test="open-access"><span class="u-color-open-access">Open Access</span></span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-15" itemprop="datePublished">15 Oct 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-9-6"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02418-z" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Effective genome editing with an enhanced ISDra2 TnpB system and deep learning-predicted ωRNAs</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>This work introduces engineered TnpBmax proteins with enhanced efficiency and an expanded targeting range. By leveraging an extensive dataset on editing efficiencies, it also integrates a deep learning model to predict guide RNA activity.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Kim Fabiano Marquart</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Nicolas Mathis</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Gerald Schwank</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Article</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-09-23" itemprop="datePublished">23 Sept 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-9-7"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02456-7" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Multiplexed profiling of intracellular protein abundance, activity, interactions and druggability with LABEL-seq</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>Labeling with barcodes and enrichment for biochemical analysis by sequencing (LABEL-seq) enables massively parallel profiling of thousands of pooled protein variants in cells, yielding insight into protein function, interactions and druggability.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Jessica J. Simon</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Douglas M. Fowler</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Dustin J. Maly</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Article</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-21" itemprop="datePublished">21 Oct 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-9-8"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02437-w" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">De novo protein design with a denoising diffusion network independent of pretrained structure prediction models</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>SCUBA-D is a denoising diffusion probabilistic model that can perform a variety of protein backbone design tasks, including generation of backbones from random noise, from user-sketched designs, and backbones to scaffold predefined motifs that can bind small molecules or other proteins.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Yufeng Liu</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Sheng Wang</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Haiyan Liu</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Article</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-09" itemprop="datePublished">09 Oct 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-9-9"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02464-7" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Restoring protein glycosylation with GlycoShape</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>GlycoShape is an open-access web-based platform designed to supplement three-dimensional glycoprotein structures with missing structural information on glycans. To link them, the Re-Glyco algorithm evaluates the steric complementarity of glycans using their conformational ensemble with the protein surface.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Callum M. Ives</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Ojas Singh</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Elisa Fadda</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Article</span> </span> <span class="c-meta__item c-meta__item--block-at-lg" itemprop="openAccess" data-test="open-access"><span class="u-color-open-access">Open Access</span></span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-14" itemprop="datePublished">14 Oct 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-9-10"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02454-9" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Single-shot 20-fold expansion microscopy</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>20ExM achieves isotropic ~20× expansion of cells and tissues in a single shot for super-resolution imaging with <20-nm resolution on a conventional microscope.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Shiwei Wang</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Tay Won Shin</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Edward S. Boyden</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Article</span> </span> <span class="c-meta__item c-meta__item--block-at-lg" itemprop="openAccess" data-test="open-access"><span class="u-color-open-access">Open Access</span></span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-11" itemprop="datePublished">11 Oct 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-9-11"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02455-8" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>A protocol for differentiating visceral sensory ganglion organoids from induced pluripotent stem cells allows the establishment of an in vitro model for the gut–visceral nerve–brain axis and study of the propagation of pathogenic proteins involved in Alzheimer’s disease along the vagus nerve.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Kyusik Ahn</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Hwee-Seon Park</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Inhee Mook-Jung</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Article</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-22" itemprop="datePublished">22 Oct 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-9-12"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02412-5" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">A polarized FGF8 source specifies frontotemporal signatures in spatially oriented cell populations of cortical assembloids</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>Cortical development is influenced by morphogen gradients. To mimic patterning events during brain development, polarized cortical assembloids are generated with the help of a localized FGF8 source.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Camilla Bosone</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Davide Castaldi</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Jürgen Arthur Knoblich</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Article</span> </span> <span class="c-meta__item c-meta__item--block-at-lg" itemprop="openAccess" data-test="open-access"><span class="u-color-open-access">Open Access</span></span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-09-18" itemprop="datePublished">18 Sept 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-9-13"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02458-5" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Volumetric voltage imaging of neuronal populations in the mouse brain by confocal light-field microscopy</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>Confocal light-field microscopy allows volumetric voltage imaging in the mouse brain at speeds sufficiently high to extract the spiking activity of hundreds of neurons.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Lu Bai</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Lin Cong</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Kai Wang</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Article</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-08" itemprop="datePublished">08 Oct 2024</time> </div> </article> </div> </li> <li class="app-article-list-row__item" data-test="issue-page-article-9-14"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02434-z" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Brain-wide neural recordings in mice navigating physical spaces enabled by robotic neural recording headstages</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>To avoid head fixation or drawbacks of miniaturized devices for freely moving rodents, a robotic device can move a headstage for microscopy or electrophysiology with the animal, thereby enabling naturalistic behavior.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">James Hope</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Travis M. Beckerle</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Suhasa B. Kodandaramaiah</span></li> </ul> </div> </div> <div class="c-meta "> <span class="c-meta__item c-meta__item--block-at-lg" > <span class="c-meta__type">Article</span> </span> <time class="c-meta__item c-meta__item--block-at-lg" datetime="2024-10-07" itemprop="datePublished">07 Oct 2024</time> </div> </article> </div> </li> </ul> <a href="#toc">Top of page ⤴</a></section> <section id="Analysis" aria-labelledby="Analysis" class="u-mb-48 u-mt-48" data-container-type=issue-section-list data-track-component="issue section list"> <div class="c-section-heading" data-test="title"> <h2>Analysis</h2> </div> <ul class="app-article-list-row"> <li class="app-article-list-row__item" data-test="issue-page-article-10-0"> <div class="u-full-height"> <article class="u-full-height c-card c-card--flush" itemscope itemtype="http://schema.org/ScholarlyArticle"> <div class="c-card__layout u-full-height"> <div class="c-card__body u-display-flex u-flex-direction-column"> <h3 class="c-card__title" itemprop="name headline"> <a href="/articles/s41592-024-02429-w" class="u-link-inherit" itemprop="url" data-track="click" data-track-action="view article" data-track-label="link">Benchmarking algorithms for single-cell multi-omics prediction and integration</a> </h3> <div class="c-card__summary u-mb-16 u-hide-sm-max" itemprop="description"> <p>This Analysis study compares computational methods for single-cell multi-omics prediction and integration, generating useful insights for method users and developers working with different analysis purposes and biological problems.</p> </div> <ul data-test="author-list" class="c-author-list c-author-list--compact c-author-list--truncated u-mb-16"> <li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Yinlei Hu</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span itemprop="name">Siyuan Wan</span></li><li itemprop="creator" itemscope="" itemtype="http://schema.org/Person"><span 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Volume 21 Issue 11, November 2024