Table of Contents — November 2024, 34 (11)

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class="cit-first-element cit-title-group">Revolutionizing genomics and medicine—one long molecule at a time </h4> <ul class="cit-auth-list"> <li class="first-item">Ana Conesa, </li> <li>Alexander Hoischen, </li> <li class="last-item">and Fritz J. Sedlazeck</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: ix-xi; doi:10.1101/gr.280179.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/ix.extract" rel="extract">Extract</a></li> <li><a href="/content/34/11/ix.full" rel="full-text">Full Text</a></li> <li class="last-item"><a href="/content/34/11/ix.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> </ul> </div> </li> </ul> </div> <div class="gca-buttons"> <input type="reset" name="reset" value="Clear" /> <input type="submit" name="submit" value="Get All Checked Abstracts" /> </div> <div class="toc-level level1 pub-section-Reviews no-children no-parent"> <h2 id="Reviews"><a class="toc-section-return" href="#content-block"></a>Reviews</h2> <ul class="cit-list"> <li class="cit openaccess creative-commons creative-commons-by-nc/4.0/ from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1701" /><label for="gca-form-cb-d485550e124Reviews">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Leveraging the power of long reads for targeted sequencing </h4> <ul class="cit-auth-list"> <li class="first-item">Shruti V. Iyer, </li> <li>Sara Goodwin, </li> <li class="last-item">and William Richard McCombie</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1701-1718; doi:10.1101/gr.279168.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1701.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1701.full" rel="full-text">Full Text</a></li> <li class="last-item"><a href="/content/34/11/1701.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> </ul> OPEN ACCESS ARTICLE </div> </li> <li class="cit openaccess creative-commons creative-commons-by/4.0/ from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1719" /><label for="gca-form-cb-d485550e125Reviews">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Challenges in identifying mRNA transcript starts and ends from long-read sequencing data </h4> <ul class="cit-auth-list"> <li class="first-item">Ezequiel Calvo-Roitberg, </li> <li>Rachel F. Daniels, </li> <li class="last-item">and Athma A. Pai</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1719-1734; doi:10.1101/gr.279559.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1719.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1719.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1719.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1719/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> OPEN ACCESS ARTICLE </div> </li> <li class="cit openaccess creative-commons creative-commons-by-nc/4.0/ from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1735" /><label for="gca-form-cb-d485550e126Reviews">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics </h4> <ul class="cit-auth-list"> <li class="first-item">Natan Belchikov, </li> <li>Justine Hsu, </li> <li>Xiang Jennie Li, </li> <li>Julien Jarroux, </li> <li>Wen Hu, </li> <li>Anoushka Joglekar, </li> <li class="last-item">and Hagen U. Tilgner</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1735-1746; doi:10.1101/gr.279640.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1735.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1735.full" rel="full-text">Full Text</a></li> <li class="last-item"><a href="/content/34/11/1735.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> </ul> OPEN ACCESS ARTICLE </div> </li> </ul> </div> <div class="gca-buttons"> <input type="reset" name="reset" value="Clear" /> <input type="submit" name="submit" value="Get All Checked Abstracts" /> </div> <div class="toc-level level1 pub-section-Research no-children no-parent"> <h2 id="Research"><a class="toc-section-return" href="#content-block"></a>Research</h2> <ul class="cit-list"> <li class="cit creative-commons creative-commons-by-nc/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1747" /><label for="gca-form-cb-d485550e135Research">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders </h4> <ul class="cit-auth-list"> <li class="first-item">Susan M. Hiatt, </li> <li>James M.J. Lawlor, </li> <li>Lori H. Handley, </li> <li>Donald R. Latner, </li> <li>Zachary T. Bonnstetter, </li> <li>Candice R. Finnila, </li> <li>Michelle L. Thompson, </li> <li>Lori Beth Boston, </li> <li>Melissa Williams, </li> <li>Ivan Rodriguez Nunez, </li> <li>Jerry Jenkins, </li> <li>Whitley V. Kelley, </li> <li>E. Martina Bebin, </li> <li>Michael A. Lopez, </li> <li>Anna C.E. Hurst, </li> <li>Bruce R. Korf, </li> <li>Jeremy Schmutz, </li> <li>Jane Grimwood, </li> <li class="last-item">and Gregory M. Cooper</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1747-1762; Published in Advance September 19, 2024, doi:10.1101/gr.279227.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1747.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1747.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1747.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1747/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> </div> </li> <li class="cit openaccess creative-commons creative-commons-by-nc/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1763" /><label for="gca-form-cb-d485550e136Research">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing </h4> <ul class="cit-auth-list"> <li class="first-item">Jesper Eisfeldt, </li> <li>Edward J. Higginbotham, </li> <li>Felix Lenner, </li> <li>Jennifer Howe, </li> <li>Bridget A. Fernandez, </li> <li>Anna Lindstrand, </li> <li>Stephen W. Scherer, </li> <li class="last-item">and Lars Feuk</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1763-1773; Published in Advance October 29, 2024, doi:10.1101/gr.279263.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1763.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1763.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1763.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1763/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> OPEN ACCESS ARTICLE </div> </li> <li class="cit openaccess creative-commons creative-commons-by/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1774" /><label for="gca-form-cb-d485550e137Research">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities </h4> <ul class="cit-auth-list"> <li class="first-item">Jesper Eisfeldt, </li> <li>Adam Ameur, </li> <li>Felix Lenner, </li> <li>Esmee Ten Berk de Boer, </li> <li>Marlene Ek, </li> <li>Josephine Wincent, </li> <li>Raquel Vaz, </li> <li>Jesper Ottosson, </li> <li>Tord Jonson, </li> <li>Sofie Ivarsson, </li> <li>Sofia Thunström, </li> <li>Alexandra Topa, </li> <li>Simon Stenberg, </li> <li>Anna Rohlin, </li> <li>Anna Sandestig, </li> <li>Margareta Nordling, </li> <li>Pia Palmebäck, </li> <li>Magnus Burstedt, </li> <li>Frida Nordin, </li> <li>Eva-Lena Stattin, </li> <li>Maria Sobol, </li> <li>Panagiotis Baliakas, </li> <li>Marie-Louise Bondeson, </li> <li>Ida Höijer, </li> <li>Kristine Bilgrav Saether, </li> <li>Lovisa Lovmar, </li> <li>Hans Ehrencrona, </li> <li>Malin Melin, </li> <li>Lars Feuk, </li> <li class="last-item">and Anna Lindstrand</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1774-1784; Published in Advance October 29, 2024, doi:10.1101/gr.279510.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1774.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1774.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1774.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1774/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> OPEN ACCESS ARTICLE </div> </li> <li class="cit openaccess creative-commons creative-commons-by/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1785" /><label for="gca-form-cb-d485550e138Research">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps </h4> <ul class="cit-auth-list"> <li class="first-item">Kristine Bilgrav Saether, </li> <li>Jesper Eisfeldt, </li> <li>Jesse D. Bengtsson, </li> <li>Ming Yin Lun, </li> <li>Christopher M. Grochowski, </li> <li>Medhat Mahmoud, </li> <li>Hsiao-Tuan Chao, </li> <li>Jill A. Rosenfeld, </li> <li>Pengfei Liu, </li> <li>Marlene Ek, </li> <li>Jakob Schuy, </li> <li>Adam Ameur, </li> <li>Hongzheng Dai, </li> <li>Undiagnosed Diseases Network, </li> <li>James Paul Hwang, </li> <li>Fritz J. Sedlazeck, </li> <li>Weimin Bi, </li> <li>Ronit Marom, </li> <li>Josephine Wincent, </li> <li>Ann Nordgren, </li> <li>Claudia M.B. Carvalho, </li> <li class="last-item">and Anna Lindstrand</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1785-1797; Published in Advance November 1, 2024, doi:10.1101/gr.279346.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1785.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1785.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1785.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1785/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> OPEN ACCESS ARTICLE </div> </li> <li class="cit openaccess creative-commons creative-commons-by/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1798" /><label for="gca-form-cb-d485550e139Research">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans </h4> <ul class="cit-auth-list"> <li class="first-item">Xavi Guitart, </li> <li>David Porubsky, </li> <li>DongAhn Yoo, </li> <li>Max L. Dougherty, </li> <li>Philip C. Dishuck, </li> <li>Katherine M. Munson, </li> <li>Alexandra P. Lewis, </li> <li>Kendra Hoekzema, </li> <li>Jordan Knuth, </li> <li>Stephen Chang, </li> <li>Tomi Pastinen, </li> <li class="last-item">and Evan E. Eichler</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1798-1810; Published in Advance August 6, 2024, doi:10.1101/gr.279299.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1798.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1798.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1798.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1798/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> OPEN ACCESS ARTICLE </div> </li> <li class="cit openaccess creative-commons creative-commons-by/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1811" /><label for="gca-form-cb-d485550e140Research">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques </h4> <ul class="cit-auth-list"> <li class="first-item">Nanine de Groot, </li> <li>Marit van der Wiel, </li> <li>Ngoc Giang Le, </li> <li>Natasja G. de Groot, </li> <li>Jesse Bruijnesteijn, </li> <li class="last-item">and Ronald E. Bontrop</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1811-1824; Published in Advance October 23, 2024, doi:10.1101/gr.278968.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1811.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1811.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1811.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1811/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> OPEN ACCESS ARTICLE </div> </li> <li class="cit creative-commons creative-commons-by-nc/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1825" /><label for="gca-form-cb-d485550e141Research">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes </h4> <ul class="cit-auth-list"> <li class="first-item">Suleyman Gulsuner, </li> <li>Amal AbuRayyan, </li> <li>Jessica B. Mandell, </li> <li>Ming K. Lee, </li> <li>Greta V. Bernier, </li> <li>Barbara M. Norquist, </li> <li>Sarah B. 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Vasudev, </li> <li class="last-item">and Dimitris Lagos</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1849-1864; Published in Advance September 16, 2024, doi:10.1101/gr.278801.123 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1849.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1849.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1849.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1849/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> OPEN ACCESS ARTICLE </div> </li> <li class="cit creative-commons creative-commons-by-nc/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1865" /><label for="gca-form-cb-d485550e144Research">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models </h4> <ul class="cit-auth-list"> <li class="first-item">Gregor Diensthuber, </li> <li>Leszek P. Pryszcz, </li> <li>Laia Llovera, </li> <li>Morghan C. Lucas, </li> <li>Anna Delgado-Tejedor, </li> <li>Sonia Cruciani, </li> <li>Jean-Yves Roignant, </li> <li>Oguzhan Begik, </li> <li class="last-item">and Eva Maria Novoa</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1865-1877; Published in Advance September 13, 2024, doi:10.1101/gr.278849.123 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1865.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1865.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1865.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1865/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> </div> </li> <li class="cit openaccess creative-commons creative-commons-by-nc/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1878" /><label for="gca-form-cb-d485550e145Research">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events </h4> <ul class="cit-auth-list"> <li class="first-item">Marin Volarić, </li> <li>Evelin Despot-Slade, </li> <li>Damira Veseljak, </li> <li>Brankica Mravinac, </li> <li class="last-item">and Nevenka Meštrović</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1878.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1878.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1878.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1878/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> OPEN ACCESS ARTICLE </div> </li> <li class="cit openaccess creative-commons creative-commons-by/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1895" /><label for="gca-form-cb-d485550e147Research">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of blaKPC </h4> <ul class="cit-auth-list"> <li class="first-item">Angela Gomez-Simmonds, </li> <li>Medini K. 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Hokunson, </li> <li>Heekuk Park, </li> <li class="last-item">and Anne-Catrin Uhlemann</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1895-1907; Published in Advance October 4, 2024, doi:10.1101/gr.279355.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1895.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1895.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1895.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1895/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> OPEN ACCESS ARTICLE </div> </li> </ul> </div> <div class="gca-buttons"> <input type="reset" name="reset" value="Clear" /> <input type="submit" name="submit" value="Get All Checked Abstracts" /> </div> <div class="toc-level level1 pub-section-Methods no-children no-parent"> <h2 id="Methods"><a class="toc-section-return" href="#content-block"></a>Methods</h2> <ul class="cit-list"> <li class="cit creative-commons creative-commons-by-nc/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1908" /><label for="gca-form-cb-d485550e156Methods">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Telomere-to-telomere assembly by preserving contained reads </h4> <ul class="cit-auth-list"> <li class="first-item">Sudhanva Shyam Kamath, </li> <li>Mehak Bindra, </li> <li>Debnath Pal, </li> <li class="last-item">and Chirag Jain</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1908-1918; Published in Advance October 15, 2024, doi:10.1101/gr.279311.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1908.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1908.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1908.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1908/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> </div> </li> <li class="cit creative-commons creative-commons-by-nc/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1919" /><label for="gca-form-cb-d485550e157Methods">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Gapless assembly of complete human and plant chromosomes using only nanopore sequencing </h4> <ul class="cit-auth-list"> <li class="first-item">Sergey Koren, </li> <li>Zhigui Bao, </li> <li>Andrea Guarracino, </li> <li>Shujun Ou, </li> <li>Sara Goodwin, </li> <li>Katharine M. Jenike, </li> <li>Julian Lucas, </li> <li>Brandy McNulty, </li> <li>Jimin Park, </li> <li>Mikko Rautiainen, </li> <li>Arang Rhie, </li> <li>Dick Roelofs, </li> <li>Harrie Schneiders, </li> <li>Ilse Vrijenhoek, </li> <li>Koen Nijbroek, </li> <li>Olle Nordesjo, </li> <li>Sergey Nurk, </li> <li>Mike Vella, </li> <li>Katherine R. Lawrence, </li> <li>Doreen Ware, </li> <li>Michael C. Schatz, </li> <li>Erik Garrison, </li> <li>Sanwen Huang, </li> <li>William Richard McCombie, </li> <li>Karen H. Miga, </li> <li>Alexander H.J. Wittenberg, </li> <li class="last-item">and Adam M. Phillippy</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1919.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1919.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1919.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1919/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> </div> </li> <li class="cit creative-commons creative-commons-by-nc/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1931" /><label for="gca-form-cb-d485550e158Methods">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Full-resolution HLA and KIR gene annotations for human genome assemblies </h4> <ul class="cit-auth-list"> <li class="first-item">Ying Zhou, </li> <li>Li Song, </li> <li class="last-item">and Heng Li</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1931.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1931.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1931.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1931/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> </div> </li> <li class="cit openaccess creative-commons creative-commons-by-nc/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1942" /><label for="gca-form-cb-d485550e159Methods">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter </h4> <ul class="cit-auth-list"> <li class="first-item">Niccoló Tesi, </li> <li>Alex Salazar, </li> <li>Yaran Zhang, </li> <li>Sven van der Lee, </li> <li>Marc Hulsman, </li> <li>Lydian Knoop, </li> <li>Sanduni Wijesekera, </li> <li>Jana Krizova, </li> <li>Anne-Fleur Schneider, </li> <li>Maartje Pennings, </li> <li>Kristel Sleegers, </li> <li>Erik-Jan Kamsteeg, </li> <li>Marcel Reinders, </li> <li class="last-item">and Henne Holstege</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1942-1953; Published in Advance October 15, 2024, doi:10.1101/gr.279351.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1942.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1942.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1942.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1942/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> OPEN ACCESS ARTICLE </div> </li> <li class="cit creative-commons creative-commons-by-nc/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1954" /><label for="gca-form-cb-d485550e160Methods">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing </h4> <ul class="cit-auth-list"> <li class="first-item">Sena A. Gocuk, </li> <li>James Lancaster, </li> <li>Shian Su, </li> <li>Jasleen K. Jolly, </li> <li>Thomas L. Edwards, </li> <li>Doron G. Hickey, </li> <li>Matthew E. Ritchie, </li> <li>Marnie E. Blewitt, </li> <li>Lauren N. Ayton, </li> <li class="last-item">and Quentin Gouil</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1954-1965; Published in Advance September 16, 2024, doi:10.1101/gr.279396.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1954.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1954.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1954.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1954/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> </div> </li> <li class="cit creative-commons creative-commons-by-nc/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1966" /><label for="gca-form-cb-d485550e161Methods">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing </h4> <ul class="cit-auth-list"> <li class="first-item">Kathleen Zeglinski, </li> <li>Christian Montellese, </li> <li>Matthew E. Ritchie, </li> <li>Monther Alhamdoosh, </li> <li>Cédric Vonarburg, </li> <li>Rory Bowden, </li> <li>Monika Jordi, </li> <li>Quentin Gouil, </li> <li>Florian Aeschimann, </li> <li class="last-item">and Arthur Hsu</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1966-1975; Published in Advance October 28, 2024, doi:10.1101/gr.279405.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1966.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1966.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1966.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1966/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> </div> </li> <li class="cit creative-commons creative-commons-by-nc/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1976" /><label for="gca-form-cb-d485550e162Methods">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools </h4> <ul class="cit-auth-list"> <li class="first-item">Anupama Jha, </li> <li>Stephanie C. Bohaczuk, </li> <li>Yizi Mao, </li> <li>Jane Ranchalis, </li> <li>Benjamin J. Mallory, </li> <li>Alan T. Min, </li> <li>Morgan O. Hamm, </li> <li>Elliott Swanson, </li> <li>Danilo Dubocanin, </li> <li>Connor Finkbeiner, </li> <li>Tony Li, </li> <li>Dale Whittington, </li> <li>William Stafford Noble, </li> <li>Andrew B. Stergachis, </li> <li class="last-item">and Mitchell R. Vollger</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1976-1986; Published in Advance June 7, 2024, doi:10.1101/gr.279095.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1976.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1976.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1976.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1976/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> </div> </li> <li class="cit openaccess creative-commons creative-commons-by-nc/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/1987" /><label for="gca-form-cb-d485550e163Methods">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework </h4> <ul class="cit-auth-list"> <li class="first-item">Haotian Teng, </li> <li>Marcus Stoiber, </li> <li>Ziv Bar-Joseph, </li> <li class="last-item">and Carl Kingsford</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 1987-1999; Published in Advance October 15, 2024, doi:10.1101/gr.278960.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/1987.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/1987.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/1987.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/1987/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> OPEN ACCESS ARTICLE </div> </li> <li class="cit openaccess creative-commons creative-commons-by-nc/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/2000" /><label for="gca-form-cb-d485550e164Methods">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation </h4> <ul class="cit-auth-list"> <li class="first-item">Alexander J. 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Slizovskiy, </li> <li>Nathalie Bonin, </li> <li>Jonathan E. Bravo, </li> <li>Peter M. Ferm, </li> <li>Jacob Singer, </li> <li>Christina Boucher, </li> <li class="last-item">and Noelle R. 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Jensen, </li> <li>Esther Robb, </li> <li>The 1000 Genomes ONT Sequencing Consortium, </li> <li>University of Washington Center for Rare Disease Research (UW-CRDR), </li> <li>Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium, </li> <li>William Richard McCombie, </li> <li>Fritz J. Sedlazeck, </li> <li>Justin M. Zook, </li> <li>Stephen B. Montgomery, </li> <li>Erik Garrison, </li> <li>Mikhail Kolmogorov, </li> <li>Michael C. Schatz, </li> <li>Richard N. McLaughlin, Jr., </li> <li>Harriet Dashnow, </li> <li>Michael C. Zody, </li> <li>Matt Loose, </li> <li>Miten Jain, </li> <li>Evan E. Eichler, </li> <li class="last-item">and Danny E. 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Smith, </li> <li>J. Chris Blazier, </li> <li>Kelli J. Kochan, </li> <li>Jonathan M.D. Wood, </li> <li>Kerstin Howe, </li> <li>Anne E. Kwitek, </li> <li>Melinda R. Dwinell, </li> <li>Hao Chen, </li> <li>Julia L. Ciosek, </li> <li>Patrick Masterson, </li> <li>Terence D. Murphy, </li> <li>Theodore S. Kalbfleisch, </li> <li class="last-item">and Peter A. 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Byerly, </li> <li>Alina von Thaden, </li> <li>Evgeny Leushkin, </li> <li>Leon Hilgers, </li> <li>Shenglin Liu, </li> <li>Sven Winter, </li> <li>Tilman Schell, </li> <li>Charlotte Gerheim, </li> <li> Alexander Ben Hamadou, </li> <li>Carola Greve, </li> <li>Christian Betz, </li> <li>Hanno J. Bolz, </li> <li>Sven Büchner, </li> <li>Johannes Lang, </li> <li>Holger Meinig, </li> <li>Evax Marie Famira-Parcsetich, </li> <li> Sarah P. Stubbe, </li> <li>Alice Mouton, </li> <li>Sandro Bertolino, </li> <li>Goedele Verbeylen, </li> <li>Thomas Briner, </li> <li>Lídia Freixas, </li> <li>Lorenzo Vinciguerra, </li> <li>Sarah A. Mueller, </li> <li>Carsten Nowak, </li> <li class="last-item">and Michael Hiller</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/2094.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/2094.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/2094.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/2094/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> </div> </li> <li class="cit openaccess creative-commons creative-commons-by-nc/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/2108" /><label for="gca-form-cb-d485550e182Resources">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Generation and analysis of a mouse multitissue genome annotation atlas </h4> <ul class="cit-auth-list"> <li class="first-item">Matthew Adams and</li> <li class="last-item">Christopher Vollmers</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 2108-2117; Published in Advance October 23, 2024, doi:10.1101/gr.279217.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/2108.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/2108.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/2108.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/2108/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> OPEN ACCESS ARTICLE </div> </li> <li class="cit creative-commons creative-commons-by-nc/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/2118" /><label for="gca-form-cb-d485550e183Resources">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations </h4> <ul class="cit-auth-list"> <li class="first-item">Wenyu Zhang, </li> <li>Anja Guenther, </li> <li>Yuanxiao Gao, </li> <li>Kristian Ullrich, </li> <li>Bruno Huettel, </li> <li>Aftab Ahmad, </li> <li>Lei Duan, </li> <li>Kaizong Wei, </li> <li class="last-item">and Diethard Tautz</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/2118.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/2118.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/2118.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/2118/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> </div> </li> <li class="cit creative-commons creative-commons-by-nc/4.0/ has-earlier-version from-current-issue toc-cit"> <div class="cit-form-select"><input class="gca-checkbox" type="checkbox" name="gca" value="genome;34/11/2133" /><label for="gca-form-cb-d485550e184Resources">Select this article</label></div> <div class="cit-metadata"> <h4 class="cit-first-element cit-title-group">Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization </h4> <ul class="cit-auth-list"> <li class="first-item">Cory Gardner, </li> <li>Junhao Chen, </li> <li>Christina Hadfield, </li> <li>Zhaolian Lu, </li> <li>David Debruin, </li> <li>Yu Zhan, </li> <li>Maureen J. Donlin, </li> <li>Tae-Hyuk Ahn, </li> <li class="last-item">and Zhenguo Lin</li> </ul> <cite><abbr title="Genome Research" class="site-title">Genome Res.</abbr> November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124 </cite> </div> <div class="cit-extra"> <ul class="cit-views"> <li class="first-item"><a href="/content/34/11/2133.abstract" rel="abstract">Abstract</a></li> <li><a href="/content/34/11/2133.full" rel="full-text">Full Text</a></li> <li><a href="/content/34/11/2133.full.pdf+html" rel="full-text.pdf">Full Text (PDF)</a></li> <li class="last-item"><a href="/content/34/11/2133/suppl/DC1" rel="supplemental-data" class="dslink-supplemental-material">Supplemental Material</a></li> </ul> </div> </li> </ul> </div> <div class="gca-buttons"> <input type="reset" name="reset" value="Clear" /> <input type="submit" name="submit" value="Get All Checked Abstracts" /> </div> </form> <div id="content-end-sb" class="sb-div"></div> </div> <div id="col-2"> 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Table of Contents — November 2024, 34 (11)