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Genomics
<!DOCTYPE html> <html lang="en"> <head> <title>Genomics </title> <meta name="viewport" content="width=device-width, initial-scale=1"> <link rel="apple-touch-icon" sizes="180x180" href="/static/browse/0.3.4/images/icons/apple-touch-icon.png"> <link rel="icon" type="image/png" sizes="32x32" href="/static/browse/0.3.4/images/icons/favicon-32x32.png"> <link rel="icon" type="image/png" sizes="16x16" href="/static/browse/0.3.4/images/icons/favicon-16x16.png"> <link rel="manifest" href="/static/browse/0.3.4/images/icons/site.webmanifest"> <link rel="mask-icon" href="/static/browse/0.3.4/images/icons/safari-pinned-tab.svg" color="#5bbad5"> <meta name="msapplication-TileColor" content="#da532c"> <meta name="theme-color" content="#ffffff"> <link rel="stylesheet" type="text/css" media="screen" href="/static/browse/0.3.4/css/arXiv.css?v=20241206" /> <link rel="stylesheet" type="text/css" media="print" href="/static/browse/0.3.4/css/arXiv-print.css?v=20200611" /> <link rel="stylesheet" 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</li><li> <a href="/list/q-bio.GN/recent?skip=6&show=50"> Wed, 19 Mar 2025 </a> </li></ul> <p>See today's <a id="new-q-bio.GN" aria-labelledby="new-q-bio.GN" href="/list/q-bio.GN/new">new</a> changes</p> <div class='paging'>Total of 6 entries </div> <div class='morefewer'>Showing up to 50 entries per page: <a href=/list/q-bio.GN/recent?skip=0&show=25 rel="nofollow"> fewer</a> | <span style="color: #454545">more</span> | <span style="color: #454545">all</span> </div> <dl id='articles'> <h3>Tue, 25 Mar 2025 (showing 3 of 3 entries )</h3> <dt> <a name='item1'>[1]</a> <a href ="/abs/2503.18810" title="Abstract" id="2503.18810"> arXiv:2503.18810 </a> [<a href="/pdf/2503.18810" title="Download PDF" id="pdf-2503.18810" aria-labelledby="pdf-2503.18810">pdf</a>, <a href="/format/2503.18810" title="Other formats" id="oth-2503.18810" aria-labelledby="oth-2503.18810">other</a>] </dt> <dd> <div class='meta'> <div class='list-title mathjax'><span class='descriptor'>Title:</span> Combining multiplexed functional data to improve variant classification </div> <div class='list-authors'><a href="https://arxiv.org/search/q-bio?searchtype=author&query=Alliance,+A+o+V+E">Atlas of Variant Effects Alliance</a>: <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Calhoun,+J+D">Jeffrey D. Calhoun</a> (1), <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Dawood,+M">Moez Dawood</a> (2,3,4), <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Rowlands,+C+F">Charlie F. Rowlands</a> (5), <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Fayer,+S">Shawn Fayer</a> (6,7), <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Radford,+E+J">Elizabeth J. Radford</a> (8,9), <a href="https://arxiv.org/search/q-bio?searchtype=author&query=McEwen,+A+E">Abbye E. McEwen</a> (6,7,10), <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Turnbull,+C">Clare Turnbull</a> (11), <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Spurdle,+A+B">Amanda B. Spurdle</a> (12,13), <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Starita,+L+M">Lea M. Starita</a> (5,6), <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Jagannathan,+S">Sujatha Jagannathan</a> (14,15), (1)Ken, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Neurology,+R+D+D+o">Ruth Davee Department of Neurology</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Medicine,+N+F+S+o">Northwestern Feinberg School of Medicine</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Chicago">Chicago</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Illinois">Illinois</a> (2)<a href="https://arxiv.org/search/q-bio?searchtype=author&query=Center,+H+G+S">Human Genome Sequencing Center</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Medicine,+B+C+o">Baylor College of Medicine</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Houston">Houston</a>, TX, USA (3)<a href="https://arxiv.org/search/q-bio?searchtype=author&query=Molecular,+D+o">Department of Molecular</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Genetics,+H">Human Genetics</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Medicine,+B+C+o">Baylor College of Medicine</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Houston">Houston</a>, TX, USA (4)<a href="https://arxiv.org/search/q-bio?searchtype=author&query=Program,+M+S+T">Medical Scientist Training Program</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Medicine,+B+C+o">Baylor College of Medicine</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Houston">Houston</a>, TX, USA (5)<a href="https://arxiv.org/search/q-bio?searchtype=author&query=Genetics,+D+o">Division of Genetics</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Epidemiology">Epidemiology</a>, The <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Research,+I+o+C">Institute of Cancer Research</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=London">London</a>, UK. (6)<a href="https://arxiv.org/search/q-bio?searchtype=author&query=Medicine,+B+B+I+f+P">Brotman Baty Institute for Precision Medicine</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Seattle">Seattle</a>, WA, USA (7)<a href="https://arxiv.org/search/q-bio?searchtype=author&query=Sciences,+D+o+G">Department of Genome Sciences</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Washington,+U+o">University of Washington</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Seattle">Seattle</a>, WA, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=USA.">USA.</a> (8)<a href="https://arxiv.org/search/q-bio?searchtype=author&query=Institute,+W+S">Wellcome Sanger Institute</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Hinxton">Hinxton</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=1SA,+C">CB10 1SA</a>, UK. (9)<a href="https://arxiv.org/search/q-bio?searchtype=author&query=Pediatrics,+D+o">Department of Pediatrics</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Cambridge,+U+o">University of Cambridge</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=8,+L">Level 8</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Campus,+C+B">Cambridge Biomedical Campus</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Cambridge">Cambridge</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=0QQ,+C">CB2 0QQ</a>, UK. (10)<a href="https://arxiv.org/search/q-bio?searchtype=author&query=Medicine,+D+o+L">Department of Laboratory Medicine</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Pathology">Pathology</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Washington,+U+o">University of Washington</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Seattle">Seattle</a>, USA (11)<a href="https://arxiv.org/search/q-bio?searchtype=author&query=Genetics,+D+o">Division of Genetics</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Epidemiology">Epidemiology</a>, The <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Research,+I+o+C">Institute of Cancer Research</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=London">London</a>, UK (12)<a href="https://arxiv.org/search/q-bio?searchtype=author&query=Program,+P+H">Population Health Program</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Institute,+Q+B+M+R">QIMR Berghofer Medical Research Institute</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Herston">Herston</a>, QLD, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=4006">4006</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Australia">Australia</a> (13)<a href="https://arxiv.org/search/q-bio?searchtype=author&query=Medicine,+F+o">Faculty of Medicine</a>, The <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Queensland,+U+o">University of Queensland</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Brisbane">Brisbane</a>, QLD, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=4006">4006</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Australia">Australia</a> (14)<a href="https://arxiv.org/search/q-bio?searchtype=author&query=Biochemistry,+D+o">Department of Biochemistry</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Genetics,+M">Molecular Genetics</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Campus,+U+o+C+A+M">University of Colorado Anschutz Medical Campus</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Aurora">Aurora</a>, CO, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=USA.">USA.</a> (15)<a href="https://arxiv.org/search/q-bio?searchtype=author&query=Initiative,+R+B">RNA Bioscience Initiative</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Campus,+U+o+C+A+M">University of Colorado Anschutz Medical Campus</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Aurora">Aurora</a>, CO, USA</div> <div class='list-subjects'><span class='descriptor'>Subjects:</span> <span class="primary-subject">Genomics (q-bio.GN)</span> </div> </div> </dd> <dt> <a name='item2'>[2]</a> <a href ="/abs/2503.18472" title="Abstract" id="2503.18472"> arXiv:2503.18472 </a> [<a href="/pdf/2503.18472" title="Download PDF" id="pdf-2503.18472" aria-labelledby="pdf-2503.18472">pdf</a>, <a href="https://arxiv.org/html/2503.18472v1" title="View HTML" id="html-2503.18472" aria-labelledby="html-2503.18472" rel="noopener noreferrer" target="_blank">html</a>, <a href="/format/2503.18472" title="Other formats" id="oth-2503.18472" aria-labelledby="oth-2503.18472">other</a>] </dt> <dd> <div class='meta'> <div class='list-title mathjax'><span class='descriptor'>Title:</span> A Graph-based Approach to Variant Extraction </div> <div class='list-authors'><a href="https://arxiv.org/search/q-bio?searchtype=author&query=Santcroos,+M+A">Mark A. Santcroos</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Kosters,+W+A">Walter A. Kosters</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Lefter,+M">Mihai Lefter</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Laros,+J+F">Jeroen F.J. Laros</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Vis,+J+K">Jonathan K. Vis</a></div> <div class='list-subjects'><span class='descriptor'>Subjects:</span> <span class="primary-subject">Genomics (q-bio.GN)</span>; Data Structures and Algorithms (cs.DS) </div> </div> </dd> <dt> <a name='item3'>[3]</a> <a href ="/abs/2503.17418" title="Abstract" id="2503.17418"> arXiv:2503.17418 </a> [<a href="/pdf/2503.17418" title="Download PDF" id="pdf-2503.17418" aria-labelledby="pdf-2503.17418">pdf</a>, <a href="/format/2503.17418" title="Other formats" id="oth-2503.17418" aria-labelledby="oth-2503.17418">other</a>] </dt> <dd> <div class='meta'> <div class='list-title mathjax'><span class='descriptor'>Title:</span> Application of Single-cell Deep Learning in Elucidating the Mapping Relationship Between Visceral and Body Surface Inflammatory Patterns </div> <div class='list-authors'><a href="https://arxiv.org/search/q-bio?searchtype=author&query=Huang,+H">Haixiang Huang</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Shen,+B">Bingbing Shen</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Zhang,+Z">Zhenwei Zhang</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Yue,+J">Jianming Yue</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Mei,+L">Lu Mei</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Chen,+Q">Qiusheng Chen</a></div> <div class='list-comments mathjax'><span class='descriptor'>Comments:</span> 25pages, 7 figures, under review </div> <div class='list-subjects'><span class='descriptor'>Subjects:</span> <span class="primary-subject">Genomics (q-bio.GN)</span> </div> </div> </dd> </dl> <dl id='articles'> <h3>Mon, 24 Mar 2025 (showing 1 of 1 entries )</h3> <dt> <a name='item4'>[4]</a> <a href ="/abs/2503.16582" title="Abstract" id="2503.16582"> arXiv:2503.16582 </a> (cross-list from cs.LG) [<a href="/pdf/2503.16582" title="Download PDF" id="pdf-2503.16582" aria-labelledby="pdf-2503.16582">pdf</a>, <a href="/format/2503.16582" title="Other formats" id="oth-2503.16582" aria-labelledby="oth-2503.16582">other</a>] </dt> <dd> <div class='meta'> <div class='list-title mathjax'><span class='descriptor'>Title:</span> Machine Learning-Based Genomic Linguistic Analysis (Gene Sequence Feature Learning): A Case Study on Predicting Heavy Metal Response Genes in Rice </div> <div class='list-authors'><a href="https://arxiv.org/search/cs?searchtype=author&query=Yang,+R">Ruiqi Yang</a>, <a href="https://arxiv.org/search/cs?searchtype=author&query=Wang,+J">Jianxu Wang</a>, <a href="https://arxiv.org/search/cs?searchtype=author&query=Yuan,+W">Wei Yuan</a>, <a href="https://arxiv.org/search/cs?searchtype=author&query=Wang,+X">Xun Wang</a>, <a href="https://arxiv.org/search/cs?searchtype=author&query=Li,+M">Mei Li</a></div> <div class='list-subjects'><span class='descriptor'>Subjects:</span> <span class="primary-subject">Machine Learning (cs.LG)</span>; Artificial Intelligence (cs.AI); Genomics (q-bio.GN) </div> </div> </dd> </dl> <dl id='articles'> <h3>Fri, 21 Mar 2025 (showing 1 of 1 entries )</h3> <dt> <a name='item5'>[5]</a> <a href ="/abs/2503.16351" title="Abstract" id="2503.16351"> arXiv:2503.16351 </a> (cross-list from cs.LG) [<a href="/pdf/2503.16351" title="Download PDF" id="pdf-2503.16351" aria-labelledby="pdf-2503.16351">pdf</a>, <a href="https://arxiv.org/html/2503.16351v1" title="View HTML" id="html-2503.16351" aria-labelledby="html-2503.16351" rel="noopener noreferrer" target="_blank">html</a>, <a href="/format/2503.16351" title="Other formats" id="oth-2503.16351" aria-labelledby="oth-2503.16351">other</a>] </dt> <dd> <div class='meta'> <div class='list-title mathjax'><span class='descriptor'>Title:</span> Lyra: An Efficient and Expressive Subquadratic Architecture for Modeling Biological Sequences </div> <div class='list-authors'><a href="https://arxiv.org/search/cs?searchtype=author&query=Ramesh,+K">Krithik Ramesh</a> (1 and 2), <a href="https://arxiv.org/search/cs?searchtype=author&query=Siddiqui,+S+M">Sameed M. Siddiqui</a> (1 and 3), <a href="https://arxiv.org/search/cs?searchtype=author&query=Gu,+A">Albert Gu</a> (4), <a href="https://arxiv.org/search/cs?searchtype=author&query=Mitzenmacher,+M+D">Michael D. Mitzenmacher</a> (1 and 5), <a href="https://arxiv.org/search/cs?searchtype=author&query=Sabeti,+P+C">Pardis C. Sabeti</a> (1 and 6 and 7 and 8) ((1) Broad Institute of MIT and Harvard, (2) Massachusetts Institute of Technology, (3) Computational and Systems Biology Program, Massachusetts Institute of Technology, (4) Machine Learning Department, Carnegie Mellon University, (5) School of Engineering and Applied Sciences, Harvard University, (6) Department of Organismic and Evolutionary Biology, Harvard University, (7) Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, (8) Howard Hughes Medical Institute)</div> <div class='list-comments mathjax'><span class='descriptor'>Comments:</span> 53 pages, 5 figures </div> <div class='list-subjects'><span class='descriptor'>Subjects:</span> <span class="primary-subject">Machine Learning (cs.LG)</span>; Genomics (q-bio.GN) </div> </div> </dd> </dl> <dl id='articles'> <h3>Thu, 20 Mar 2025 (showing 1 of 1 entries )</h3> <dt> <a name='item6'>[6]</a> <a href ="/abs/2503.14520" title="Abstract" id="2503.14520"> arXiv:2503.14520 </a> [<a href="/pdf/2503.14520" title="Download PDF" id="pdf-2503.14520" aria-labelledby="pdf-2503.14520">pdf</a>, <a href="https://arxiv.org/html/2503.14520v1" title="View HTML" id="html-2503.14520" aria-labelledby="html-2503.14520" rel="noopener noreferrer" target="_blank">html</a>, <a href="/format/2503.14520" title="Other formats" id="oth-2503.14520" aria-labelledby="oth-2503.14520">other</a>] </dt> <dd> <div class='meta'> <div class='list-title mathjax'><span class='descriptor'>Title:</span> From de Bruijn graphs to variation graphs-relationships between pangenome models </div> <div class='list-authors'><a href="https://arxiv.org/search/q-bio?searchtype=author&query=Cicherski,+A">Adam Cicherski</a>, <a href="https://arxiv.org/search/q-bio?searchtype=author&query=Dojer,+N">Norbert Dojer</a></div> <div class='list-comments mathjax'><span class='descriptor'>Comments:</span> Submitted to International Symposium on String Processing and Information Retrieval. Cham: Springer Nature Switzerland, 2023 (SPIRE2023). This preprint has not undergone peer review or any post-submission improvements or corrections. The Version of Record of this contribution is published in LNCS, volume 14240, and is available online at <a href="https://doi.org/10.1007/978-3-031-43980-3_10" rel="external noopener nofollow" class="link-external link-https">this https URL</a> </div> <div class='list-subjects'><span class='descriptor'>Subjects:</span> <span class="primary-subject">Genomics (q-bio.GN)</span>; Combinatorics (math.CO) </div> </div> </dd> </dl> <dl id='articles'> <h3>Wed, 19 Mar 2025</h3> <p>No updates for this time period.</p> </dl> <div class='paging'>Total of 6 entries </div> <div class='morefewer'>Showing up to 50 entries per page: <a href=/list/q-bio.GN/recent?skip=0&show=25 rel="nofollow"> fewer</a> | <span style="color: #454545">more</span> | <span style="color: #454545">all</span> </div> </div> </div> </div> </main> <footer style="clear: both;"> <div class="columns is-desktop" role="navigation" aria-label="Secondary" style="margin: -0.75em -0.75em 0.75em -0.75em"> <!-- Macro-Column 1 --> <div class="column" style="padding: 0;"> <div class="columns"> <div class="column"> <ul style="list-style: none; 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