deploy: a8e7b98

Author: aabiddanda

.doctrees/environment.pickle

@@ -7,10 +7,12 @@
 
 Arun Das, <strong> Arjun Biddanda</strong>, Rajiv C. McCoy, Michael C. Schatz. Assembling unmapped reads reveals hidden variation in South Asian genomes. _bioRxiv_ | [Full Text](https://www.biorxiv.org/content/10.1101/2025.05.14.653340v1)
 
-Sara A. Carioscia*, <strong>Arjun Biddanda*</strong>, Margaret R. Starostik, Xiaona Tang, Eva R. Hoffmann, Zachary P. Demko, Rajiv C. McCoy. Common variation in meiosis genes shapes human recombination phenotypes and aneuploidy risk. _medRxiv_ | [Full Text](https://www.medrxiv.org/content/10.1101/2025.04.02.25325097v1)
-
 ### Peer-Reviewed 
 
+#### 2026
+
+Sara A. Carioscia*, <strong>Arjun Biddanda*</strong>, Margaret R. Starostik, Xiaona Tang, Eva R. Hoffmann, Zachary P. Demko, Rajiv C. McCoy. Common variation in meiosis genes shapes human recombination phenotypes and aneuploidy risk. _Nature (in press)_ | [medRxiv preprint](https://www.medrxiv.org/content/10.1101/2025.04.02.25325097v1)
+
 #### 2025
 
 Jose A Urban Aragon, ... ,<strong>Arjun Biddanda</strong>, ..., Niraj Rai, Maanasa Raghavan. Population histories of the Indigenous Adivasi and Sinhalese from Sri Lanka using whole genomes. _Current Biology_ | [Full Text](https://doi.org/10.1016/j.cub.2025.04.039)

.doctrees/publications.doctree

@@ -249,49 +249,52 @@ <h1>Publications<a class="headerlink" href="#publications" title="Link to this h
 <section id="preprints">
 <h2>Preprints<a class="headerlink" href="#preprints" title="Link to this heading">¶</a></h2>
 <p>Arun Das, <strong> Arjun Biddanda</strong>, Rajiv C. McCoy, Michael C. Schatz. Assembling unmapped reads reveals hidden variation in South Asian genomes. <em>bioRxiv</em> | <a class="reference external" href="https://www.biorxiv.org/content/10.1101/2025.05.14.653340v1">Full Text</a></p>
-<p>Sara A. Carioscia*, <strong>Arjun Biddanda*</strong>, Margaret R. Starostik, Xiaona Tang, Eva R. Hoffmann, Zachary P. Demko, Rajiv C. McCoy. Common variation in meiosis genes shapes human recombination phenotypes and aneuploidy risk. <em>medRxiv</em> | <a class="reference external" href="https://www.medrxiv.org/content/10.1101/2025.04.02.25325097v1">Full Text</a></p>
 </section>
 <section id="peer-reviewed">
 <h2>Peer-Reviewed<a class="headerlink" href="#peer-reviewed" title="Link to this heading">¶</a></h2>
 <section id="id1">
-<h3>2025<a class="headerlink" href="#id1" title="Link to this heading">¶</a></h3>
+<h3>2026<a class="headerlink" href="#id1" title="Link to this heading">¶</a></h3>
+<p>Sara A. Carioscia*, <strong>Arjun Biddanda*</strong>, Margaret R. Starostik, Xiaona Tang, Eva R. Hoffmann, Zachary P. Demko, Rajiv C. McCoy. Common variation in meiosis genes shapes human recombination phenotypes and aneuploidy risk. <em>Nature (in press)</em> | <a class="reference external" href="https://www.medrxiv.org/content/10.1101/2025.04.02.25325097v1">medRxiv preprint</a></p>
+</section>
+<section id="id2">
+<h3>2025<a class="headerlink" href="#id2" title="Link to this heading">¶</a></h3>
 <p>Jose A Urban Aragon, … ,<strong>Arjun Biddanda</strong>, …, Niraj Rai, Maanasa Raghavan. Population histories of the Indigenous Adivasi and Sinhalese from Sri Lanka using whole genomes. <em>Current Biology</em> | <a class="reference external" href="https://doi.org/10.1016/j.cub.2025.04.039">Full Text</a></p>
 <p>Margaret C. Steiner,  Daniel P. Rice, <strong>Arjun Biddanda</strong>,  Mariadaria K. Ianni-Ravn, Christian Porras, John Novembre. Study design and the sampling of deleterious rare variants in biobank-scale datasets. <em>PNAS</em> | <a class="reference external" href="https://www.pnas.org/doi/10.1073/pnas.2425196122">Full Text</a></p>
 <p>DongAhn Yoo,  Arang Rhie, …, <strong> Arjun Biddanda </strong>, …,  Adam M. Phillippy, Evan E. Eichler. Complete sequencing of ape genomes. <em>Nature</em> | <a class="reference external" href="https://www.nature.com/articles/s41586-025-08816-3">Full Text</a></p>
 </section>
-<section id="id2">
-<h3>2024<a class="headerlink" href="#id2" title="Link to this heading">¶</a></h3>
+<section id="id3">
+<h3>2024<a class="headerlink" href="#id3" title="Link to this heading">¶</a></h3>
 <p>Dylan J. Taylor, Surya B. Chhetri, Michael G. Tassia, <strong>Arjun Biddanda</strong>, Stephanie M. Yan, Genevieve L. Wojcik, Alexis Battle, Rajiv C. McCoy. (2024) Sources of gene expression variation in a globally diverse human cohort. <em>Nature</em> | <a class="reference external" href="https://www.nature.com/articles/s41586-024-07708-2">Full Text</a> | <a class="reference external" href="https://github.com/mccoy-lab/MAGE/tree/main">Software</a></p>
 <p>Kateryna D. Makova, Brandon D. Pickett, …, <strong>Arjun Biddanda</strong>, …, Evan E. Eichler, Adam M. Phillippy. (2024). The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. <em>Nature</em> | <a class="reference external" href="https://www.nature.com/articles/s41586-024-07473-2">Full Text</a></p>
 <p><strong>Arjun Biddanda*</strong>, Esha Bandyopadhyay*, Constanza de la Fuente Castro*, David Witonsky, … , Niraj Rai, Maanasa Raghavan. (2024) Distinct positions of genetic and oral histories - Perspectives from India. <em>HGG Advances</em> | <a class="reference external" href="https://www.cell.com/hgg-advances/fulltext/S2666-2477(24)00044-7">Full Text</a></p>
 </section>
-<section id="id3">
-<h3>2023<a class="headerlink" href="#id3" title="Link to this heading">¶</a></h3>
+<section id="id4">
+<h3>2023<a class="headerlink" href="#id4" title="Link to this heading">¶</a></h3>
 <p>Esha Joshi, <strong>Arjun Biddanda</strong>, Jumi Popoola, … , Abasi Ene-Obong, Colm O’Dushlaine. (2023) Whole-genome sequencing across 449 samples spanning 47 ethnolinguistic groups provides insights into genetic diversity in Nigeria. <em>Cell Genomics</em> | <a class="reference external" href="https://www.cell.com/cell-genomics/fulltext/S2666-979X(23)00175-1">Full Text</a></p>
 <p>M. Elise Lauterbur, Maria Izabel A. Cavassim, …, <strong>Arjun Biddanda</strong> , …, Peter L. Ralph, Daniel R. Schrider, Ilan Gronau. (2023) Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations. | <a class="reference external" href="https://elifesciences.org/reviewed-preprints/84874v2">Full Text</a> | <a class="reference external" href="https://popsim-consortium.github.io/stdpopsim-docs/stable/index.html">Software</a></p>
 <p>Brian C Zhang, <strong>Arjun Biddanda</strong>, Árni F Gunnarsson, Fergus Cooper, Pier Francesco Palamara. (2023) Biobank-scale inference of ancestral recombination graphs enables genealogy-based mixed model association of complex traits. <em>Nature Genetics</em> | <a class="reference external" href="https://www.nature.com/articles/s41588-023-01379-x">Full Text</a> | <a class="reference external" href="https://palamaralab.github.io/software/argneedle/">Software</a></p>
 </section>
-<section id="id4">
-<h3>2022<a class="headerlink" href="#id4" title="Link to this heading">¶</a></h3>
+<section id="id5">
+<h3>2022<a class="headerlink" href="#id5" title="Link to this heading">¶</a></h3>
 <p>Charles Washington III, Matthew Dapas, <strong>Arjun Biddanda</strong>, Kevin M Magnaye, … , Christopher G McKennan, Carole Ober. (2022) African-specific alleles modify risk for asthma at the 17q12-q21 locus in African Americans <em>Genome Medicine</em> | <a class="reference external" href="https://link.springer.com/article/10.1186/s13073-022-01114-x">Full Text</a></p>
 <p><strong>Arjun Biddanda</strong>, Matthias Steinrücken, John Novembre. (2022) Properties of Two-Locus Genealogies and Linkage Disequilibrium in Temporally Structured Samples. <em>Genetics</em> | <a class="reference external" href="https://doi.org/10.1093/genetics/iyac038">Full Text</a> | <a class="reference external" href="https://aabiddanda.github.io/aDNA_LD_public/">Software</a></p>
 </section>
-<section id="id5">
-<h3>2020<a class="headerlink" href="#id5" title="Link to this heading">¶</a></h3>
+<section id="id6">
+<h3>2020<a class="headerlink" href="#id6" title="Link to this heading">¶</a></h3>
 <p><strong>Arjun Biddanda</strong>, Daniel P Rice, John Novembre. (2020). Geographic patterns of human allele frequency variation - a variant-centric perspective. <em>eLife</em> | <a class="reference external" href="https://elifesciences.org/articles/60107">Full Text</a> | <a class="reference external" href="https://aabiddanda.github.io/geovar/">Software</a></p>
 </section>
-<section id="id6">
-<h3>2018<a class="headerlink" href="#id6" title="Link to this heading">¶</a></h3>
+<section id="id7">
+<h3>2018<a class="headerlink" href="#id7" title="Link to this heading">¶</a></h3>
 <p>Charleston W K Chiang, Joseph H Marcus, Carlo Sidore, <strong>Arjun Biddanda</strong>, Hussein Al-Asadi, Magdalena Zoledziewska, Maristella Pitzalis, Fabio Busonero, Andrea Maschio, Giorgio Pistis, Maristella Steri, Andrea Angius, Kirk E Lohmueller, Gonçalo R Abecasis, David Schlessinger, Francesco Cucca, John Novembre. (2018) Genomic history of the Sardinian population. <em>Nature Genetics</em> | <a class="reference external" href="https://doi.org/10.1038/s41588-018-0215-8">Full Text</a></p>
 <p>Peter de Barros Damgaard, Rui Martiniano, Jack Kamm, Jose Victor Moreno-Mayar, …, <strong>Arjun Biddanda</strong>, …, Richard Durbin, Eske Willerslev. (2018) The first horse herders and the impact of early Bronze Age steppe expansions into Asia. <em>Science</em> | <a class="reference external" href="http://science.sciencemag.org/content/early/2018/05/08/science.aar7711.abstract">Full Text</a></p>
 </section>
-<section id="id7">
-<h3>2016<a class="headerlink" href="#id7" title="Link to this heading">¶</a></h3>
+<section id="id8">
+<h3>2016<a class="headerlink" href="#id8" title="Link to this heading">¶</a></h3>
 <p>Yedael Y. Waldman, <strong>Arjun Biddanda</strong>, Maya Dubrovsky, Christopher L. Campbell, Carole Oddoux, Eitan Friedman, Gil Atzmon, Eran Halperin, Harry Ostrer, Alon Keinan. (2016) The genetic history of Cochin Jews from India. <em>Human Genetics</em> | <a class="reference external" href="https://www.ncbi.nlm.nih.gov/pubmed/27377974">Full Text</a></p>
 <p>Yedael Y. Waldman*, <strong>Arjun Biddanda*</strong>, Natalie R. Davidson, Paul Billing-Ross, Maya Dubrovsky, Christopher L. Campbell, Carole Oddoux, Eitan Friedman, Gil Atzmon, Eran Halperin, Harry Ostrer, Alon Keinan. (2016) The genetics of Bene Israel from India Reveals Both Substantial Jewish and Indian Ancestry. <em>Plos One</em>  | <a class="reference external" href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152056">Full Text</a></p>
 </section>
-<section id="id8">
-<h3>2015<a class="headerlink" href="#id8" title="Link to this heading">¶</a></h3>
+<section id="id9">
+<h3>2015<a class="headerlink" href="#id9" title="Link to this heading">¶</a></h3>
 <p>Feng Gao*, Diana Chang*, <strong>Arjun Biddanda*</strong>, Li Ma, Yingjie Guo, Zilu Zhou, Alon Keinan. (2015) XWAS - A Software Toolset for Genetic Data Analysis and Association Studies of the X Chromosome. <em>Journal of Heredity</em> | <a class="reference external" href="https://www.ncbi.nlm.nih.gov/pubmed/26268243">Full Text</a> | <a class="reference external" href="http://keinanlab.cb.bscb.cornell.edu/content/xwas">Software</a></p>
 </section>
 </section>
@@ -372,14 +375,15 @@ <h2>Technical Reports<a class="headerlink" href="#technical-reports" title="Link
 <li><a class="reference internal" href="#">Publications</a><ul>
 <li><a class="reference internal" href="#preprints">Preprints</a></li>
 <li><a class="reference internal" href="#peer-reviewed">Peer-Reviewed</a><ul>
-<li><a class="reference internal" href="#id1">2025</a></li>
-<li><a class="reference internal" href="#id2">2024</a></li>
-<li><a class="reference internal" href="#id3">2023</a></li>
-<li><a class="reference internal" href="#id4">2022</a></li>
-<li><a class="reference internal" href="#id5">2020</a></li>
-<li><a class="reference internal" href="#id6">2018</a></li>
-<li><a class="reference internal" href="#id7">2016</a></li>
-<li><a class="reference internal" href="#id8">2015</a></li>
+<li><a class="reference internal" href="#id1">2026</a></li>
+<li><a class="reference internal" href="#id2">2025</a></li>
+<li><a class="reference internal" href="#id3">2024</a></li>
+<li><a class="reference internal" href="#id4">2023</a></li>
+<li><a class="reference internal" href="#id5">2022</a></li>
+<li><a class="reference internal" href="#id6">2020</a></li>
+<li><a class="reference internal" href="#id7">2018</a></li>
+<li><a class="reference internal" href="#id8">2016</a></li>
+<li><a class="reference internal" href="#id9">2015</a></li>
 </ul>
 </li>
 <li><a class="reference internal" href="#technical-reports">Technical Reports</a></li>