## Publications

<sup>* indicates equal contribution</sup>

### Preprints

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. _bioRxiv_ | [Full Text](https://www.biorxiv.org/content/10.1101/2024.12.02.626424v1)

DongAhn Yoo,  Arang Rhie, ..., <strong> Arjun Biddanda </strong>, ...,  Adam M. Phillippy, Evan E. Eichler. Complete sequencing of ape genomes. _bioRxiv_ | [Full Text](https://www.biorxiv.org/content/10.1101/2024.07.31.605654v2)

### Peer-Reviewed 

#### 2024

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. _Nature_ | [Full Text](https://www.nature.com/articles/s41586-024-07708-2 ) | [Software](https://github.com/mccoy-lab/MAGE/tree/main)

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. _Nature_ | [Full Text](https://www.nature.com/articles/s41586-024-07473-2)

<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. _HGG Advances_ | [Full Text](https://www.cell.com/hgg-advances/fulltext/S2666-2477(24)00044-7)

#### 2023


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. _Cell Genomics_ | [Full Text](https://www.cell.com/cell-genomics/fulltext/S2666-979X(23)00175-1)

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. | [Full Text](https://elifesciences.org/reviewed-preprints/84874v2) | [Software](https://popsim-consortium.github.io/stdpopsim-docs/stable/index.html)

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. _Nature Genetics_ | [Full Text](https://www.nature.com/articles/s41588-023-01379-x) | [Software](https://palamaralab.github.io/software/argneedle/)

#### 2022

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 _Genome Medicine_ | [Full Text](https://link.springer.com/article/10.1186/s13073-022-01114-x)

<strong>Arjun Biddanda</strong>, Matthias Steinrücken, John Novembre. (2022) Properties of Two-Locus Genealogies and Linkage Disequilibrium in Temporally Structured Samples. _Genetics_ | [Full Text](https://doi.org/10.1093/genetics/iyac038) | [Software](https://aabiddanda.github.io/aDNA_LD_public/)

#### 2020

<strong>Arjun Biddanda</strong>, Daniel P Rice, John Novembre. (2020). Geographic patterns of human allele frequency variation - a variant-centric perspective. _eLife_ | [Full Text](https://elifesciences.org/articles/60107) | [Software](https://aabiddanda.github.io/geovar/)

#### 2018

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. _Nature Genetics_ | [Full Text](https://doi.org/10.1038/s41588-018-0215-8)


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. _Science_ | [Full Text](http://science.sciencemag.org/content/early/2018/05/08/science.aar7711.abstract)

#### 2016

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. _Human Genetics_ | [Full Text](https://www.ncbi.nlm.nih.gov/pubmed/27377974)

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. _Plos One_  | [Full Text](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152056)

#### 2015

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. _Journal of Heredity_ | [Full Text](https://www.ncbi.nlm.nih.gov/pubmed/26268243) | [Software](http://keinanlab.cb.bscb.cornell.edu/content/xwas)


### Technical Reports

<strong>Arjun Biddanda</strong>, Karen Perez de Arce, ... , Abasi Ene-Obong, Jumi Popoola, Colm O'Dushlaine, Peter Fekkes. (2023) A survey of proteomic variation across two ethnic groups in Nigeria and its relationship to obesity risk. _bioRxiv_ | [Full Text](https://www.biorxiv.org/content/10.1101/2022.12.09.519773v1) | [Software](https://54gene-olink-qc.readthedocs.io/en/latest/)