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Articles by Arjun Biddanda
Recovering signatures of archaic hominin introgression using ancestral recombination graphs
Abstract Results Discussion Acknowledgments References and Notes Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract Admixture between modern humans and extinct hominins has shaped the genomes of present-day individuals, but reconstructing this history has been constrained by the scarcity of archaic samples and unadmixed outgroup populations.
Assembling unmapped reads reveals hidden variation in South Asian genomes
Abstract Conventional genome mapping-based approaches systematically overlook genetic variation, particularly in regions that substantially differ from the reference. To explore this hidden variation, here we examine unmapped and poorly mapped reads from the genomes of 640 human individuals from South Asian populations in the 1000 Genomes Project and the Simons Genome Diversity Project.
Common variation in meiosis genes shapes human recombination and aneuploidy - Nature
Abstract The leading cause of human pregnancy loss is aneuploidy, often tracing to errors in chromosome segregation during female meiosis1,2. Although abnormal crossover recombination is known to confer risk for aneuploidy3,4, limited data have hindered understanding of the potential shared genetic basis of these key molecular phenotypes.
Complete sequencing of ape genomes - Nature
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Abstract The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies1,2,3. Consequently, our understanding of the evolution of our species is incomplete. Here we present haplotype-resolved reference genomes and comparative analyses of six ape species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang.
By DongAhn Yoo, Arang Rhie, Prajna hebbar, Francesca Antonacci, Glennis A. Logsdon, Brandon Pickett, Yana Safonova, Francesco Montinaro, Yanting Luo, Abigail N. Sequeira, Glenn Hickey, Graciela Monfort Anez, Christine R. Beck, Arjun Biddanda, Gerard G. Bouffard, Lucia Carbone, Laura Carrel, Agnes Chan, Juyun Crawford, Mark Diekhans, Gage H. Garcia, David Gilbert, Richard Green, Andrea Guarracino, Gabrielle Hartley, Michael Hiller, Manolis Kellis, William Lees, Mark Loftus, Jian Ma, Yafei Mao, Rajiv C. McCoy, Sean McKinney, Britta Meyer, Karen H Miga, Katherine Munson, Matt Pennell, Pavel A. Pevzner, David Porubsky, Tamara A. Potapova, Joana Rocha, Oliver A. Ryder, Swati Saha, Takayo Sasaki, Michael C Schatz, Nicholas J. Schork, Linnéa Smeds, Dongmin Son, Alexander P. Sweeten, Michael Tassia, Francoise Thibaud-Nissen, Julie Wertz, Shilong Zhang, Sarah Zhao, Erich D. Jarvis, Jennifer L. Gerton, Benedict Paten, Christian D. Huber, Tobias Lenz, Miriam K. Konkel, Soojin V. Yi, Stefan Canzar, Corey T. Watson, Peter H. Sudmant, Erin K Molloy, Erik Garrison, Craig B. Lowe, Mario Ventura, Rachel O’Neill, Sergey Koren, Kateryna D. Makova, Adam M. Phillippy
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Nature
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Sources of gene expression variation in a globally diverse human cohort - Nature
Abstract Genetic variation that influences gene expression and splicing is a key source of phenotypic diversity1,2,3,4,5. Although invaluable, studies investigating these links in humans have been strongly biased towards participants of European ancestries, which constrains generalizability and hinders evolutionary research.
Distinct positions of genetic and oral histories: Perspectives from India
Over the past decade, genomic data has contributed to several insights on global human population histories. These studies have been met both with interest and critically, particularly by populations with oral histories that are records of their past and often reference their origins.
Distinct positions of genetic and oral histories: Perspectives from India
Abstract Over the past decade, genomic data has contributed to several insights on global human population histories. These studies have been met both with interest and critically, particularly by populations with oral histories that are records of their past and often reference their origins.
Sources of gene expression variation in a globally diverse cohort
Abstract Genetic variation influencing gene expression and splicing is a key source of phenotypic diversity. Though invaluable, studies investigating these links in humans have been strongly biased toward participants of European ancestries, diminishing generalizability and hindering evolutionary research.
Sources of gene expression variation in a globally diverse human cohort
Abstract Genetic variation influencing gene expression and splicing is a key source of phenotypic diversity. Though invaluable, studies investigating these links in humans have been strongly biased toward participants of European ancestries, diminishing generalizability and hindering evolutionary research.
Integrating genetic and oral histories of Southwest Indian populations
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Properties of Two-Locus Genealogies and Linkage Disequilibrium in Temporally Structured Samples
Abstract Archaeogenetics has been revolutionary, revealing insights into demographic history and recent positive selection in many organisms. However, most studies to date have ignored the non-random association of genetic variants at different loci (i.e., linkage disequilibrium, LD). This may be in part because basic properties of LD in samples from different times are still not well understood.
Genomic history of the Sardinian population
Marrosu, M. G. et al. The co-inheritance of type 1 diabetes and multiple sclerosis in Sardinia cannot be explained by genotype variation in the HLA region alone. Hum. Mol. Genet. 13, 2919–2924 (2004). Dyson, S. L., & Rowland, R. J. Archaeology and History in Sardinia from the Stone Age to the Middle Ages: Shepherds, Sailors, & Conquerors (University of Pennsylvania Museum of Archaeology and Anthropology: Philadelphia, PA, USA, 2007). Eaves, I. A. et al.
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