2.2k citations · 3.1k across the 14 of their papers we have counts for
14 papers
Diversity in immunogenomics: the value and the challenge
Kerui Peng, Yana Safonova, Mikhail Shugay +32
With the advent of high-throughput sequencing technologies, the fields of immunogenomics and adaptive immune receptor repertoire research are facing both opportunities and challeng…
Addressing Ancestry Disparities in Genomic Medicine: A Geographic-aware Algorithm
Daniel Mas Montserrat, Arvind Kumar, Carlos Bustamante +1
With declining sequencing costs a promising and affordable tool is emerging in cancer diagnostics: genomics. By using association studies, genomic variants that predispose patients…
LAI-Net: Local-Ancestry Inference with Neural Networks
Daniel Mas Montserrat, Carlos Bustamante, Alexander Ioannidis
Local-ancestry inference (LAI), also referred to as ancestry deconvolution, provides high-resolution ancestry estimation along the human genome. In both research and industry, LAI…
Class-Conditional VAE-GAN for Local-Ancestry Simulation
Daniel Mas Montserrat, Carlos Bustamante, Alexander Ioannidis
Local ancestry inference (LAI) allows identification of the ancestry of all chromosomal segments in admixed individuals, and it is a critical step in the analysis of human genomes…
LitGen: Genetic Literature Recommendation Guided by Human Explanations
Allen Nie, Arturo L. Pineda, Matt W. Wright Hannah Wand +5
As genetic sequencing costs decrease, the lack of clinical interpretation of variants has become the bottleneck in using genetics data. A major rate limiting step in clinical inter…
DeepTag: inferring all-cause diagnoses from clinical notes in under-resourced medical domain
Allen Nie, Ashley Zehnder, Rodney L. Page +4
Large scale veterinary clinical records can become a powerful resource for patient care and research. However, clinicians lack the time and resource to annotate patient records wit…
Network Enhancement: a general method to denoise weighted biological networks
Bo Wang, Armin Pourshafeie, Marinka Zitnik +4
Networks are ubiquitous in biology where they encode connectivity patterns at all scales of organization, from molecular to the biome. However, biological networks are noisy due to…
Genome Sequencing Highlights Genes Under Selection and the Dynamic Early History of Dogs
Adam H. Freedman, Rena M. Schweizer, Ilan Gronau +27
To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we analyzed novel high-quality genome sequences of three gray wolves, one…
Reconstructing the Population Genetic History of the Caribbean
Andres Moreno-Estrada, Simon Gravel, Fouad Zakharia +18
The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, by making use of genome-wide SNP array dat…
Reconstructing Native American Migrations from Whole-genome and Whole-exome Data
Simon Gravel, Fouad Zakharia, Andres Moreno-Estrada +17
There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent we…
Genetic recombination is targeted towards gene promoter regions in dogs
Adam Auton, Ying Rui Li, Jeffrey Kidd +9
The identification of the H3K4 trimethylase, PRDM9, as the gene responsible for recombination hotspot localization has provided considerable insight into the mechanisms by which re…
Improved haplotyping of rare variants using next-generation sequence data
Fouad Zakharia, Carlos Bustamante
Accurate identification of haplotypes in sequenced human genomes can provide invaluable information about population demography and fine-scale correlations along the genome, thus e…
The genetic prehistory of southern Africa
Joseph K. Pickrell, Nick Patterson, Chiara Barbieri +18
Southern and eastern African populations that speak non-Bantu languages with click consonants are known to harbour some of the most ancient genetic lineages in humans, but their re…
Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data
Ryan N. Gutenkunst, Ryan D. Hernandez, Scott H. Williamson +1
Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an infer…