Peter H. Sudmant

This study constructs a pangenome for deer mice to reveal extensive structural variation and its evolutionary implications.

The paper identifies CypA as a molecular barrier preventing lentivirus from Eastern chimpanzees from infecting humans, due to its restriction of replication through a unique capsid feature.

The paper examines introgression and population structure in Pacific rockfishes, finding Copper shows higher differentiation while Quillback shows panmixia and introgression from 13-16 other species.

A sequence-only convolutional neural network and an annotation-based random forest predict human structural variant breakpoints from 400 bp windows (AUROC 0.903, 0.904); their ensemble reaches 0.916.

This study identifies 35.3 million structural variants across vertebrates, showing significant variation in their abundance, mechanisms, and functional impact across species.

This study analyzes tandem repeat variation in humans and chimpanzees to identify signatures of selection, revealing roles in neural evolution and adaptive expression.

This study identifies two melanic pigmentation patterns in Xiphophorus nezahualcoyotl linked to the sex chromosome-linked oncogene xmrk through long-read sequencing and GWAS.

This study presents a pan-pangenome of humans, chimpanzees, and bonobos, revealing structural variation, selection patterns, and adaptations related to immunity and malaria resistance.

The paper characterizes structural variation at the 17q21.31 locus in humans and great apes, identifying new haplotypes and evolutionary dynamics.

This study identifies GBP5 as a key antiviral gene in bats, showing its evolutionary adaptations and functional specificity in restricting viral infections.

The paper uses phyloGWAS to link genotypes to longevity in Sebastes rockfishes despite high genealogical discordance, identifying variants associated with longevity.

COSIGT improves genotyping accuracy at low sequencing depths by matching coverage patterns to pangenome haplotypes using cosine similarity, enabling population-scale analysis of complex variation.

The paper compares lysosomal characteristics between fibroblasts of two mouse species, finding elevated lysosomal mass and enzyme activity in M. spretus compared to M. musculus.

Splice Ninja predicts tissue-specific splicing events using splicing factor expression, achieving accurate results on unseen tissues.

This study identifies ancient immune convergence between prokaryotes and primates through SAMD9/9L proteins and reveals recent adaptations in bonobos and chimps enhancing HIV resistance.

The paper directly identifies de novo mobile element insertions in human sperm using long-read sequencing and finds age-related increases in retrotransposition rates.

TRACK is a pipeline for identifying and comparing tandem repeats across species, offering tools for cataloging, filtering, and population genetic analysis.

This paper introduces PGGB, a pipeline for building pangenome graphs that includes all variation without bias, enabling variation detection, conservation measurement, recombination event detection, and phylogenetic inference.

This study identifies genetic adaptations in Myotis bats linked to longevity and viral tolerance through genome analysis and functional experiments.

This study examines amylase structural haplotypes in humans, finding increased copy numbers in agricultural populations and evidence of recent selection over the last 12,000 years.

The paper uses long-read sperm sequencing to analyze non-crossover recombination events, finding variation in recombination rates and distinct mechanisms for non-crossover gene conversions.

The paper produces gapless assemblies of ape sex chromosomes for five great apes and a lesser ape, revealing divergence in Y chromosomes and evolutionary dynamics.

The paper shows neuronal activity modulates BBB permeability in the healthy brain, linking it to synaptic plasticity and sensory learning.

The paper introduces a pangenome research toolkit to analyze complex genomic variations across multiple scales, improving the interpretation of repetitive and clinically relevant genes.

The paper examines how mitochondrial haplotype and mito-nuclear matching influence somatic mutation and selection in aging mice across tissues.

This study identifies transcriptomic differences in the amygdala and hippocampus of stress-susceptible and resilient rats, revealing gene expression patterns associated with vulnerability and resilience to anxiety-like behavior.

This study quantifies how aging and genetics influence gene expression across 27 human tissues, finding tissue-specific differences in their contributions and identifying signatures of aging and selection.

The paper constructs and analyzes meiotic cDNA libraries in yeast to identify gene isoforms and mitochondrial proteins affecting competitive fitness and respiration.

This study shows that reduced proteasome activity in aging brains leads to ribosome stoichiometry loss and aggregation, increasing mortality risk in killifish.

This study shows BBB dysfunction in aging leads to TGF-beta hyperactivation in astrocytes, causing neural dysfunction, which can be reversed by inhibiting TGF-beta signaling.