Peter H. Sudmant

Pangenome analyses uncover the scale and evolutionary consequences of structural variation in a wild mammal

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

CypA is a molecular barrier to HIV emergence from Eastern chimpanzees

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.

Phylogenetically diverse introgression drives subtle population structure in Pacific rockfishes

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.

Machine learning-based prediction of human structural variation and characterization of associated sequence determinants

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.

The evolution of structural variation across 500 million years of vertebrate evolution

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

Tandem repeat variation within and between species reveals signatures of selection in humans and chimpanzees

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

Two melanic pigment patterns are associated with a sex chromosome-linked oncogene in the mountain swordtail Xiphophorus nezahualcoyotl

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

A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos

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

Recurrent structural variation and recent turnover at the 17q21.31 locus in humans and great apes

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

Genomic and functional adaptations in guanylate-binding protein 5 (GBP5) highlight specificities of bat antiviral innate immunity

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

Linking genotype to longevity under genealogical discordance in Sebastes rockfishes

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

Population-scalable genotyping from low-coverage sequencing data using pangenome graphs

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.

Elevated lysosomal mass and enzyme activity in fibroblasts of the Mediterranean mouse Mus spretus

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.

Sequence models conditioned on splicing factor expression predict splicing in unseen tissues

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

Ancient convergence with prokaryote defense and recent adaptations to lentiviruses in primates characterize the ancestral immune factors SAMD9s

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.

Direct identification of de novo mobile element insertions from single molecule sequencing of human sperm

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

TRACKing Tandem Repeats: a customizable pipeline for identification and cross-species comparisons

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

Building pangenome graphs

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.

Extensive longevity and DNA virus-driven adaptation in nearctic Myotis bats

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

Insights into non-crossover recombination from long-read sperm sequencing

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 Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

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.

Cortical Plasticity is associated with Blood-Brain-Barrier Modulation

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

Multiscale Analysis of Pangenome Enables Improved Representation of Genomic Diversity For Repetitive And Clinical Relevant Genes

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

Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection throughout aging

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

Transcriptomic profiles of stress susceptibility and resilience in the amygdala and hippocampus

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.

Tissue-specific impacts of aging and genetics on gene expression patterns in humans

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.

Comprehensive analysis of meiosis-derived cDNA libraries reveals gene isoforms and mitochondrial proteins important for competitive fitness

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

Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation

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

Blood-brain barrier dysfunction in aging induces hyper-activation of TGF-beta signaling and chronic yet reversible neural dysfunction

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.

Integrated Clinical and Omics Approach to Rare Diseases: Novel Genes and Oligogenic Inheritance in Holoprosencephaly

This study identifies novel HPE genes and oligogenic inheritance patterns in holoprosencephaly by integrating clinical data with exome sequencing and gene prioritization.