Peter J. Park

Recurrent mitotic error and purifying selection shape chromosomal mosaicism across human tissues

This study identifies mosaic chromosomal alterations in healthy human tissues, revealing tissue-specific patterns of mitotic errors and purifying selection across aging.

Perinatal Elimination of Genetically Aberrant Neurons from Human Cerebral Cortex

The paper investigates somatic copy number variants (CNVs) in human neurons across development, finding that perinatal elimination of neurons with aberrant genomes reduces CNV prevalence and targets dosage-sensitive genes.

Complete timing of copy-number amplification histories reveals whole-genome duplication dynamics and coincident oncogene amplification bursts

The paper introduces a method to time copy-number amplification events in cancer genomes, revealing that whole-genome duplication (WGD) enables bursts of oncogene amplification.

Somatic mutations and single-nucleus transcriptomics reveal uniquely human properties of neuronal aging

The paper compares somatic mutation rates and transcriptomic changes in neurons across six mammalian species, finding higher mutation accumulation and distinct age-related dysregulation in human neurons.

Correlation-aware discovery of co-occurring mutational signatures in cancer

Cornet improves mutational signature discovery by modeling correlations, identifying new signatures in cancer genomes.

Integrated map of somatic mosaicism across human tissues in 25 individuals

The paper presents an integrated analysis of somatic mosaicism across 25 individuals, revealing tissue-specific mutational processes and epigenetic states.

Replication fork directionality reveals how structural variants arise under replication stress

The paper identifies a novel mechanism for large tandem duplications in cancer by analyzing replication fork directionality and develops a classifier to distinguish SV phenotypes based on replication features.

Recurrent patterns of TOP1-mediated neuronal genomic damage shared by major neurodegenerative disorders

The paper identifies a shared TOP1-mediated mutagenic mechanism in ALS, FTD, and AD through single-cell genomic analysis and experimental validation.

Topographical archetypes of somatic mutagenesis in cancer

The paper introduces MuTopia, a framework that identifies topographic archetypes of mutagenesis in cancer genomes, revealing that mutational processes are constrained by replication timing and chromatin state.

A recurrent sequencing artifact on Illumina sequencers with two-color fluorescent dye chemistry and its impact on somatic variant detection

The paper identifies a sequencing artifact in Illumina NovaSeq 6000 two-color chemistry that causes T>G substitutions, affecting low-VAF somatic variant detection.

The Common Fund Data Ecosystem (CFDE)

The paper describes the Common Fund Data Ecosystem (CFDE), which integrates NIH Common Fund data resources to enable discovery, analysis, and collaboration across heterogeneous datasets.

Efficient near telomere-to-telomere assembly of Nanopore Simplex reads

The paper introduces hifiasm (ONT), an algorithm that enables near telomere-to-telomere genome assembly using standard ONT Simplex reads, reducing computational demands and improving chromosome reconstruction.

An integrated view of the structure and function of the human 4D nucleome

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

Benchmarking of duplex sequencing approaches to reveal somatic mutation landscapes

This study benchmarks six duplex sequencing technologies to evaluate their performance in detecting somatic mutations across different genomic contexts and tissue types.

Nanopore whole-genome sequencing reveals conserved chromosome-specific telomere architecture across tissues and populations

This study uses Nanopore whole-genome sequencing to show conserved chromosome-specific telomere length patterns across tissues and populations, revealing coordinated regulation and potential disease risk factors.

A comprehensive view of somatic mosaicism by single-cell DNA analysis

The paper uses single-cell DNA sequencing to analyze somatic mosaicism in postmortem lung and colon tissues, revealing mutation heterogeneity, chromosomal abnormalities, and cellular ancestry.

Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes

This study evaluates diploid donor-specific assemblies for improving somatic structural variant detection in cancer genomes, finding they identify more variants and reduce artifacts compared to standard references.

Systematic artifacts from Illumina two-color chemistry confound variant identification and actionability in clinical panels

This study identifies systematic T>G sequencing artifacts in Illumina two-color chemistry that can create false pathogenic variants and inflate tumor mutational burden in clinical panels.

Timing the onset of homologous recombination deficiency before breast cancer diagnosis

The paper estimates the timing of homologous recombination deficiency (HRD) onset in breast cancers using HRDTimer, finding HRD occurs years before diagnosis in different subtypes.

Tissue specificity and chromosomal alterations shape divergent immune programs in HRD tumors

This study identifies two immune archetypes in HRD tumors—immune-inflamed and immune-evasive—linked to chromosomal instability and lineage, informing biomarker-driven therapies.

Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read data

The paper benchmarks somatic variant and indel detection at low allele fractions using short- and long-read data, finding sensitivity and precision around 80% at 300x coverage.

Multi-platform framework for mapping somatic retrotransposition in human tissues

The paper develops a framework to detect and trace somatic retrotransposition events in human tissues, identifying rare L1 insertions and improving detection accuracy.

Comprehensive benchmarking of somatic structural variant detection at ultra-low allele fractions

The paper benchmarks somatic structural variant detection at ultra-low allele fractions using synthetic data and evaluates 12 pipelines, finding long-read sequencing provides higher accuracy than short-read methods.

The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data

The paper introduces a knowledge graph framework for integrating and querying biomedical data across domains, demonstrating its utility in eight use cases.

High-resolution detection of copy number alterations in single cells with HiScanner

HiScanner detects high-resolution copy number alterations in single cells, outperforming existing methods and revealing distinct CNA patterns in neurons and oligodendrocytes.

Contribution of de novo retroelements to birth defects and childhood cancers

The paper identifies de novo retroelements in birth defects and childhood cancers using whole-genome sequencing data and an improved computational tool.

Accurate and sensitive mutational signature analysis with MuSiCal

MuSiCal improves mutational signature analysis by outperforming existing methods in discovery and assignment, revealing new signatures and resolving ambiguities in cancer genomes.

Predicting response to immune checkpoint blockade therapy among mismatch repair-deficient patients using mutational signatures

The paper identifies mutational signatures SBS26 and SBS54 in MMRD tumors that correlate with immune checkpoint blockade response and survival, suggesting their use as prognostic biomarkers.

Cell lineage analysis with somatic mutations reveals late divergence of neuronal cell types and cortical areas in human cerebral cortex

The paper uses somatic mutations to analyze lineage divergence in human cortical regions, finding late divergence of neuronal cell types and regional inhomogeneities in progenitor proliferation.

Contrasting patterns of somatic mutations in neurons and glia reveal differential predisposition to disease in the aging human brain

The paper compares somatic mutation rates in neurons and oligodendrocytes across aging human brains, finding faster mutation accumulation in oligodendrocytes and distinct genomic distribution patterns.