Daniel C. Nachun

Integrating sequence-to-omics predictions and personal multi-omics for rare variant prioritization

The paper introduces Watershed-DL, a framework integrating sequence-to-omics predictions and multi-omics data to prioritize rare variants, finding it increases prioritized variants by 61.4% and identifies candidate disease alleles.

MetaDome 2027: a comprehensively updated resource for aggregating missense variant evidence across homologous human protein domains

MetaDome now supports GRCh38 alongside GRCh37, adds coordinate lookup, and identifies 52,463 GRCh38 ClinVar missense variants of uncertain significance with uncontradicted pathogenic evidence at homologous Pfam-domain positions.

A Multi-Context Regulome-Wide Association Atlas for Genetic Studies of Aging Brain Disorders

This paper introduces FGMB, a multi-context regulome-wide association atlas, and applies it to Alzheimer's disease to identify 327 regulatory associations and resolve 86 gene-molecular-trait pairs.

Somatic mutations reveal the ontogeny of human microglia

This study uses somatic mutations to track marrow-derived cell infiltration into the human brain, finding widespread microglia replenishment and a protective link between clonal hematopoiesis and Alzheimer's disease.

Focus on single gene effects limits discovery and interpretation of complex trait-associated variants

The paper introduces a multi-gene eQTL mapping framework to detect variants influencing multiple neighboring genes, finding novel loci and improving colocalization with GWAS variants.

SuSiE 2.0: improved methods and implementations for genetic fine-mapping and phenotype prediction

SuSiE 2.0 improves genetic fine-mapping and phenotype prediction with faster performance, better calibration, and new methods like SuSiE-ash.

Long-read genome sequencing and multi-omics in aging and neurodegeneration

The paper uses long-read genome sequencing and multi-omics data to identify structural variants associated with aging and neurodegenerative diseases, finding that SVs are more likely to be causal than SNVs.

Mapping the regulatory effects of common and rare non-coding variants across cellular and developmental contexts in the brain and heart

The paper predicts the regulatory effects of non-coding variants across brain and heart cellular contexts using deep learning, identifying rare variants with significant developmental impacts.

The GENCODE CLS project: massively expanding the lncRNA catalog through capture long-read RNA sequencing

The paper expands the lncRNA catalog using capture long-read RNA sequencing, significantly increasing the number of annotated transcripts in human and mouse genomes.

Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue

This study examines how endurance exercise training affects rat subcutaneous white adipose tissue, revealing sex-specific molecular responses and differences in adiposity and metabolism.

regionalpcs: improved discovery of DNA methylation associations with complex traits

The paper introduces regionalpcs, a method for summarizing DNA methylation patterns, showing improved sensitivity in detecting associations with Alzheimer's disease traits.

Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects

The paper maps interaction QTLs (iQTLs) for cell type, age, and other variables in blood multi-omic data to identify context-specific genetic regulatory effects.

Transcriptomics and chromatin accessibility in multiple African population samples

The paper identifies novel transcripts, eQTLs, and caQTLs in African populations and fine-maps GWAS signals for complex diseases.

Multiset correlation and factor analysis enables exploration of multi-omic data

This paper introduces MCFA, an unsupervised integration method for multi-omic data, and applies it to five omics types across 614 samples to infer shared and private factors.

PRC2 clock: a universal biomarker of aging and rejuvenation

The paper identifies PRC2 low-methylated regions as a universal biomarker of aging and rejuvenation, showing they account for most age-related DNA methylation gain across tissues.

Integration of genetic colocalizations with physiological and pharmacological perturbations identifies cardiometabolic disease genes

The paper integrates genetic colocalizations with physiological and pharmacological perturbations to identify causal genes for cardiometabolic diseases.

An integrated approach to identify environmental modulators of genetic risk factors for complex traits

The paper identifies environmental modulators of genetic risk factors for complex traits by integrating perturbation data with GWAS.

Nonsense-mediated decay is highly stable across individuals and tissues.

The paper assesses NMD efficiency for PTVs across tissues and individuals, finding high concordance and demonstrating in silico prediction using peripheral tissues.

A vast resource of allelic expression data spanning human tissues

The paper presents a large ASE resource from GTEx v8 with 431 million SNP-level and 153 million haplotype-level measurements, and extends phASER to estimate cis regulatory variant effect sizes.

Cell type specific genetic regulation of gene expression across human tissues

The paper uses bulk RNA-seq data to estimate cell type abundances and identifies cell type interaction QTLs that provide finer resolution of tissue specificity than bulk cis-eQTLs.

Determinants of telomere length across human tissues

The paper examines telomere length variation across 6,391 tissue samples from 952 individuals, showing tissue-specific differences, positive correlations between tissues, and associations with age and ancestry.

Diverse transcriptomic signatures across human tissues identify functional rare genetic variation

Integrating expression, allelic expression and splicing across tissues identifies rare variants with relevance to traits.

A Quantitative Proteome Map of the Human Body

The paper quantifies protein levels across 32 human tissues and compares them to transcriptome data, revealing insights into post-transcriptional regulation and disease mechanisms.

Systems analysis of blood transcriptomes in dementia patients reveals an innate immune response shared across disorders

The paper analyzes blood transcriptomes from dementia patients and controls, identifying a shared innate immune response across multiple dementia disorders.

Long non-coding RNA gene regulation and trait associations across human tissues

The paper identifies distinct regulatory patterns and trait associations of lncRNA genes compared to protein-coding genes across human tissues.

Synaptic and Gene Regulatory Mechanisms in Schizophrenia, Autism, and 22q11.2 CNV Mediated Risk for Neuropsychiatric Disorders

The paper integrates transcriptomic, genomic, and proteomic data to identify gene networks and pathways involved in schizophrenia and autism risk, with a focus on 22q11.2 CNVs.

Transcriptional profiling of isogenic Friedreich ataxia induced pluripotent stem cell-derived neurons

This study uses isogenic iPSC-derived neurons to analyze the transcriptomic effects of GAA*TTC repeat expansion in Friedreich ataxia and shows partial restoration with HDACi treatment.