David Wesley Craig

This study develops a custom probe-based spatial transcriptomics method for detecting microbiomes in FFPE colorectal cancer tissue, showing spatially patterned bacterial signals and preserving host transcriptomic structure.

This paper introduces a causal inference framework using extrachromosomal DNA as an instrumental variable to disentangle oncogene dosage effects from downstream cellular effects in spatial multi-omics data.

This study uses single-cell whole genome sequencing and spatial transcriptomics to uncover intra-tumoral heterogeneity in ovarian cancer, revealing evolutionary relationships and functionally consequential copy number alterations.

This study links elevated methylglyoxal-adducts and GLO1 genetic variants in African American/Black men with prostate cancer progression through metabolic reprogramming and impaired detoxification.

This study identifies distinct molecular features of early-onset colorectal cancer in Hispanic/Latino patients through multi-omics analysis, revealing significant WNT pathway alterations and potential therapeutic targets.

The paper identifies decreased SNCA expression in Parkinson's Disease blood samples after correcting for immune cell effects, suggesting it as a potential transcriptomic biomarker.

The paper presents a multi-omics dataset for genetic subtypes of frontotemporal dementia to identify molecular mechanisms disrupted in the disease.

The paper presents a multi-layered molecular dataset from iPSC-derived dopaminergic neurons to model Parkinson's disease genetic risk and provides a data browser for accessing these resources.

This paper develops an automated ML model to predict Parkinson's Disease using multi-modal data, achieving high AUC scores and constructing gene networks relevant to PD.

The paper identifies genomic subtypes of multiple myeloma using the MMRF CoMMpass study and finds that 25.5% of patients transition to a high-risk expression subtype at progression, which expresses immunotherapy targets.

The paper identifies human-lineage-specific genomic elements, called CNCRs, and shows their enrichment in neurological disease genes and APOE intron-3 retention transcripts in Alzheimer's disease.

The paper analyzes sncRNA-seq data from the PPMI cohort to identify miRNAs associated with Parkinson's disease progression and systemic inflammation.

The paper quantifies technical variability in whole blood transcriptome data from the PPMI study using pooled reference samples and describes the dataset's availability.

miEAA 2.0 enhances miRNA enrichment analysis by supporting multiple species, adding new categories, and providing API access, with case studies in human and mouse data.

The paper identifies genes associated with Rett syndrome-like (RTT-L) phenotype through whole exome sequencing and protein-protein interaction network analysis, revealing shared pathways with classical Rett syndrome.

The paper examines common genetic variants' contribution to bipolar disorder risk in multiplex families and finds higher polygenic risk scores in affected individuals compared to controls and unaffected family members.

Across 37,688 Parkinson's cases, 18,618 proxy-cases and 1.4M controls, 90 risk signals map to 78 loci (37 new); an 1805-variant polygenic score explains 26-36% of heritability.

This study identifies 73 genome-wide significant loci for mood disorders, revealing shared and distinct genetic factors between major depressive disorder and bipolar disorder.

The paper uses single-cell sequencing of genomic DNA to resolve sub-clonal heterogeneity in the COLO829 cell line, identifying four major sub-clones and explaining conflicting bulk sequencing results.

This study identifies 30 genome-wide significant loci associated with bipolar disorder, including novel genes involved in ion channels, neurotransmitters, and synaptic components.

This study identifies 114 genome-wide significant loci for schizophrenia and bipolar disorder, with specific subphenotype associations and four genes distinguishing the disorders.