Alexander W. Charney

The paper introduces a diploid genomic foundation model to represent diploid genotypes in genomic language models, improving variant discrimination in compound-heterozygous cases.

Wrap a genomic foundation model's inference methods once to score it on supervised and zero-shot GUE, VariantBenchmarks, BEND, TraitGym and ClinVar tasks; code is promised upon acceptance.

This study identifies 207 height-associated genes using rare protein-altering variants from over 1.4 million individuals, showing large effect sizes and overlap with Mendelian height syndromes.

This study compares gene expression in living and postmortem human brain tissue, finding significant differences that challenge the assumption that postmortem data accurately represents living brain gene expression.

The paper maps T cell epitopes in SARS-CoV-2, showing that immunodominant regions are conserved across variants and important for immune surveillance.

This study evaluates imputation performance of reference panels in a Pakistani population, finding that ex1KG outperforms TOPMed despite its smaller size.

This study compares A-to-I RNA editing in postmortem and living human brain tissues, revealing significant differences in editing levels and their association with cellular processes and neurological conditions.

The paper compares gene expression differences between living and postmortem human brain samples using snRNA-seq and develops a model to account for these differences in analysis.

The paper identifies IL10RB as a key regulator of COVID-19 host susceptibility and severity through integrative analysis of genetic and transcriptomic data, and validates potential drug repositioning candidates.

The paper identifies regulatory mechanisms for 21 Alzheimer's disease risk loci in human microglia using transcriptome and chromatin accessibility profiling.

The paper identifies three H1 sub-haplotypes at the 17q21.31 locus associated with Parkinson's disease risk and links them to LRRC37A/2 expression in astrocytes.

This study evaluates the association of genetic risk scores with depression and anxiety diagnoses, finding distinct genetic contributions to their comorbidity.

This study uses transcriptomic imputation to translate AN GWAS findings into gene expression associations, revealing 47 genes linked to AN and their clinical consequences in a biobank cohort.

The paper investigates the conservation of rare schizophrenia risk variants across diverse populations and finds consistent burden in constrained genes.

This study evaluates the prognostic value of polygenic risk scores for schizophrenia and finds they do not improve outcome prediction beyond clinical features.

Meta-analysis of 41,917 European-ancestry bipolar disorder cases versus 371,549 controls yields 64 risk loci (33 novel), neuronal and synaptic gene enrichment, and 15 eQTL-prioritized genes.

This study identifies shared molecular signatures between chronic fatigue syndrome and other fatiguing illnesses using RNA-sequencing data from blood samples.

This paper performs a large-scale eQTL meta-analysis across cerebral cortical and cerebellar brain regions, identifying distinct eQTL patterns and demonstrating improved power over existing studies.

The paper functionally annotates rare structural variants in the human brain by integrating SV calling with RNA-seq data to assess their regulatory effects and prioritize pathogenic deletions.

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.

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

This study evaluates polygenic risk scores for schizophrenia in electronic health records, finding strong associations with schizophrenia and pleiotropic effects on other psychiatric and medical conditions.

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

The study finds that rare copy number variants (CNVs) contribute to bipolar disorder risk primarily in schizoaffective disorder bipolar type cases, with differences in CNV burden and schizophrenia polygenic risk scores between subtypes.

The paper introduces a Bayesian framework to prioritize risk genes for complex diseases by integrating gene-set information with variant counts, identifying novel epilepsy risk genes and linking them to immune pathways and drug targets.

The paper identifies VGF as a key regulator of Alzheimer’s disease using multiscale causal network models and validates its protective role in mouse models.

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

This paper validates EHR-based BD phenotyping algorithms by showing their genetic correlation with traditional BD cases, suggesting they identify genetically similar cases.