Nicholas J. Schork

This paper introduces a benchmarking framework for predicting perturbation signatures across biological contexts, showing that projection and network-based methods perform well across diverse datasets and contexts.

This study uses human iPSC-derived cortical organoids to model familial Alzheimer's disease and shows that autophagy activators reduce pathological Tau and Aβ accumulation and rescue synaptic loss.

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

This study identifies genetic variants associated with liver fat in normal-weight individuals using GWAS and TWAS, highlighting potential causal genes like SAMM50 and novel associations like RFXANK.

The paper introduces a method to detect boolean asymmetric relationships in gene expression data, identifying heterogeneity driven by asymmetric gene interactions and showing improved classifier performance.

Autism-like MEF2C+/- patient hiPSC models show miRNA-mediated overproduction of astrocytes and hyperactivity of neurons.

The paper identifies genetic subtypes of Alzheimer's disease using PCA and biclustering, finding two disease-specific genetic signatures associated with cognitive decline and pathological markers.

The paper introduces yQTL Pipeline, a tool for QTL discovery and visualization, applied to metabolomics data from NECS, identifying 14,983 mQTLs with improved efficiency.

This paper analyzes 25-year longitudinal blood biomarker data from dolphins to identify age-related interactions and biological variation, showing significant directed interactions and correlated variation between biomarkers.

The paper evaluates 54 polygenic risk scores in long-lived individuals and their offspring, finding lower genetic risk for Alzheimer's, CAD, and lupus, but not for dementia in long-lived individuals.

The paper identifies unique sequence signatures in the 3’-UTR of SARS-CoV-2 and explores their potential role in viral replication, host interaction, and as therapeutic targets.

This study examines how polygenic risk scores for cancer and longevity-associated variants relate to cancer risk and finds that longevity scores do not significantly improve cancer risk prediction beyond cancer-specific scores.

Bisbee detects differential splicing and identifies splice outliers with improved sensitivity and specificity using proteomics validated methods.

The paper identifies von Economo neurons as a regionally specialized subtype of extratelencephalic-projecting excitatory neurons using single nucleus RNA-sequencing and cross-species comparisons.

The paper shows that single-nucleus and single-cell RNA-seq can equally identify neuronal cell types in mouse visual cortex when intronic sequences are included.

The paper identifies a novel human cortical GABAergic interneuron subtype with unique transcriptomic, morphological, and physiological features not observed in rodents.

This study identifies technical artifacts in TCGA germline variant calls, showing how batch effects from DNA amplification confound germline-tumor type associations and recommends removing amplified DNA samples.

This paper improves TWAS power by incorporating prediction uncertainty, finding 45 TWAS genes with 17 novel associations and replicating only 2 of 40 previously reported genes.