Paul T. Spellman

Advancing Precision Health Discovery in a Genetically Diverse Health System

The paper analyzes genetic and health record data from a diverse population to uncover gene-phenotype associations and assess polygenic score performance across ancestries.

Genome-wide classification of tumor-derived reads from bulk long-read sequencing

ROCIT classifies tumor or non-tumor origin of reads from bulk long-read sequencing with high accuracy, improving somatic variant calling in tumors.

Autosomal Allelic Inactivation: Variable Replication and Dosage Sensitivity

The paper identifies and characterizes Autosomal Inactivation/Stability Centers (I/SCs) as loci with allele-specific epigenetic regulation of replication timing and gene expression, showing dosage sensitivity and implications for human diseases.

Methylation dynamics in the decades preceding acute myeloid leukaemia

The paper tracks DNA methylation changes in blood samples up to 15 years before AML diagnosis, identifying DMRs linked to clonal expansions and epigenetic reprogramming.

The history of chromosomal instability in genome doubled tumors

This paper introduces GRITIC, a method to time genomic gains in tumors, finding that copy number gains often accumulate after genome duplication.

ASAR lncRNAs control DNA replication timing through interactions with multiple hnRNP/RNA binding proteins

The paper identifies ASAR lncRNAs as regulators of DNA replication timing through interactions with hnRNP proteins, showing their role in chromosome stability and replication synchronization.

An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences

The paper presents a cost-effective, non-commercial protocol for normalizing TCRβ CDR3 sequencing data to correct amplification bias in bulk TCR repertoire profiling.

Supervised learning of high-confidence phenotypic subpopulations from single-cell data

PENCIL identifies phenotype-relevant cell subpopulations from single-cell data using a supervised learning framework with feature selection and trajectory prediction capabilities.

Epigenetic Control of Hundreds of Chromosome-Associated lncRNA Genes Essential for Replication and Stability

The paper identifies hundreds of epigenetically controlled long noncoding RNA genes essential for chromosome replication and stability, validating their role in chromosomal integrity.

Causal interactions from proteomic profiles: molecular data meets pathway knowledge

The paper introduces a computational method to generate causal explanations for proteomic profiles by integrating molecular data with prior biological pathway knowledge, demonstrating its application in various biological contexts.

Large-scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines

The paper compiles protein response data from cancer cell lines to drug perturbations, showing improved drug sensitivity prediction and building a protein-drug connectivity map with an accessible data portal.

Phenotype-guided subpopulation identification from single-cell sequencing data

Scissor identifies cell subpopulations from single-cell data correlated with specific phenotypes using clinical information, revealing biologically relevant subpopulations in lung and melanoma cancers.

Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6.

The paper identifies a new lncRNA gene, ASAR6-141, that regulates replication timing of human chromosome 6 through reciprocal monoallelic expression and inactivation/stability centers.

Comprehensive characterization of genomic, transcriptomic and epigenomic artifacts introduced in formalin-fixed, paraffin-embedded tissues.

This study characterizes genomic, transcriptomic, and epigenomic artifacts in FFPE tissues and provides best practices to mitigate their impact on molecular analysis.

Context-specificity in causal signaling networks revealed by phosphoprotein profiling

The paper investigates context-specificity in signaling networks using phosphoprotein profiling in breast cancer cell lines under various stimuli and kinase inhibition.