Shawn Levy

CellCage™ Technology Enables High-throughput Isolation of Defined Cell Combinations to Resolve the Determinants of CAR-T mediated Cytotoxicity

The paper introduces CellCage™ technology to isolate defined cell combinations for high-throughput analysis of CAR-T cell cytotoxicity, revealing functional heterogeneity and cooperative behavior in T cell-mediated killing.

Scalable longitudinal imaging and transcriptomics of cells in dynamic enclosures

This paper develops a platform for longitudinal imaging and transcriptomics of live cells, revealing adaptive drug-resistant states and key drivers of cellular function through integrated analysis.

Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance

The paper presents T2T reference genomes from a multi-generational pedigree to study genetic and epigenetic inheritance across the complete genome.

Accurate human genome analysis with Element Avidity sequencing

This study compares Element Avidity sequencing to Illumina sequencing, finding higher accuracy in mapping and variant calling, especially at lower coverages and in challenging genomic regions.

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

The paper describes a comprehensive genomic dataset from a tumor-normal pair with broad consent, generated using multiple sequencing technologies for benchmarking somatic variant detection.

FLEXIBLE, PRODUCTION-SCALE, HUMAN WHOLE GENOME SEQUENCING ON A BENCHTOP SEQUENCER

This paper demonstrates high-quality, scalable human whole-genome sequencing on a benchtop sequencer, achieving 30x coverage with flexibility and cost-effectiveness.

A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree

The paper uses a four-generation family to systematically assess de novo mutations and recombination, finding high mutation rates and paternal bias, along with a detailed recombination map.

A common flanking variant is associated with enhanced meiotic stability of the FGF14-SCA27B locus

The paper identifies a common flanking variant linked to increased meiotic stability at the FGF14-SCA27B repeat locus.

Characterizing and addressing error modes to improve sequencing accuracy

The paper demonstrates achieving over 70% Q50 accuracy on the AVITI sequencer by improving sequencing quality and mitigating library preparation and analysis errors.

Utility of long-read sequencing for All of Us

The paper compares short-read and long-read sequencing in the All of Us initiative, finding HiFi reads provide the most accurate variant calling and presents a cloud-based pipeline for long-read analysis.

Sequencing by avidity enables high accuracy with low reagent consumption

This paper introduces avidity sequencing, a new chemistry that improves sequencing accuracy and reduces reagent use, enabling applications like single-cell RNA-seq and whole-genome sequencing.

Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases

GEM, an AI-based tool, ranks causal genes highly for rare genetic diseases, improving diagnostic efficiency and reducing manual effort.

Combinatorial transcription factor profiles predict mature and functional human islet α and β cells

The paper identifies combinatorial transcription factor expression in human islet cells and shows it correlates with functional maturity and electrophysiological activity.

Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions

This study uses rapid diagnostics and metatranscriptomics to analyze SARS-CoV-2 infection, revealing viral evolution, host responses, and drug interactions in NYC samples.

Quality Control Metrics for Whole Blood Transcriptome Analysis in the Parkinson's Progression Markers Initiative (PPMI)

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

Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study

The paper assesses DNA sequencing performance across multiple platforms using human and bacterial reference genomes to evaluate quality and reproducibility.

Single-Cell, Human Sperm Transcriptomes and Variants from Fathers of Autistic and Healthy Children

The paper analyzes single-cell sperm RNA-seq data from fathers of autistic and healthy children to identify mutation clusters and expression differences associated with ASD risk.

Extremely rare variants reveal patterns of germline mutation rate heterogeneity in humans

The paper analyzes rare variants to uncover mutation rate heterogeneity in the human genome, identifying genomic features that influence mutation rates.

Genomic sequencing identifies secondary findings in a cohort of parent study participants

The paper reports secondary findings in parents of children with developmental delay through genomic sequencing, identifying clinically relevant variants in 9% of participants.

Narrow-sense heritability estimation of complex traits using identity-by-descent information.

This paper estimates narrow-sense heritability using identity-by-descent information in unrelated individuals and finds that IBD-based methods can capture rare variant contributions but are affected by stratification.

Comprehensive Benchmarking and Ensemble Approaches for Metagenomic Classifiers

This study benchmarks eleven metagenomic classifiers using 846 species and evaluates strategies to reduce false positives in taxonomic classification.