Bryan R. Lajoie

The paper introduces a platform that directly sequences 3'UTRs and guide RNAs in fixed cells alongside protein abundance and morphology, enabling CRISPR screening in lung cancer cells.

This paper introduces a simplified hybrid capture method that eliminates PCR and bead-based steps while maintaining specificity and improving variant calling.

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.

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.

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

The paper develops a benchmark for detecting low-frequency mosaic variants in the HG002 reference material using high-coverage sequencing data and validates its utility across multiple technologies.

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

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.

The paper evaluates variant calling in difficult genomic regions using short- and long-read sequencing, showing improved performance with new methods and multi-technology approaches.

ExpansionHunter Denovo detects known and novel repeat expansions in short-read sequencing data without requiring predefined repeat catalogs.

A haplotype-resolved Hi-C approach reveals structured homolog pairing in early Drosophila embryos, correlated with Zelda-mediated chromatin accessibility.

The paper uses haplotype-resolved Hi-C to reveal structured homolog pairing and its global impact on gene activity in hybrid Drosophila cells.

ExpansionHunter is a tool for accurately genotyping short tandem repeats, particularly in complex regions with adjacent variants or imperfect repeats.

The paper evaluates reproducibility and quality measures for Hi-C data using real and simulated datasets, showing that specialized methods outperform simple correlation analysis.

This study develops a method to probe mRNA 3D structures and finds that pre-translational mRNPs form linear rod-like structures without strong end interactions.

This study evaluates copy number variant detection in clinical whole genome sequencing, finding it as sensitive as microarrays with additional variants, and identifies clinically significant CNVs in 15% of cases.

This paper presents an integrative framework to detect structural variants in cancer genomes using multiple methods and finds that non-coding structural variation significantly impacts genome function in cancer cells.

This paper investigates the mechanism of nuclear inversion in rod photoreceptors by combining Hi-C, microscopy, and polymer modeling, revealing that heterochromatin interactions drive phase separation and that lamina interactions maintain conventional nuclear organization.

The paper introduces ExpansionHunter, a tool for detecting long repeat expansions from PCR-free WGS data, achieving high sensitivity and specificity in identifying pathogenic expansions.