Jay Shendure

This paper introduces crisprQTL mapping to identify gene regulation by using CRISPR perturbations and single-cell RNA-seq in human cells, finding 128 cis-regulatory elements affecting nearby genes.

The paper shows Dxz4 orientation controls long-range contacts on the inactive X chromosome, maintaining its bipartite structure through CTCF motif direction.

The paper introduces sci-MET, a scalable single-cell DNA methylation sequencing method, achieving 69% read alignment rates and successfully deconvolving a mixture of three human cell lines.

The paper introduces scGESTALT, a method that combines single-cell RNA sequencing with lineage tracking to identify cell types and their developmental relationships in the zebrafish brain.

The paper profiles chromatin accessibility in Drosophila embryos to uncover cis-regulatory programs and cell fate determinants during development.

The paper identifies a major issue with CRISPR-based single cell screens due to guide-barcode swapping and presents an optimized method to improve accuracy.

This paper introduces DNase Hi-C and targeted DNase Hi-C methods for high-resolution mapping of chromatin interactions, overcoming limitations of traditional Hi-C techniques.

This paper introduces THEMIS, a method for analyzing tumor heterogeneity across multiple biopsies, showing improved accuracy over existing methods and applications in tracking cancer progression and treatment resistance.

The paper outlines the goals and structure of the 4D Nucleome Project, which aims to map the spatial and temporal dynamics of the genome in human and mouse cells.

The paper uses Hi-C to assemble genomes from a mixed beer sample, identifying a novel yeast hybrid between Pichia membranifaciens and an undescribed yeast.

This paper introduces sci-RNA-seq, a combinatorial indexing method for single-cell RNA sequencing, and applies it to profile 42,035 C. elegans cells, identifying 27 cell types and their specific genes.

This paper introduces ScanDel, a CRISPR-based method to systematically delete non-coding regions of a gene locus, revealing that distal regulatory elements are not critical for HPRT1 function.

The paper introduces Cicero, a statistical method to link regulatory elements to target genes using single-cell chromatin accessibility data, and applies it to study myogenesis.

This study examines the 3D genome organization in diploid yeast, finding dynamic homolog proximity and environment-induced gene relocalization.

This paper introduces combinatorial single cell Hi-C, a method for measuring chromosome conformation in single cells, and shows its ability to distinguish cell types and reveal chromosomal heterogeneity.

The paper compares chromosomal and episomal enhancer activity using a novel assay, finding significant differences in activity and predictability.

This paper presents a de novo mammalian genome assembly for the domestic goat using long-read sequencing, short-read validation, and chromatin interaction mapping, achieving high contiguity and resolving repetitive regions.

This study introduces a genome editing method to trace whole organism lineages by accumulating mutations in DNA barcodes, showing that most adult zebrafish cells originate from few embryonic progenitors.

MIPSTR is a method for accurate genotyping of STR variation in germ-line and somatic contexts across many individuals, using targeted capture and single-molecule mapping to overcome sequencing challenges.