Doron Lipson

The paper develops RoboATAC, an automated ATAC-seq method, to study how TF dosage affects chromatin accessibility and gene expression, finding that DNA sequence predicts dosage sensitivity and nucleosome positioning patterns vary by TF.

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.

The paper uses Perturb-seq to systematically identify signaling regulator targets across multiple cell lines and contexts, introducing Mixscale to improve analysis and infer pathway activation changes.

This study shows that early colorectal cancer loses promoter-enhancer connectivity, leading to gene expression changes and a two-phase model of transcriptional regulation.

The paper characterizes age-related and inter-individual variation in circulating hematopoietic stem cells and establishes a normal reference to identify hematological disorders.

The paper benchmarks PIPseq, a single-cell RNA sequencing method, across different scales and models, showing its ability to detect cell types and differentially expressed genes.

This study applies low-cost whole genome sequencing to detect circulating tumor DNA at high sensitivity in plasma samples, achieving error rates as low as 10^-7 and enabling cancer monitoring without matched tumor sequencing.

The paper performs genome-scale Perturb-seq to map genotype-phenotype relationships, uncovering new gene functions and stress-specific mitochondrial regulation.

The paper uses ultra high-throughput methylation sequencing to study DNA methylation changes during colorectal cancer progression from normal tissue to adenocarcinoma.

Open flow cell on a circular wafer with mostly natural nucleotides and no reversible terminators: about 300 bp reads at $1/Gb, 99.6% SNP accuracy on reference human genomes.

The paper benchmarks a new low-cost sequencing by synthesis method for scRNA-seq, showing comparable results to existing technologies and enabling cost-effective large-scale applications.