Renhe Luo

Open-source STAR binary for five transcriptomic assays runs 3.9- to 6.2-fold faster than Cell Ranger 9.0.1 for scRNA-seq and Perturb-seq, 17- to 41-fold for Flex, with closely concordant counts.

FourC identifies significant and differential contacts in 4C-seq data using a Bayesian model and Gaussian processes to address duplication and model spatial patterns.

The paper identifies pre-established chromatin regions in human ESCs that enable rapid activation of lineage-specific genes during differentiation.

This paper develops a human organoid model of early PDAC that identifies genetic and epigenetic barriers to lineage plasticity, showing CDKN2A loss is essential with KRAS/TP53 mutations and TET1 suppression links ERK signaling to transcription factor silencing.

This study uses a knockout village framework to analyze how mutations in diabetes genes alter pancreatic beta cell development, revealing non-canonical cell fate shifts and identifying ISL1 as a key regulator.

This study uses Perturb-seq to analyze how varying levels of pluripotency regulators affect hESC self-renewal and differentiation through single-cell RNA-seq.

The paper identifies two NANOG enhancers in human embryonic stem cells and shows their critical role in maintaining self-renewal and preventing differentiation.

ChromaFold predicts 3D chromatin contact maps from scATAC-seq data, outperforming bulk-based methods and enabling cell-type-specific interaction analysis.

The paper uses CRISPR-Cas9 screens to identify genes affecting stem cell fitness versus pluripotency identity, finding distinct and overlapping roles for chromatin and metabolic regulators.

The paper identifies a long-range enhancer for ONECUT1 involved in pancreatic differentiation and links a diabetes risk variant to disrupted transcription factor binding.

The paper uses a CRISPRi screen in hESC differentiation to identify enhancers with nonlinear regulatory activity, revealing a CTCF loop-constrained model for improved enhancer prediction.