Daniel E. Bauer

The paper shows DNA replication stress redistributes G9a to stalled forks, activates gamma-globin genes, and explains how hydroxyurea increases fetal hemoglobin in sickle cell anemia.

This study identifies IGF2BP1 as a direct and indirect regulator of fetal globin transcripts through m6A modification and interaction with HIC2 and BCL11A.

The paper develops a modular platform for synthesizing bio-orthogonal macromolecular conjugates (BMCs) to enable targeted delivery of macromolecular therapeutics with improved efficiency and specificity.

CRISPRLungo is a computational pipeline for analyzing long-read CRISPR experiments, improving accuracy in detecting structural variants and small indels through UMI-based error correction and benchmarking.

This paper discovers and characterizes SH6, a small molecule degrader of ZBTB7A that increases fetal hemoglobin expression in erythroid cells and shows therapeutic potential for β-hemoglobinopathies.

This paper introduces a method for targeted genomic integration and rearrangement in human cells using CRISPR-targeted dual flap synthesis, enabling DNA sequence assembly without requiring double-stranded DNA donors or cell cycle progression.

This study shows that gene editing of HSCs without ex vivo culture reduces genotoxicity while maintaining therapeutic efficacy for beta-hemoglobinopathy treatment.

This study shows that RNA methylation, specifically m6A, regulates stress granule formation and function during erythropoiesis by modulating ATXN2 expression and RNA translation.

CRISPR-CLEAR maps regulatory elements at nucleotide resolution by directly assessing genotype-phenotype effects through targeted sequencing of CRISPR-introduced alleles.

The paper develops ABSOLVE-seq to assess genome editing off-targets linked to genetic variants using primary cells and sequencing, enabling evaluation of human genetic diversity's impact on gene editing specificity.

This study develops stabilized Cas-embedded base editors (sCE_CBEs) that enable efficient and accurate C-to-T editing with minimal off-target effects in hematopoietic stem and progenitor cells.

This study shows that nucleotide metabolism limits prime editing efficiency in HSPCs and that deoxynucleoside supplementation and Vpx-mediated SAMHD1 degradation enhance it.

Dictys infers dynamic gene regulatory networks from single-cell multi-omics data, revealing context-specific and developmental GRNs in human blood and mouse skin.

The paper develops CRISPRme, a tool that integrates genetic diversity data to assess off-target risks of gene editing, finding allele-specific off-target effects in clinical gRNAs.

This study optimizes the nuclear localization signal (NLS) of Cas12a to enhance editing efficiency in human primary cells without compromising specificity.

This study identifies ZNF410 as a novel repressor of fetal globin by targeting the NuRD complex, offering a new therapeutic target for beta-hemoglobinopathies.

STREAM is an interactive pipeline for reconstructing and visualizing complex branching trajectories from single-cell transcriptomic and epigenomic data.

CRISPResso2 is a software tool for analyzing genome editing data, providing allele-specific quantification and scalable alignment to assess editing efficiency and safety.

CRISPR-SURF deconvolves CRISPR tiling screen data to identify functional regulatory elements across CRISPR-Cas, CRISPRi, and CRISPRa experiments.

CRISPRO maps guide RNA functional scores to genomic and structural coordinates, enabling structure-function relationship analysis and improved guide RNA efficacy prediction.

The paper introduces AmpUMI, a tool for designing and analyzing UMI-based amplicon sequencing experiments, providing a model to determine optimal UMI length and quality control features.

The paper presents a protocol for designing, executing, and analyzing CRISPR genome editing experiments using CRISPOR and CRISPResso.