W. J. Greenleaf

Rampant transcription replication conflict creates therapeutic vulnerability in extrachromosomal DNA containing cancers

This paper identifies transcription-replication conflict as a vulnerability in ecDNA-containing cancers and demonstrates that CHK1 inhibition selectively kills these tumors.

Epigenetic signature and key transcriptional regulators of human antigen-specific type 1 regulatory T cells

This study identifies the epigenetic signature and key transcription factors regulating human antigen-specific Tr1 cells, revealing their unique biology and potential for therapeutic applications.

High-Throughput DNA melt measurements enable improved models of DNA folding thermodynamics

This paper introduces a high-throughput method to measure DNA melting and develops models to improve DNA folding thermodynamics predictions.

Expression of terminal deoxynucleotidyl transferase (TdT) identifies lymphoid-primed progenitors in human bone marrow

The paper identifies TdT-expressing progenitors in human bone marrow that show lymphoid potential while retaining myeloid capacity, redefining the lympho-myeloid axis.

Short tandem repeats bind transcription factors to tune eukaryotic gene expression

This study shows STRs modulate TF-DNA interactions by altering binding affinities and on rates, impacting gene expression through increased TF density near target sites.

Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH

This study introduces CRISPR-CATCH, a method to purify and analyze extrachromosomal DNA, revealing hypomethylation and structural details of ecDNA in cancer cells.

The STAT5-IRF4-BATF pathway drives heightened epigenetic remodeling in naïve CD4+ T cell responses of older adults

The paper examines age-related changes in T cell responses by analyzing transcriptional and epigenetic profiles of naive CD4+ T cells from young and older adults, identifying increased epigenetic remodeling and effector cell differentiation.

LKB1 inactivation modulates chromatin accessibility to drive metastatic progression

This study shows that LKB1 inactivation alters chromatin accessibility, promoting metastatic progression in lung cancer through SOX17 activation.

Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19

Single-cell multi-omic profiling identifies immune dysregulation in severe COVID-19, including neutrophil hyperactivation and anti-inflammatory monocytes.

Quantification of Cas9 binding and cleavage across diverse guide sequences maps landscapes of target engagement

The paper quantifies Cas9 binding and cleavage across diverse guide sequences, revealing sequence-specific variations in efficacy and specificity, and develops a predictive biophysical model.

Automated design of highly diverse riboswitches

This paper introduces an automated method, RiboLogic, to design diverse riboswitches and validates them experimentally, showing improved performance in modulating molecular interactions.

Quantitative high-throughput tests of ubiquitous RNA secondary structure prediction algorithms via RNA/protein binding

The paper quantitatively tests RNA secondary structure prediction algorithms using RNA-MaP, revealing significant deviations between predictions and experimental stabilities.

A quantitative and predictive model for RNA binding by human Pumilio proteins

The paper develops a predictive model for RNA binding by human PUM1 and PUM2 using RNA-MaP data, showing residue flipping and positional coupling, and validates it against in vivo crosslinking data.