Jennifer A. Mitchell

A Broad-Spectrum Chemokine Inhibitor Prevents Preterm Labor in Mice by Suppressing Inflammation Induced by Intra-Amniotic Injection of Interleukin-1 alpha

This study shows that BSCI prevents preterm labor in mice by reducing inflammation and uterine gene expression changes caused by IL-1.

Temporal chromatin and transcriptome dynamics driven by JUND and progesterone receptor binding in the pregnant mouse myometrium

The paper identifies JUND and progesterone receptor binding dynamics in the pregnant mouse myometrium, linking chromatin accessibility changes to gene expression during pregnancy, labor, and postpartum.

Evolutionary conditioning enables guided generation of functionally diverse enhancers

This paper introduces EnhancAR, a deep learning model that generates functionally diverse enhancers using evolutionary homologs instead of cell type labels.

Enhancers mediate euchromatin hopping at chromatin contact points

The paper shows enhancers mediate euchromatin hopping, spreading euchromatin features to distal regions through chromatin looping, redefining enhancer identification using chromatin features.

Transcriptional repression of SOX2 by p53 in cancer cells regulates cell identity and migration

This paper shows that TP53 represses SOX2 in cancer cells, affecting cell identity and migration, with implications for metastasis in breast cancer.

JUND plays a genome-wide role in the quiescent to contractile switch in the pregnant human myometrium

This study identifies JUND's genome-wide role in regulating the myometrial transition from quiescence to contractility during labor.

A Sox2 Enhancer Cluster Regulates Region-Specific Neural Fates from Mouse Embryonic Stem Cells

This study identifies a cis-regulatory enhancer cluster, SRR2-18, that regulates Sox2 transcription in mouse neural stem/progenitor cells, affecting their regional identity and differentiation into posterior neural fates.

THE CELLS ARE ALL-RIGHT: Regulation of the Lefty genes by separate enhancers in mouse embryonic stem cells

The paper shows that Lefty1 and Lefty2 genes in mouse embryonic stem cells are regulated by separate enhancers despite being in the same TAD.

SOX4 exerts contrasting regulatory effects on labor-associated gene promoters in myometrial cells

This study shows SOX4 regulates labor-associated gene promoters in myometrial cells through interactions with AP-1 factors, with varying effects on different promoters.

Improving the performance of supervised deep learning for regulatory genomics using phylogenetic augmentation

This paper improves supervised deep learning for regulatory genomics by using phylogenetic augmentation to enhance model performance on small datasets.

Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung cancer

The paper identifies an enhancer cluster that drives SOX2 overexpression in breast and lung cancer by altering chromatin accessibility and regulatory mechanisms.

Functional similarity of non-coding regions is revealed in phylogenetic average motif score representations

The paper defines a feature space for non-coding DNA sequences using phylogenetic average motif scores, revealing functional similarity among promoters and 3' UTRs.

High affinity enhancer-promoter interactions can bypass CTCF/cohesin-mediated insulation and contribute to phenotypic robustness

The paper shows that high affinity enhancer-promoter interactions can bypass CTCF/cohesin insulation and maintain gene expression in some tissues but not others.

MYB and ELF3 differentially modulate labor-inducing gene expression in myometrial cells

The paper identifies MYB and ELF3 as transcription factors that differentially regulate labor-inducing gene expression in myometrial cells, with opposing effects on promoter activity.

Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-κB binding

The paper analyzes RELA-bound transposable elements across species to show their ancient and lineage-specific contributions to NF-κB binding and inflammation.

Transcriptional regulation and chromatin architecture maintenance are decoupled modular functions at the Sox2 locus

The paper shows that transcriptional control and chromatin architecture at the Sox2 locus are decoupled, with distinct regulatory mechanisms.

A flexible repertoire of transcription factor binding sites and diversity threshold determines enhancer activity in embryonic stem cells

The paper identifies a diversity threshold of transcription factor binding sites (TFBS) required for enhancer activity in embryonic stem cells, showing that a diverse set of TFBS can replace optimized regulatory sequences.

The pregnant myometrium is epigenetically activated at contractility-driving gene loci prior to the onset of labor in mice

The paper identifies epigenetic activation of contractility-driving genes in the mouse myometrium before labor onset, revealing early H3K27ac enrichment and transcriptional changes during active labor.

KLF4 protein stability regulated by interaction with pluripotency transcription factors overrides transcriptional control

The paper shows that KLF4 protein stability, regulated by interactions with pluripotency factors, overrides transcriptional control in ES cells, and mutations affecting stability prevent differentiation.

Variational Infinite Heterogeneous Mixture Model for Semi-supervised Clustering of Heart Enhancers

The paper introduces a semi-supervised clustering model for identifying active enhancers in mouse heart tissues using heterogeneous genomic data.