Michael Levine

FiberBrowser converts diverse single-molecule footprinting datasets into a unified representation for analyzing chromatin structure and function across assays.

This study identifies genetic and cellular mechanisms underlying visual system evolution in Heliconius butterflies by analyzing compound eye cell types across species.

The paper tracks regulatory divergence in hybrid embryos of Ciona species, showing how allelic differences are maintained or remodeled in lineage-specific ways and how GRN hierarchy influences allelic divergence.

The paper identifies chromosomal metaloops in Drosophila brains and shows their role in organizing gene expression patterns through metadomains.

The paper introduces Domino, a deep learning framework that models sequence-to-function relationships to uncover the context-specific grammar of Drosophila chromatin insulation.

The paper identifies distal and interchromosomal chromatin interactions in T cells using a new algorithm and links them to gene regulation through epigenomic analysis.

This paper investigates the role of Lmx1 in Ciona neural tube closure, finding that its knockdown causes defects and overexpression disrupts cell intercalation, suggesting a conserved role in chordate morphogenesis.

The paper investigates how cohesin-mediated loop extrusion and tethering elements contribute to enhancer-promoter interactions in Drosophila embryos using imaging, genetics, and simulations.

The paper shows that cell number control via Cdkn1.b in Ciona embryos affects cell fate, leading to heart development failure when cell division is arrested early.

The paper identifies cis-regulatory modules in Drosophila that act as an intrinsic chromatin timer, setting temporal thresholds for gene expression during development.

The paper identifies a transcriptional network involving Lmx1, Cdkn1b, and Msx that coordinates neural tube closure in Ciona, showing a pair-rule-like pattern and cell-cycle regulation.

This paper examines corticostriatal development in the R6/2 mouse model of juvenile Huntington disease, finding early cortical malformations and transient synaptic deficits that normalize by postnatal day 21.

The paper presents a proteome atlas of Ciona covering eight developmental stages and ~7,000 genes, showing maximal divergence during mid-developmental stages contrary to the hourglass model.

The paper shows that lncRNA read-through from the Fub-1 boundary in Drosophila inactivates its insulating activity in PS6/A1.

The paper studies the timing of zygotic genome activation in Ciona intestinalis using FGF signaling and finds that two Prdm1 homologs are the earliest genes induced, with a sharp transition in FGF responsiveness between 8- and 16-cell stages.

The paper investigates cereblon's role in muscle differentiation in Ciona embryos, finding it regulates contractility gene expression timing through interactions with Tbx6 and Snail.

The paper shows ERK signaling dissolves ERF repression condensates in Ciona embryos through dynamic phase separation regulated by cell signaling.

DeepArk uses deep learning to model cis-regulatory codes in four model species, accurately predicting regulatory features and variant impacts.

The paper shows that 3D chromatin organisation and gene regulation are independent during Drosophila dorsoventral patterning, with chromatin structure maintaining consistency across tissues despite differences in gene expression.

The paper investigates the role of liquid-liquid phase separation in transcriptional repression by studying Hes/Gro complexes in Ciona embryos and their behavior during cell cycles.