Bomyi Lim

Live Droplet Single-Cell RNA Sequencing

The paper introduces Live D-seq, a method for longitudinal, non-destructive single-cell RNA sequencing, and demonstrates its ability to track cellular dynamics over time.

Insulators As Dynamic, Tunable Regulators of Enhancer-Promoter Coordination in Living Drosophila Embryos

This study shows insulators dynamically enhance enhancer-promoter coordination in Drosophila embryos through looping and coordination of transcriptional bursts.

Enhancer Placement Impacts Transcriptional Dynamics in Drosophila Embryos

This study shows that enhancer-promoter configurations in Drosophila embryos affect transcriptional dynamics, with downstream enhancer positioning reducing mRNA output by 70%.

SCO-pH: Microfluidic dynamic phenotyping platform for high-throughput screening of single cell acidification

SCO-pH enables high-throughput single-cell acidification analysis by compartmentalizing cells in microfluidic droplets and measuring extracellular pH changes to distinguish metabolic states.

Regulation of Transcriptional Bursting and Spatial Patterning in Early Drosophila Embryo Development

The paper analyzes transcriptional bursting in Drosophila embryos to understand how spatial gene expression patterns are established despite variability in transcriptional activity.

MYC and AP-1 oncogenes synergistically bind enhancers to rewire transcription

The paper identifies TRE motifs as indirect MYC binding sites that synergize with AP-1 at enhancers, leading to transcriptional rewiring in cancer.

Heterogeneous Sox2 transcriptional dynamics mediate pluripotency maintenance in mESCs in response to LIF signaling perturbations

This study investigates how LIF signaling perturbations affect Sox2 transcriptional dynamics in mESCs, revealing that reduced Sox2 expression, not complete loss, drives pluripotency loss.

3D dynamics of trans enhancer-promoter interactions in living Drosophila embryos reveals spatiotemporal thresholds for transcription activation

The paper investigates the spatiotemporal requirements for transcription activation by analyzing enhancer-promoter interactions in living Drosophila embryos using transvection and 3D imaging.

Multifaceted effects on even-skipped transcriptional dynamics upon Kruppel dosage changes

This study examines how halving Kruppel dosage affects even-skipped transcriptional dynamics in Drosophila embryos, revealing nonlinear relationships between TF dosage and developmental phenotypes through direct and indirect interactions.

Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos

The paper investigates how multiple TF binding sites modulate enhancer activity in Drosophila embryos, showing that cooperative binding increases transcriptional output and affects promoter dynamics.

Enhancer-promoter competition between homologous alleles leads to reduced transcription in early Drosophila embryos

The paper investigates allelic competition in Drosophila embryos, finding that homozygous alleles produce fewer RNAs than hemizygous alleles due to transcriptional machinery interference.

The nuclear to cytoplasmic ratio directly regulates zygotic transcription in Drosophila through multiple modalities

This study shows that the nuclear to cytoplasmic ratio regulates zygotic transcription in Drosophila through multiple mechanisms, independent of cell cycle length.

Synthesizing developmental trajectories

The paper develops a semi-supervised learning framework to integrate heterogeneous biological data and demonstrates its application in analyzing Drosophila pattern formation.

A Novel function for Cactus/IκB inhibitor to promote Toll signals in the Drosophila embryo

The paper shows that Cactus promotes Toll signals in Drosophila embryos by modulating Dorsal nuclear localization, revealing differential behavior of the Dorsal gradient in response to Cactus concentrations.