Hernán G. García

The paper uses live-imaging and computational modeling to show that Dorsal hub formation in Drosophila embryos depends on TF-DNA binding kinetics, not enhancer sequence or higher-order regulatory structures.

This study measures single-cell transcriptional dynamics in zebrafish embryos using MS2-MCP labeling and light sheet microscopy, revealing discrete transcriptional bursts in the segmentation clock.

The paper introduces an algorithm to identify condition-dependent transcription factor binding sites by compressing promoter sequences into hyperletters, validated on E. coli data.

This paper introduces DARSI, a deep learning model that predicts gene expression and transcription factor binding sites from DNA sequences using MPRA data.

This paper uses statistical mechanical models to study how endogenous signaling parameters, such as effector concentrations, influence the stability of genetic circuits in living cells, contrasting with traditional approaches that rely on Hill functions and manually tuned parameters.

The paper quantifies Dorsal concentration, binding, and mobility in Drosophila embryos, revealing threshold-based formation of DNA-bound and mobile clusters linked to gene regulation.

The paper investigates spatial patterns of antimicrobial peptide expression in Drosophila larval fat body, finding that these patterns are predetermined and correlate with fluid flow.

The paper introduces a model linking chromatin and enhancer states to transcriptional bursting dynamics, using the Monod-Wyman-Changeux framework to predict bursting behavior in C. elegans.

The paper proposes exploratory dynamics as a framework for understanding biological processes that achieve specific outcomes through repeated, random trajectories.

The paper introduces four new fluorescent protein fusions for Dorsal to study its dynamics in fruit fly embryos.

The paper investigates transcriptional bursting strategies in endogenous and ectopic even-skipped expression in fruit flies, finding consistent bursting patterns despite different regulatory contexts.

This paper introduces Energy Aware Technology Mapping to design genetic logic circuits with energy efficiency and functionality, showing energy efficiency improves by 37.2% over functionally optimized variants.

The paper develops a method to generate variant libraries in vivo using base editing to study gene regulatory programs in multicellular organisms.

The paper creates synthetic single-cell gene expression data using thermodynamic models to better understand and optimize MPRA experiments for regulatory architecture inference.

The paper shows that temperature affects transcription dynamics in Drosophila embryos, with relative rates and total mRNA production remaining temperature-independent.

The paper uses live imaging and mathematical modeling to show that the ftz autoregulatory module in fruit flies is bistable and commits cells to binary fates.

The paper shows that DRMY1 sustains translation of cytokinin signaling inhibitors, ensuring robust sepal development in Arabidopsis by maintaining auxin patterning.

The paper uses a minimal synthetic enhancer in Drosophila to show that a single Dorsal binding site can regulate transcriptional engagement probability and timing in response to a morphogen gradient.

The paper uses live imaging to study the transcriptional dynamics of the Drosophila even-skipped gene, revealing how transcriptional bursting shapes its stripe expression pattern.

The paper quantifies the relationship between bacterial growth rate, cell size, and protein content in E. coli using proteomic data, finding ribosome biogenesis as a primary determinant of growth rate.

This paper introduces a genetically-encoded fluorescent biosensor that detects protein expression in live cells within seconds, significantly faster than standard fluorescent protein fusions.

The paper studies how transcriptional burst frequency and transcription timing control mRNA pattern formation in Drosophila embryos.

The paper shows how enhancers decode Notch signaling by altering transcription burst duration and requiring priming by transcription factors for sustained activity.

The paper investigates how the Drosophila pioneer factor Zelda enhances transcriptional output of the Dorsal target gene sog by modulating the nuclear microenvironment and increasing Dorsal accumulation at the enhancer.

The paper uses live imaging in Drosophila embryos to show that Bicoid binds DNA with a rapid off-rate and forms localized hubs that enable concentration-sensitive regulation.