Hernán G. García
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View article: Biological Processes as Exploratory Dynamics
Biological Processes as Exploratory Dynamics Open
Many biological processes can be thought of as the result of an underlying dynamics in which the system repeatedly undergoes distinct and abortive trajectories with the dynamical process only ending when some specific process, purpose, str…
View article: Biological Processes as Exploratory Dynamics
Biological Processes as Exploratory Dynamics Open
Many biological processes can be thought of as the result of an underlying dynamics in which the system repeatedly undergoes distinct and abortive trajectories with the dynamical process only ending when some specific process, purpose, str…
View article: The Dynamics of Inducible Genetic Circuits
The Dynamics of Inducible Genetic Circuits Open
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches a…
View article: Novel Fluorescent and Photoconvertible Fusions Reveal Dorsal Activator Dynamics
Novel Fluorescent and Photoconvertible Fusions Reveal Dorsal Activator Dynamics Open
Over the last two decades, new in vivo and in cellulo imaging technologies have uncovered the inherently dynamic nature of transcriptional regulation in embryonic development and, in particular, in the fruit fly D. melanogaster . These tec…
View article: Global maps of transcription factor properties reveal threshold-based formation of DNA-bound and mobile clusters
Global maps of transcription factor properties reveal threshold-based formation of DNA-bound and mobile clusters Open
The relationship between bulk transcription factor concentration and DNA binding has been a central question in gene regulation for decades. Recent studies propose that DNA-bound transcription factor hubs, or clusters, aid in fast and prec…
View article: Transcription factor hubs exhibit gene-specific properties that tune expression
Transcription factor hubs exhibit gene-specific properties that tune expression Open
The spatial and temporal control of gene expression relies on transcription factors binding to and occupying their target sites. Transcription factor hubs—localized, high-concentration microenvironments—promote transcription by facilitatin…
View article: Deciphering regulatory architectures of bacterial promoters from synthetic expression patterns
Deciphering regulatory architectures of bacterial promoters from synthetic expression patterns Open
For the vast majority of genes in sequenced genomes, there is limited understanding of how they are regulated. Without such knowledge, it is not possible to perform a quantitative theory-experiment dialogue on how such genes give rise to p…
View article: Predictive Modeling of Gene Expression and Localization of DNA Binding Site Using Deep Convolutional Neural Networks
Predictive Modeling of Gene Expression and Localization of DNA Binding Site Using Deep Convolutional Neural Networks Open
Despite the sequencing revolution, large swaths of the genomes sequenced to date lack any information about the arrangement of transcription factor binding sites on regulatory DNA. Massively Parallel Reporter Assays (MPRAs) have the potent…
View article: Author response: Unified bursting strategies in ectopic and endogenous even-skipped expression patterns
Author response: Unified bursting strategies in ectopic and endogenous even-skipped expression patterns Open
View article: Unified bursting strategies in ectopic and endogenous even-skipped expression patterns
Unified bursting strategies in ectopic and endogenous even-skipped expression patterns Open
Transcription often occurs in bursts as gene promoters switch stochastically between active and inactive states. Enhancers can dictate transcriptional activity in animal development through the modulation of burst frequency, duration, or a…
View article: Flexibility and sensitivity in gene regulation out of equilibrium
Flexibility and sensitivity in gene regulation out of equilibrium Open
Cells adapt to environments and tune gene expression by controlling the concentrations of proteins and their kinetics in regulatory networks. In both eukaryotes and prokaryotes, experiments and theory increasingly attest that these network…
View article: Optogenetic dissection of transcriptional repression in a multicellular organism
Optogenetic dissection of transcriptional repression in a multicellular organism Open
View article: Energy Aware Technology Mapping of Genetic Logic Circuits
Energy Aware Technology Mapping of Genetic Logic Circuits Open
Energy and its dissipation are fundamental to all living systems, including cells. Insufficient abundance of energy carriers─as caused by the additional burden of artificial genetic circuits─shifts a cell's priority to survival, also impai…
View article: Author response: Unified bursting strategies in ectopic and endogenous even-skipped expression patterns
Author response: Unified bursting strategies in ectopic and endogenous even-skipped expression patterns Open
View article: Unified bursting strategies in ectopic and endogenous even-skipped expression patterns
Unified bursting strategies in ectopic and endogenous even-skipped expression patterns Open
Transcription often occurs in bursts as gene promoters switch stochastically between active and inactive states. Enhancers can dictate transcriptional activity in animal development through the modulation of burst frequency, duration, or a…
View article: Spatial microenvironments tune immune response dynamics in the <i>Drosophila</i> larval fat body
Spatial microenvironments tune immune response dynamics in the <i>Drosophila</i> larval fat body Open
Immune responses in tissues display complex spatial patterns of gene expression that are linked to disease outcomes. However, the mechanisms that generate these patterns—including the relative roles of noisy gene expression dynamics, micro…
View article: Energy Aware Technology Mapping of Genetic Logic Circuits
Energy Aware Technology Mapping of Genetic Logic Circuits Open
Energy and its dissipation are fundamental to all living systems, including cells. Insufficient abundance of energy carriers -as caused by the additional burden of artificial genetic circuits-shifts a cell’s priority to survival, also impa…
View article: Targeted mutagenesis of specific genomic DNA sequences in animals for the<i>in vivo</i>generation of variant libraries
Targeted mutagenesis of specific genomic DNA sequences in animals for the<i>in vivo</i>generation of variant libraries Open
Understanding how the number, placement and affinity of transcription factor binding sites dictates gene regulatory programs remains a major unsolved challenge in biology, particularly in the context of multicellular organisms. To uncover …
View article: Deciphering regulatory architectures from synthetic single-cell expression patterns
Deciphering regulatory architectures from synthetic single-cell expression patterns Open
For the vast majority of genes in sequenced genomes, there is limited understanding of how they are regulated. Without such knowledge, it is not possible to perform a quantitative theory-experiment dialogue on how such genes give rise to p…
View article: Single-cell transcriptional dynamics in a living vertebrate
Single-cell transcriptional dynamics in a living vertebrate Open
The ability to quantify transcriptional dynamics in individual cells via live imaging has revolutionized our understanding of gene regulation. However, such measurements are lacking in the context of vertebrate embryos. We addressed this d…
View article: Optogenetic control of YAP reveals a dynamic communication code for stem cell fate and proliferation
Optogenetic control of YAP reveals a dynamic communication code for stem cell fate and proliferation Open
View article: Temperature variation drives coordinated scaling of temporal and dynamic features of transcription in embryonic development
Temperature variation drives coordinated scaling of temporal and dynamic features of transcription in embryonic development Open
Temperature affects the timing of development in most poikilothermic organisms that cannot regulate their internal body temperature. In the fruit fly, Drosophila melanogaster , similar quantitative trends characterize changes in the timing…
View article: Unified bursting strategies in ectopic and endogenous even-skipped expression patterns
Unified bursting strategies in ectopic and endogenous even-skipped expression patterns Open
Transcription often occurs in bursts as gene promoters switch stochastically between active and inactive states. Enhancers can dictate transcriptional activity in animal development through the modulation of burst frequency, duration, or a…
View article: Unified bursting strategies in ectopic and endogenous even-skipped expression patterns
Unified bursting strategies in ectopic and endogenous even-skipped expression patterns Open
Transcription often occurs in bursts as gene promoters switch stochastically between active and inactive states. Enhancers can dictate transcriptional activity in animal development through the modulation of burst frequency, duration, or a…
View article: Author Response: Unified bursting strategies in ectopic and endogenous even-skipped expression patterns
Author Response: Unified bursting strategies in ectopic and endogenous even-skipped expression patterns Open
Transcription often occurs in bursts as gene promoters switch stochastically between active and inactive states. Enhancers can dictate transcriptional activity in animal development through the modulation of burst frequency, duration, or a…
View article: A bistable autoregulatory module in the developing embryo commits cells to binary expression fates
A bistable autoregulatory module in the developing embryo commits cells to binary expression fates Open
Bistable autoactivation has been proposed as a mechanism for cells to adopt binary fates during embryonic development. However, it is unclear whether the autoactivating modules found within developmental gene regulatory networks are bistab…
View article: Flexibility and sensitivity in gene regulation out of equilibrium
Flexibility and sensitivity in gene regulation out of equilibrium Open
Cells adapt to environments and tune gene expression by controlling the concentrations of proteins and their kinetics in regulatory networks. In both eukaryotes and prokaryotes, experiments and theory increasingly attest that these network…
View article: DRMY1 promotes robust morphogenesis by sustaining the translation of cytokinin signaling inhibitor proteins
DRMY1 promotes robust morphogenesis by sustaining the translation of cytokinin signaling inhibitor proteins Open
SUMMARY Robustness is the invariant development of phenotype despite environmental changes and genetic perturbations. In the Arabidopsis flower bud, four sepals robustly initiate and grow to constant size to enclose and protect the inner f…
View article: Competing constraints shape the nonequilibrium limits of cellular decision-making
Competing constraints shape the nonequilibrium limits of cellular decision-making Open
Gene regulation is central to cellular function. Yet, despite decades of work, we lack quantitative models that can predict how transcriptional control emerges from molecular interactions at the gene locus. Thermodynamic models of transcri…
View article: Unified bursting strategies in ectopic and endogenous even-skipped expression patterns - Supplemental Data
Unified bursting strategies in ectopic and endogenous even-skipped expression patterns - Supplemental Data Open
This dataset contains the supplemental data of the article "Unified bursting strategies in ectopic and endogenous even-skipped expression patterns".