Héctor García Martín

Genome-scale mapping of plant transcription factor effector domains reveals conserved regulatory principles across eukaryotes

The paper maps transcription factor effector domains in plants and compares their function across eukaryotes, revealing conserved and lineage-specific regulatory principles.

CAZyme domain architectures suggest fine-scale functional differentiation among anaerobic fungi and bacteria during lignocellulose conversion to volatile fatty acids

Prediction of metabolic dynamics through deep learning and high-throughput multiomics data

This paper trains a deep learning model on multiomics data to predict metabolic dynamics in synthetic biology, achieving high accuracy in predicting product and metabolite levels.

Predictive genome-wide CRISPR-mediated gene downregulation for enhanced bioproduction

This study introduces two methods, FluxRETAP and VAMMPIRE, to improve CRISPRi-mediated gene downregulation for bioproduction by enhancing target identification and multiplexed construct assembly.

BioPKS Pipeline: An integrated platform for merging the computational design of chimeric type I polyketide synthases with enzymatic pathways for chemical biosynthesis

BioPKS Pipeline automates the design of chimeric type I polyketide synthases and enzymatic pathways to synthesize target chemicals, achieving exact designs for 93 of 155 tested molecules and proposing routes for complex natural products.

Guide RNA structure design enables combinatorial CRISPRa programs for biosynthetic profiling

The paper designs guide RNA structures for CRISPRa to optimize multi-gene expression in bacterial metabolic pathways, achieving higher product titers and identifying pathway bottlenecks.

Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida

This paper engineers Pseudomonas putida for isoprenol production using computational modeling and strain optimization, achieving a titer of 3.5 g/L.

BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale

BayFlux quantifies metabolic fluxes and their uncertainty using Bayesian inference, showing genome-scale models reduce flux uncertainty compared to core models and improve knockout predictions.

Scalable and Automated CRISPR-Based Strain Engineering Using Droplet Microfluidics

The paper describes a microfluidic system for high-throughput CRISPR-based gene editing and screening, demonstrating its ability to perform parallel genetic modifications in E. coli.

Multiomics data collection, visualization, and utilization for guiding metabolic engineering

The paper presents tools for storing, visualizing, and leveraging multiomics data to predict outcomes of bioengineering efforts.

Identification, characterization, and application of a highly sensitive lactam biosensor from Pseudomonas putida

The paper develops a highly sensitive biosensor for caprolactam and valerolactam from Pseudomonas putida, capable of detecting product titers above background at ~6 g/L.

Robust characterization of two distinct glutarate sensing transcription factors found in Pseudomonas putida L-lysine metabolism

The paper characterizes two glutarate-sensing transcription factors in Pseudomonas putida and develops biosensors to detect glutarate flux for metabolic engineering.