Ian K. Blaby

Sorghum Metabolic Atlas: Large-Scale Subcellular Localization Resource for Sorghum Metabolic Enzymes

The paper experimentally determines subcellular localization of 234 metabolic enzymes in sorghum, providing a resource for metabolic organization studies.

Expanding the Promoter Toolbox for Metabolic Engineering in the Lignocellulolytic Thermophile Anaerocellum bescii

This study identifies and characterizes new promoters in Anaerocellum bescii to enhance metabolic engineering capabilities for ethanol production.

Mapping Genome-wide Transcription Factor Binding Sites in two Rhodanobacter strains Isolated from Extreme Environments

The paper identifies target genes for 31 transcription factors in two Rhodanobacter strains using DAP-seq and comparative genomics, revealing conserved regulatory networks and a key global regulator Clp.

DAP-seq Reveals Cluster-Situated Regulator Control of Numerous Streptomyces Natural Product Biosynthetic Genes

The paper uses DAP-seq to identify CSR regulators of NP biosynthetic genes in Streptomyces, revealing their broad regulatory impact and overlap in BGC control.

Biosensor-Driven Strain Engineering Reveals Key Cellular Processes for Maximizing Isoprenol Production in Pseudomonas putida

The paper uses a biosensor-driven strategy to enhance isoprenol production in Pseudomonas putida through combinatorial strain engineering and omics analysis.

TOR inhibition drives accumulation of amino acids through transcriptional activation in algae

This study shows that TOR inhibition in algae increases amino acid levels through transcriptional activation of biosynthesis pathways and identifies a conserved transcription factor involved in nitrogen metabolism.

Mining thermophile photosynthesis genes: a synthetic operon expressing Chloroflexota species reaction center genes in Rhodobacter sphaeroides

The paper expresses heterologous photosynthesis genes from Chloroflexota in Rhodobacter sphaeroides to study thermophilic photosynthesis and provides metagenomic analysis of high-temperature reaction center sequences.

Recruitment, rewiring, and deep conservation in flowering plant gene regulation

The paper presents a scalable TFBS assay to create an atlas of 3,000 genome-wide binding site maps for 360 TFs across 10 flowering plant species, revealing conservation and rewiring of regulatory elements.

Enzymatic carbon-fluorine bond cleavage by human gut microbes

This paper discovers that human gut microbes can cleave carbon-fluorine bonds using defluorinases, identifies structural features predictive of this activity, and develops a screening assay for detecting such enzymes.

Genome-wide exploration of the transcriptional regulatory landscape in the early-diverging fungus R. microsporus reveals pervasive DNA methyl adenine regulatory network

The paper uses DAP-seq to analyze TF binding sites in R. microsporus, revealing DNA methylation's role in gene regulation and expanding fungal motif catalogs.

Synthetic genomes unveil the effects of synonymous recoding

This study uses synthetic genomes to investigate how synonymous codon recoding affects organismal fitness and develops a workflow to overcome lethal effects of codon swaps.

Functional genomic screening in Komagataella phaffii enabled by high-activity CRISPR-Cas9 library

The paper develops a high-activity CRISPR-Cas9 library for Komagataella phaffii and uses it to identify essential genes related to protein production, secretion, and glycosylation.

Sensitivity analysis of genome-scale metabolic flux prediction

The paper develops a sensitivity analysis strategy for genome-scale metabolic flux prediction using TRIMER, showing its utility in guiding optimal experimental design for metabolic engineering.

TRIMER: Transcription Regulation Integrated with MEtabolic Regulation

TRIMER integrates transcriptional and metabolic regulation to predict metabolic fluxes and gene states, outperforming existing methods on simulated and experimental data.

ManiNetCluster: A Manifold Learning Approach to Reveal the Functional Linkages Across Multiple Gene Networks

ManiNetCluster aligns and clusters multiple gene networks to reveal functional linkages across datasets, showing better alignment of orthologous genes than existing methods.