Leo A. Baumgart

Evolved microbial diversity enables combinatoric biosensing in complex environments

The paper develops a framework using evolved microbial diversity and machine learning to enable combinatoric biosensing of multiple analytes in complex environments.

Positional grammar of transcription factor binding partitions developmental and stress-response regulation in plants

The paper investigates how transcription factor binding site position and chromatin context influence gene regulation in plants, revealing distinct regulatory roles for different genomic locations.

A global regulatory atlas of Streptomyces reveals conserved and diversified transcriptional networks across actinomycetes

The paper constructs a regulatory atlas of Streptomyces and related actinomycetes using DAP-seq and ChIP-seq, revealing conserved and divergent transcriptional networks.

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.

The transcription factor SiROCX controls a monocot-specific CAZyme program for host cell wall remodeling during symbiotic root colonization

This study identifies SiROCX as a transcription factor regulating a monocot-specific CAZyme program for host cell wall remodeling during fungal symbiosis.

CRAGE-RB-PI-seq enables transcriptional profiling of rhizobacteria during plant-root colonization

The paper develops CRAGE-RB-PI-seq to profile rhizobacterial transcription during plant root colonization, revealing key transcriptional changes involved in immune evasion and colonization success.

Dopamine biosynthesis in plants

The paper identifies dopamine biosynthesis pathway in plants using metabolite-based genome-wide association studies and demonstrates its role in tissue browning and stress tolerance.

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.

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.

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.