Rafael Silva‐Rocha

The paper uses transcriptomic data from Rhodosporidium toruloides to identify novel cis-regulatory elements by predicting transcription factor binding motifs under stress and substrate conditions.

ChiMera is a pipeline that reconstructs, evaluates, and visualizes bacterial genome-scale metabolic models using efficient tools and a user-friendly interface.

The paper compares chromatin activities in two A. fumigatus isolates, finding higher genome instability in Af293 and identifying a variant with chromosomal alterations linked to increased virulence.

The paper standardizes an inducible expression system for bacterial hosts by refactoring the AlkS/PalkB module to improve predictability and interoperability.

PredicTF predicts bacterial transcription factors in microbial communities using genomic and metagenomic data from environmental isolates and anammox bioreactors.

The paper benchmarks bacterial promoter prediction tools using validated and control datasets, finding that some tools perform better than others.

This study engineers Escherichia coli to tolerate extreme acidity by combining metagenomic genes in synthetic operons, significantly increasing survival under acidic shock conditions.

The paper identifies and characterizes 20 constitutive promoters in Rhodosporidium toruloides for use in genetic engineering and metabolic pathway optimization.

The paper constructs synthetic promoters in E. coli to study how cis-regulatory element arrangements affect transcription factor binding and gene expression outcomes.

This paper identifies novel broad host-range transcriptional terminators from metagenomic data for use in Proteobacteria.

TFound is a software tool for visualizing transcription factor binding sites in yeast genomes using PWMs, with support for custom sequences and genomes.

The paper identifies an amino acid critical for inducer recognition in bacterial regulators and creates engineered TFs responsive to aspirin.

The paper studies synthetic bacterial promoters to show emergent properties from combinations of CRP and IHF binding sites.

The paper identifies false positives in metagenomic screenings using lacZα-based vectors due to small DNA insertions within the lacZα gene, highlighting the need to report screening boundaries.