Samuel E. Clamons

REViewer: Haplotype-resolved visualization of read alignments in and around tandem repeats

REViewer visualizes sequencing data around long repeat expansions by reconstructing haplotypes and aligning reads, improving the assessment of repeat genotype calls and detecting interruptions.

Modeling Dynamic Transcriptional Circuits with CRISPRi

The paper models dynamic transcriptional circuits using CRISPRi and identifies key parameters for their construction.

How to model DNA replication in stochastic models of synthetic genetic circuits (and why)

The paper describes a stable DNA replication mechanism for synthetic genetic circuits and explains its derivation from a mechanistic model of ColE1 replication.

Analysis of Circuits for Dosage Control in Microbial Populations

The paper analyzes genetic circuits for dosage control in microbial populations using the Lux quorum sensing system and demonstrates the effects of negative feedback and degradase activity on circuit robustness.

Enabling community-based metrology for wood-degrading fungi

The paper establishes standardized methods and reference materials for measuring wood-degrading fungi growth to enable reproducible and scalable bioproduction.

Modeling predicts that CRISPR-based activators, unlike CRISPR-based repressors, scale well with increasing gRNA competition and dCas9 bottlenecking

The paper models CRISPRa and CRISPRi systems in E. coli, finding CRISPRa is less affected by dCas9 competition and can support more gRNAs with high activation.