Seth L. Shipman

DeSTAR is a machine learning model that ranks target sites for RNA sensors, improving performance across different transcripts.

This paper determines the cryo-EM structure of retron-Kva2 and designs synthetic triggers to activate its antimicrobial activity.

This paper introduces Detectrons, RNA-to-DNA transduction biosensors for phage-host interaction screening, enabling multiplexed detection and quantitative susceptibility profiling.

This study generates corticospinal-like neurons from SOX6+/NG2+ cortical progenitors using a multi-component transcriptional construct, achieving high fidelity in morphology, molecular, transcriptomic, and electrophysiological characteristics.

This study identifies Retron-Eco11 as a bacterial defense system that uses helicase proteins to trigger effector toxicity against phage infection.

The paper describes a non-canonical mechanism in Type VI retrons where reverse transcribed ssDNA derepresses translation of an antiviral toxin, providing phage defense without detectable msDNA.

MitoScribe records graded molecular signals into mitochondrial DNA, enabling high-resolution tracking of cellular states during differentiation.

This study demonstrates that retron-mediated recombineering can be applied across multiple bacterial species, achieving high editing efficiencies in several phyla.

The paper isolates and characterizes novel retrons from environmental bacteria, tests their phage defense mechanisms, and engineers them for genome editing in E. coli.

This study identifies SspA as a transcriptional regulator of CRISPR adaptation in E. coli using a CRISPRi-based screen and proposes a model of independent cellular control of adaptation and interference by SspA.

The paper uses high-throughput variant libraries and machine learning to identify design rules for improving retron gene editors in both yeast and human genome editing.

The paper experimentally characterizes retrons to determine their RT-DNA sequences, production rates, and editing efficacy across bacterial, phage, and human genomes.

The paper tests fluorescent timer proteins to synchronize cortical progenitor cell differentiation from hPSCs but finds they fail to achieve synchronized fluorescence kinetics.

The paper develops a high-throughput pipeline to assess mitochondrial targeting signal efficacy across different protein types by quantifying colocalization.

This paper introduces a method to record transcriptional event timing in living genomes using CRISPR-integrated retron barcodes.

The paper improves retron architectures to enhance DNA production across different organisms, leading to more efficient genome editing.

This paper introduces RLR, a high-throughput method for screening genetic variants using in-vivo single-stranded DNA production, demonstrating its utility in antibiotic resistance studies.

This study investigates the portability of RecT-mediated homologous recombination across bacterial species, finding that compatibility with the host's single-stranded DNA-binding protein determines functionality.