Jacob Beal

Fungal Highways Enable Underground Biosensors

This study develops underground biosensors using fungal-bacterial networks to propagate synthetic genetic signals through soil.

The Limits of Sequence-Based Biosecurity Screening Tools in the Age of AI-Assisted Protein Design

This study evaluates the effectiveness of biosecurity screening tools against AI-generated synthetic homologs of proteins of concern, finding some tools can detect fragments as short as 50 nucleotides.

Developing a Standard Definition for Sequences of Concern

The paper develops a rubric to define sequences of concern by analyzing test sequences and refining categorization through stakeholder review, reducing disputed categorization by 44.3% for controlled viruses.

Ontology-driven software engineering using LLMs for knowledge graphs in engineering biology

The paper presents an ontology-driven approach using LLMs to create software libraries for knowledge graphs in engineering biology, demonstrating it with the SBOL3 Ontology and sbol-script library.

Inter-tool analysis of a NIST dataset for assessing baseline nucleic acid sequence screening

The paper evaluates sequence screening tools using a NIST dataset to assess their consistency in identifying sequences of concern.

Defending Synthetic DNA Orders Against Splitting-Based Obfuscation

The paper evaluates vulnerabilities in biosecurity screening tools by testing their ability to detect splitting-based obfuscation of synthetic DNA sequences.

Simulations Predict Stronger CRISPRi Transcriptional Repression in Plants for Identical than Heterogeneous gRNA Target Sites

The paper uses simulations to show that identical gRNA target sites provide stronger transcriptional repression in plant CRISPRi than heterogeneous sites.

Toward AI-Resilient Screening of Nucleic Acid Synthesis Orders: Process, Results, and Recommendations

The paper evaluates biosecurity screening tools for detecting AI-generated synthetic protein homologs and reports improved detection rates through patches.

Building an Open Representation for Biological Protocols

The paper introduces PAML, an open protocol representation language for biological protocols, enabling precise interpretation, automation, and reuse across different contexts.

Studying Pathogens Degrades BLAST-based Pathogen Identification

The paper highlights limitations of BLAST-based pathogen identification and suggests moving to specialized biosecurity tools.

Excel-SBOL Converter: Creating SBOL from Excel Templates and Vice Versa

The paper introduces an Excel-SBOL Converter that facilitates bidirectional conversion between Excel templates and SBOL, enhancing usability of SBOL standards in synthetic biology workflows.

Robustness and reproducibility of simple and complex synthetic logic circuit designs using a DBTL loop

This paper introduces DART, a DBTL loop for synthetic genetic circuit design, showing that complex circuits can be more robust and reproducible than simpler ones in budding yeast.

Computational Prediction of Synthetic Circuit Function Across Growth Conditions

The paper develops a computational method to predict synthetic circuit robustness across growth conditions and validates it with experimental results in budding yeast.

Meeting Measurement Precision Requirements for Effective Engineering of Genetic Regulatory Networks

The paper derives an Engineering Error Inequality to estimate measurement precision requirements for genetic regulatory network engineering and validates these requirements using flow cytometry data.

Highly-Automated, High-Throughput Replication of Yeast-based Logic Circuit Design Assessments

The paper replicates yeast-based logic circuit design assessments using a high-throughput robotic framework, generating more flow cytometry data than the original study.

Data Representation in the DARPA SD2 Program

The paper describes challenges in scientific collaboration and presents a flexible data-sharing model to improve information flow and experimentation in multidisciplinary research.

Robust Estimation of Bacterial Cell Count from Optical Density

The paper evaluates three OD calibration protocols for bacterial cell count estimation and recommends serial dilution of silica microspheres for its precision and compatibility with flow cytometry.

Capturing Multicellular System Designs Using the Synthetic Biology Open Language (SBOL)

The paper demonstrates how the SBOL standard can represent multicellular biological systems, enabling better sharing of complex designs across multiple cells.

SBOL Visual 2 Ontology

The paper introduces the SBOL Visual 2 Ontology to standardize the mapping of genetic elements to visual glyphs, facilitating tool development and integration with biological standards.

Highly Distinguished Amino Acid Sequences of 2019-nCoV (Wuhan Coronavirus)

The paper identifies unique amino acid sequences in 2019-nCoV that distinguish it from other Coronaviridae viruses.

High-performance chemical and light-inducible recombinases in mammalian cells and mice

The paper introduces a library of inducible split recombinases for precise and multiplexed gene expression control in mammalian cells and mice.