Alfonso Jaramillo

A genetically encoded local learning rule enables physical learning in engineered bacteria

This paper demonstrates physical learning in engineered bacteria using a genetically encoded local learning rule that updates analogue weights through environmental inputs and differential growth.

Engineering P4 satellite phage particles with single and dual antimicrobial actions

This study engineers P4-like phage particles with single and dual antimicrobial actions for bacterial infection treatment, demonstrating improved production and payload delivery.

Engineering compact bacterial combinatorial promoters for two-input chemical AND switching

The paper designs and evaluates compact bacterial promoters that respond to two chemical inputs with AND logic, finding that utility depends on minimizing leakage and matching operator-scaffold compatibility.

High-yield bioproduction of virus-free virus-like P4-EKORhE multi-lysin transducing particles as an antimicrobial gene therapeutic

This paper describes the construction and high-yield production of virus-like particles for delivering antimicrobial genes, demonstrating their effectiveness in bacterial cultures and human cell models.

T7 phage-assisted evolution of riboswitches using error-prone replication and dual selection

This paper describes a dual-selection system using T7 phage to evolve functional theophylline riboswitches by alternating selection pressures in ON and OFF states.

Quantification of genetic variants in bacterial cultures by Sanger sequencing

The paper introduces a method to quantify genetic variants in bacterial cultures using Sanger sequencing, validated with engineered plasmids and showing cost reduction compared to qPCR.

Engineered sensor bacteria evolve master-level gameplay through accelerated adaptation

This paper describes a system of engineered bacteria that evolve to play tic-tac-toe, demonstrating complex decision-making through gene circuits.

Comparison of CRISPR and marker based methods for the engineering of phage T7

This study compares CRISPR and marker-based methods for engineering phage T7, finding marker-based selection most efficient and type II CRISPR-Cas easier to use than type I.

Engineering the smallest transcription factor: accelerated evolution of a 63-amino acid peptide dual activator-repressor

This paper engineers a 63-amino acid peptide that functions as both an activator and repressor, demonstrating that minimal transcription factor activity is achievable through directed evolution.

Quantitative characterization of translational riboregulators using an in vitro transcription-translation system

This paper quantitatively characterizes in silico designed riboregulators using a cell-free TX-TL system to measure their performance and dissociation constants.

Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression

This paper designs and characterizes RNA circuits that dynamically process signals to control gene expression in live cells.

Cooperative riboregulation in living cells through allosteric programming of toehold activation

The paper designs cooperative riboregulation in E. coli using a hierarchical toehold activation cascade and a de novo sequence design algorithm.

Engineering a circular riboregulator in Escherichia coli

This study engineers a circular riboregulator in E. coli using group I PIE sequences, showing increased gene expression activation compared to linear forms.

Regulatory RNA design through evolutionary computation and strand displacement

This paper presents an evolutionary computation method combined with strand displacement techniques to systematically design riboregulators for genetic control systems in bacteria.