Carlos G. Acevedo‐Rocha

Translating chemical reactions into enzyme sequences enables formate dehydrogenase engineering

This paper introduces REXzyme, a model translating chemical reactions into enzyme sequences, and demonstrates its ability to generate active formate dehydrogenases for CO2 reduction.

Biocatalytic Production of Galantamine in Yeast through Cytochrome P450 Optimization

This paper demonstrates the production of galantamine in yeast through pathway engineering and optimization, achieving a 173-fold improvement over the parental strain.

Engineering Biosensors to Enhance Monoterpene Indole Alkaloid Production in Yeast

This study develops biosensors for MIAs and identifies metabolic engineering hits to enhance MIA production in yeast.

Unlocking substrate specificities of human solute carrier proteins using untargeted metabolomics

The paper presents a Xenopus oocyte-based platform to discover transporter substrates using untargeted metabolomics, identifying known and novel substrates for five human SLC transporters.

Hybrid quantum-classical de novo design of MHC-binding peptides

This paper introduces a hybrid quantum-classical pipeline for designing MHC-binding peptides, showing that quantum-derived priors improve the yield of strong binders, especially for understudied HLA alleles.

Mycol: A user-friendly app for automating analysis of microscopy images

Mycol provides an accessible, open-source platform for microscopy image analysis using machine learning, enabling non-specialists to perform segmentation, classification, and quality control with minimal setup.

growthcurves: A platform for human-in-the-loop analysis of biological growth curves

The paper introduces growthcurves, a Python package and web tools for analyzing biological growth curves with human-in-the-loop workflows, providing automated fitting and interactive inspection.

ProteusAI: An Open-Source and User-Friendly Platform for Machine Learning-Guided Protein Design and Engineering

ProteusAI is an open-source platform that streamlines ML-guided protein design and engineering, improving proteins and enzymes efficiently within the DBTL cycle.

Metabolic engineering of yeast for de novo production of kratom monoterpene indole alkaloids

This study engineering yeast to produce kratom monoterpene indole alkaloids through synthetic pathway reconstruction and optimization, achieving a titer of ~290 µg/L.

Labels as a Feature: Network Homophily for Systematically Discovering human GPCR Drug-Target Interactions

The paper introduces a model called CSNN that uses network homophily to improve in-distribution predictions of drug-target interactions for human GPCRs.