The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering, Nature Communications
The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering, Nature Communications

30 August 2022

We believe that the synthetic biology and metabolic engineering communities need to be provided with easily acessible and usable computational tools enabling them to apply

Large scale active-learning-guided exploration for in vitro protein production optimization, Nature Communications
Large scale active-learning-guided exploration for in vitro protein production optimization, Nature Communications

24 April 2020

Cell-free lysates are a major platform for in vitro protein production but batch-to-batch variation makes production difficult to predict. A research team from the Micalis

RetroPath RL: Reinforcement Learning for Bioretrosynthesis, ACS Synthetic Biology
RetroPath RL: Reinforcement Learning for Bioretrosynthesis, ACS Synthetic Biology

24 April 2020

Metabolic engineering aims to produce chemicals of interest from living organisms, to advance toward greener chemistry. Despite efforts, the research and development process

Metabolic Perceptrons for Neural Computing in Biological Systems, Nature Communications
Metabolic Perceptrons for Neural Computing in Biological Systems, Nature Communications

29 August 2019

While machine learning methods are used in many areas, including human health, interfacing these methods with the living world has been little explored at the molecular level.

Optimizing Cell-Free Biosensors to Monitor Enzymatic Production, ACS Synthetic Biology
Optimizing Cell-Free Biosensors to Monitor Enzymatic Production, ACS Synthetic Biology

19 August 2019

Synthetic biology is the field of engineering biology inspired by engineering in computation, standardization, and construction to develop new devices composed of biological

RetroRules: A database of reaction rules for engineering biology, Nucleic Acids Research
RetroRules: A database of reaction rules for engineering biology, Nucleic Acids Research

3 October 2018

RetroRules is a database of reaction rules for metabolic engineering (). Reaction rules are generic descriptions of chemical reactions that can be used in retrosynthesis workflows

RetroPath2.0: A retrosynthesis workflow for metabolic engineers, Metab. Eng.
RetroPath2.0: A retrosynthesis workflow for metabolic engineers, Metab. Eng.

25 September 2017

Synthetic biology applied to industrial biotechnology is transforming the way we produce chemicals. However, despite advances in the scale and scope of metabolic engineering,

SensiPath: computer-aided design of sensing-enabling metabolic pathways, Nucleic Acids Research
SensiPath: computer-aided design of sensing-enabling metabolic pathways, Nucleic Acids Research

13 April 2016

Genetically-encoded biosensors offer a wide range of opportunities to develop advanced synthetic biology applications. Circuits with the ability of detecting and quantifying

Expanding Biosensing Abilities through Computer-Aided Design of Metabolic Pathways, ACS Synthetic Biology
Expanding Biosensing Abilities through Computer-Aided Design of Metabolic Pathways, ACS Synthetic Biology

1 April 2016

Detection of chemical signals is critical for cells in nature as well as in synthetic biology, where they serve as inputs for designer circuits. Important progress has been

Semi-supervised Gaussian Process for Automated Enzyme Search, ACS Synthetic Biology
Semi-supervised Gaussian Process for Automated Enzyme Search, ACS Synthetic Biology

24 March 2016

Synthetic biology is today harnessing the design of novel and greener biosynthesis routes for the production of added-value chemicals and natural products. The design of novel

Stereo Signature Molecular Descriptor, J Chem Info Model
Stereo Signature Molecular Descriptor, J Chem Info Model

5 April 2013

We present an algorithm to compute molecular graph descriptors considering the stereochemistry of the molecular structure based on our previously introduced signature molecular

A retrosynthetic biology approach to metabolic pathway design for therapeutic production, BMC Systems Biology
A retrosynthetic biology approach to metabolic pathway design for therapeutic production, BMC Systems Biology

5 August 2011

Retrosynthetic map connecting reachable compounds to E. coli metabolism (blue)Synthetic biology is used to develop cell factories for production of chemicals by constructively

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↬ Welcome

Our group is interested in synthetic biology and systems metabolic engineering in whole-cell and cell-free systems. We develop in silico and experimental methods to search and design chemical and biological networks constrained by experimental data. The applications of our work include synthetic metabolic pathway design, build and test for bioproduction, biosensing, and biocomputing. Other activities include structure-activity, sequence-function relationships, and design of experiments using active and reinforcement machine learning methods.

↬ Open Positions