12 Result(s)

Article

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

Leveraging riboswitches, non-coding mRNA fragments pivotal to gene regulation, poses a challenge in effectively selecting and enriching these functional genetic sensors, which can toggle between ON and OFF sta...

Eduardo Goicoechea Serrano, Carlos Blázquez-Bondia, Alfonso Jaramillo in Scientific Reports (2024)

Article

Engineering orthogonal dual transcription factors for multi-input synthetic promoters

Synthetic biology has seen an explosive growth in the capability of engineering artificial gene circuits from transcription factors (TFs), particularly in bacteria. However, most artificial networks still empl...

Andreas K. Brödel, Alfonso Jaramillo, Mark Isalan in Nature Communications (2016)

Article

Automated design of bacterial genome sequences

Organisms have evolved ways of regulating transcription to better adapt to varying environments. Could the current functional genomics data and models support the possibility of engineering a genome with compl...

Javier Carrera, Alfonso Jaramillo in BMC Systems Biology (2013)

Article

Synthetic biology gains momentum in Europe

David Gilbert, Alfonso Jaramillo, Natalio Krasnogor… in Systems and Synthetic Biology (2010)

Article

Robust dynamical pattern formation from a multifunctional minimal genetic circuit

A practical problem during the analysis of natural networks is their complexity, thus the use of synthetic circuits would allow to unveil the natural mechanisms of operation. Autocatalytic gene regulatory netw...

Guillermo Rodrigo, Javier Carrera, Santiago F Elena… in BMC Systems Biology (2010)

Article

Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions

Understanding the molecular mechanisms plants have evolved to adapt their biological activities to a constantly changing environment is an intriguing question and one that requires a systems biology approach. ...

Javier Carrera, Guillermo Rodrigo, Alfonso Jaramillo, Santiago F Elena in Genome Biology (2009)

Article

PROTDES: CHARMM toolbox for computational protein design

We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PRO...

María Suárez, Pablo Tortosa, Alfonso Jaramillo in Systems and Synthetic Biology (2008)

Article

Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus

Tobacco etch potyvirus (TEV) has been extensively used as model system for the study of positive-sense RNA virus infecting plants. TEV ability to infect Arabidopsis thaliana varies among ecotypes. In this study, ...

Patricia Agudelo-Romero, Pablo Carbonell, Francisca de la Iglesia… in Virology Journal (2008)

Article

Asmparts: assembly of biological model parts

We propose a new computational tool to produce models of biological systems by assembling models from biological parts. Our software not only takes advantage of modularity, but it also enforces standardisation...

Guillermo Rodrigo, Javier Carrera, Alfonso Jaramillo in Systems and Synthetic Biology (2007)

Article

Computational design of digital and memory biological devices

The use of combinatorial optimization techniques with computational design allows the development of automated methods to design biological systems. Automatic design integrates design principles in an unsuperv...

Guillermo Rodrigo, Alfonso Jaramillo in Systems and Synthetic Biology (2007)

Article

Computational design of proteins with new functions

Alfonso Jaramillo, Pablo Tortosa, Guillermo Rodrigo, Maria Suarez… in BMC Systems Biology (2007)

Article

ECOLITASTER: cellular biosensor

Guillermo Rodrigo, Javier Carreral, Alfonso Jaramillo in BMC Systems Biology (2007)