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Grupo LIA - UPM

 

Synthetic Biology (the engineering of biology) is the application of the engineering principles to biology in order to build synthetic biological systems. This is a new and fascinating interdisciplinary field (born in 2000 in MIT Artificial Intelligence Lab), where engineers, physicists, and computer scientists have a new opportunity to apply their engineering concepts and tools: Biology is the new hardware that can be programmed.

In our group we address the following research questions:

 

  1. Biological information processing: how cells communicate, process biological signals and take decisions?
  2. Synthetic Biology and DNA Computing confluence: how to engineer and program new biological systems (based on DNA, RNA or proteins) that can interact with cell and/or can sense and respond to biological signals?  How can we design new DNA Computing devices able to operate in vivo?
  3. Artificial Intelligence in vivo: How to use algorithmic ideas developed in Artificial Intelligence field to program smart cellular computers? Or, how to apply evolutionary computing ideas in the design of new biocircuits?
  4. Heterotic living computing and non-digital SynBio: Most biocircuits developed so far are based on Boolean algebra and use a digital/binary abstraction to operate with biological signals. How could we design new robust analog, and/or probabilistic and/or multicellular biocircuits?
  5. Bio-design automation and Programmable Biology: We produce software to simulate multicellular genetic circuits and to automatize biology protocols.

 

Our FP7 EU FET-Proactive research projects: www.plaswires.eu and www.evoprog.eu

 

PhD studentship offer. If you are an engineer or physicist that likes biology and wants to program cells and DNA, code biology or engineer life contact us. Deadline: June 21st, 2016. We love people passionate about research that wants to deep into the unknown.

 

PhD studentship offer. 4 years. Reseach to be done in LIA Lab - UPM and collaborating in the European research projects PLAWIRES and EVOPROG. Topics of research: Synthetic Biology, Systems Biology, DNA Computing, Lab Automation, Programmable Biology. Candidates background and profile: Highly motivated candidates with excellent transcripts. Strong mathematical background and programming skills are mandatory requirements. No biology knowledge is required but the applicant must be willing to acquire it. Good working knowledge in English. Applicants should preferably hold a Degree or a Master in Bioengineering, Biophysics, Computer Science, Electrical, Industrial, Mechanical, Aerospace Engineering or a related discipline. Applicants please send an email to Alfonso Rodríguez-Patón, arpaton@fi.upm.es with CV, grade transcripts, motivation letter, and two letters of recommendation. Deadline: July 21st, 2015.

We are coordinating the European project funded under FP7 - FET Proactive area and titled PLASWIRES: "Engineering Multicellular Biocircuits: Programming Cell-Cell Communication Using PLASmids as WIRES". Duration of the project: 36 months. Start: October, 2013. Additional information in: www.plaswires.eu

We are also partners in the project on synthetic biology called EVOPROG: "General-Purpose Programmable Evolution Machine on a Chip".  Start: October, 2013. Duration of the project: 36 months.

Our project "ENGINEERING and PROGRAMMING BIOCIRCUITS: DESIGN and IN SILICO MODELING" which was selected for funding by the Spanish Government (project code TIN2012-36992) is also running.

Offering one PhD studentship in Synthetic Biology and Microfludic Systems. Detailed information about the offered PhD grant may be seen HERE. Deadline for applications: September 10th, 2013.

 

Synthetic Biology European project BACTOCOM (Bacterial Computing with Engineered Populations) finished on July, 2013. www.bactocom.eu

New LIA Group patent. El grupo LIA ha conseguido en 2012 una patente biotecnológica con aplicaciones potenciales en el campo del diagnóstico genético. Información adicional aquí.

New paper accepted in PLoS ONE describing a new way of generating robust oscillations with a genetic circuit with only one gene:

Miró-Bueno JM, Rodríguez-Patón A (2011) A Simple Negative Interaction in the Positive Transcriptional Feedback of a Single Gene Is Sufficient to Produce Reliable Oscillations. PLoS ONE 6(11): e27414. doi:10.1371/journal.pone.0027414 (pdf version)

 

Research topics

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  • DNA Computing - Synthetic Biology

  • Biomolecular computing

  • Membrane computing - P Systems

  • Systems Biology

  • Evolutionary computation

  • Nanobiotechnology

  • Formal languages and automata theory



Publications

 

News:

PhD studentship offer. If you are an engineer or physicist that likes biology and wants to program cells and DNA, code biology or engineering life contact us. Deadline: June 21st, 2016.


Our team will participate in two new European research projects in Synthetic Biology field: EVOPROG and PLASWIRES that will begin in October, 2013.

PLASWIRES project (coordinated by LIA group) has been funded by European Commision. It will start in October 2013. www.plaswires.eu

-Our next Synthetic Biology research project will be financed by Spanish Government:

Project code: TIN2012-36992.
Project Title: "PROGRAMACIÓN E INGENIERÍA DE BIOCIRCUITOS: DISEÑO Y
MODELADO IN SILICO".
Duration: 3 years. Begins at January 2013. Ends at December 2015.

A new Ph.D. grant position of 4 years (Spanish "beca FPI") will be available associated to this project TIN2012-36992

-Seminar announcement:

"Systems Biology of Cell-Cell Interactions" by Joao B. Xavier from Memorial Sloan-Kettering Cancer Center, New York, USA. May 2012

-New Paper accepted in PLoS ONE:

Miró-Bueno JM, Rodríguez-Patón A (2011) A Simple Negative Interaction in the Positive Transcriptional Feedback of a Single Gene Is Sufficient to Produce Reliable Oscillations. PLoS ONE 6(11): e27414. doi:10.1371/journal.pone.0027414

- Patent grant. New patent awarded to LIA group in genetic diagnostic. El grupo LIA logra una patente biotecnológica con aplicaciones potenciales en el campo del diagnóstico genético.

-BACTOCOM in The Guardian: Brainy bacteria could revolutionise healthcare

-ROBOTS MICROSCÓPICOS RECORRERÁN NUESTRO ORGANISMO (INDAGANDO TV):


Robots microscópicos recorrerán nuestro organismo
por IndagandoTV

-Natural Computing And Synthetic Biology Techniques Advanced For Treating Diseases

-Investigadores de la Facultad contribuyen al tratamiento de enfermedades con técnicas de Computación Natural y Biología Sintética

Noticia en Facultad de Informática

Noticia en UPM

 

Seminars LIA Group 2011-2012:

"Systems Biology of Cell-Cell Interactions" by Joao B. Xavier from Memorial Sloan-Kettering Cancer Center, New York, USA. May 2012. Anuncio del seminario de Joao B. Xavier.

Master/PhD Seminars LIA Group 2009-2010:

Milan Stojanovic, Christof Teuscher, Martyn Amos, Friedrich Simmel

Master/PhD Seminars LIA Group 2008-2009:

George Paun, Alfonso JaramilloMilan Stojanovic, Matteo Cavaliere, Friedrich Simmel.

 


 

 


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