Logic of Genomic Systems laboratory; Juan F Poyatos (CNB-CSIC)

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I am currently teaching Systems and Synthetic Biology at the Polytechnic University of Madrid (UPM). I have also been part over the last years of several Masters and PhD courses. Interested on what we discussed back then? See the info below




Social dilemmas ... and how bacteria and humans solve them (2012-2013)

We will try to understand how individual decision-making can contribute to the resolution of social dilemmas. We will first discuss some basic ideas by introducing the language of game theory to then identify a fundamental principle of social behavior, i.e., conditional cooperation, that will then be further illustrated with examples in systems as different as bacteria and ... humans! Lectures: day 1, day 2, day 3.


The mathematics of Biology (2011-2012)

Can we compute with biological systems? If so, how? And how can different systems exhibiting complex behaviours, such as clocks, work together? Moreover, if we want systems to work together, why not designing them to cooperate? We will discuss these issues using mathematics and biology by means of three topic lectures by Matteo Cavaliere (Engineering automata in biological systems), Saúl Ares (The rise and fall of synchrony in biological clocks) and myself (How to design cooperative communities).


Conflict and cooperation in microorganisms II (2010-2011)

How do altruistic traits evolve? Which are the main theories linked to the evolution of cooperation? How are they related? And to what extent microbial systems could help us to understand these issues? We discussed these topics in class with some introductory lectures (based on last year notes) and the discussion of recently published works. Exercises: Ex.


Conflict and cooperation in microorganisms (2009-2010)

These are the notes for the lectures of the Master in Biophysics at Autónoma University, Madrid, Spain. We discussed the problem of cooperation (and conflict) in biological systems. I first introduced the theoretical background, e.g., frequency-dependent selection, game theory, prisoner's dilemma, kin selection, Price's theorem, etc. Then, I discussed several recent experimental works on the evolution of cooperation in microbial systems. Lectures: day 1, day 2, day 3. Exercises: Ex.


Noise in Gene Expression (2008-2009)

These are the notes for the lectures of the Master in Biophysics and Master in Biosciences at Autónoma University, Madrid, Spain. I first asked why gene expression is noisy. Second, I introduced some mathematics to understand the current models describing noisy genes -Master equations, Gillespie's algorithm, etc- to then discuss about the implications of noisy genes in prokaryotic and eukaryotic Biology. Lectures: day 1, day 2, day 3, day 4, day 5, summary. Matlab codes: code1.m, code1equations.m, code2.m, code2equations.m.

 


Introduction to SYSTEMS BIOLOGY and SYNTHETIC BIOLOGY(2006-2007)

(Curso de doctorado en Biología de Sistemas y Biología Sintética)

Introduction. Biological research is in the midst of a radical transformation. Within the last few years, experimental advances derived from genome sequence projects are transforming Biology in a data rich discipline where complex mechanisms of cellular evolution and function can be deciphered. This has promoted the emergence of two new research areas: Systems Biology and Synthetic Biology, a combination of disciplines such as Mathematical Biology, Genetic Engineering or Bioinformatics.

Course goals. The aim of this course is to introduce some aspects of this new interdisciplinary areas with special emphasis on showing how the integration of experimental and theoretical approaches my help us to address fundamental biological questions. A very important goal of this course is to promote the interaction among students with very different backgrounds, e.g., Biology or Physics, and to make them aware of the existing research opportunities and the rapidly accumulating information in this new field.

Description. The course will consist of several instructor lectures introducing each week's topic, a journal club and a personal project. One of the papers will be explained and discussed on class at the end of the week. A "course project" related to these topics should be done by each student. The goal of these projects is to investigate some biological question in a more quantitative way, either with mathematics or simulations.

Time & Place. This PhD course will be held next fall (academic year 2006-2007). Three lectures per week. Schedule to be arranged. (see course 2005-2006)

If you have some questions, please e-mail me

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COURSE BRIEF OUTLINE (see also info course 05-06)

1. Recurrent units of cellular information processing: Networks motifs.

2. Cellular decision making: Positive feedback loops, ultrasensitivity, bistability, epigenetic differentiation.

3. Molecular oscillations: Negative feedback loops, relaxation-based clocks.

4. Spatial and Temporal organization: Just-in-time kinetics, principles of cellular patterning.

5. Robustness in cellular networks.

 


V Master in Biophysics course

Are genes noisy? What do we mean by that? How can noisy genes enable robust function? We will address these questions by first introducing the required mathematical framework to then discuss some recent experimental results. Lectures: day 1, day 2, day 3, day 4.


IV Master in Biophysics course

These lectures are a (very) brief introduction to deterministic and stochastic dynamics in biological systems. The course is part of the IV Master in Biophysics (2006 - 2007) at Universidad Autónoma, Madrid, and it will be taught in collaboration with Raúl Guantes who is teaching deterministic biodynamics. I will be discussing recent experimental reports on stochastic gene expression and also introducing some theoretical and computational approaches to analyse them. Lectures: day 1, day 2, day 3, day 4.


III Master in Biophysics course

The course is a (very) brief introduction to dynamics in biological systems (genetic switches, cellular clocks, molecular motors, noisy dynamics and population dynamics). The course is part of the III Master in Biophysics (2005 - 2006) at Universidad Autónoma, Madrid and it will be taught in collaboration with Raúl Guantes. We will be discussing recent experimental results and also introducing some theoretical and computational approaches to analyse them. Lectures not yet available.


II Master in Biophysics course

The course is a (very) brief introduction to the study of noise in gene expression. The course is part of the II Master in Biophysics (2004 - 2005) at Universidad Autónoma, Madrid. We will be discussing recent experimental results and also introducing some theoretical and computational approaches to analyse them. These are the lectures: [alldays].


I Master in Biophysics course

The course is a (very) brief introduction to Biodynamics. The course is part of the I Master in Biophysics (2003 - 2004) at Universidad Autónoma, Madrid. We will be discussing multistability, bifurcations and oscillations in cellular systems, focused in particular on the lambda phage and the cell cycle cases.These are the lectures (in spanish): [alldays].