Teaching
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
------
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].