Topic outline

  • General

    Markov processes

    Lausanne, 1-4 October 2013

    Organiser: Nicolas Salamin and Patricia Palagi

    Course description:

    Markov models play an important role in biological modelling. They are involved in many areas of biology including gene and motif predictions to phylogenetics and macroevolution. The goal of this course is to give a broad theoretical overview of these models and the biological processes that can be studied with them. The course will be divided in four days as follow:

    • Day 1: Introduction to Markov models (Andrea Kraus) - The initial day will be used to introduce the theoretical background on Markov models. The idea is to present the main concepts and theorems that are necessary to understand how to use Makov models in biology.
    • Day 2: Macroevolutionary modeling (Nicolas Salamin) - This day will be used to explore the use of Markov models outside molecular data. There is a rich suite of applications that use these processes to model how phenotypic variation evolve through time. This will lead to the introduction of branching processes and will finish with a practical illustration of the use of these models in macroevolution.
    • Day 3: Hidden-Markov models for motif predictions (Frédéric Schütz) - Motif prediction is a key element to identify structural component of genomic data. The first part of this day will introduce how hidden Markov models are defined and how they work. The afternoon will be spent using existing software to analyse motifs in DNA sequences.
    • Day 4: Markov models in phylogenetics (Brian O'Meara) - Probabilistic methods in phylogenetics are based on Markov processes to model how changes in DNA sequences occur along the branches of a phylogenetic tree. The first part of this day will be spent developing the idea of Maximum likelihood estimation of Markov model parameters and how this is applied in phylogenetics. The afternoon will be used to get practical experience of how these models work.


    The course will take place in room 2020 in the Genopode building (University of Lausanne). The courses start at 9am and finish around 5 pm.


    Participants will need to bring their laptops.


    Registration is closed.

    The registration fee for academics is 200 CHF. (Some doctoral programs may subsidize the course; please contact your doctoral program for more information). Participants from the industry should contact us. The fees include course content material, coffee breaks and a social dinner on Wednesday 2 October).

    We have received many more applications than the number of places. If you want to add your name to the waiting list just follow this link.

    The deadline for free-of-charge cancellations is 19 September 2013.

    ECTS accreditation: 1 credit

    Important: participating graduate students will have to inquire if this credit is accepted by their respective graduate schools.

    For more information, please contact