November 4 – 9 , 2018, Dagstuhl Seminar 18451

Genomics, Pattern Avoidance, and Statistical Mechanics


Michael Albert (University of Otago, NZ)
David Bevan (University of Strathclyde – Glasgow, GB)
Miklós Bóna (University of Florida – Gainesville, US)
István Miklós (Alfréd Rényi Institute of Mathematics – Budapest, HU)

For support, please contact

Jutka Gasiorowski for administrative matters

Michael Gerke for scientific matters


List of Participants
Shared Documents
Dagstuhl Seminar Schedule [pdf]


This event will bring together computational and mathematical biologists who are active in the field of genomics, computer scientists and mathematicians studying pattern avoidance, and mathematicians and physicists whose area of research is statistical mechanics.

There are many tantalising connections between these three fields. Examples include the following.

In the simplest form the problem of gene rearrangements corresponds to sorting by reversals. The permutations that are hardest to sort in this way are known as increasing oscillations, and are fundamental to the study of permutation classes.

The partially asymmetric simple exclusion process (PASEP) is a generalization of a one-dimensional gas model, exhibiting boundary-driven phase transitions and spontaneous symmetry-breaking. Properties of the PASEP are directly connected to counting occurrences of the vincular pattern 2-13 in permutations and to the combinatorics of permutation tableaux.

Evolution in viral populations can be modelled by theories of quasi-species. These theories have captured the attention of the statistical mechanics community since it was shown that they could be represented by a type of two-dimensional Ising model, the macroscopic distribution of the population corresponding to surface magnetization.

However, despite the existence of these links, there is little interaction between the different communities. The goals of this seminar are to

  • build bridges between the three areas by bringing together experts from each field,
  • identify themes and models that are common across the three areas,
  • detail avenues of possible future research and define project ideas for cooperation between the communities.

In addition to presentations of recent research results, the Dagstuhl Seminar will include expository talks explaining the specific interests and questions of each community to the other two. The programme will also contain lectures surveying the interfaces between each pair of communities. In addition, there will be sessions on questions that are common to two or more of the fields. Opportunities will be provided for the discussion of open problems and other topics of shared interest.

  Creative Commons BY 3.0 DE
  Michael Albert, David Bevan, Miklós Bóna, and István Miklós

Related Dagstuhl Seminar


  • Bioinformatics
  • Data Structures / Algorithms / Complexity
  • Modelling / Simulation


  • Permutation patterns
  • Genomics
  • Algorithms
  • Modeling
  • Evolutionary distance

Book exhibition

Books from the participants of the current Seminar 

Book exhibition in the library, ground floor, during the seminar week.


In the series Dagstuhl Reports each Dagstuhl Seminar and Dagstuhl Perspectives Workshop is documented. The seminar organizers, in cooperation with the collector, prepare a report that includes contributions from the participants' talks together with a summary of the seminar.


Download overview leaflet (PDF).


Furthermore, a comprehensive peer-reviewed collection of research papers can be published in the series Dagstuhl Follow-Ups.

Dagstuhl's Impact

Please inform us when a publication was published as a result from your seminar. These publications are listed in the category Dagstuhl's Impact and are presented on a special shelf on the ground floor of the library.

NSF young researcher support