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Gene Assembly in Ciliates

Seminar Series on Gene Assembly in Ciliates

We are running seminar series on computational aspects of gene assembly in ciliates. The purpose of our seminars is to bring people from our group and all others interested in together, to make brainstorming sessions, to learn new techniques, to identify open questions in the area, etc. We will review the work already done in our group and elsewhere and we will try to identify the challenges posed by this research. All interested in are warmly welcome.



24th of February

The initial seminar session was held


10th of March

  • Vladimir Rogojin presented “Simple Operations for Gene Assembly in Ciliates”. The PDF file is available here
  • Miika Langille presented “Simple Gene Assembly is Deterministic”. The PDF file is available here


24th of March

  • We discussed paper “The DNA of Ciliated Protozoa” by David M Prescott.
  • Chang Li made a short survey on biology of ciliates. Her presentation is available here.


7th of April

  • Dr. Ion Petre will talk about templates
  • We are planning to consider some more biological features of ciliates

5th of May

  • Robert Brijder (University of Leiden, the Netherlands) gave a guest lecture on “Breakpoint graphs for gene assembly in ciliates”. The abstract is available here.

17th of May

  • Professor Adrian Atanasiu (University of Bucharest) gave a guest lecture on “Binary amiable words”. The abstract is available here. The lecture notes are available here.


9th of June

  • Andreas Lawast will talk about complexity in Gene Assembly
  • Tseren-Onolt Ishdroj will give a short survey on Membrane Computing

Binary Amiable Words

Binary amiable words Abstract Using the fact that the Parikh matrix mapping is not an injective mapping, the paper investigates some properties of the set of the binary words having the same Parikh matrix; these words are called “amiable”. Some results concerning the conditions when the equivalence classes of amiable words have more than one …

Breakpoint Graphs for Gene Assembly in Ciliates

Breakpoint graphs for gene assembly in ciliates Abstract Gene assembly is a very involved DNA transformation process which occurs in an extremely old group of organisms called stichotrichous ciliates. The process transforms one nucleus, the micronucleus, into a radically different nucleus, the macronucleus. Sound formal models have been developed for this process based on string …