TOM 31.01.2018

Venue: Biomedicum 1 Seminar room 3

Timing: 15:30 onwards

Presenter: Jarkko Toivonen

MODER: discovering structures of dimeric transcription factor binding sites

Transcription factor (TF) binding sites can be modeled with the usual
Position-specific Probability Matrices (PPMs).
However, when using these models to scan the genome, too many
putative binding sites are predicted. This binding site discovery
can be alleviated by incorporating additional information
about the binding process. One source of additional information
is the collaborative binding of TFs. To obtain information
of collaborative binding we have developed an algorithm
and a program called MODER, which learns a total probability model
which includes monomeric models for binding sites and for
their dimeric interactions.

In this talk I will first briefly introduce the problem MODER
solves. After that I will show examples of running MODER and
introduce the visualization of the results.

MODER is freely available at:

For more reading:

TOM Spring schedule 2018

Tentative schedule for Spring session 2018


Date Presenter  Title of presentation
31.01 Jarkko Toivonen

MODER: Discovering structures of dimeric transcription factor binding sites


Ilida Sulemanyova 

A deep convolutional neural network approach for astrocyte detection


Julia Casado

CYTO – single cell analysis powered by Anduril


Rishi Das Roy

For RNA-seq: a pipeline for RNA-seq analysis


Tuomas Puoliväli

MultiPy: Multiple hypothesis testing in Python