Poster presentations

Project students are encouraged to present their work at an appropriate conference

ISMB/ECCB 2013
Poster - A008
Caribbean Medicinal Plant Ontology
Alana Abdool, The University of Manchester, Trinidad and Tobago
Short Abstract: This study aims to initiate the construction of an ontology that represents the concepts
and their relationships of indigenous knowledge of medicinal plants in the Caribbean region. This is
vital as the herbal industry has been growing rapidly in the Caribbean and the popularity of herbal
products is increasing in both the developing and developed world. There are numerous concerns over
the safety of herbal use and there exists the potential for unforeseen negative allopathic drug-herb
reactions. The cons of herbal commercial activities should not outweigh the pros nor the potential for
new and exciting drug discovery potential. It is imperative that the necessary steps be taken and active
stakeholder involvement take place to effectively document and research indigenous knowledge so
that this resource is not lost.An analysis of online and other database resources on plants and
medicinal plants and their attributes in the Caribbean region revealed a lack of semantically
meaningful query facilities, lack of standards, data linkages and there are no unique identifiers for
entries. The ontology was created utilizing information gathered from domain experts and medicinal
plant literature. The success of the ontology, it is suggested, will drive the concurrent development of
other databases and ensure a higher standard of data, semantically meaningful querying and
interoperability.

Poster - N097
Noncoding RNA alignment and homology search using extended RNA secondary structure
Eduardo De Paiva Alves (University of Manchester) Sam Griffiths-Jones (University of Manchester,
Faculty of Life Sciences United Kingdom);
Short Abstract: Non-coding RNAs have low sequence conservation and therefore HMM based
alignment and homology search methods often do not perform well. Their base-paired secondary
structures on the other hand are usually highly conserved. RNA sequence alignment and homology
search algorithms have been developed to use structure information. These algorithms usually use a
simplified RNA secondary structure consisting of 1-diagrams where each nucleotide interacts with at
most one partner and only canonical base pairs are allowed. Many nucleotides however form noncanonical base pairs and interact with two other nucleotides forming base-triplets. Recent attempts to
include this information include RNAwolf which applies a base-triplet grammar combined with a
simple version of the standard Turner energy model to single-sequence non-coding RNA structure
prediction. Here we describe an application of a probabilistic base-triplet grammar to alignment and
homology search. The grammar was implemented in Haskell using Algebraic Dynamic Programming
and the transition and emission probabilities were estimated using FR3D annotations from PDB. The
grammar was then used to generate covariance models for a set of Rfam families. These models were
used to filter the results from a Infernal genome search for the same families. The results show that
the filtering produces a lower false negative rate which can be attributed to the additional restrictions
imposed on the structure.

Poster - O003
A Generalized Framework for Interactomes with Time-varying Topology
Mahmoud Ibrahim, Max Delbrck Center for Molecular Medicine, Germany; Steffen Waldherr (Ottovon-Guericke-Universitt Madgeburg, CDS Biosystems Engineering Germany); Heather Vincent
(University of Manchester, Faculty of Life Sciences United Kingdom); Daniella Schittler (University
of Stuttgart, Institute for Systems Theory and Automatic Control Germany);
Short Abstract: Topological analyses of interactomes have focused on static overall networks that
represent interactions regardless of their temporal context. However, even if one assumes that no false
interactions are included in the network, not all network interactions occur at the same time.
Therefore, conclusions based on the topology of such overall networks may not be valid.
Consequently, one must consider interactomes to have dynamic topology that affects and is affected
by the functions they perform.
We introduce a generalized framework for simulation and integration of dynamic interactomes, and
provide an example for its implementation. The framework describes a network as an evolving system
partitioned into an edge evolution model and a node evolution model. This framework can be used to
simulate and integrate interactomes of varying types, sizes and complexities and it can serve as a basis
towards facilitating the study and analysis of dynamic interactomes. In addition, we also demonstrate
that time-varying topological node metrics (like time-average betweenness-centrality) correlates to the
nodes' functional context more than metrics measured on the overall static network.

Poster - O057
Approaches to Modelling the Mouse Response to Trypanosomiasis
Heather Vincent, University of Manchester, United Kingdom; Sarah Bailey (University of
Manchester, Faculty of Life Sciences United Kingdom); Mahmoud Ibrahim (Max-Delbrueck-Center
for Molecular Medicine, Berlin Institute for Medical Systems Biology Germany);
Short Abstract: Mouse models for trypanosomiasis have been studied extensively in order to reveal
the differences between the immune response in Trypanosoma congolense resistant and susceptible
mice. However, despite the availability of high-throughput gene expression data for susceptible and
resistant strains, there is a lack of a network systems understanding on how genes interact during
infection, and how these interactions might relate to the difference in susceptibility between mouse
strains.
For each strain, A/J and C57BL/6, theoretical Boolean interaction networks were built from known
pathways for Natural Killer (NK) cells. The state of the networks in the uninfected strains was first
simulated using Cytoscape with the SimBoolNet plugin. We also checked the models using a
generalized framework for interactomes, which can be used to investigate time-varying topology.
When the results were compared against microarray gene expression data we found a close similarity
between the network simulation results and gene expression for both strains.
The principal difference between these initial murine models of the NK cell network was found in the
CD2 superfamily of receptors, including 2B4 and Ly9, which contain switch motifs. Also, the model
of the susceptible A/J strain suggests the receptor NK-P1B is not expressed.
This preliminary work highlights the importance of adopting a differential networks approach to
understanding the difference in immune response between different strains. We will now extend the
work to model the differences in response to infection.