SARA C. MADEIRA
- Universidade de Lisboa
Thursday, December 10, 2015
14:45 rinfresco; 15:00 inizio seminario
Biclustering, the discovery of sets of objects with a coherent pattern across a subset of conditions, is key to study a wide-set of biomedical problems, where molecular units or patients are meaningfully related with a set of properties. The challenging combinatorial nature of this task led to the development of several approaches with restrictions on the allowed type, number and quality of biclusters, subsets of rows exhibiting a coherent pattern over a subset of columns found by analysing a data matrix. State of the art biclustering approaches relying on efficient string processing and mining techniques, in the case of temporal data, and based on pattern mining, in the general case, allow an exhaustive yet efficient space exploration together with the possibility to discover flexible structures of biclusters with parameterizable coherency and noise-tolerance.
This talk introduces the biclustering problem and then tackles the problem of biclustering temporal data. Follows focusing on biclustering algorithms for the analysis of gene expression time series obtained from transcriptomics using microarrays or RNA-seq technologies. In this context, the ability to monitor changes in expression patterns over time, and to observe the emergence of coherent temporal responses using gene expression time series, is shown to be critical to advance our understanding of complex biological processes, such as complex diseases. This talk presents efficient biclustering algorithms to analyse expression time series, able to effectively unravel coherent coexpression patterns and important aspects of gene regulation, as anticorrelation and time-lagged relationships. On going work on new biclustering algorithms to simultaneouly analyse multiple expression time series, together with their application to biomedical problems, are also be discussed.