Thesis Topic Details

Topic ID:
3465
Title:
Decoding the language of life: epigenomic determinants for cell-type-specific signalling response
Supervisor:
Joshua Ho
Research Area:
Bioinformatics, Natural Language Processing, Systems biology
Associated Staff
Assessor:
Bruno Gaeta
Topic Details
Status:
Active
Type:
Research
Programs:
CS CE BIOM BINF SE
Group Suitable:
No
Industrial:
Yes
Pre-requisites:
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Description:
It is curious that stimulation of the same signalling pathway (e.g., Wnt pathway) can often lead to expression of different genes in different cell types (e.g., embryonic stem cells vs. differentiated intestinal cells). Recent findings based on genome-wide chromatin analysis (e.g., ChIP-chip/ChIP-seq) suggested that both the chromatin environment and DNA sequencing composition play an important role in genomic targeting of transcription factors, opening up the possibility we could learn a 'grammar' to describe and predict cell-type specific signalling response. To test this hypothesis, this project will compile and perform meta-analysis on published genome-wide datasets (ChIP-chip, ChIP-seq, DNase-seq, and RNA-seq from ENCODE/modENCODE consortia for example) as well as in-house data generated by local and international collaborators. We will adapt and develop computational linguistics and machine learning methods to analyse these data.
Comments:
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Past Student Reports
 
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