COMPUTATIONAL PHENOMICS

PLATFORM LEADER

Functional Genomics aims at elucidating the complex associations underpinning an organism’s genome and its phenotypes. This is achieved mostly through functional and chemical genomics-based high-throughput/high-content screening (HTS/HCS) to comprehensively interrogate the genome in different genetic and environmental settings and quantifying the phenotypic changes. Computationally, it requires a "big data" approach to combine various –omics dimensions into a holistic view of how a given genomic profile gives rise to its phenome.

The key mission of the Computational Phenomics platform is to enable functional genomic research in GIS and beyond. Through a strong partnership with the CHiP-GIS platform, research programmes in GIS and other institutions in Singapore and abroad, industry and clinical advocates, we aim to establish an integrated computational platform which encompasses:

  • High-throughput computational methods and tools for quantifying morphological, physiological, and other phenotypic readouts. We focus on the development of analysis tools and novel descriptors for complex phenotypes (morphological features) to facilitate functional genomic studies linked to phenotypical outcomes, with important implications in the treatment of human diseases.
  • System-level integration of various –omics (transcriptomics, genomics, proteomics, phenomics) datasets in a clinical relevant setup in order to derive models valuable for understanding disease mechanisms and response evaluation, and towards personalised treatment such as precision oncology.
  • Computational infrastructure supporting HTS/HCS in CHiP-GIS, including LIMS development, data management and database server development, website and web server development, automation of data processing/quality control/analysis pipelines for screens conducted in CHiP-GIS, and high content image analysis and visualisation.

The platform has established expertise in high content image analysis, database development, machine learning, and system biology/network interference to support a spectrum of analyses and application developments including:

  • 3-Dimensional High Content Screening (3D-HCS)
  • Microscopic image analysis of various cellular models including primary cultures, co-cultures, spheroids and organoids
  • Disease-specific chemical pathway profiling
  • Synthetic lethality (Loss-of-function/Gain-of-function) profiling
  • Development of integrative genomics and/or phenomics databases

With an integrated effort to bridge between genomics and phenomics, the platform aims to bring together research, industry and clinical efforts, through multi-disciplinary collaborations, to advance genomics research in Singapore and beyond.

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