Amit Mandal

My research focusses on deciphering tumour evolution in the context of cell differentiation routes, mutation backgrounds or drug sensitivity. To that end, I use bioinformatics and computational approaches on bulk/ single-cell sequencing datasets from organoid models of colorectal cancers.

I aim to identify alterations correlated across the regulatory layers of DNA, RNA or chromatin and hopefully create genomic signatures with predictive value over regulatory layer(s) or developmental trajectory. These signatures can then be used to predict patient prognosis/ drug response using a minimal set of genomic measures (say gene expression only) derived from organoid models or biopsy tissue.

I am also interested in integrating publicly available large-scale cancer cohorts.

I completed my PhD from CSIR-IGIB (New Delhi), on transposable elements (‘selfish genes’) embedded in the human transcriptome and the phenotypic plasticity created due to that in mRNA isoforms and non-coding RNAs. From there I have moved to studying ‘selfish cells’ (tumours) during post-doctoral research. In my previous post-doctoral positions, I have worked on skin and lung cancers.