Transcriptome Engineering

Transcriptome engineering means genetically modifying a cell's transcription factor network in order to change its transcriptional state (the amount of RNA present from each gene) to some desired objective. Transcriptome engineering is most frequently used to convert cells of one type (e.g. skin cells) in to another type (e.g. liver cells).

In 2016, we published a paper on our transcriptome engineering algorithm, NetSurgeon, in Proceedings of the National Academy of Sciences . That algorithm used only a binary TF network map (see Mapping TF networks ). Now, we aim to develop more sophisticated algorithms engineering that make use of TF activity inference (see TF activity inference ) to pinpoint the required interventions.

NetSurgeon scores are calculated using the hypergeometric probability function with draws, positives, and successes as indicated. Arrowheads indicate activation, and T heads indicate repression.

Current Students:

Yiming Kang

Email: yiming.kang[at]