Network approach to navigating the human genome

A method for reprogramming cells of a subject, comprising:

• receiving a biological sample of a sample cell from the subject, where the sample cell has a given cell type;
• determining gene expression data for the sample cell from the biological sample;
• constructing a graph for a genome, where each node in the graph represents a gene in the genome and each edge in the graph quantifies the relationship between two genes;
• forming an adjacency matrix from the graph;
• receiving gene expression data for a target cell having a target cell type, where the target cell type differs from the given cell type;
• computing a regulatory set for a set of transcription factors, where the regulatory set quantifies influence of the transcription factors in the set of transcription factors on a genome;
• expressing reprogramming of the sample cell to the target cell with a state-space representation of a linear system, where the gene expression data for the target cell serves as an output vector in the state-space representation, the adjacency matrix serves as a state transition matrix, the gene expression data for the sample cell serves as a state vector in the state-space representation, the regulatory set for the given transcription factor serves as an input matrix in the state-space representation, and an input vector in the state-space representation represents the given transcription factor;
• solving for the input vector in the state-space representation;
• and
• manipulating at least one transcription factor in a particular cell of the subject, where the particular cell has the given cell type and the at least one transcription factor is in the input vector.