Columbia University

Harmen J Bussemaker

Barrett C Foat

Eunjee Lee

Ronald G Tepper

The disclosed subject matter is directed to genetic linkage methods for identifying genetic determinants of transcription factor activity. An inferred transcription factor activity profile is generated based on a nucleotide sequence-specific mathematical model of gene expression regulation. Genetic linkage analysis is performed to identify at least one genetic determinant linked to a specific transcription factor segregant based on the inferred transcription factor profile.

Method for identifying aQTL regions whose genotype modulates transcription factor activity

Systems and methods for determining free energy parameters for predicting binding affinities of nucleotide sequences are provided. The disclosed subject matter obtains phenotypic measurements for nucleotide sequences (for example a DNA sequence or RNA sequence), links the phenotypic measurements to the nucleotide sequences to obtain linked pairs of phenotypic measurements and nucleotide sequences, estimates a relationship between the phenotypic measurements and the nucleotide sequences using the linked pairs, and obtains sequence specific affinity parameters from the estimated relationship.

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New York, NY, United States of America

Harmen J Bussemaker