J. B. Kinney

This study develops quantitative models to understand how splice-modifying drugs work, showing drug-specific mechanisms and revealing widespread drug synergy and cooperativity.

This paper identifies the structural basis of σ-dependent transcriptional pausing by showing that it involves backtracked or scrunched states of RNA polymerase, depending on the presence of GreB.

The paper identifies promoter sequence determinants and structural basis of primer-dependent transcription initiation in E. coli using MASTER and biochemical studies.

This paper introduces a method to model higher-order genetic interactions from partially observed data and applies it to predict phenotypes in antibody-binding domains and splicing efficiency.

The paper introduces a method to characterize promoter regulation in E. coli by analyzing 100 promoters across 12 growth conditions, identifying regulatory elements and transcription factors.

The paper introduces a method to measure the Gibbs free energy of TF-DNA and TF-TF interactions in living cells using allelic manifolds and reporter assays, achieving precision of ~0.1 kcal/mol.

The paper shows that small non-additive contributions to folding free energy are essential for protein stability, compatible with observed additive mutation effects.

This study develops a method to map DNA sequences to transcription factor binding energy using in vivo data, achieving predictions within 1 kBT of measured values and exploring sequence-context relationships.

The paper introduces a systematic method combining assays and modeling to dissect bacterial promoter mechanisms at nucleotide resolution.

This paper introduces TiteSeq, a method to measure binding affinities of thousands of antibody variants, revealing structural insights and the role of secondary CDR loops in stability.