Niles A. Pierce

This paper introduces transfer matrix and tensor models for nucleic acid secondary structure thermodynamics, achieving higher accuracy with fewer parameters and improved computational efficiency.

The paper develops mixed-material models and dynamic programming algorithms for analyzing equilibrium base-pairing properties of nucleic acid systems containing RNA, DNA, and 2'OMe-RNA strands.

The paper introduces k-spaces, a probabilistic framework for simultaneous dimension reduction, clustering, and latent space learning, demonstrating its application in genomic settings.

This paper develops a method to image protein:protein complexes with high resolution and quantitation using hybridization chain reaction, demonstrating its effectiveness in various biological samples.

This paper introduces a method using hybridization chain reaction for multiplexed, quantitative, high-resolution imaging of both proteins and RNA in challenging tissues.

This paper introduces conditional guide RNAs (cgRNAs) that control CRISPR/Cas activity via RNA triggers, enabling programmable gene regulation in E. coli with varying dynamic ranges and crosstalk levels.

The paper demonstrates scRNAs that perform conditional RNA interference in human cell lysate, showing programmable signal transduction between mRNAs X and Y with a 20-fold response difference.

This paper introduces third-generation in situ HCR with automatic background suppression, enabling multiplexed, quantitative mRNA imaging and flow cytometry with improved performance and ease-of-use.

This paper introduces a method to quantitatively analyze mRNA expression in whole vertebrate embryos with subcellular resolution, enabling both anatomical to expression and expression to anatomical queries.