Lindsay K. Pino

Ptarmigan-1 uses contrastive learning to predict small molecule-protein interactions without requiring 3D structure, outperforming traditional methods on challenging targets.

MSstatsBioNet integrates differential proteomics results with biomolecular networks to enable mechanistic interpretation of biological changes.

The paper identifies two classes of Pol2-mediated chromatin clusters and shows CpG island density predicts CBP/p300 dependency.

Carafe2 generates high-quality in silico spectral libraries for timsTOF DIA proteomics by fine-tuning deep learning models on DIA data, outperforming DDA-trained models in multiple applications.

This paper introduces a method to profile the regulome across human cell lines and perturbations, revealing transcription factor dynamics and drug responses.

The paper identifies neuropeptides that specify and reprogram division of labor in leafcutter ants, showing their role in behavior and transcriptomic changes.

The paper introduces nf-encyclopedia, a NextFlow pipeline for DIA proteomics analysis, showing it works well on cloud and local platforms and improves protein quantification with MSstats.

The paper identifies and characterizes small ORFs and microproteins in adipose cells, showing their metabolic relevance and potential roles in obesity and inflammation.

The paper examines the role of epigenetics in the transition from unicellular to multicellular states in Dictyostelium discoideum, identifying conserved genes and validating their necessity or sufficiency for multicellularity.

This study develops a method to quantify nuclear protein dynamics by isolating chromatin compartments and using mass spectrometry, revealing chromatin remodeling during BET protein degradation.