Cristina Chiva

This paper introduces a normalization framework to decouple protocol and instrument effects in multicenter proteomics studies, demonstrating its application to the PME13 dataset.

The paper profiles histone post-translational modifications across eukaryotic lineages to assess conservation of chromatin states, finding conserved euchromatin states but diverse repressive heterochromatin configurations.

The paper investigates genomic mechanisms underlying independent transitions to terrestrial life across species, finding lineage-specific gene changes that converge functionally.

The paper generates a benchmark dataset to evaluate proteomics instruments and workflows using high-throughput LC gradients across multiple platforms and organisms.

iDeepLC improves retention time prediction for peptides with unseen modifications by incorporating chemical structural information, outperforming previous models.

ProteoBench provides a centralized platform for comparing proteomics data analysis workflows, enabling benchmarking and community collaboration.

The paper introduces TMTCal, a TMT-based multipoint internal calibration method for proteomics, demonstrating its application in quantifying proteome changes in ovarian cancer cells under cisplatin treatment.

This study identifies gene gain and regulatory shifts in terrestrial planarians as key mechanisms for terrestrialization, showing distinct stress response toolkits compared to freshwater relatives.

This study compares toxin and mucus protein evolution in aquatic and terrestrial flatworms, finding broader toxin gene repertoires and distinct functional expansions in terrestrial species.

This study harmonizes quality controls across proteomics core facilities to improve data comparability and reliability through a 4-year longitudinal dataset and common processing software.