Jason Derks

Proteome asymmetry in mouse and human embryos before fate specification

The paper shows proteomic asymmetry in mouse and human embryos that influences lineage segregation.

Ubiquitin-Proteasome System Dysregulation in Alzheimer's Disease Impacts Protein Abundance

This study identifies proteomic changes in Alzheimer's disease, revealing decreased 20S proteasome levels and altered ubiquitin system enzymes contributing to protein accumulation.

JMod: Joint modeling of mass spectra for empowering multiplexed DIA proteomics

JMod improves sequence identification and quantification in multiplexed DIA proteomics by jointly modeling overlapping mass spectra, enabling higher throughput with maintained accuracy.

timePlex: Increasing mass spectrometry throughput using time-encoded sample multiplexing

timePlex increases LC-MS throughput by multiplexing samples in the time domain, achieving combinatorial scaling and enabling high-throughput proteomics.

Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y

The paper shows that DDX3X and DDX3Y exhibit post-transcriptional cross- and auto-regulation, buffering their expression levels in human cells.

Inferring post-transcriptional regulation within and across cell types in human testis

The paper quantifies proteomes and RNA levels in human testis cells to infer post-transcriptional regulation using a Bayesian model called BayesPG.

Single-nucleus proteomics identifies regulators of protein transport

The paper identifies regulators of nucleocytoplasmic protein transport in macrophages using single-nucleus proteomics and validates findings through knockdown experiments.

Strategies for increasing the depth and throughput of protein analysis by plexDIA

This paper introduces plexDIA, a framework for increasing proteomics throughput and depth through multiplexed DIA, enabling more accurate protein quantification and single-cell analysis.

Increasing the throughput of sensitive proteomics by plexDIA

Multiplexing nonisobaric isotopologous mass tags (mTRAQ) with data-independent acquisition and DIA-NN increases sensitive proteomics throughput 3-fold while cutting missing data below 3% in bulk and single cells.