Ben C. Collins

Spectronaut-nf is a Nextflow pipeline that enables parallel processing of DIA proteomics data on HPC systems, reducing analysis time compared to single workstation execution.

The paper introduces a multi-omics framework to analyze protein activity in context-specific networks, demonstrating its utility in linking molecular profiles to phenotypic outcomes using HeLa and Kyoto cell lines.

The paper uses long-read assemblies and proteogenomic analysis to discover novel small proteins in Mycobacterium tuberculosis strains.

The paper presents a comprehensive spatial proteome map of human tissues and cancers, enabling drug response analysis and target discovery.

This study identifies lineage-specific transcriptional network rewiring in Mtb by analyzing proteomic and transcriptomic data from L1 and L2 strains, revealing key regulators like Rv1985c that drive phenotypic differences.

This study generates and benchmarks iPSC-derived macrophages (iMacs) as a model for human inflammasome signaling, showing they respond to multiple inflammasome stimuli and activate unique pathways.

The paper introduces an ion mobility-integrated gas phase fractionation (IM-GPF) method for rapid diaPASEF library generation, outperforming direct deconvolution and approaching offline fractionation performance.

The paper presents a rapid workflow combining experimental and computational methods to profile protein complex re-organization in cellular states, showing distinct changes during differentiation and macrophage stimulation.

This paper introduces a data-driven method to detect functional proteoform groups from bottom-up proteomic datasets, identifying state-specific proteoform groups linked to molecular mechanisms.

SECAT quantifies differential protein-protein interaction states across cellular states by analyzing PPI networks, showing improved scalability and effectiveness over previous methods.

The paper introduces a new DIA scan mode that improves peptide precursor ion sampling and identification specificity using ion mobility, achieving high proteome coverage and accuracy.

The paper quantifies proteome assembly state changes during mitosis using SEC-SWATH-MS and identifies new mitotic complex disassembly events.

The paper introduces a method to quantify protein complexes using SEC-SWATH-MS and identifies 462 complexes from HEK293 cells.

The paper investigates the fitness cost of rifampicin resistance in Mycobacterium tuberculosis using transcriptomic and proteomic profiling, finding that aberrant gene expression causes the cost and that this burden can be suppressed.