Dieter L. D. Deforce

This paper develops a method to identify species in mixed palaeoproteomic samples by analyzing both physical and genetic mixtures, revealing new faunal information from ancient bone fragments.

LCM-FFPEseq enables high-sensitivity transcriptomics from FFPE tissues with single-cell resolution, detecting over 14,000 genes per sample using as few as 30 cells.

This study characterizes multimeric artefacts in RPA and identifies temperature and T4 UvsX concentration as ways to reduce them.

The paper constructs a multi-omics biomolecular network in AML using proteins, metabolites, and histone PTMs to reveal functional entanglement between biomolecules.

The paper uses mass spectrometry to profile histone post-translational modifications in T-ALL cell lines and identifies drug response signatures, but finds discrepancies between in vitro and in vivo models.

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

This paper develops a mass spectrometry-based method to profile single-cell histone post-translational modifications, demonstrating its ability to detect treatment responses and chromatin heterogeneity.

This study evaluates Recombinase Polymerase Amplification (RPA) for amplifying forensic STR loci, showing successful singleplex amplification but challenges in multiplex formats.

The paper develops a multimodal model integrating chemical structure and transcriptomics to predict toxicity, achieving robust performance across multiple assays and providing mechanistic insights.

This paper uses proteomics alongside use-wear and microscopy analyses to identify bovine, plant, and human proteins on Mesolithic-Neolithic tools, demonstrating the potential of palaeoproteomics for understanding prehistoric activities.

This study examines genetic responses of Circaea lutetiana to forest edge dynamics, finding delayed genetic changes and highlighting the role of historical forest configuration in shaping current genetic diversity.

ClassiCOL improves species classification from ancient collagen LC-MS/MS data by resolving peptide ambiguity through isoBLAST and taxonomic branching analysis.

The paper develops a targeted LC-MS method to quantify SARS-CoV-2 spike protein expression and enables proteome profiling of infected cells.

The paper investigates methylome stability and parental effects in Lombardy poplar, finding stable CG methylation patterns and weak parental carry-over effects on phenotypic traits.

The paper develops a genotyping assay to accurately determine CYP2D6-CYP2D7 hybrid alleles using optimized nanopore sequencing and a new analysis pipeline.

The paper presents a comprehensive benchmark dataset for evaluating label-free quantification methods across various proteomics acquisition strategies.

The paper provides a roadmap for selecting a bottom-up mass spectrometry protocol for histone analysis by comparing four methods and introducing a new enzyme.

The paper removes the dependency on DDA libraries in DIA by using predicted spectral libraries, making the workflow deterministic and improving standardization in clinical proteomics.

The paper introduces ion-networks, a data format for DIA MS that captures full data integrity by representing reproducible fragment ions and their consistent co-elution across runs.

This study evaluates the use of Oxford Nanopore MinION sequencer for forensic STR profiling using standard primers and shows it can generate partial forensic profiles despite high error rates.