Michael Lund Nielsen

The paper develops an MS-based workflow to detect Glu/Asp-ADPr modifications, identifies over 600 sites in cytokine-stimulated cells, and reveals residue-specific ADPr dynamics in immune signaling.

The paper introduces MaxSBM, a MaxQuant module for identifying sequence-based modifiers like SUMO, improving peptide identification rates and spectral annotation.

The paper reports the structure of a novel contractile injection system in Salmonella enterica subsp. salamae and identifies a new CIS cluster.

The paper uses proteomics and phosphoproteomics to show GCs activate TLR and Rho GTPase signaling in neutrophil-like cells, leading to abnormal activation and aging.

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

This study presents the cryo-EM structures of PlPVC1 in extended and contracted states, revealing structural features and contraction mechanism insights.

The paper uses proteomics to analyze protein dynamics during replication origin firing in human cells, identifying NCAPH2 as a novel factor required for efficient origin firing.

The paper identifies TOPORS as a SUMO-targeted ubiquitin ligase (STUbL) essential for SUMO-dependent DNA-protein crosslink repair and stress responses, showing its cooperative function with RNF4.

The paper identifies 14,056 citrullination sites across 4,008 proteins using mass spectrometry, revealing widespread citrullination and its functional roles in histone marks and autoantigens.

The paper introduces UBIMAX, a method to profile ubiquitylation, and identifies Dbn1 as a novel DNA damage-induced ubiquitylation target regulated by SCFβTRCP.

This study identifies catalytic and non-catalytic functions of DNA polymerase kappa in translesion DNA synthesis using CRISPR screening and TLS analysis.

This paper identifies VCF1 as a novel p97 cofactor that enhances p97-UFD1-NPL4 interactions with ubiquitylated substrates, promoting proteasomal degradation.

This study identifies the dual role of sumoylation in adipocyte differentiation by regulating gene expression and transcriptional network rewiring through SLAMseq and ChIPseq.

The paper identifies ADP-ribosylation sites regulated by HPF1 and ARH3 using proteomics, revealing widespread mono-ADP-ribosylation and challenges existing assumptions about PARP1 target residues.

The paper introduces AI-ETD for MS-based proteomics analysis of physiological ADP-ribosylation, identifying more ADPr sites than existing methods.

The paper identifies RNA binding proteins and RNAs interacting with Sox2 in mouse embryonic stem cells, showing coexistence in a ribonucleoprotein complex without evidence of chromatin recruitment regulation.

This study shows that PADI2-mediated citrullination is essential for oligodendrocyte differentiation, myelination, and motor function, with implications for remyelination therapies.

The paper introduces an advanced proteomics strategy using mass spectrometry to comprehensively profile ADP-ribosylation sites, identifying over 11,000 unique peptides and 7,000 sites in HeLa cells.