Danielle L. Swaney

This study uses co-fractionation mass spectrometry to map host-pathogen and pathogen-pathogen interactions in jumbophages infecting Pseudomonas aeruginosa, revealing over 6000 interactions and novel viral components.

The paper systematically analyzes proteomic and genomic data of SARS-CoV-2 variants to identify how mutations affect viral gene expression, host interactions, and immune evasion.

The paper shows apoE4 increases VASP phosphorylation, disrupting actin interactions and affecting neurite outgrowth in Neuro-2a cells.

This paper evaluates a DIA proteomics approach using three proteases to increase proteome sequence coverage, achieving higher peptide and amino acid detection rates compared to trypsin alone.

The paper maps Tau interactomes in neurons using APEX and AP-MS to reveal activity-dependent interactions and FTD mutation effects on mitochondrial associations in neurodegenerative diseases.

This study identifies TRIM1 as an E3 ligase that ubiquitinates LRRK2, regulating its localization, degradation, and toxicity in Parkinson's Disease.

The paper investigates how the GTPase Ran/Gsp1 achieves functional multi-specificity through biophysical and genetic perturbations, revealing that its effects are linked to kinetic parameters of the switch cycle rather than direct interaction sites.

The paper develops a proteomics workflow using orthogonal proteases to generate spectral libraries, enabling comprehensive plasma proteome analysis and identifying TB-related proteins.

The paper generates and provides computational predictions of the effects of all possible SARS-CoV-2 missense variants to support variant analysis and experimental validation.

This paper identifies Isr1 as a negative regulator of the hexosamine biosynthesis pathway in yeast, showing it inhibits Gfa1 and modulates UDP-GlcNAc synthesis in response to cell cycle and nutrient signals.

Affinity-purification mass spectrometry of 26 SARS-CoV-2 proteins in HEK293T cells yields 332 high-confidence host interactions and 67 druggable human proteins with known compounds.

The paper creates a comprehensive human phosphoproteome by integrating 6,801 phospho-enriched mass spectrometry experiments and prioritizes functional phosphosites using machine learning.

The paper identifies NOSEMPE in brown adipocytes as a cause of mitochondrial ETC imbalance and shows it drives nonmitochondrial thermogenesis and metabolic improvement via ATF4 activation.

The paper uses proteomic analysis to identify TAX1BP1 as a mediator of autophagy targeting M. tuberculosis during macrophage infection.

The paper uses deep mutational scanning to explore how chemical perturbations affect ubiquitin's mutational tolerance, revealing sensitization of most positions except two.