Danielle L. Swaney

The paper identifies tau as an m6A-associated RNA binding protein that causes RNA dysregulation in MAPT coding-variant patients and V337M iNeurons.

The paper identifies aggrecan as an extracellular matrix protein that stabilizes fear memories by altering neuronal excitability in the hippocampal dentate gyrus.

The paper identifies an operon in MRSA encoding two secreted nucleases that contribute to virulence, showing attenuation in a mouse model when mutated.

This paper introduces EYClamp, a de novo designed enzyme for photo-proximity labeling of E3 ligase neighborhoods in live cells, identifying over 1,500 candidate neighbors for four E3 ligases.

This study shows APOE4 disrupts neuronal proteome dynamics by impairing proteostasis, leading to protein accumulation and cellular stress before Alzheimer's disease onset.

This study shows HIV-1 infected immune cells alter cervical cancer pathways through paracrine signals, with upregulated PI3K-AKT and interferon-stimulated genes.

The paper uses multi-omic analysis to study MAPT V337M neurons, finding altered axonogenesis and tau phosphorylation, with p38 MAPK pathway involvement in tau phosphorylation in V337M neurons.

This study identifies the COX2-PGE2-PKA axis as a negative regulator of mtDNA-STING signaling, which suppresses antiviral immunity by inhibiting STING activation through mitophagy.

The paper shows ECM proteolysis, specifically via MMP14 and brevican, maintains dynamic synapse plasticity during brain development in zebrafish and human iPSC-derived cultures.

This study investigates how RNA editing in cephalopods alters protein function through proteomics and biochemical assays, revealing its impact on protein stability, localization, and interactions.

This study identifies Mac1 as a therapeutic target for SARS-CoV-2 and demonstrates that AVI-4206, a small molecule inhibitor, reduces viral replication and improves survival in an animal model.

This study shows Tax1bp1 promotes Mtb growth in alveolar macrophages and enhances inflammatory responses, while restricting Mtb in bone marrow-derived macrophages.

The paper profiles RNA content in P-bodies across vertebrate species, showing that RNA sequestration in condensates is linked to cell fate transitions through miRNA-dependent mechanisms.

This study identifies lysosomal proteome changes caused by apoE4, linking them to lysosomal dysfunction and Alzheimer's disease pathology.

This study develops a biophysical model to show how lipid binding and mutations affect Orf9b's conformational equilibrium and its interaction with Tom70, influencing interferon suppression.

This paper develops RocASO, a molecular glue-oligonucleotide conjugate that selectively inhibits mRNA translation by targeting specific sequences, showing potent antiviral activity against SARS-CoV-2.

This paper describes the discovery of new coronavirus MPro inhibitors with improved pharmacokinetics, broad-spectrum antiviral activity, and superior in vivo efficacy compared to existing drugs.

This study identifies the L260F mutation in NSP6 as enhancing RNA replication and pathogenesis in recent SARS-CoV-2 variants, independent of Spike function.

The paper identifies a lipid-based compartment in early phage infection that protects phage DNA and supports early transcription and translation.

This paper identifies the interaction between Chlamydia trachomatis effector Tri1 and host TRAF7, showing Tri1 displaces TRAF7's native binding partners to alter its signaling during infection.

This study identifies a spatial mechanism of sensory adaptation in Pseudomonas aeruginosa, revealing how enzyme localization modulates mechanosensing and virulence.

The paper constructs a PPI network of 100 high-confidence ASD genes, identifies novel interactions, and uses AlphaFold-Multimer to prioritize variants for functional validation in organoids.

This study investigates the functional impact of a BAG3 allele associated with reduced heart failure risk, showing it enhances cardiomyocyte stress resistance through altered protein interactions.

The paper introduces Chronologer, a deep learning tool for accurate peptide retention time prediction, outperforming existing methods by leveraging harmonized datasets of post-translational modifications.

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.