A5018388583- Bioinformatics and Genomic Networks
- Alzheimer's disease research and treatments
- Advanced Proteomics Techniques and Applications
- Computational Drug Discovery Methods
- Metabolomics and Mass Spectrometry Studies
- Biotin and Related Studies
- Endoplasmic Reticulum Stress and Disease
- RNA Research and Splicing
- Fungal Biology and Applications
- Chronic Lymphocytic Leukemia Research
- Fermentation and Sensory Analysis
- Mass Spectrometry Techniques and Applications
- Celiac Disease Research and Management
- Renal Diseases and Glomerulopathies
- Acute Lymphoblastic Leukemia research
- Viral-associated cancers and disorders
- interferon and immune responses
- Fungal and yeast genetics research
- Cell Adhesion Molecules Research
- Caveolin-1 and cellular processes
- Inflammasome and immune disorders
- BRCA gene mutations in cancer
St. Jude Children's Research Hospital
2021-2025
Boston Children's Hospital
2024
Harvard University
2023-2024
Rhodes College
2019
Murine models of Alzheimer's disease (AD) are crucial for elucidating mechanisms but have limitations in fully representing AD molecular complexities. Here we present the comprehensive, age-dependent brain proteome and phosphoproteome across multiple mouse amyloidosis. We identified shared pathways by integrating with human metadata prioritized components multi-omics analysis. Collectively, two commonly used (5xFAD APP-KI) replicate 30% protein alterations; additional genetic incorporation...
Epstein-Barr virus (EBV) causes infectious mononucleosis, triggers multiple sclerosis, and is associated with 200,000 cancers/year. EBV colonizes the human B cell compartment periodically reactivates, inducing expression of 80 viral proteins. However, much remains unknown about how remodels host cells dismantles key antiviral responses. We therefore created a map EBV-host EBV-EBV interactions in undergoing replication, uncovering conserved herpesvirus versus EBV-specific targets. The...
Tandem mass tag (TMT) spectrometry is a mainstream isobaric chemical labeling strategy for profiling proteomes. Here we present 29-plex TMT method to combine the 11-plex and 18-plex strategies. The was examined with pooled sample composed of 1×, 3×, 10× Escherichia coli peptides 100× human background peptides, which generated two E. datasets (TMT11 TMT18), displaying distorted ratios 1.0:1.7:4.2 1.0:1.8:4.9, respectively. This ratio compression from expected 1:3:10 caused by co-isolated...
With recent advances in mass spectrometry-based proteomics technologies, deep profiling of hundreds proteomes has become increasingly feasible. However, deriving biological insights from such valuable datasets is challenging. Here we introduce a systems biology-based software JUMPn, and its associated protocol to organize the proteome into protein co-expression clusters across samples protein-protein interaction (PPI) networks connected by modules (e.g., complexes). Using R/Shiny platform,...
Mass spectrometry (MS)-based proteomic analysis of posttranslational modifications (PTMs) usually requires the pre-enrichment modified proteins or peptides. However, recent ultra-deep whole proteome profiling generates millions spectra in a single experiment, leaving many unassigned spectra, some which may be derived from PTM peptides.Here we present JUMPptm, an integrative computational pipeline, to extract PTMs unenriched proteome. JUMPptm combines advantages JUMP, MSFragger and Comet...
With recent advances in mass spectrometry-based proteomics technologies, deep profiling of hundreds proteomes has become increasingly feasible. However, deriving biological insights from such valuable datasets is challenging. Here we introduce a systems biology-based software JUMPn, and its associated protocol to organize the proteome into protein co-expression clusters across samples protein-protein interaction (PPI) networks connected by modules (e.g., complexes). Using R/Shiny platform,...
Abstract Murine models of Alzheimer’s disease (AD) are crucial for elucidating mechanisms but have limitations in fully representing AD molecular complexities. We comprehensively profiled age-dependent brain proteome and phosphoproteome ( n > 10,000 both) across multiple mouse amyloidosis. identified shared pathways by integrating with human metadata, prioritized novel components multi-omics analysis. Collectively, two commonly used (5xFAD APP-KI) replicate 30% the protein alterations;...
<title>Abstract</title> Murine models of Alzheimer’s disease (AD) are crucial for elucidating mechanisms but have limitations in fully representing AD molecular complexities. We comprehensively profiled age-dependent brain proteome and phosphoproteome (n > 10,000 both) across multiple mouse amyloidosis. identified shared pathways by integrating with human metadata, prioritized novel components multi-omics analysis. Collectively, two commonly used (5xFAD APP-KI) replicate 30% the protein...
Cell division in filamentous fungi involves coalescence and subsequent constriction of a contractile actomyosin ring (CAR), as other metazoans. In fungi, the CAR is followed by deposition cell wall material resulting septum. model organism, Aspergillus nidulans , many proteins are involved septation including protein kinase C (PkcA), formin SepA, GTPase Rho4. The current study focuses on relationships among PkcA, Rho‐type GTPases during septation. PkcA contains two putative N ‐terminal Rho...