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ModelsLorenz2026 - Wright-Fisher model with negative frequency-dependent selection (NFDS) for vaccine-replacement dynamics in S. pneumoniae
A compartmental Wright-Fisher model that describes the replacement dynamics in Streptococcus pneumoniae populations after the introduction of vaccines. Free parameters in the model are vaccine impact, negative frequency-dependent selection (NFDS), and immigration rate.
2026-09-27 | MODEL2609210001 | BioModels
ProteomicsNucleosome recognition and DNA distortion by the Chd1 remodeler revealed at 2.6 Å resolution
Chromatin remodelers are ATP-dependent enzymes that reorganize nucleosomes within all eukaryotic genomes. The Chd1 remodeler specializes in shifting nucleosomes into evenly spaced arrays, a defining characteristic of chromatin in gene bodies that blocks spurious transcription initiation. Linked to s...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) Xenopus laevis (African clawed frog) 
2022-02-23 | PXD025287 | Pride
Chd1 Nucleosome Xl-ms Chromatin remodeler 
UnknownT-cell receptor beta variable gene polymorphism predicts immune-related adverse events during checkpoint blockade immunotherapy.
Not available
S-EPMC10445351 | biostudies-literature
ProteomicsAn Intrinsically Disordered Region of Ubp10 Governs its Specificity for Deubiquitinating H2A/H2B Dimers over Nucleosomes
Histone modifications perform a vast array of functions in regulating gene expression, DNA replication, and repair. Monoubiquitination of histone H2B at K123 in yeast (K120 in humans) is an intriguing modification because it is deposited cotranscriptionally, mediates the installation of several othe...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2025-07-16 | PXD051971 | Pride
Deubiqutinase Crosslinking mass spectrometry Ubiquitinated histone Ubp10 Single molecule fret Fact 
ProteomicsCatechol-O-Methyltransferase connects dopamine homeostasis to redox signaling, metal homeostasis and protein folding in schizophrenia
Dysregulation of dopamine (DA) signaling and redox homeostasis contributes to multiple neuropsychiatric and neurodegenerative disorders. Polymorphisms that influence the activity of catechol‑O‑methyltransferase (COMT), an enzyme critical for degrading dopamine (DA) in the dorsolateral prefrontal cor...
ORGANISM(S): Rattus norvegicus (Rat) 
2026-09-28 | PXD075030 | Pride
Limited proteolysis Thermo-fisher ascend Rat Pc12 cells 
TranscriptomicsInstitute of Aquaculture Lepeophtheirus salmonis analysis of gene expression induced by in vitro exposure to emamectin benzoate
Caligid copepods, also called sea lice, are common ectoparasites of wild and farmed marine fish. The salmon louse Lepeophtheirus salmonis (KrM-xyer, 1837) has emerged as a serious problem for salmon farming in the Northern hemisphere. The annual cost of sea lice to the global salmon mariculture indu...
ORGANISM(S): Lepeophtheirus salmonis 
2013-11-06 | E-MTAB-1478 | biostudies-arrayexpress
MetabolomicsRA-MAP: mapping the molecular immunological landscape in early rheumatoid arthritis with vaccine controls

Rheumatoid arthritis (RA) is a chronic inflammatory disorder with poorly defined aetiology characterised by synovial inflammation with variable disease severity and drug responsiveness. To investigate the peripheral blood immune cell landscape of RA, we performed comprehensive clinical and molecu...

2021-06-16 | MTBLS1497 | MetaboLights
TranscriptomicsInstitute of Aquaculture Lepeophtheirus salmonis constitutive gene expression analysis
Caligid copepods, also called sea lice, are common ectoparasites of wild and farmed marine fish. The salmon louse Lepeophtheirus salmonis (KrM-xyer, 1837) has emerged as a serious problem for salmon farming in the Northern hemisphere. The annual cost of sea lice to the global salmon mariculture indu...
ORGANISM(S): Lepeophtheirus salmonis 
2013-11-06 | E-MTAB-1484 | biostudies-arrayexpress
MetabolomicsHeadspace volatile organic compounds from bacteria implicated in ventilator-associated pneumonia analysed by TD-GC/MS
Ventilator-associated pneumonia (VAP) is a healthcare-acquired infection arising from the invasion of the lower respiratory tract by opportunistic pathogens in ventilated patients. The current method of diagnosis requires the culture of an airway sample such as bronchoalveolar lavage, which is invas...
2018-08-08 | MTBLS497 | MetaboLights
ProteomicsDeciphering Staphylococcus aureus-host dynamics using dual Activity-based protein profiling of ATP-interacting proteins
This study focuses on ATP-binding proteins to dissect the complex interplay between Staphylococcus aureus and human cells, particularly macrophages (THP-1) and keratinocytes (HaCaT), during the course of an intracellular infection. A snapshot of the various protein activity and function is provided ...
ORGANISM(S): Homo sapiens (Human) Staphylococcus aureus 
2024-04-22 | PXD049003 | Pride
Atp-interacting proteins Thp-1 cell infection Staphylococcus aureus Activity-based protein profiling Hacat cel infectionl Host-pathogen interaction 
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