Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis
Nature Communications, 2020 Genomics-based neoantigen discovery can be enhanced by proteomic evidence, but there remains a lack of consensus on the performance of different quality control methods for variant peptide identification in proteogenomics.
Bo Wen, Kai Li, Yun Zhang, Bing Zhang
semanticscholar +1 more source
Understanding Neurodegenerative Diseases From the −Omics Perspective: Lessons Learnt
Annals of Neurology, EarlyView.As the population ages, certain neurodegenerative diseases (NDs) are becoming a major health issue. For this reason, this review will focus on the most common ND with onset after 65 years old; Alzheimer's disease, Parkinson's disease, Lewy body dementia, and frontotemporal dementia.
Laura Ibanez +5 more
wiley +1 more source
Proteogenomic and V(D)J Analysis of Human Decidual T Cells Highlights Unique Transcriptional Programming and Clonal Distribution [PDF]
, 2023 Deborah Chasman +8 more
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A unified mediation analysis framework for integrative cancer proteogenomics with clinical outcomes
Bioinform., 2023 Motivation Multilevel molecular profiling of tumors and the integrative analysis with clinical outcomes have enabled a deeper characterization of cancer treatment.
Licai Huang +5 more
semanticscholar +1 more source
Animal Research and One Health, EarlyView.We conducted a longitudinal trial across nursery, growing, and finishing phases, showing that phytochemical supplementation as a potential antibiotic alternative reduced potential pathogens and promoted beneficial Lactobacillus amylovorus in the nursery phase, and enriched amino acid and carbohydrate metabolism pathways (prediction) during finishing ...
Ziyu Liu +11 more
wiley +1 more source
Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol. [PDF]
, 2019 Stable isotope probing (SIP) enables tracking the nutrient flows from isotopically labeled substrates to specific microorganisms in microbial communities. In proteomic SIP, labeled proteins synthesized by the microbial consumers of labeled substrates are
Banfield, Jillian F +10 more
core +1 more source
Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont [PDF]
, 2020 The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50 % pseudogenes containing mutations ...
Beynon, R +9 more
core +2 more sources
bioRxiv, 2023 Here we describe the histopathology-driven proteogenomic landscape of 142 treatment-naïve metastatic melanoma samples. We identified five proteomic subtypes that integrate the immune and stroma microenvironment components, and associate with clinical and
M. Kuras +30 more
semanticscholar +1 more source
Protein glycosylation in lung cancer from a mass spectrometry perspective
Mass Spectrometry Reviews, EarlyView.Abstract Lung cancer is a severe disease for which better diagnostic and therapeutic approaches are urgently needed. Increasing evidence implies that aberrant protein glycosylation plays a crucial role in the pathogenesis and progression of lung cancer.
Mirjam Balbisi +2 more
wiley +1 more source
Proteogenomics of synaptosomal mitochondrial oxidative stress [PDF]
Free Radical Biology and Medicine, 2012 Oxidative stress is frequently implicated in the pathology of neurodegenerative disease. The chief source of this stress is mitochondrial respiration, via the passage of reducing equivalents through the respiratory chain resulting in a small but potentially pathological production of superoxide. The superoxide that is produced during normal respiration
James M, Flynn +6 more
openaire +2 more sources