Proteomics
Methods and Protocols
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Article
Open AccessAZGP1 deficiency promotes angiogenesis in prostate cancer
Loss of AZGP1 expression is a biomarker associated with progression to castration resistance, development of metastasis, and poor disease-specific survival in prostate cancer. However, high expression of AZGP1...
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Article
Nano-omics: nanotechnology-based multidimensional harvesting of the blood-circulating cancerome
Over the past decade, the development of ‘simple’ blood tests that enable cancer screening, diagnosis or monitoring and facilitate the design of personalized therapies without the need for invasive tumour biop...
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Chapter and Conference Paper
A Dataset Generation Framework for Evaluating Megapixel Image Classifiers and Their Explanations
Deep learning-based megapixel image classifiers have exceptional prediction performance in a number of domains, including clinical pathology. However, extracting reliable, human-interpretable model explanation...
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Article
Open AccessModular fluorescent nanoparticle DNA probes for detection of peptides and proteins
Fluorescently labeled antibody and aptamer probes are used in biological studies to characterize binding interactions, measure concentrations of analytes, and sort cells. Fluorescent nanoparticle labels offer ...
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Article
Open AccessTranscriptome and genome evolution during HER2-amplified breast neoplasia
The acquisition of oncogenic drivers is a critical feature of cancer progression. For some carcinomas, it is clear that certain genetic drivers occur early in neoplasia and others late. Why these drivers are s...
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Article
Sanjiv ‘Sam’ Gambhir (1962–2020)
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Article
Open AccessMulticompartment modeling of protein shedding kinetics during vascularized tumor growth
Identification of protein biomarkers for cancer diagnosis and prognosis remains a critical unmet clinical need. A major reason is that the dynamic relationship between proliferating and necrotic cell populatio...
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Article
Open AccessImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network
While technological advances have made it possible to profile the immune system at high resolution, translating high-throughput data into knowledge of immune mechanisms has been challenged by the complexity of...
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Article
Loss of ER retention motif of AGR2 can impact mTORC signaling and promote cancer metastasis
Anterior gradient 2 (AGR2) is a member of the protein disulfide isomerase (PDI) family, which plays a role in the regulation of protein homeostasis and the unfolded protein response pathway (UPR). AGR2 has als...
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Article
Open AccessImproving Precursor Selectivity in Data-Independent Acquisition Using Overlap** Windows
A major goal of proteomics research is the accurate and sensitive identification and quantification of a broad range of proteins within a sample. Data-independent acquisition (DIA) approaches that acquire MS/M...
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Article
Open AccessA Temporal Examination of Platelet Counts as a Predictor of Prognosis in Lung, Prostate, and Colon Cancer Patients
Platelets, components of hemostasis, when present in excess (>400 K/μL, thrombocytosis) have also been associated with worse outcomes in lung, ovarian, breast, renal, and colorectal cancer patients. Associatio...
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Article
Open AccessMulti-lectin Affinity Chromatography and Quantitative Proteomic Analysis Reveal Differential Glycoform Levels between Prostate Cancer and Benign Prostatic Hyperplasia Sera
Currently prostate-specific antigen is used for prostate cancer (PCa) screening, however it lacks the necessary specificity for differentiating PCa from other diseases of the prostate such as benign prostatic ...
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Article
How many human proteoforms are there?
Despite decades of accumulated knowledge about proteins and their post-translational modifications (PTMs), numerous questions remain regarding their molecular composition and biological function. One of the mo...
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Article
Open AccessAssessing biological and technological variability in protein levels measured in pre-diagnostic plasma samples of women with breast cancer
Quantitative proteomics allows for the discovery and functional investigation of blood-based pre-diagnostic biomarkers for early cancer detection. However, a major limitation of proteomic investigations in bio...
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Book
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Protocol
A Robust Protocol for Protein Extraction and Digestion
Proteins play a key role in all aspects of cellular homeostasis. Proteomics, the large-scale study of proteins, provides in-depth data on protein properties, including abundances and post-translational modific...
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Chapter and Conference Paper
A Bayesian Active Learning Experimental Design for Inferring Signaling Networks
Machine learning methods for learning network structure, applied to quantitative proteomics experiments, reverse-engineer intracellular signal transduction networks. They provide insight into the rewiring of s...
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Protocol
Data Conversion with ProteoWizard msConvert
Recent advances in proteome informatics have led to an explosion in tools to analyze mass spectrometry data. These tools operate across the analysis pipeline doing everything from assessing quality control to ...
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Article
Open AccessSingle cell dynamic phenoty**
Live cell imaging has improved our ability to measure phenotypic heterogeneity. However, bottlenecks in imaging and image processing often make it difficult to differentiate interesting biological behavior fro...
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Article
Open AccessA high-content image-based method for quantitatively studying context-dependent cell population dynamics
Tumor progression results from a complex interplay between cellular heterogeneity, treatment response, microenvironment and heterocellular interactions. Existing approaches to characterize this interplay suffe...
