AIMC Topic: Proteome

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Engineered nanoparticles enable deep proteomics studies at scale by leveraging tunable nano-bio interactions.

Proceedings of the National Academy of Sciences of the United States of America Mar 11, 2022
SignificanceDeep profiling of the plasma proteome at scale has been a challenge for traditional approaches. We achieve superior performance across the dimensions of precision, depth, and throughput using a panel of surface-functionalized superparamag...
Proteomics Proteome Deep Learning Blood Proteins Nanoparticles Protein Corona
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PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning.

Journal of molecular biology Mar 5, 2022
Proteome-wide identification of protein-protein interactions is a formidable task which has yet to be sufficiently addressed by experimental methodologies. Many computational methods have been developed to predict proteome-wide interaction networks, ...
SARS-CoV-2 Proteomics Proteome Bayes Theorem Machine Learning Software COVID-19 Protein Interaction Mapping Humans
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Using deep learning to annotate the protein universe.

Nature biotechnology Feb 21, 2022
Understanding the relationship between amino acid sequence and protein function is a long-standing challenge with far-reaching scientific and translational implications. State-of-the-art alignment-based techniques cannot predict function for one-thir...
Molecular Sequence Annotation Proteome Databases, Protein Amino Acid Sequence Deep Learning Proteomics Humans
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Deep learning methods for 3D structural proteome and interactome modeling.

Current opinion in structural biology Feb 6, 2022
Bolstered by recent methodological and hardware advances, deep learning has increasingly been applied to biological problems and structural proteomics. Such approaches have achieved remarkable improvements over traditional machine learning methods in...
Deep Learning Computational Biology Proteome Protein Conformation Protein Folding
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Inferring protein expression changes from mRNA in Alzheimer's dementia using deep neural networks.

Nature communications Feb 3, 2022
Identifying the molecular systems and proteins that modify the progression of Alzheimer's disease and related dementias (ADRD) is central to drug target selection. However, discordance between mRNA and protein abundance, and the scarcity of proteomic...
Neural Networks, Computer Brain Female Aged Humans RNA, Messenger Proteomics Proteome Protein Biosynthesis Mass Spectrometry Alzheimer Disease Deep Learning Cognitive Dysfunction Dementia RNA-Seq Aged, 80 and over Male Transcriptome
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Precipitate-Supported Thermal Proteome Profiling Coupled with Deep Learning for Comprehensive Screening of Drug Target Proteins.

ACS chemical biology Jan 6, 2022
Although thermal proteome profiling (TPP) acts as a popular modification-free approach for drug target deconvolution, some key problems are still limiting screening sensitivity. In the prevailing TPP workflow, only the soluble fractions are analyzed ...
Proteins Chemical Precipitation Hot Temperature K562 Cells Deep Learning Proteomics Proteome Humans Algorithms Drug Delivery Systems
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Deep learning approaches for data-independent acquisition proteomics.

Expert review of proteomics Dec 28, 2021
INTRODUCTION: Data-independent acquisition (DIA) is an emerging technology for large-scale proteomic studies. DIA data analysis methods are evolving rapidly, and deep learning has cut a conspicuous figure in this field.
Deep Learning Proteomics Proteome Protein Processing, Post-Translational Humans Peptides
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A novel strategy to uncover specific GO terms/phosphorylation pathways in phosphoproteomic data in Arabidopsis thaliana.

BMC plant biology Dec 14, 2021
BACKGROUND: Proteins are the workforce of the cell and their phosphorylation status tailors specific responses efficiently. One of the main challenges of phosphoproteomic approaches is to deconvolute biological processes that specifically respond to ...
Phosphorylation Seedlings Phosphoproteins Microtubules RNA, Messenger Proteome Databases, Protein Arabidopsis Proteins Arabidopsis RNA, Plant Gene Ontology Genes, Plant RNA Splicing
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Integrated Multiomics Analysis Identifies a Novel Biomarker Associated with Prognosis in Intracerebral Hemorrhage.

Oxidative medicine and cellular longevity Dec 14, 2021
Existing treatments for intracerebral hemorrhage (ICH) are unable to satisfactorily prevent development of secondary brain injury after ICH and multiple pathological mechanisms are involved in the development of the injury. In this study, we aimed to...
Sphingolipids Animals Male Proteome Mice Humans Brain Injuries Biomarkers Collagenases Mice, Inbred C57BL Prognosis Inflammasomes Cerebral Hemorrhage Interleukin-12
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Computed structures of core eukaryotic protein complexes.

Science (New York, N.Y.) Dec 10, 2021
Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions not yet identified. We take advantage of advances in proteome-wide amino acid coe...
Computer Simulation Deep Learning Protein Interaction Maps Membrane Proteins Evolution, Molecular Computational Biology Proteome Protein Biosynthesis Ribosomes Multiprotein Complexes Chromosome Segregation Ligases Acyltransferases Homologous Recombination Ubiquitin Protein Interaction Mapping Saccharomyces cerevisiae Proteins DNA Repair Models, Molecular Protein Conformation Saccharomyces cerevisiae
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