AIMC Topic: Proteome

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Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs.

Scientific reports
Apart from some model organisms, the interactome of most organisms is largely unidentified. High-throughput experimental techniques to determine protein-protein interactions (PPIs) are resource intensive and highly susceptible to noise. Computational...

Machine Learning and Network Analyses Reveal Disease Subtypes of Pancreatic Cancer and their Molecular Characteristics.

Scientific reports
Given that the biological processes governing the oncogenesis of pancreatic cancers could present useful therapeutic targets, there is a pressing need to molecularly distinguish between different clinically relevant pancreatic cancer subtypes. To add...

MMPdb and MitoPredictor: Tools for facilitating comparative analysis of animal mitochondrial proteomes.

Mitochondrion
Data on experimentally-characterized animal mitochondrial proteomes (mt-proteomes) are limited to a few model organisms and are scattered across multiple databases, impeding a comparative analysis. We developed two resources to address these problems...

In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics.

Nature communications
Data-independent acquisition (DIA) is an emerging technology for quantitative proteomic analysis of large cohorts of samples. However, sample-specific spectral libraries built by data-dependent acquisition (DDA) experiments are required prior to DIA ...

Joint learning improves protein abundance prediction in cancers.

BMC biology
BACKGROUND: The classic central dogma in biology is the information flow from DNA to mRNA to protein, yet complicated regulatory mechanisms underlying protein translation often lead to weak correlations between mRNA and protein abundances. This is pa...

Identification of distinct blood-based biomarkers in early stage of Parkinson's disease.

Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology
Parkinson's disease (PD) is a slowly progressive geriatric disease, which can be one of the leading causes of serious socioeconomic burden in the aging society. Clinical trials suggest that prompt treatment of early-stage Parkinson's disease (EPD) ma...

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput.

Nature methods
We present an easy-to-use integrated software suite, DIA-NN, that exploits deep neural networks and new quantification and signal correction strategies for the processing of data-independent acquisition (DIA) proteomics experiments. DIA-NN improves t...

GSIAR: gene-subcategory interaction-based improved deep representation learning for breast cancer subcategorical analysis using gene expression, applicable for precision medicine.

Medical & biological engineering & computing
Tumor subclass detection and diagnosis is inevitable requirement for personalized medical treatment and refinement of the effects that the somatic cells show towards other clinical conditions. The genome of these somatic cells exhibits mutations and ...

Investigation of machine learning techniques on proteomics: A comprehensive survey.

Progress in biophysics and molecular biology
Proteomics is the extensive investigation of proteins which has empowered the recognizable proof of consistently expanding quantities of protein. Proteins are necessary part of living life form, with numerous capacities. The proteome is the complete ...