AIMC Topic: Protein Interaction Maps

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Support vector machine classifier for prediction of the metastasis of colorectal cancer.

International journal of molecular medicine Jan 2, 2018
Colorectal cancer (CRC) is one of the most common cancers and a major cause of mortality. The present study aimed to identify potential biomarkers for CRC metastasis and uncover the mechanisms underlying the etiology of the disease. The five datasets...
Colorectal Neoplasms Gene Expression Profiling Cell Line, Tumor Humans Reproducibility of Results Databases, Genetic Quality Control Neoplasm Metastasis Protein Interaction Maps Gene Expression Regulation, Neoplastic Support Vector Machine
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Document triage for identifying protein-protein interactions affected by mutations: a neural network ensemble approach.

Database : the journal of biological databases and curation Jan 1, 2018
The precision medicine (PM) initiative promises to identify individualized treatment depending on a patients' genetic profile and their related responses. In order to help health professionals and researchers in the PM endeavor, BioCreative VI organi...
Neural Networks, Computer Algorithms Protein Interaction Maps Databases, Protein Mutation
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An end-to-end deep learning architecture for extracting protein-protein interactions affected by genetic mutations.

Database : the journal of biological databases and curation Jan 1, 2018
The BioCreative VI Track IV (mining protein interactions and mutations for precision medicine) challenge was organized in 2017 with the goal of applying biomedical text mining methods to support advancements in precision medicine approaches. As part ...
Machine Learning Algorithms Protein Interaction Maps Neural Networks, Computer Databases, Protein Mutation
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Hierarchical bi-directional attention-based RNNs for supporting document classification on protein-protein interactions affected by genetic mutations.

Database : the journal of biological databases and curation Jan 1, 2018
In this paper, we describe a hierarchical bi-directional attention-based Re-current Neural Network (RNN) as a reusable sequence encoder architecture, which is used as sentence and document encoder for document classification. The sequence encoder is ...
Protein Interaction Maps Neural Networks, Computer Models, Theoretical Algorithms Support Vector Machine Databases, Protein Reproducibility of Results Mutation Data Mining
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Construction of a 26‑feature gene support vector machine classifier for smoking and non‑smoking lung adenocarcinoma sample classification.

Molecular medicine reports Dec 7, 2017
The present study aimed to identify the feature genes associated with smoking in lung adenocarcinoma (LAC) samples and explore the underlying mechanism. Three gene expression datasets of LAC samples were downloaded from the Gene Expression Omnibus da...
Smoking Adenocarcinoma of Lung Gene Expression Regulation, Neoplastic Adenocarcinoma Support Vector Machine Databases, Genetic Cluster Analysis Gene Expression Profiling Protein Interaction Maps Lung Neoplasms Humans
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Disease Gene Prediction by Integrating PPI Networks, Clinical RNA-Seq Data and OMIM Data.

IEEE/ACM transactions on computational biology and bioinformatics Nov 7, 2017
Disease gene prediction is a challenging task that has a variety of applications such as early diagnosis and drug development. The existing machine learning methods suffer from the imbalanced sample issue because the number of known disease genes (po...
ROC Curve Sequence Analysis, RNA Humans Protein Interaction Maps Databases, Genetic Computational Biology Neoplasms RNA
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Revealing protein functions based on relationships of interacting proteins and GO terms.

Journal of biomedical semantics Sep 20, 2017
BACKGROUND: In recent years, numerous computational methods predicted protein function based on the protein-protein interaction (PPI) network. These methods supposed that two proteins share the same function if they interact with each other. However,...
Protein Interaction Maps Computational Biology Proteins Databases, Protein Gene Ontology Saccharomyces cerevisiae Proteins
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A support vector machine classifier for the prediction of osteosarcoma metastasis with high accuracy.

International journal of molecular medicine Sep 7, 2017
In this study, gene expression profiles of osteosarcoma (OS) were analyzed to identify critical genes associated with metastasis. Five gene expression datasets were screened and downloaded from Gene Expression Omnibus (GEO). Following assessment by M...
Protein Interaction Mapping Signal Transduction Support Vector Machine Osteosarcoma Gene Expression Profiling Bone Neoplasms Humans Protein Interaction Maps Neoplasm Staging Reproducibility of Results Gene Expression Regulation, Neoplastic Neoplasm Metastasis
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A Type-2 fuzzy data fusion approach for building reliable weighted protein interaction networks with application in protein complex detection.

Computers in biology and medicine Jun 23, 2017
Detecting the protein complexes is an important task in analyzing the protein interaction networks. Although many algorithms predict protein complexes in different ways, surveys on the interaction networks indicate that about 50% of detected interact...
Fuzzy Logic Algorithms Databases, Protein Semantics Protein Interaction Maps Gene Expression Profiling Protein Interaction Mapping Computational Biology Multiprotein Complexes
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Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase.

Scientific reports Jun 16, 2017
The human protein disulfide isomerase (hPDI), is an essential four-domain multifunctional enzyme. As a result of disulfide shuffling in its terminal domains, hPDI exists in two oxidation states with different conformational preferences which are impo...
Protein Interaction Mapping Protein Disulfide-Isomerases Protein Interaction Domains and Motifs Machine Learning Molecular Dynamics Simulation Protein Conformation Protein Interaction Maps Oxidation-Reduction Humans
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