AIMC Topic: DNA-Binding Proteins

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Predicting 3D genome folding from DNA sequence with Akita.

Nature methods Oct 12, 2020
In interphase, the human genome sequence folds in three dimensions into a rich variety of locus-specific contact patterns. Cohesin and CTCF (CCCTC-binding factor) are key regulators; perturbing the levels of either greatly disrupts genome-wide foldin...
Humans Neural Networks, Computer Models, Genetic Sequence Analysis, DNA Cell Cycle Proteins CCCTC-Binding Factor Chromosomal Proteins, Non-Histone Cohesins DNA-Binding Proteins Gene Expression Regulation Genome, Human
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iDRBP_MMC: Identifying DNA-Binding Proteins and RNA-Binding Proteins Based on Multi-Label Learning Model and Motif-Based Convolutional Neural Network.

Journal of molecular biology Sep 11, 2020
DNA-binding protein (DBP) and RNA-binding protein (RBP) are playing crucial roles in gene expression. Accurate identification of them is of great significance, and accurately computational predictors are highly required. In previous studies, DBP reco...
DNA-Binding Proteins RNA Binding Sites Humans Neural Networks, Computer Computational Biology Machine Learning RNA-Binding Proteins Protein Binding
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Use Chou's 5-Step Rule to Predict DNA-Binding Proteins with Evolutionary Information.

BioMed research international Jul 27, 2020
The knowledge of DNA-binding proteins would help to understand the functions of proteins better in cellular biological processes. Research on the prediction of DNA-binding proteins can promote the research of drug proteins and computer acidified drug...
Computational Biology DNA-Binding Proteins Support Vector Machine Evolution, Molecular Databases, Protein
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Clinical-Grade Detection of Microsatellite Instability in Colorectal Tumors by Deep Learning.

Gastroenterology Jun 17, 2020
BACKGROUND & AIMS: Microsatellite instability (MSI) and mismatch-repair deficiency (dMMR) in colorectal tumors are used to select treatment for patients. Deep learning can detect MSI and dMMR in tumor samples on routine histology slides faster and le...
Humans Female Adult Middle Aged Deep Learning Cohort Studies ROC Curve Colorectal Neoplasms Brain Neoplasms Male MutS Homolog 2 Protein MutL Protein Homolog 1 Neoplastic Syndromes, Hereditary Mismatch Repair Endonuclease PMS2 Predictive Value of Tests Microsatellite Instability DNA-Binding Proteins
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PredDBP-Stack: Prediction of DNA-Binding Proteins from HMM Profiles using a Stacked Ensemble Method.

BioMed research international Apr 13, 2020
DNA-binding proteins (DBPs) play vital roles in all aspects of genetic activities. However, the identification of DBPs by using wet-lab experimental approaches is often time-consuming and laborious. In this study, we develop a novel computational met...
DNA-Binding Proteins Software Support Vector Machine Databases, Protein
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HMMPred: Accurate Prediction of DNA-Binding Proteins Based on HMM Profiles and XGBoost Feature Selection.

Computational and mathematical methods in medicine Mar 28, 2020
Prediction of DNA-binding proteins (DBPs) has become a popular research topic in protein science due to its crucial role in all aspects of biological activities. Even though considerable efforts have been devoted to developing powerful computational ...
Computational Biology Support Vector Machine Databases, Protein Amino Acid Sequence Markov Chains Humans Amino Acids Machine Learning DNA-Binding Proteins Algorithms ROC Curve
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Identification of Methylated Gene Biomarkers in Patients with Alzheimer's Disease Based on Machine Learning.

BioMed research international Mar 26, 2020
BACKGROUND: Alzheimer's disease (AD) is a neurodegenerative disorder and characterized by the cognitive impairments. It is essential to identify potential gene biomarkers for AD pathology.
Carrier Proteins DNA-Binding Proteins Genetic Markers Peptide Hydrolases Mitochondrial Proteins Alzheimer Disease Patients Gene Expression Regulation, Neoplastic Transcription Factors DNA Methylation Humans Machine Learning Microfilament Proteins Cyclin-Dependent Kinase Inhibitor p57 Protein Tyrosine Phosphatases
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Deep learning approaches for sleep disorder prediction in an asthma cohort.

The Journal of asthma : official journal of the Association for the Care of Asthma Mar 18, 2020
OBJECTIVE: Sleep is a natural activity of humans that affects physical and mental health; therefore, sleep disturbance may lead to fatigue and lower productivity. This study examined 1 million samples included in the Taiwan National Health Insurance ...
Sleep Wake Disorders Nerve Tissue Proteins Predictive Value of Tests DNA-Binding Proteins Male Middle Aged Infant Child, Preschool Child Deep Learning Adolescent Young Adult Adult Asthma Humans Artificial Intelligence Female
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iProDNA-CapsNet: identifying protein-DNA binding residues using capsule neural networks.

BMC bioinformatics Dec 27, 2019
BACKGROUND: Since protein-DNA interactions are highly essential to diverse biological events, accurately positioning the location of the DNA-binding residues is necessary. This biological issue, however, is currently a challenging task in the age of ...
Amino Acid Sequence Position-Specific Scoring Matrices Humans DNA Neural Networks, Computer Reproducibility of Results Amino Acids ROC Curve Software DNA-Binding Proteins Algorithms
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An improved deep learning method for predicting DNA-binding proteins based on contextual features in amino acid sequences.

PloS one Nov 14, 2019
As the number of known proteins has expanded, how to accurately identify DNA binding proteins has become a significant biological challenge. At present, various computational methods have been proposed to recognize DNA-binding proteins from only amin...
Memory, Long-Term Deep Learning Neural Networks, Computer DNA-Binding Proteins Algorithms Amino Acid Sequence Reproducibility of Results
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