AIMC Topic: Computational Biology

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DeepPSP: A Global-Local Information-Based Deep Neural Network for the Prediction of Protein Phosphorylation Sites.

Journal of proteome research
Identification of phosphorylation sites is an important step in the function study and drug design of proteins. In recent years, there have been increasing applications of the computational method in the identification of phosphorylation sites becaus...

Identification and validation of 174 COVID-19 vaccine candidate epitopes reveals low performance of common epitope prediction tools.

Scientific reports
The outbreak of SARS-CoV-2 (2019-nCoV) virus has highlighted the need for fast and efficacious vaccine development. Stimulation of a proper immune response that leads to protection is highly dependent on presentation of epitopes to circulating T-cell...

Transforming the study of organisms: Phenomic data models and knowledge bases.

PLoS computational biology
The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanie...

Broad Learning Enhanced H-MRS for Early Diagnosis of Neuropsychiatric Systemic Lupus Erythematosus.

Computational and mathematical methods in medicine
In this paper, we explore the potential of using the multivoxel proton magnetic resonance spectroscopy (H-MRS) to diagnose neuropsychiatric systemic lupus erythematosus (NPSLE) with the assistance of a support vector machine broad learning system (BL...

PredAmyl-MLP: Prediction of Amyloid Proteins Using Multilayer Perceptron.

Computational and mathematical methods in medicine
Amyloid is generally an aggregate of insoluble fibrin; its abnormal deposition is the pathogenic mechanism of various diseases, such as Alzheimer's disease and type II diabetes. Therefore, accurately identifying amyloid is necessary to understand its...

Machine-Learning and Chemicogenomics Approach Defines and Predicts Cross-Talk of Hippo and MAPK Pathways.

Cancer discovery
Hippo pathway dysregulation occurs in multiple cancers through genetic and nongenetic alterations, resulting in translocation of YAP to the nucleus and activation of the TEAD family of transcription factors. Unlike other oncogenic pathways such as RA...

DeepFrag-k: a fragment-based deep learning approach for protein fold recognition.

BMC bioinformatics
BACKGROUND: One of the most essential problems in structural bioinformatics is protein fold recognition. In this paper, we design a novel deep learning architecture, so-called DeepFrag-k, which identifies fold discriminative features at fragment leve...

GODoc: high-throughput protein function prediction using novel k-nearest-neighbor and voting algorithms.

BMC bioinformatics
BACKGROUND: Biological data has grown explosively with the advance of next-generation sequencing. However, annotating protein function with wet lab experiments is time-consuming. Fortunately, computational function prediction can help wet labs formul...

DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier.

PLoS computational biology
Predicting the phenotypes resulting from molecular perturbations is one of the key challenges in genetics. Both forward and reverse genetic screen are employed to identify the molecular mechanisms underlying phenotypes and disease, and these resulted...

Classifying the superfamily of small heat shock proteins by using g-gap dipeptide compositions.

International journal of biological macromolecules
Small heat shock protein (sHSP) is a superfamily of molecular chaperone and is found from archaea to human. Recent researches have demonstrated that sHSPs participate in a series of biological processes and are even closely associated with serious di...