16 Result(s)
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Jiangning Song
Bioinformatics
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Article
Open AccessDiCleave: a deep learning model for predicting human Dicer cleavage sites
MicroRNAs (miRNAs) are a class of non-coding RNAs that play a pivotal role as gene expression regulators. These miRNAs are typically approximately 20 to 25 nucleotides long. The maturation of miRNAs requires D...
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Article
Open AccessGenetic algorithm-based feature selection with manifold learning for cancer classification using microarray data
Microarray data have been widely utilized for cancer classification. The main characteristic of microarray data is “large p and small n” in that data contain a small number of subjects but a large number of ge...
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Article
Open AccessPreAcrs: a machine learning framework for identifying anti-CRISPR proteins
Anti-CRISPR proteins are potent modulators that inhibit the CRISPR-Cas immunity system and have huge potential in gene editing and gene therapy as a genome-editing tool. Extensive studies have shown that anti-...
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Systematic Characterization of Lysine Post-translational Modification Sites Using MUscADEL
Among various types of protein post-translational modifications (PTMs), lysine PTMs play an important role in regulating a wide range of functions and biological processes. Due to the generation and accumulat...
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Article
PCprophet: a framework for protein complex prediction and differential analysis using proteomic data
Despite the availability of methods for analyzing protein complexes, systematic analysis of complexes under multiple conditions remains challenging. Approaches based on biochemical fractionation of intact, nat...
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Open AccessReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites
Human dicer is an enzyme that cleaves pre-miRNAs into miRNAs. Several models have been developed to predict human dicer cleavage sites, including PHDCleav and LBSizeCleav. Given an input sequence, these models...
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Open AccessSIMLIN: a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models
S-sulphenylation is a ubiquitous protein post-translational modification (PTM) where an S-hydroxyl (−SOH) bond is formed via the reversible oxidation on the Sulfhydryl group of cysteine (C). Recent experimenta...
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Open AccessPositive-unlabelled learning of glycosylation sites in the human proteome
As an important type of post-translational modification (PTM), protein glycosylation plays a crucial role in protein stability and protein function. The abundance and ubiquity of protein glycosylation across t...
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Inference Method for Develo** Mathematical Models of Cell Signaling Pathways Using Proteomic Datasets
The progress in proteomics technologies has led to a rapid accumulation of large-scale proteomic datasets in recent years, which provides an unprecedented opportunity and valuable resources to understand how l...
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Article
Open AccessPrediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso
To uncover molecular functions and networks in biological cellular systems, it is important to dissect interactions between proteins and RNAs. Many studies have been performed to investigate and analyze intera...
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Article
Open AccessThe drug cocktail network
Combination of different agents is widely used in clinic to combat complex diseases with improved therapy and reduced side effects. However, the identification of effective drug combinations remains a challeng...
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Article
Open AccessExploring drug combinations in genetic interaction network
Drug combination that consists of distinctive agents is an attractive strategy to combat complex diseases and has been widely used clinically with improved therapeutic effects. However, the identification of e...
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Open AccessConditional random field approach to prediction of protein-protein interactions using domain information
For understanding cellular systems and biological networks, it is important to analyze functions and interactions of proteins and domains. Many methods for predicting protein-protein interactions have been dev...
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Open AccessAPIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility
It is well known that most of the binding free energy of protein interaction is contributed by a few key hot spot residues. These residues are crucial for understanding the function of proteins and studying th...
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Open AccessPredicting residue-wise contact orders in proteins by support vector regression
The residue-wise contact order (RWCO) describes the sequence separations between the residues of interest and its contacting residues in a protein sequence. It is a new kind of one-dimensional protein structur...
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Open AccessPrediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information
The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomeri...
