15 Result(s)
within
Jiangning Song
Science, Humanities and Social Sciences, multidisciplinary
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Article
Open AccessA polytherapy based approach to combat antimicrobial resistance using cubosomes
A depleted antimicrobial drug pipeline combined with an increasing prevalence of Gram-negative ‘superbugs’ has increased interest in nano therapies to treat antibiotic resistance. As cubosomes and polymyxins d...
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Open AccessCharacterization of the Src-regulated kinome identifies SGK1 as a key mediator of Src-induced transformation
Despite significant progress, our understanding of how specific oncogenes transform cells is still limited and likely underestimates the complexity of downstream signalling events. To address this gap, we use ...
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Article
Open AccessPhosContext2vec: a distributed representation of residue-level sequence contexts and its application to general and kinase-specific phosphorylation site prediction
Phosphorylation is the most important type of protein post-translational modification. Accordingly, reliable identification of kinase-mediated phosphorylation has important implications for functional annotati...
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Article
Open AccessPhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection
Protein phosphorylation is a major form of post-translational modification (PTM) that regulates diverse cellular processes. In silico methods for phosphorylation site prediction can provide a useful and complemen...
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Article
Open AccessKnowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites
Matrix Metalloproteases (MMPs) are an important family of proteases that play crucial roles in key cellular and disease processes. Therefore, MMPs constitute important targets for drug design, development and ...
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Article
Open AccessHIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency
Measuring the altered gene expression level and identifying differentially expressed genes/proteins during HIV infection, replication and latency is fundamental for broadening our understanding of the mechanis...
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Article
Open AccessSecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems
Bacteria translocate effector molecules to host cells through highly evolved secretion systems. By definition, the function of these effector proteins is to manipulate host cell biology and the sequence, struc...
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Open AccessGlycoMinestruct: a new bioinformatics tool for highly accurate map** of the human N-linked and O-linked glycoproteomes by incorporating structural features
Glycosylation plays an important role in cell-cell adhesion, ligand-binding and subcellular recognition. Current approaches for predicting protein glycosylation are primarily based on sequence-derived features...
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Open AccessDephosSite: a machine learning approach for discovering phosphotase-specific dephosphorylation sites
Protein dephosphorylation, which is an inverse process of phosphorylation, plays a crucial role in a myriad of cellular processes, including mitotic cycle, proliferation, differentiation and cell growth. Compa...
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Article
Open AccessPeriscope: quantitative prediction of soluble protein expression in the periplasm of Escherichia coli
Periplasmic expression of soluble proteins in Escherichia coli not only offers a much-simplified downstream purification process, but also enhances the probability of obtaining correctly folded and biologically a...
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Article
Open AccessGlobal metabolic analyses identify key differences in metabolite levels between polymyxin-susceptible and polymyxin-resistant Acinetobacter baumannii
Multidrug-resistant Acinetobacter baumannii presents a global medical crisis and polymyxins are used as the last-line therapy. This study aimed to identify metabolic differences between polymyxin-susceptible and ...
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Article
Open AccessCrysalis: an integrated server for computational analysis and design of protein crystallization
The failure of multi-step experimental procedures to yield diffraction-quality crystals is a major bottleneck in protein structure determination. Accordingly, several bioinformatics methods have been successfu...
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Open AccessUsing contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes
Most protein complex detection methods utilize unsupervised techniques to cluster densely connected nodes in a protein-protein interaction (PPI) network, in spite of the fact that many true complexes are not d...
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Article
Open AccessThe exploration of network motifs as potential drug targets from post-translational regulatory networks
Phosphorylation and proteolysis are among the most common post-translational modifications (PTMs), and play critical roles in various biological processes. More recent discoveries imply that the crosstalks bet...
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Article
Open AccessAccurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features
Lysine acetylation is a reversible post-translational modification, playing an important role in cytokine signaling, transcriptional regulation and apoptosis. To fully understand acetylation mechanisms, identi...
