Jiangning Song

Jiangning Song
Monash University (Australia) · Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology

41.81
 · 
Ph.D.
About
249
Research items
29,268
Reads
2,338
Citations
Introduction
My research interests are at the frontier and interface of computer science, data science and computational biomedicine. I am highly motivated to design, develop and deploy cutting-edge, data-driven statistical and computational algorithms, models, web servers, tools, and pipelines to address a range of challenging problems in computational biomedicine. I am passionate about solving the statistical and analytical challenges posed by the scale and complexity of biomedical big data in the era of Data Science and Analytics.
Research Experience
Jan 2019
Monash University (Australia)
Position
  • Associate Professor, Group Leader
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Projects
Projects (3)
Project
Proteases are pivotal enzymes during birth, life, ageing and death of all organisms. They can regulate most physiological processes by controlling protein activation, synthesis and turnover and are essential for replication and spread of viruses, bacteria and parasites that cause infectious diseases. Proteases thus have central roles in “life and death” processes. The key to our better understanding of the mechanisms that control such processes is to identify the natural substrates of the proteases. To address this, we will develop a series of bioinformatic tools for the accurate prediction of protease-specific substrates and their cleavage sites. These high-throughput and cost-effective tools will add significant values to the current protease research. Such efforts will also promote national and international collaborations to improve our understanding of biology, and encourage exploitation of proteases/inhibitors/receptors for pharmaceutical and industrial applications.
Project
The overall goal of this collaborative project is to create a comprehensive web-based platform to accurately predict functions and conformations of structured and intrinsically disordered proteins from their sequences. A more specific aim it to provide accurate and runtime-efficient computational predictors that annotate protein-DNA, protein-RNA, protein-protein, protein-small ligand and protein-drug binding at the residue and protein levels. We are also working on methods that provide several types of putative functional annotations for the challenging class of intrinsically disordered proteins. The need for these methods is motivated by the rapidly expanding "dark" space of millions of protein sequences that lack functional annotations.
Research
Research items (249)
Article
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Motivation: Glycosylation is a ubiquitous type of protein post-translational modification (PTM) in eukaryotic cells, which plays vital roles in various biological processes such as cellular communication, ligand recognition, and subcellular recognition. It is estimated that >50% of the entire human proteome is glycosylated. However, it is still a s...
Article
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Caspases and granzyme B (GrB) are important proteases involved in fundamental cellular processes and play essential roles in programmed cell death, necrosis and inflammation. Although a number of substrates for both types have been experimentally identified, the complete repertoire of caspases and granzyme B substrates remained to be fully characte...
Article
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The ability to catalytically cleave protein substrates after synthesis is fundamental for all forms of life. Accordingly, site-specific proteolysis is one of the most important post-translational modifications. The key to understanding the physiological role of a protease is to identify its natural substrate(s). Knowledge of the substrate specifici...
Article
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The caspase family of cysteine proteases play essential roles in key biological processes such as programmed cell death, differentiation, proliferation, necrosis and inflammation. The complete repertoire of caspase substrates remains to be fully characterized. Accordingly, systematic computational screening studies of caspase substrate cleavage sit...
Article
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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 their interactions. Experimental hot spots detection methods such as alanine scanning mutagenesis are not applicable on a large scale since the...
Article
This is our response to the Technical Comment by Rolfs et al. where we point out errors in their reanalysis of our data.
Article
RNA post-transcriptional modifications play a crucial role in a myriad of biological processes and cellular functions. To date, >160 RNA modifications have been discovered; therefore, accurate identification of RNA-modification sites is fundamental for a better understanding of RNA-mediated biological functions and mechanisms. However, due to limit...
Article
Motivation: Gram-positive bacteria have developed secretion systems to transport proteins across their cell wall, a process that plays an important role during host infection. These secretion mechanisms have also been harnessed for therapeutic purposes in many biotechnology applications. Accordingly, the identification of features that select a pro...
Article
Post-translational modifications (PTMs) play very important roles in various cell signaling pathways and biological process. Due to PTMs' extremely important roles, many major PTMs have been studied, while the functional and mechanical characterization of major PTMs is well documented in several databases. However, most currently available database...
Article
Cancer subtype identification is an unmet need in precision diagnosis. Recently, evolutionary conservation has been indicated to contain informative signatures for functional significance in cancers. However, the importance of evolutionary conservation in distinguishing cancer subtypes remains largely unclear. Here, we identified the evolutionarily...
Article
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With the explosive growth of biological sequences generated in the post-genomic era, one of the most challenging problems in bioinformatics and computational biology is to computationally characterize sequences, structures, and functions in an efficient, accurate and high-throughput manner. A number of online web servers and stand-alone tools have...
Article
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Human leukocyte antigen class I (HLA-I) molecules are encoded by major histocompatibility complex (MHC) class I loci in humans. The binding and interaction between HLA-I molecules and intracellular peptides derived from a variety of proteolytic mechanisms plays a crucial role in subsequent T cell recognition of target cells and the specificity of t...
Article
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Approximately 50% of prostate cancers harbor the TMPRSS2:ERG fusion, resulting in elevated expression of the ERG transcription factor. Despite the identification of this subclass of prostate cancers, no personalized therapeutic strategies have achieved clinical implementation. Kinases are attractive therapeutic targets as signaling networks are com...
Article
Full-text available
Post-translational modifications (PTMs) play very important roles in various cell signalling pathways and biological process. Due to PTMs’ extremely important roles, many major PTMs have been stud-ied, while the functional and mechanical characterization of major PTMs is well-documented in sever-al databases. However, most currently available datab...
Article
Full-text available
Background: 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 three domains of life involving Eukarya, Bacteria and Archaea demonstrate its roles in regulating a variety of signalling and meta...
Article
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Despite significant progress, our understanding of how specific oncogenes transform cells is still limited and likely underestimates the complexity of downstream signalling events. Herein, we describe a novel, integrated approach that addresses this knowledge gap. This utilizes mass spectrometry-based chemical proteomics to characterize the global...
Article
Motivation: Promoters are short DNA consensus sequences that are localized proximal to the transcription start sites of genes, allowing transcription initiation of particular genes. However, the precise prediction of promoters remains a challenging task because individual promoters often differ from the consensus at one or more positions. Results:...
Article
Full-text available
Motivation: Type III secreted effectors (T3SEs) can be injected into host cell cytoplasm via type III secretion systems (T3SSs) to modulate interactions between Gram-negative bacterial pathogens and their hosts. Due to their relevance in pathogen-host interactions, significant computational efforts have been put toward identification of T3SEs and t...
Article
The diversity of peptides displayed by class I human leukocyte antigen (HLA) plays an essential role in T cell immunity. The peptide repertoire is extended by various posttranslational modifications, including proteasomal splicing of peptide fragments from distinct regions of an antigen to form nongenomically templated cis-spliced sequences. Previo...
Article
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Quorum sensing peptides (QSPs) are the signal molecules that are closely associated with diverse cellular processes, such as cell-cell communication, and gene expression regulation in Gram-positive bacteria. It is therefore of great importance to identify QSPs for better understanding and in-depth revealing of their functional mechanisms in physiol...
Article
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Lysine post-translational modifications (PTMs) play a crucial role in regulating diverse functions and biological processes of proteins. However, due to the large volumes of sequencing data generated from genome sequencing projects, systematic identification of different types of lysine PTM substrates and PTM sites in the entire proteome remains a...
Article
Growth rate of the protein sequence universe dramatically exceeds the speed of expansion for the protein structure universe, generating an immense dark proteome that includes proteins with unknown structure. We perform a whole‐proteome scale analysis of 5.4 million proteins from 987 proteomes in the three domains of life and viruses to systematical...
Article
Full-text available
Iron is essential for life. Accessing iron from the environment can be a limiting factor that determines success in a given environmental niche. For bacteria, access of chelated iron from the environment is often mediated by TonB-dependent transporters (TBDTs), which are β-barrel proteins that form sophisticated channels in the outer membrane. Repo...
Data
Structural comparisons of the catalytic lobes of MPP and FusC. The β-subunit of MPP houses the active site and is represented here in silver coloring. The side-chains of catalytically important residues are shown as sticks, with the metal (Zn2+) cofactor designated as a gray sphere. The equivalent domain of FusC is represented in yellow, and its st...
Data
FusC:ferredoxin interface statistics. (PDF)
Data
Disparate acquisition of fusC genes in Klebsiella spp. Klebsiella genome sequences were visualized using Figtree v1.4.3 (http://tree.bio.ed.ac.uk/software/figtree/). Each terminal node, representing a genome, was colored according to the geographical location for the isolate, based on metadata obtained from the NCBI Pathogen Detection project datab...
Data
Biophysical characterization of purified FusC. Analytical-SEC (upper panel) and analytical ultracentrifugation (lower panel) showing that purified FusC is a monomer of approximately 104 kDa. SEC, size-exclusion chromatography. (PDF)
Data
Data underlying this paper. (XLSX)
Data
Sequence accession data for plants M16 sequences used in the CLANS analysis. CLANS, cluster analysis of sequences. (PDF)
Data
Data underlying this paper. (XLSX)
Data
The FusC:ferredoxin crystal structure electron density. Stereo electron density and model of the refined FusC:ferredoxin crystal structures. Density was prepared through generation of a composite omit map and is contoured to 1.0 σ. (PDF)
Data
Cocrystallization and structural modeling are consistent in suggesting a partial unfolding of ferredoxin in the FusC:ferredoxin complex. (A) The crystal structure of full-length Arabidopsis ferredoxin (4ZHO), docked into the FusC cavity by superimposition with the ferredoxin fragment located at binding site F2. This docking results in a large numbe...
Data
FusC:ferredoxin crystallographic data collection and refinement statistics. (PDF)
Article
Full-text available
The roles of proteolytic cleavage have been intensively investigated and discussed during the past two decades. This irreversible chemical process has been frequently reported to influence a number of crucial biological processes, such as cell cycle, protein regulation and inflammation. A number of advanced studies have been published aiming at dec...
Article
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As a newly discovered post-translational modification, lysine malonylation regulates a myriad of cellular processes from prokaryotes to eukaryotes and has important implications in human diseases. Despite its functional significance, computational methods to accurately identify malonylation sites are still lacking and urgently needed. In particular...
Article
Canonical mechanisms of protein evolution include the duplication and diversification of pre-existing folds through genetic alterations that include point mutations, insertions, deletions, and copy number amplifications, as well as post-translational modifications that modify processes such as folding efficiency and cellular localization. Following...
Article
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Motivation: Kinase-regulated phosphorylation is a ubiquitous type of post-translational modification (PTM) in both eukaryotic and prokaryotic cells. Phosphorylation plays fundamental roles in many signalling pathways and biological processes, such as protein degradation and protein-protein interactions. Experimental studies have revealed that signa...
Article
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Motivation: Anti-cancer peptides (ACPs) have recently emerged as promising therapeutic agents for cancer treatment. Due to the avalanche of protein sequence data in the post-genomic era, there is an urgent need to develop automated computational methods to enable fast and accurate identification of novel ACPs within the vast number of candidate pro...
Article
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Phosphorylation is the most important type of protein post-translational modification. Accordingly, reliable identification of kinase-mediated phosphorylation has important implications for functional annotation of phosphorylated substrates and characterization of cellular signalling pathways. The local sequence context surrounding potential phosph...
Article
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As one of the few irreversible protein post-translational modifications, proteolytic cleavage is involved in nearly all aspects of cellular activities, ranging from gene regulation to cell life-cycle regulation. Among the various protease-specific types of proteolytic cleavage, cleavages by casapses/granzyme B are considered as essential in the ini...
Article
Full-text available
Regulation of proteolysis plays a critical role in a myriad of important cellular processes. The key to better understanding the mechanisms that control this process is to identify the specific substrates that each protease targets. To address this, we have developed iProt-Sub, a powerful bioinformatics tool for the accurate prediction of protease-...
Article
Protein-protein binding interaction is the most prevalent biological activity that mediates a great variety of biological processes. The increasing availability of experimental data of protein-protein interaction allows a systematic construction of protein-protein interaction networks, significantly contributing to a better understanding of protein...
Article
Full-text available
Background Pseudomonas aeruginosa often causes multidrug-resistant infections in immunocompromised patients and polymyxins are often used as the last-line therapy. Alarmingly, resistance to polymyxins has been increasingly reported worldwide recently. To rescue this last-resort class of antibiotics, it is necessary to systematically understand how...
Article
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Summary: Structural and physiochemical descriptors extracted from sequence data have been widely used to represent sequences and predict structural, functional, expression and interaction profiles of proteins and peptides as well as DNAs/RNAs. Here, we present iFeature, a versatile Python-based toolkit for generating various numerical feature repre...
Article
Motivation: Many Gram-negative bacteria use type VI secretion systems (T6SS) to export effector proteins into adjacent target cells. These secreted effectors (T6SEs) play vital roles in the competitive survival in bacterial populations, as well as pathogenesis of bacteria. Although various computational analyses have been previously applied to iden...
Article
Objective: This study was designed to investigate the impacts of Staphylococcus aureus isolated from sperm of male infertility patients, and explore the mechanism of the spermatozoa immobilization attributed to S. aureus. Methods: S. aureus MJ015 and MJ163, the representative strains of immobilization positive and negative group respectively, we...
Article
In recent years, large-scale data, such as microarray, phenotype and sequencing data at multiple levels in the fields of biology and biomedicine, have emerged. Mining the hidden and valuable information underlying such data is useful for improving our understanding of the molecular-level mechanisms and causative relationships of complex diseases. I...
Article
Full-text available
Summary: Proteases are enzymes that specifically cleave the peptide backbone of their target proteins. As an important type of irreversible post-translational modification, protein cleavage underlies many key physiological processes. When dysregulated, proteases’ actions are associated with numerous diseases. Many proteases are highly specific, cle...