Kuo-Chen Chou

Gordon Life Science Institute · Computational Biology & Biomedicine

In the domain of genome annotation, the identification of DNA-binding protein is one of the crucial challenges. DNA is considered a blueprint for the cell. It contained all necessary information for building and maintaining the trait of an organism. It is DNA, which makes a living thing, a living thing. Protein interaction with DNA performs an esse...

The “Gordon Life Science” or “GLS” Institute is the first Internet Institute in the world. Established by Prof. Dr. Kuo-Chen Chou in 2003, right after he was retired from “Pfizer Global Research and Development” in San Diego, California. There is a very interesting story for the name of Institute as elaborated below. After the “gangs of four” (incl...

Introduction Hydroxylation is one of the most important post-translational modification (PTM) in cellular functions and is linked to various diseases. The addition of one of a hydroxyl group (OH) to the lysine sites produce hydroxylysine when undergoes chemical modification. Methods The method which is used in this study for identifying hydroxylys...

Piwi interacting RNA (piRNA) molecules belong to a largest class of small non coding RNA molecules which are originally discovered in animal germline cells and also occur across a variety of human somatic cells. The piRNA molecules play a significant role in many gene functions such as protecting genomic integrity, gene expression regulation and re...

Identification of the sites of post-translational modifications (PTMs) in protein, RNA, and DNA sequences is currently a very hot topic. This is because the information thus obtained is very useful for in-depth understanding the biological processes at the cellular level and for developing effective drugs against major diseases including cancers as...

In this minireview paper it has been elucidated that the proposal of pseudo amino acid components represents a very important milestone for the disciplines of proteome and genome. This has been concluded by observing and analyzing the developments in the following six different sub-disciplines: (1) proteome analysis; (2) genome analysis; (3) protei...

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...

Piwi interacting RNA (piRNA) is a recognized group of small non-coding RNA molecules. The piRNA molecules are associated with multiple tumors type diagnosis and drug development. It is also linked to regulate gene expression, suppressing transposon and maintains genome integrity. Due to a vital role of piRNAs in biology, the identification of piRNA...

Facing the explosive growth of biological sequences unearthed in the post-genomic age, one of the most important but also most difficult problems in computational biology is how to express a biological sequence with a discrete model or a vector, but still keep it with considerable sequence-order information or its special pattern. To deal with such...

With the avalanche of biological sequences discovered in the postgenomic era, one of the most important but also most difficult problems in computational biology is how to express a biological sequence with a discrete model or a vector, yet still keep its considerable sequence-order information or special pattern. To deal with this problem, the ide...

During the last three decades or so, many efforts have been made to study the protein cleavage sites by some disease-causing enzyme, such as HIV (human immunodeficiency virus) protease and SARS (severe acute respiratory syndrome) coronavirus main proteinase. It has become increasingly clear via this minireview that the motivation driving the aforem...

Proteases are a type of enzymes, which perform the process of proteolysis. Proteolysis normally refers to protein and peptide degradation which is crucial for the survival, growth and wellbeing of a cell. Moreover, proteases have a strong association with therapeutics and drug development. The proteases are classified into five different types acco...

During the last three decades or so, many efforts have been made to study the protein cleavage sites by some disease-causing enzyme, such as HIV (human immunodeficiency virus) protease and SARS (severe acute respiratory syndrome) coronavirus main proteinase. It has become increasingly clear via this minireview that the motivation driving the aforem...

This article has been withdrawn at the request of the Editor-in-Chief. After a thorough investigation, the Editor has concluded that the acceptance of this article was partly based upon the positive advice of two illegitimate reviewer reports. The reports were submitted from email accounts which were provided to the journal as suggested reviewers d...

This article has been withdrawn at the request of the Editor-in-Chief. After a thorough investigation, the Editor has concluded that the acceptance of this article was partly based upon the positive advice of two illegitimate reviewer reports. The reports were submitted from email accounts which were provided to the journal as suggested reviewers d...

Protein phosphorylation is one of the key mechanism in prokaryotes and eukaryotes and is responsible for various biological functions such as protein degradation, intracellular localization, the multitude of cellular processes, molecular association, cytoskeletal dynamics, and enzymatic inhibition/activation. Phosphohistidine (PhosH) has a key role...

The smallest unit of life is a cell, which contains numerous protein molecules. Most of the functions critical to the cell’s survival are performed by these proteins located in its different organelles, usually called ‘‘subcellular locations”. Information of subcellular localization for a protein can provide useful clues about its function. To reve...

Background: Glioma is the most lethal nervous system cancer. Recent studies have made great efforts to study the occurrence and development of glioma, but the molecular mechanisms are still unclear. This study was designed to reveal the molecular mechanisms of glioma based on protein-protein interaction network combined with machine learning metho...

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...

The humanized cytotoxic T lymphocyte-associated antigen 4 immunoglobulin (CTLA-4-Ig) has been used to treat Lupus nephritis (LN) based on CTLA-4s negative regulation of T-cell activation through competent to binding with CD80/CD86, the inherent genetic factors influencing the CTLA-4-Ig treatment efficacy are widely unknown. Here, 62 nonsynonymous s...

The protein prenylation (or S-prenylation) is one of the most essential modifications, required for the association of membrane of a plethora of signalling proteins with the key biological process such as protein trafficking, cell growth, proliferation and differentiation. Due to the ubiquitous nature of S-prenylation and its role in cellular funct...

Introduction: In various biological processes and cell functions, Post Translational Modifications (PTMs) bear critical significance. Hydroxylation of proline residue is one kind of PTM, which occurs following protein synthesis. The experimental determination of hydroxyproline sites in an uncharacterized protein sequence requires extensive, time-co...

Motivation: 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 thoroughly studied, while the functional and mechanical characterization of major PTMs is well-documented in several databases. However, currently...

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:...

Abstract The biological process known as post-translational modification (PTM) contributes to diversifying the proteome hence affecting many aspects of normal cell biology and pathogenesis. There have been many recently reported PTMs, but lysine phosphoglycerylation has emerged as the most recent subject of interest. Despite a large number of prote...

Background/objective: Information of protein subcellular localization is crucially important for both basic research and drug development. With the explosive growth of protein sequences discovered in the post-genomic age, it is highly demanded to develop powerful bioinformatics tools for timely and effectively identifying their subcellular localiz...

Objective: Knowledge of protein subcellular localization is vitally important for both basic research and drug development. Facing the avalanche of protein sequences emerging in the post-genomic age, it is urgent to develop computational tools for timely and effectively identifying their subcellular localization based on the sequence information a...

Protein phosphorylation is one of the most fundamental types of post-translational modifications and it plays a vital role in various cellular processes of eukaryotes. Among three types of phosphorylation i.e. serine, threonine and tyrosine phosphorylation, tyrosine phosphorylation is one of the most frequent and it is important for mediation of si...

The promoter is a regulatory DNA region about 81–1000 base pairs long, usually located near the transcription start site (TSS) along upstream of a given gene. By combining a certain protein called transcription factor, the promoter provides the starting point for regulated gene transcription, and hence plays a vitally important role in gene transcr...

The structure of protein gains additional stability against various detrimental effects by the presence of disulfide bonds. The formation of correct disulfide bonds between cysteine residues ensures proper in vivo and in vitro folding of the protein. Many cysteine residues can be present in the polypeptide chain of a protein, however, not all cyste...

S-Palmitoylation is a uniquely reversible and biologically important post-translational modification as it plays an essential role in a variety of cellular processes including signal transduction, protein-membrane interactions, neuronal development, lipid raft targeting, subcellular localization and apoptosis. Due to its association with the neuron...

Background: Closely related to causes of various diseases such as rheumatoid arthritis, septic shock, and coeliac disease; tyrosine nitration is considered as one of the most important post-translational modification in proteins. Inside a cell, protein modifications occur accurately by the action of sophisticated cellular machinery. Specific enzym...

Knowledge of protein subcellular localization is vitally important for both basic research and drug development. With the avalanche of protein sequences emerging in the post-genomic age, it is highly desired to develop computational tools for timely and effectively identifying their subcellular localization based on the sequence information alone....

Background: The relationship between protein structure and its bioactivity is one of the fundamental problems for protein engineering and pharmaceutical design. Method: A new method, called SPTD (Simulated Protein Thermal Detection), was proposed for studying and improving the thermal stability of enzymes. The method was based on the evidences o...

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...

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...

Investigation into the network of protein–protein interactions (PPIs) will provide valuable insights into the inner workings of cells. Accordingly, it is crucially important to develop an automated method or high-throughput tool that can efficiently predict the PPIs. In this study, a new predictor, called “iPPI-PseAAC(CGR)” was developed by incorpo...

A cell contains numerous protein molecules. One of the fundamental goals in molecular cell biology is to determine their subcellular locations since this information is extremely important to both basic research and drug development. In this paper, we report a novel and very powerful predictor called "pLoc_bal-mHum" for predicting the subcellular l...

One of the hottest topics in molecular cell biology is to determine the subcellular localization of proteins from various different organisms. This is because it is crucially important for both basic research and drug development. Recently, a predictor called "pLoc-mGneg" was developed for identifying the subcellular localization of Gram-negative b...

As a prevalent post-transcriptional modification, N6-methyladenosine (m6A) plays key roles in a series of biological processes. Although experimental technologies have been developed and applied to identify m6A sites, they are still cost-ineffective for transcriptome-wide detections of m6A. As good complements to the experimental techniques, some c...

S-nitrosylation is one of the most prominent posttranslational modification among proteins. It involves the addition of nitrogen oxide group to cysteine thiols forming S-nitrosocysteine. Evidence suggests that S-nitrosylation plays a foremost role in numerous human diseases and disorders. The incorporation of techniques for robust identification of...

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...

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...

The occurrence of epidemic avian influenza (EAI) not only hinders the development of a country’s agricultural economy, but also seriously affects human beings’ life. Recently, the information collected from Google Trends has been increasingly used to predict various epidemics. In this study, using the relevant keywords in Google Trends as well as t...

Motivation A cell contains numerous protein molecules. One of the fundamental goals in cell biology is to determine their subcellular locations, which can provide useful clues about their functions. Knowledge of protein subcellular localization is also indispensable for prioritizing and selecting the right targets for drug development. With the ava...

Schizophrenia (SCZ) is a devastating genetic mental disorder. Identification of the SCZ risk genes in brains is helpful to understand this disease. Thus, we first used the minimum Redundancy-Maximum Relevance (mRMR) approach to integrate the genome-wide sequence analysis results on SCZ and the expression quantitative trait locus (eQTL) data from te...

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...

Motivation: Long non-coding RNAs (lncRNAs) are a class of RNA molecules with more than 200 nucleotides. They have important functions in cell development and metabolism, such as genetic markers, genome rearrangements, chromatin modifications, cell cycle regulation, transcription and translation. Their functions are generally closely related to the...

Motivation: Identification of enhancers and their strength is important because they play a critical role in controlling gene expression. Although some bioinformatics tools were developed, they are limited in discriminating enhancers from non-enhancers only. Recently, a two-layer predictor called "iEnhancer-2L" was developed that can be used to pr...

Meiotic recombination caused by meiotic double-strand DNA breaks. In some regions the frequency of DNA recombination is relatively higher, while in other regions the frequency is lower: the former is usually called “recombination hotspot”, while the latter the “recombination coldspot”. Information of the hot and cold spots may provide important clu...

Knowledge of protein subcellular localization is vitally important for both basic research and drug development. With the avalanche of protein sequences emerging in the post-genomic age, it is highly desired to develop computational tools for timely and effectively identifying their subcellular localization purely based on the sequence information...

Motivation: DNA replication is the key of the genetic information transmission, and it is initiated from the replication origins. Identifying the replication origins is crucial for understanding the mechanism of DNA replication. Although several discriminative computational predictors were proposed to identify DNA replication origins of yeast spec...

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-...