Yi-Fan Liou

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Additional file 1: Table S1. of A hydrophobic spine stabilizes a surface-exposed Îą-helix according to analysis of the solvent-accessible surface area

The physicochemical properties mined using IBCGA-SVR and used for knowledge discovery. (DOCX 15 kb)

Additional file 5: of SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides

Showing interactions between 5,022 putative BY-kinases and 586 approved drugs (from the DrugBank ... more

Additional file 2: Table S1. of SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides

Leave-one-phylum-out test is applied to evaluate SCMBYK. (DOCX 14 kb)

Additional file 1: Figure S1. of SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides

The histogram of the BY-kinase and non-BY-kinase propensity scores in the test data. (A) Statisti... more

Additional file 3: Table S2. of SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides

The propensity scores and composition (%) of amino acids in BY-kinases. (DOCX 13 kb)

Additional file 4: Table S3. of SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides

The averaged a-helices contents. (DOCX 15 kb)

SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides

BMC bioinformatics, Jan 22, 2016

Bacterial tyrosine-kinases (BY-kinases), which play an important role in numerous cellular proces... more Bacterial tyrosine-kinases (BY-kinases), which play an important role in numerous cellular processes, are characterized as a separate class of enzymes and share no structural similarity with their eukaryotic counterparts. However, in silico methods for predicting BY-kinases have not been developed yet. Since these enzymes are involved in key regulatory processes, and are promising targets for anti-bacterial drug design, it is desirable to develop a simple and easily interpretable predictor to gain new insights into bacterial tyrosine phosphorylation. This study proposes a novel SCMBYK method for predicting and characterizing BY-kinases. A dataset consisting of 797 BY-kinases and 783 non-BY-kinases was established to design the SCMBYK predictor, which achieved training and test accuracies of 97.55 and 96.73%, respectively. Furthermore, the leave-one-phylum-out method was used to predict specific bacterial phyla hosts of target sequences, gaining 97.39% average test accuracy. After an...

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Increased Risk of Major Depression in the Three Years following a Femoral Neck Fracture–A National Population-Based Follow-Up Study

PLoS ONE, 2014

Femoral neck fracture is common in the elderly, and its impact has increased in aging societies. ... more Femoral neck fracture is common in the elderly, and its impact has increased in aging societies. Comorbidities, poor levels of activity and pain may contribute to the development of depression, but these factors have not been well addressed. This study aims to investigate the frequency and risk of major depression after a femoral neck fracture using a nationwide population-based study. The Taiwan Longitudinal Health Insurance Database was used in this study. A total of 4,547 patients who were hospitalized for femoral neck fracture within 2003 to 2007 were recruited as a study group; 13,641 matched non-fracture participants were enrolled as a comparison group. Each patient was prospectively followed for 3 years to monitor the occurrence of major depression. Cox proportional-hazards models were used to compute the risk of major depression between members of the study and comparison group after adjusting for residence and sociodemographic characteristics. The most common physical comorbidities that were present after the fracture were also analyzed. The incidences of major depression were 1.2% (n = 55) and 0.7% (n = 95) in the study and comparison groups, respectively. The stratified Cox proportional analysis showed a covariate-adjusted hazard ratio of major depression among patients with femoral neck fracture that was 1.82 times greater (95% CI, 1.30-2.53) than that of the comparison group. Most major depressive episodes (34.5%) presented within the first 200 days following the fracture. In conclusion, patients with a femoral neck fracture are at an increased risk of subsequent major depression. Most importantly, major depressive episodes mainly occurred within the first 200 days following the fracture.

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Designing predictors of carbohydrate-binding proteins using informative physicochemical properties

ipcbee.com

Carbohydrate-binding proteins can interact with sugars but do not modify them, and play a pivotal... more Carbohydrate-binding proteins can interact with sugars but do not modify them, and play a pivotal role in a variety of important biological recognition processes. Most studies predict carbohydrate-binding sites, but not carbohydrate-binding proteins. The existing method of predicting carbohydrate-binding proteins with sequence identity 35% uses an amino acid based encoding method and support vector machine (SVM). The merits of this study are three-fold. First, we establish a large-scale data set of carbohydrate-binding proteins collected from three up-to-date databases, CAZy, CGF and Swiss-Prot. This data set CBPDS consists of 2380 positive and negative proteins with sequence identity 25% by removing sequence redundancy. Secondly, we propose an efficient SVMbased method for predicting carbohydrate-binding proteins using a small set of informative physicochemical properties obtained by using an inheritable bi-objective genetic algorithm. The prediction accuracy of independent test is 79.45% using 17 properties. Third, from the analysis of informative physicochemical properties, some interpretable knowledge of carbohydrate-binding and non-carbohydrate-binding proteins can be further discovered. The set of obtained physicochemical properties can also be used conveniently as the core for designing various predictors of carbohydrate-binding problems.

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Increased expression of glucose transporter 3 in gerbil brains following magnesium sulfate treatment and focal cerebral ischemic injury

Cell Biochemistry and Function, 2010

Glucose is the primary energy substrate for neurons. Glucose transporter 3 (Glut3) localizes at t... more Glucose is the primary energy substrate for neurons. Glucose transporter 3 (Glut3) localizes at the neuronal cellular membrane, which transports glucose from the extracelluar space into neurons. Ischemia results in an increased energy demand that is associated with profound changes in brain energy metabolism. Magnesium sulfate (MgSO4) ameliorates ischemia‐induced neuronal death in the rat and gerbil model. We investigated the effects of MgSO4 administration on the expression of Glut3 in cortex and hippocampus of gerbils during ischemia. The focal cerebral ischemia was produced by unilateral occlusion of the right common carotid artery and right middle cerebral artery. Following ischemia, Glut3 expression increased significantly versus non‐ischemic (contra‐lateral) cortex and hippocampus. MgSO4 treatment significantly increased the level of Glut3 expression in the non‐ischemic and ischemic cortex and hippocampus. We found that the MgSO4‐induced increase in Glut3 expression was not re...

Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties

BMC Bioinformatics, 2011

Background Existing methods of predicting DNA-binding proteins used valuable features of physicoc... more Background Existing methods of predicting DNA-binding proteins used valuable features of physicochemical properties to design support vector machine (SVM) based classifiers. Generally, selection of physicochemical properties and determination of their corresponding feature vectors rely mainly on known properties of binding mechanism and experience of designers. However, there exists a troublesome problem for designers that some different physicochemical properties have similar vectors of representing 20 amino acids and some closely related physicochemical properties have dissimilar vectors. Results This study proposes a systematic approach (named Auto-IDPCPs) to automatically identify a set of physicochemical and biochemical properties in the AAindex database to design SVM-based classifiers for predicting and analyzing DNA-binding domains/proteins. Auto-IDPCPs consists of 1) clustering 531 amino acid indices in AAindex into 20 clusters using a fuzzy c-means algorithm, 2) utilizing a...

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SCMMTP: identifying and characterizing membrane transport proteins using propensity scores of dipeptides

BMC genomics, Jan 9, 2015

Identifying putative membrane transport proteins (MTPs) and understanding the transport mechanism... more Identifying putative membrane transport proteins (MTPs) and understanding the transport mechanisms involved remain important challenges for the advancement of structural and functional genomics. However, the transporter characters are mainly acquired from MTP crystal structures which are hard to crystalize. Therefore, it is desirable to develop bioinformatics tools for the effective large-scale analysis of available sequences to identify novel transporters and characterize such transporters. This work proposes a novel method (SCMMTP) based on the scoring card method (SCM) using dipeptide composition to identify and characterize MTPs from an existing dataset containing 900 MTPs and 660 non-MTPs which are separated into a training dataset consisting 1,380 proteins and an independent dataset consisting 180 proteins. The SCMMTP produced estimating propensity scores for amino acids and dipeptides as MTPs. The SCMMTP training and test accuracy levels respectively reached 83.81% and 76.11%...

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A hydrophobic spine stabilizes a surface-exposed α-helix according to analysis of the solvent-accessible surface area

BMC bioinformatics, Jan 22, 2016

Most of hydrophilic and hydrophobic residues are thought to be exposed and buried in proteins, re... more Most of hydrophilic and hydrophobic residues are thought to be exposed and buried in proteins, respectively. In contrast to the majority of the existing studies on protein folding characteristics using protein structures, in this study, our aim was to design predictors for estimating relative solvent accessibility (RSA) of amino acid residues to discover protein folding characteristics from sequences. The proposed 20 real-value RSA predictors were designed on the basis of the support vector regression method with a set of informative physicochemical properties (PCPs) obtained by means of an optimal feature selection algorithm. Then, molecular dynamics simulations were performed for validating the knowledge discovered by analysis of the selected PCPs. The RSA predictors had the mean absolute error of 14.11% and a correlation coefficient of 0.69, better than the existing predictors. The hydrophilic-residue predictors preferred PCPs of buried amino acid residues to PCPs of exposed ones...

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SCMPSP: Prediction and characterization of photosynthetic proteins based on a scoring card method

BMC bioinformatics, 2015

Photosynthetic proteins (PSPs) greatly differ in their structure and function as they are involve... more Photosynthetic proteins (PSPs) greatly differ in their structure and function as they are involved in numerous subprocesses that take place inside an organelle called a chloroplast. Few studies predict PSPs from sequences due to their high variety of sequences and structues. This work aims to predict and characterize PSPs by establishing the datasets of PSP and non-PSP sequences and developing prediction methods. A novel bioinformatics method of predicting and characterizing PSPs based on scoring card method (SCMPSP) was used. First, a dataset consisting of 649 PSPs was established by using a Gene Ontology term GO:0015979 and 649 non-PSPs from the SwissProt database with sequence identity <= 25%.- Several prediction methods are presented based on support vector machine (SVM), decision tree J48, Bayes, BLAST, and SCM. The SVM method using dipeptide features-performed well and yielded - a test accuracy of 72.31%. The SCMPSP method uses the estimated propensity scores of 400 dipepti...

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SCMHBP: prediction and analysis of heme binding proteins using propensity scores of dipeptides

BMC Bioinformatics, 2014

Background: Heme binding proteins (HBPs) are metalloproteins that contain a heme ligand (an iron-... more Background: Heme binding proteins (HBPs) are metalloproteins that contain a heme ligand (an iron-porphyrin complex) as the prosthetic group. Several computational methods have been proposed to predict heme binding residues and thereby to understand the interactions between heme and its host proteins. However, few in silico methods for identifying HBPs have been proposed. Results: This work proposes a scoring card method (SCM) based method (named SCMHBP) for predicting and analyzing HBPs from sequences. A balanced dataset of 747 HBPs (selected using a Gene Ontology term GO:0020037) and 747 non-HBPs (selected from 91,414 putative non-HBPs) with an identity of 25% was firstly established. Consequently, a set of scores that quantified the propensity of amino acids and dipeptides to be HBPs is estimated using SCM to maximize the predictive accuracy of SCMHBP. Finally, the informative physicochemical properties of 20 amino acids are identified by utilizing the estimated propensity scores to be used to categorize HBPs. The training and mean test accuracies of SCMHBP applied to three independent test datasets are 85.90% and 71.57%, respectively. SCMHBP performs well relative to comparison with such methods as support vector machine (SVM), decision tree J48, and Bayes classifiers. The putative non-HBPs with high sequence propensity scores are potential HBPs, which can be further validated by experimental confirmation. The propensity scores of individual amino acids and dipeptides are examined to elucidate the interactions between heme and its host proteins. The following characteristics of HBPs are derived from the propensity scores: 1) aromatic side chains are important to the effectiveness of specific HBP functions; 2) a hydrophobic environment is important in the interaction between heme and binding sites; and 3) the whole HBP has low flexibility whereas the heme binding residues are relatively flexible. Conclusions: SCMHBP yields knowledge that improves our understanding of HBPs rather than merely improves the prediction accuracy in predicting HBPs.

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