E2

Taiwan Bioinformatics Institute

2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015

 

Research and Development - 2003

1. Influence of peptide conformation on oligosaccharide binding characteristics--a study using apamin-based chimeric peptide. C. W. Wu , G. Jayaraman , K. Y. Chien , Y. J. Liu , P. C. Lyu. Peptides. 24, 1853-1861 (2003).
2. Mutagenesis Study on the Zebra Fish SOX9 High-Mobility Group: Comparison of Sequence and Non-Sequence Specific HMG Domains. N. W. Hsiao, D. Samuel, Y. N. Liu, L. C. Chen, T. Y. Yang, G. Jayaraman and P. C. Lyu., Biochemistry 42,11183-93 (2003)
3. Lin, C. Y., Chen, S. H, Lo, C.Z., Cho, C.S., Hsiung, C. A. 200Primer Design Assistant (PDA): a Web-based Primer Design Tool. Nucleic Acids Res. 31: 3751-375(http://dbb.nhri.org.tw) (SCI/ 6.575)
4. Lin, C. Y., Wang, L.M., Chen, C.L., Lo, Chen, P.Y., C.Z., Cho, C.S., Hsiung, C. A. 200A Combined Experimental and Inferring Interactomes. Genome Informatics. 14:494-49(Medline Index)
5. Lin, Y.M.J., H.C. Yang, T.J. Lai, C.S.J. Fann, and H. S. Sun*. 200Receptor-mediated effect of serotonergic transmission in patients with bipolar affective disorder. J Med Genet 40:781-786.
6. Sun, H. S*., I-J. Su, Y-C. Lin, J–S. Chen, and S-Y. Fang. 200A 2.6Mb interval on Chromosome 6q25.2-q25.3 is commonly deleted in human nasal NK/T cell lymphoma. Brit J Haematology 122: 590-599.
7. Sun, H. S., Kuei-Yang Hsiao, Chih-Chao Hsu, Meng-Hsing Wu, and Shaw-Jenq Tsai*. 200Transactivation of steroidogenic acute regulatory protein in human endometriotic stromal cells is mediated by the prostaglandin EP2 receptor. Endocrinology 144: 3934-394

 

Research and Development - 2004

1. 3D-QSAR Studies on PU3 Analogues by Comparative Molecular Field Analysis.Hong-Tsong Liu, Ping-Chiang Lyu, Max K. Long, Ging-Ho Hsiue, Bioorg. Med. Chem. Lett. 14, 731-734 (2004)
2. Lipid binding in rice nonspecific lipid transfer protein-1 complexes from Oryza sativa.H. C. Cheng , P. T. Cheng , P. Peng , P. C. Lyu and Y. J. Sun . Protein Sci. 13, 2304-2315 (2004)
3. Distinct Unfolding and Refolding Pathways of Lipid Transfer Proteins LTP-1 and LTP- Chi-Hung Lin, Li Li, Ping-Chiang Lyu and Jui-Yoa Chang. The Protein Journal 23, 553-566 (2004)
4. Evaluation of Plant non-specific Lipid Transfer Proteins for Potential Application in Drug Delivery. C. S. Cheng, M. N. Chen, Y. J. Liu, L. Y. Huang, K. F. Lin and P. C. Lyu. Enzyme and Microbial Technology 35, 532-539 (2004)
5. Binding Mechanism of Non-specific Lipid Transfer Proteins and their role in Plant Defense. C. S. Cheng, D. Samuel, Y. J. Liu, J. C. Shyu,S. M. Lai, K. F. Lin and P. C. Lyu. Biochemistry 43, 13628-13636 (2004)
6. Chang, I.S. and Hsiung, C.A. (2004) “Counting process methods in survival analysis”. Encyclopedia of Biostatistics, Edited by P. Armitage and T. Colton, John Wiley and Sons, New York, U.S.A.
7. Chang, I. S., Wang, T.S., Huang, Y. H., Jiang, D.S., Yang, J.Y., Lin, T.S., Yang, C. C., Wu, Y. J., Wen, C. C., Su, I.J., and Hsiung, C. A. Survival analysis of Taiwan SARS data by a semiparametric mixture model. Mathematisches Forschungsinstitut Oberwolfach, Workshop: design and analysis of infectious disease studies, Oberwolfach Report 49.
8. Lin, C. Y., Chang C. M., Cho, C.S., Chen C.L., Lin F.K., Chen P. Y., Lo, C.Z., Hsiung, C. A. 200Deciphering the Protein Network of Caenorhabditis elegans in the Approach of Systems Biology. Genome Informatics. 15 (Medline Index)
9. Sun, H. S*., Hui-Chung Wang, Te-Jen Lai , Tso-Jen Wang, and Chih-Ming Li. 200Sequence variants and haplotype analysis of serotonin transporter gene and association with bipolar affective disorder in Taiwan. Pharmacogenetics 14:173-179.
10. Sun, H. S*., Hsu-Wen Tsai, Huei-Chen Ko, Fong-Ming Chang Tzung-Lieh Yeh. 200Association of the tryptophan hydroxylase gene polymorphism with depression, anxiety, and comorbid depression and anxiety in a population-based sample of postpartum Taiwanese women. Genes, Brain and Behavior 3: 328-336.

 

Research and Development - 2005

1. Chang, I.S., Hsiung, C.A., Wang, M.C. and Wen, C.C. (2005) An aymptotic theory for the non-parametric maximum likelihood estimate in the Cox-gene model. Bernoulli; 11:863-89
2. Chang, I.S., Hsiung, C.A., Wu, Y.J., and Yang, C.C. (2005) Bayesian survival analysis using Bernstein polynomials. Scandinavian J. Statistics; 32:447-46
3. Chen, G.W., Hsiung,C.A., Chyn, J.L., Shih, S.R., Wen, C.C. and Chang, I.S. (2005) Revealing molecular targets for Enterovirus type 71 detection by profile hidden Markov models. Virus Genes; 31:337-34
4. Characterization and structural analyses of nsLTP1 from mung bean. K.-F. Lin, Y.-N. Liu, S.-T. D. Hsu, D. Samuel, C.-S. Cheng, A. M. J. J. Bonvin, and P. C. Lyu. Biochemistry 44, 5703-5712 (2005)
5. Lin, C. Y., Chen C.L., Cho, C.S., Wang L.M., Chang C. M., Chen P. Y., Lo, C.Z., Hsiung, C. A. 200hp-DPI: Helicobacter pylori Database of Protein Interactomes, A Combined Experimental and Inferring Interactions. Bioinformatics, 21: 1288-1290.
6. Lin, C. Y., Lin, F.K., Lin, C.H., Lai, L.W., Hsu, S.J., Chen, S.H., Hsiung, C. A. 200POWER: PhylOgenetic WEb Repeater - An integrated and user-optimized framework for bio-molecular phylogenetic analysis. Nucleic Acids Res. 33: 553-556.
7. Chiu, Y.F., Chuang, L.M., Hsiao,C.F., Hung,Y.J., Lin, M.W., Chen, Y.T., Grove J., Jorgenson, E., Quertermous, T., Risch, N., and Hsiung,C.A*. ”An autosomal genome-wide scan for loci linked to pre-diabetic phenotypes in nondiabetic Chinese subjects from the Stanford Asia-Pacific Program of Hypertension and Insulin Resistance family study”. Diabetes,Vol.54, April, 2005:1200-1206
8. Chen YC, Hwang JK Prediction of disulfide connectivity from protein sequences. Proteins: Structure, Function and Bioinformatics (2005) 61, 507-512 .
9. Huang SW, Hwang JK. Computation of conformational entropy from protein sequences using the machine-learning method – Application to the study of the relationship between structural conservation and local structural stability. Proteins: Structure, Function and Bioinformatics (2005), 59, 802-80
10. Liang HK, Huang CM, Ko MT, Hwang JK. The Amino Acid-Coupling Patterns in Thermophilic Proteins. Proteins: Structure, Function and Bioinformatics (2005), 59, 58-6
11. Lin YS, Tzeng CS, Hwang JK. Reassessment of morphological characters in freshwater eels (genus Anguilla, Anguillidae) shows congruence with molecular phylogeny estimate. Zoologica Scripta (2005), 34, 225-234.
12. Sun, H. S., C. S. J. Fann, Hsien-Yuan Lane, Y-T Chang, C-J Chang,Y-L Liu, W-Y Yu, and A. T. A. Cheng. 200A functional polymorphism in the promoter region of the tryptophan hydroxylase (TPH1) gene is associated with alcohol dependence in one aboriginal group in Taiwan. Alcoholism – Clinical and Experimental Research 29 (1): 1-7.
13. Ko-Fan Chen, Yen-Yu Lai, H. Sunny Sun and Shaw-Jenq Tsai. 200Transcriptional repression of human cad gene by hypoxia inducible factor-Nucleic Acids Research 33(16):5190-5198.

 

Research and Development - 2006

1. Wang, W.C., Chang, I.S., Chang, C.H., David Curb, Ho, L.T., Hsiung, C.A.(2006) “Incorporating Endophenotypes into Allele-Sharing Based Linkage Tests”. Genetic Epidemiology. 30:133-42
2. Chi-Chung Wen, Yuh-Jenn Wu, Yung-Hsiang Huang, Wei-Chen Chen, Shu-Chen Liu, Shih-Sheng Jiang, Jyh-Lyh Juang, Chung-Yen Lin, Wen-Tsen Fang, Chao A. Hsiung, I-Shou Chang. (2006) “A Bayes Regression Approach to array-CGH Data”. Statistical Applications in Genetics and Molecular Biology: Vol. 5: No. 1, Article
3. Chang, I.S., Hsiung, C.A., Wen, C.C. and Wu, Y.J. A note on the consistency in Bayesian shape-restricted regression with random Bernstein polynomials. Festschrift in Honor Y.S. Chow, Edited by Zhiliang Ying and Cun-Hui Zhang (In press).
4. Chang, I.S., Chien L.C., Gupta Pramod K., Wen, C.C., Wu, Y.J., Jiang S.S., Juang J.L., Hsiung, C.A. (2006) A Bayes Approach to Time Course Expression Profile of a Virus Gene Based on Microarray Data.
5. Biosynthesis of fluorescent allophycocyanin alpha-subunits by autocatalytic bilin attachment. I. C. Hu, T. R. Lee, H. F. Lin, C. C. Chiueh, and P. C. Lyu. Biochemistry 13, 7092-709(2006) .
6. Solution Structure of the Plant Defensin VrD1 from Mung bean: A Possible Mechanism for Insecticidal Activity Against Bruchids. Y. J. Liu, C. S. Cheng, S. M.Lai, M.P. Hsu, C.S. Chen and P. C. Lyu. Proteins: Structure, Function, Bioinformatics. 63, 777-786 (2006).
7. Crystal structure of HP0242, a hypothetical protein from Helicobacter pylori with a novel fold. J. Y. Tsai, B. T. Chen , H. C. Cheng , H. Y. Chen , N. W. Hsaio, P. C. Lyu, Y. J. Sun. Protein Sci. 62, 1138-114(2006).
8. Hsiao CF, Chiu YF, Chiang FT, Ho LT, Lee WJ, Hung YJ, Chen YD, Donlon TA, Jorgenson E, Curb D, Risch N, Hsiung CA.(2006) Genome-wide linkage analysis of lipids in non-diabetic Chinese and Japanese from the SAPPHIRe family study. American Journal of Hypertension
9. Tsai YC, Lin YM, Yu, JSK, Hwang JK. A three-coordinate and quaruply bonded Mo-Mo-Complex, J. Am. Chem. Soc. (2006) 128:13980-13981
10. Yu CH, Chen YC, Lu CH, Hwang JK. Prediction of protein subcellular localization. Proteins: Sturcture, Function and Bioinformatics (2006), [Epub ahead of print].
11. Chen CC, Hwang JK, JM Yang. Protein structure prediction server. Nucleic Acid Research (2006), 34: W152-15(PS)2 server
12. Lu CH, Lin SH, Chen YC, Yu CS, Chang SY, Hwang JK. The fragment transformation method to detect the protein structural motifs. Proteins: Sturcture, Function and Bioinformatics (2006), 63:636-64
13. Ying-Fan Chen, Po-Lin Kou, Shaw-Jenq Tsai, Ko-Fan Chen, Hsiangan Chan, Chung Ming Chen, and H. Sunny Sun. 200Computational analysis and refinement of sequence structure on chromosome 22q11.2 region: application to the development of quantitative real-time PCR assay for clinical diagnosis. Genomics 87(2):290-297.
14. Ying-Fan Chen, Po-Lin Kou, Shaw-Jenq Tsai, Ko-Fan Chen, Hsiang–Han Chan, Chung Ming Chen, and H. Sunny Sun. 200Computational analysis and refinement of sequence structure on chromosome 22q11.2 region: application to the development of quantitative real-time PCR assay for clinical diagnosis. Genomics 87：290-297.

 

Research and Development - 2007

1. 3D-partner: a web server to infer interacting partners and binding models. Y.-C. Chen, Y.-S. Lo, W.-C. Hsu and J.-M. Yang, Nucleic Acids Research 561/567 (2007).
2. A Chaotic Micromixer Modulated by Constructive Vortices Agitation. J. T. Yang , K. J. Huang , K. Y. Tung, I. C. Hu, P. C. Lyu. J. Micromechanics and Microengineering, 17: 2084-2092 (2007).
3. A fast algorithm for the nonparametric maximum likelihood estimate in the Cox-gene model. Chang, I.S., Wen, C.C., Wu, Y.J. and Yang, C.C. Statistica Sinica, 17:841-856 (2007).
4. A profile likelihood theory for the correlated Gamma-frailty model with current status family data. Chang, I.S., Wen, C.C. and Wu, Y.J. Statistica Sinica, 17: 1023-1046 (2007)
5. A simple way to compute protein dynamics without a mechanical model. Shih CH, Huang SW, Yen SC, Lai YL, Yu SH, Hwang JK. Proteins: Structure, Function and Bioinformatics, 68/34-3 (2007)
6. Aberrant expression of leptin in human endometriotic stromal cells is induced by elevated levels of hypoxia inducible factor-1. Meng-Hsing Wu, Ko-Fan Chen, Shih-Chieh Lin, Chun-Wun Lgu and Shaw-Jenq Tsai. American Journal of Pathology, 170:590-598 (2007)
7. An overlapping crisscross micromixer. Lilin Wang, Jing-TangYang, Ping-Chiang Lyu. Chemical Engineering Science, 62:711-720. (2007)
8. Association of functional polymorphisms of the human tryptophan hydroxylase 2 gene with risk for bipolar disorder in han Chinese. Lin, Y. M., Chao, S. C., Chen, T. M., Lai, T. J., Chen, J. S., and Sun, H. S. Archives of General Psychiatry, 64(9), 1015-102(2007)
9. Bivariate genome-wide scan for metabolic phenotypes in non-diabetic Chinese individuals from the Stanford, Asia and Pacific Program of Hypertension and Insulin Resistance Family Study. Chiu YF, Chuang LM, Kao HY, Ho LT, Ting CT, Hung YJ, Chen YD, Donlon T, Curb JD, Quertermous T, Hsiung CA. The SAPPHIRe Study Group Diabetologia, 50(8)/1631-1640 (2007)
10. Challenges faced by hospital healthcare workers in using a syndrome-based surveillance system during the 2003 outbreak of severe acute respiratory syndrome in taiwan. Shih FY, Yen MY, Wu JS, Chang FK, Lin LW, Ho MS, Hsiung CA, Su IJ, Marx MA, Sobel H, King CC. Infection control and hospital epidemiology, 28(3)/354-35(2007)
11. Chronic treatment with aripiprazole induces differential gene expression in the rat frontal cortex. Cheng MC, Liao DL, Hsiung CA, Chen CY, Liao YC, Chen CH. Int J Neuropsychopharmacol, 2017/1/10 Design of a Self-Flapping Microfluidid Oscillator and Diagnosis with Fluorescence Methods. Yang, J. T., Chen, C. K., Hu, I. C., and Lyu, P. C. J. Microelectromechanical Systems, 16: 826-835 (2007)
12. fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies. C.-H. Tung and J.-M. Yang. Nucleic Acids Research, 438/443 (2007)
13. 1Hormone replacement therapy and lung cancer risk in Chinese. Chen KY, Hsiao CF, Chang GC, Tsai YH, Su WC, Perng RP, Huang MS, Hsiung CA, Chen CJ, Yang PC; GEFLAC Study Group. Cancer, 110(8)/1768-1775 (2007)
14. Identifying potential immunodominant positions and predicting antigenic variants of influenza A/H3N2 viruses. Lee MS, Chen MC, Liao YC, Hsiung CA. Vaccine, 25(48)/8133-8139 (2007)
15. Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database. C.-H. Tung, J.-W. Huang and J.-M. Yang. Genome Biology, 8-3-r31 (2007)
16. Microsatellite in the 3' untranslated region of human fibroblast growth factor 9 (FGF9) gene exhibits pleiotropic effect on modulating FGF9 protein expression. Chen, T. M., Kuo, P. L., Hsu, C. H., Tsai, S. J., Chen, M. J., Lin, C. W., and Sun, H. S. Human Mutation, 28(1), 98
17. Non-parametric Maximum-Likelihood Estimation in a Semiparametric Mixture Model for Competing-Risks Data. I-Shou Chang, Chao A. Hsiung, Chi-Chung Wen, Yuh-Jenn Wu and Che-Chi Yang. Scandinavian Journal of Statistics, 34(4)/870-895
18. On the Stereochemistry of Zn-Zn Bonds: Synthesis, Structural Transformation, and Computations. Tsai YC, Lin YM, Hwang JK, Yu JSK. Chem. Comm., 40/4125-4127
19. Optimizing severe acute respiratory syndrome response strategies: lessons learned from quarantine. Wang TH, Wei KC, Hsiung CA, Maloney SA, Eidex RB, Posey DL, Chou WH, Shih WY, Kuo HS. Am J Public Health, 97/S18 (2007)
20. pKNOT: the Protein KNOT web server Lai YL, Yen SC, Yu SH, Hwang JK. Nucleic Acids Res, 35/W420-W424 (2007)
21. Predicting disulfide connectivity patterns, Lu CH, Chen YC, Yu CS, Hwang JK. Proteins: Structure, Function and Bioinformatics, 64/262-270 (2007)
22. Protein structural similarity search by Ramachandran codes. Lo WC, Chang CH, Huang PJ, Lyu PC. BMC Bioinformatics, 8:307 (2007)
23. Reconstruction of human protein interolog network using evolutionary conserved network. Huang, T. W., Lin, C.Y., and Kao, C.Y. BMC Bioinformatics, 8(152)/1-14 (2007)
24. Shape restricted regression with random Bernstein polynomials. Chang, I.S., Chien, L.C., Hsiung, C.A., Wen, C.C., and Wu, Y.J. In R. Liu, W. Strawderman and C.H. Zhang, Complex Dataset and Inverse, 54:187-202 (2007)
25. Solution structure of family 21 carbohydrate-binding module from Rhizopus oryzae glucoamylase. Y. N. Liu, Y. T. Lai, W. I. Chou, M. D. Chang, P. C. Lyu. Biochemical Journal, 403(1):21-30 (2007)
26. Structure-based protein engineering for alpha-amylase inhibitory activity of plant defensin. K. F. Lin, T. R. Lee, P. H. Tsai, M. P. Hsu, C. S. Chen, and P. C. Lyu. Proteins: Structure, Function, Bioinformatics, 68(2):530-40 (2007)
27. TAG: a comprehensive database for cancer research. Chan, H. H., Tsai, S. J., and Sun, H. S. Nucleic Acids Research Molecular Biology Database Collection, #922 (2007)
28. Chang, I.S., Wen, C.C. and Wu, Y.J. (2007) A profile likelihood theory for the correlated Gamma-frailty model with current status family data. Statistica Sinica 17, 1023-1046
29. Chang, I.S., Wen, C.C., Wu, Y.J. and Yang, C.C. (2007) A fast algorithm for the nonparametric maximum likelihood estimate in the Cox-gene model. Statistica Sinica 17:841-856..
30. Chang, I.S., Chien, L.C., Hsiung, C.A., Wen, C.C., and Wu, Y.J. (2007). Shape restricted regression with random Bernstein polynomials. Vardi Volume, IMS Lecture Notes – Monograph Series Vol. 54 (2007) 187–202.

 

Research and Development - 2008

1. Association analysis of monoamine oxidase A gene and bipolar affective disorder in Han Chinese. Lin, Yi-Mei J., Fabian Davamani, Wei-Chih Yang, Te-Jen Lai, and H. Sunny Sun. Behavioral and Brain Functions, 04:21
2. Bioinformatics models for predicting antigenic variants of influenza A/H3N2 virus. Liao, YC; Lee, MS; Ko, CY; Hsiung, CA. Bioinformatics, 24(4)/505-512
3. Comment: Quantifying the Fraction of Missing Information for Hypothesis Testing in Statistical and Genetic Studies. I-Shou Chang, Chung-Hsing Chen, Li-Chu Chien and Chao A. Hsiung. Statistical Science, 23(3)/318-320
4. CPSARST – An efficient circular permutation search tool applied to the detection of novel protein structural relationships. Lo WC and Lyu PC. Genome Biology, 9:R11
5. Deriving protein dynamical properties from weighted protein contact number. Lin CP, Huang SW, Lai YL, Yen SC, Shih CH, Lu CH, Huang CC, Hwang JK. Proteins: Structure, Function and Bioinformatics, 72/929-935
6. Diagnosis of insulin resistance in hypertensive patients by the metabolic syndrome: AHA vs. IDF definitions. Hwu CM, Hsiung CA,Wu KD, LeeWJ, Shih KC, Grove J, Chen YD, Rodriguez BL, Curb JD; The SAPPHIRe Study Group. International Journal of Clinical Practice, 62(9)/1141-1146
7. Effects of ligand binding on the dynamics of rice nonspecific lipid transfer protein 1: A model from molecular simulations has been exported. Y. T. Lai, C. S. Cheng, K. F. Lin, Y. J. Liu, P. C. Lyu. Proteins: Structure, Function, Bioinformatics, 72(4):1189-98
8. HLA-A33 is associated with susceptibility to enterovirus 71 infection. Chang, L.Y., Chang, I.S., Chen, W.J., Huang, Y.C., Chen, G.W., Shih, S.R., Juang, J.L., H.M., Shih, Hsiung, C.A., Lin, T.Y., and Huang, L.M. Pediatrics, 122(6)/1271-1276
9. Hubba: hub objects analyzer - a framework of interactome hubs identification for network biology. Lin, CY; Chin, CH; Wu, HH; Chen, SH; Ho, CW; Ko, MT. Nucleic Acids Research, 36/W438-W443
10. Induction of pyruvate dehydrogenase kinase 3 by hypoxia-inducible factor-1 promotes metabolic switch and drug resistance. Chun-Wun Lu, Shih-Chieh Lin, Ko-Fan Chen, Yen-Yu Lai and Shaw-Jenq Tsai. The Journal of Biological Chemistry, 283:28106-28114
11. 1miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. Hsu SD, Chu CH, Tsou AP, Chen SJ, Chen HC, Hsu PW, Wong YH, Chen YH, Chen GH, Huang HD. Nucleic Acids Res., 36(Database issue): D165-9
12. 1Modeling and predicting extrapolated probabilities with outlooks - Comments. Chang, IS; Chien, LC; Hsiung, CA. Statistica Sinica, 18(1)/40-43
13. 1Mutagenesis Study of Rice Nonspecific Lipid Transfer Protein 2 Reveals Residues that Contribute to Structure and Ligand Binding. C. S. Cheng, M. N. Chen, Y. T. Lai, T. Chen, K. F. Lin, Y. J. Liu, P. C. Lyu. Proteins: Structure, Function, Bioinformatics, 70(3):695-706
14. 1On the relationship between the protein structure and protein dynamics. Lu CH, Huang SW, Lai YL, Lin CP, Shih CH, Huang CC, Hsu WL, Hwang JK. Proteins: Structure, Function and Bioinformatics, 72/625-634
15. 1Prediction of NMR order parameters in proteins using weighted protein contact-number model. Huang SW, Shih CH, Lin CP, Hwang JK. Theor Chem Acc, 121/197-200
16. 1Regulation of CD151 by hypoxia controls cell adhesion and metastasis in colorectal cancer. Chun-Wei Chien, Shih-Chieh Lin, Yen-Yu Lai, Bo-Wen Lin, Shao-Chieh Lin, Jenq-Chang Lee and Shaw-Jenq Tsai. Clinical Cancer Research, 14:8043-8051
17. 1Soft energy function and generic evolutionary method for discriminating native from non-native protein conformations. Chiu, YY, Hwang JK, Yang JM. J. Comp. Chem., 29/1364-1373 The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays. Chen, S.H., Tsai, M.K., Lo, C.Z., Hsiung, C. A., Lin, C. Y. BMC Bioinformatics, 9(S8)

 

Research and Development - 2009

1. PPISearch: a web server for searching homologous protein-protein interactions across multiple species. C.-C. Chen, C.-Y Lin, Y.-S Lo and J.-M. Yang. Nucleic Acids Research, 376/383
2. A Polymorphism in the APE1 Gene Promoter is Associated with Lung Cancer Risk. Lo YL, Jou YS, Hsiao CF, Chang GC, Tsai YH, Su WC, Chen KY, Chen YM, Huang MS, Hu CY, Chen CJ, Hsiung CA. Cancer Epidemiology Biomarkers & Prevention, 18(1)/223-229
3. Alanine substitutions of noncysteine residues in the cysteine-stabilized alphabeta motif. Yang YF, Cheng KC, Tsai PH, Liu CC, Lee TR, Lyu PC. Protein Sci., 18(7):1498-506
4. Association of an EGFR Intron 1 SNP with nonsmoking female lung adenocarcinoma patients. Jou YS, Lo YL, Hsiao CF, Chang GC, Tsai YH, Su WC, Chen YM, Huang MS, Chen HL, Chen CJ, Yang PC, Hsiung CA. Lung Cancer, 64(3)/251-256
5. ATIVS: analytical tool for influenza virus surveillance. Liao YC, Ko CY, Tsai MH, Lee MS, Hsiung CA. Nucleic Acids Research, 37/W643-W646
6. CAPIH: A Web interface for comparative analyses and visualization of host-HIV protein-protein interactions. Lin FK, Pan CL, Chuang TJ, and Chen FC. BMC Microbiology, 9(164)
7. CNVVdb: a database of copy number variations across vertebrate genomes. Chen FC, Chen YZ, and Chuang TJ. Bioinformatics, 25(11)/1419-1421
8. CPDB: a database of circular permutation in proteins. Lo WC, Lee CC, Lee CY, Lyu PC. Nucleic Acids Res., 37(Database issue): D328-32
9. FMM: a web server for metabolic pathway reconstruction and comparative analysis. Chou CH, Chang WC, Chiu CM, Huang CC, Huang HD. Nucleic Acids Res., 37(Web Server issue): W129-34
10. Identification of trypsin-inhibitory site and structure determination of human SPINK2 serine proteinase inhibitor. Chen T, Lee TR, Liang WG, Chang WS, Lyu PC. Proteins, 77(1):209-19
11. iSARST: an integrated SARST web server for rapid protein structural similarity searches. Lo WC, Lee CY, Lee CC, Lyu PC. Nucleic Acids Res., 37(Web Server issue): W545-51
12. miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. Wang WC, Lin FM, Chang WC, Lin KY, Huang HD, Lin NS. BMC Bioinformatics, 10:328
13. PALM: A Parallel and Integrated Framework with the Substitution Model Estimation for Phylogenetic Inference. Chen, S.H., Su, S.Y., Lo, C.Z., Huang. T. G., Kuo, P. H., Lin, C. Y. PLoS One, 4(12):e8116
14. Population-specific functional variant of the TPH2 gene 2755C>A polymorphism contributes risk association to major depression and anxiety in Chinese peripartum women. Lin, Yi-Mei J., Huei-Chen Ko, Fong-Ming Chang, Tzung-Lieh Yeh, and H. Sunny Sun. Arch Women Ment Health, 12(6): 401-408
15. Profiling time course expression of virus genes - an illustration of Bayesian inference under shape restrictions. Li-Chu Chien, I-Shou Chang, Shih Sheng Jiang, Pramod K. Gupta, Chi-Chung Wen, Yuh-Jenn Wu, and Chao A. Hsiung. Annals of Applied Statistics., 3(4)/1542-1565
16. PS2-v2: template-based protein structure prediction server. Chen CC, Hwang JK, Yang JM. BMC Bioinformatics, 10/366

 

Research and Development - 2010

1. Huang PJ, Liu YC, Lee CC, Lin WC, Gan RR, Lyu PC*, Tang P*. DSAP: deep-sequencing small RNA analysis pipeline. Nucleic Acids Res. 2010 July. W385-91.
2. Hsiung CA, Lan Q, Hong YC, Chen CJ, Hosgood HD, Chang IS, Chatterjee N, Brennan P, Wu C, Zheng W, Chang GC, Wu T, Park JY, Hsiao CF, Kim YH, Shen H, Seow A, Yeager M, Tsai YH, Kim YT, Chow WH, Guo H, Wang WC, Sung SW, Hu Z, Chen KY, Kim JH, Chen Y, Huang L, Lee KM, Lo YL, Gao YT, Kim JH, Liu L, Huang MS, Jung TH, Jin G, Caporaso N, Yu D, Kim CH, Su WC, Shu XO, Xu P, Kim IS, Chen YM, Ma H, Shen M, Cha SI, Tan W, Chang CH, Sung JS, Zhang M, Yang TY, Park KH, Yuenger J, Wang CL, Ryu JS, Xiang Y, Deng Q, Hutchinson A, Kim JS, Cai Q, Landi MT, Yu CJ, Park JY, Tucker M, Hung JY, Lin CC, Perng RP, Boffetta P, Chen CY, Chen KC, Yang SY, Hu CY, Chang CK, Fraumeni JF Jr, Chanock S, Yang PC, Rothman N, Lin D. “The 5p15.33 locus is associated with risk of lung adenocarcinoma in never-smoking females in Asia.” PLoS Genet. 2010 Aug 5;6(8). pii: e1001051.
3. Tsai HJ, Hsiao CF, Ho LT, Chuang LM, He CT, Curb JD, Quertermos T, Hsiung CA, Sheu WH. “Genetic variants of human urea transporter-2 are associated with metabolic syndrome in Asian population.” Clin Chim Acta. 2010 Dec 14;411(23-24):2009-1Epub 2010 Aug 23.
4. Chiu YF, Chuang LM, Kao HY, Shih KC, Lin MW, Lee WJ, Quertermous T, Curb JD, Chen I, Rodriguez BL, Hsiung CA. “Sex-specific genetic architecture of human fatness in Chinese: the SAPPHIRe Study.” Hum Genet. 2010 Nov;128(5):501-1Epub 2010 Aug 20.
5. Chen TM, Hsu CH, Tsai SJ, Sun HS. AUF1 p42 isoform selectively controls both steady-state and PGE2-induced FGF9 mRNA decay. Nucleic Acids Res. 2010;38(22):8061-71.
6. Shin-Chih Chao, Jia–Shing Chen , Cheng-Hsien Tsai, Joy Yi-Mei Lin, Yuh-Jyh Lin, and H. Sunny Sun*. 2010. Novel exon nucleotide substitution at the splice junction causes a neonatal Marfan syndrome. Clinical Genetics 77:453-463.
7. Wu MH, Lu CW, Chuang PC, Tsai SJ* 2010 Prostaglandin E2: the master of endometriosis? (review) Exp Biol Med 235: 668–677.
8. Chuang PC, Lin YJ, Wu MH, Wing LYC, Shoji Y, and Tsai SJ* 2010 Inhibition of CD36-dependent phagocytosis by prostaglandin E2 contributes to the development of endometriosis Am J Pathol 176:850-860.
9. Wu MH, Huang MF, Chang FM, Tsai SJ* 2010 Leptin on peritoneal macrophages of patients with endometriosis. Am J Reprod Immunol 63:214-221.
10. Weng MP and Liao BY (2010) MamPhEA: a Web tool for Mammalian Phenotype Enrichment Analysis. Bioinformatics 26: 2212-2213
11. Liao YC, Chen FC, Hsiung CA. ” Contrasting substitution patterns between HA proteins of avian and human influenza viruses: Implication for monitoring human influenza epidemics.” Vaccine. 2010 Nov 23;28(50):7890-Epub 2010 Oct
12. Hsieh YJ, Yu JS*, Lyu PC*. Characterization of photodynamic therapy responses elicited in A431 cells containing intracellular organelle-localized photofrin. J Cell Biochem. 2010 Nov 1;111(4):821-3
13. Y.-S. Lo, C.-Y Lin, and J.-M. Yang*, "PCFamily: a web server for searching homologous protein complexes," Nucleic Acids Research, W516-W522, 2010. (IF: 7.479)
14. Y.-F. Chen, K.-C. Hsu, S.-R. Lin, W.-C. Wang, Y.-C. Huang and J.-M. Yang*, " SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties," Nucleic Acids Research, W424 - W430, 2010. (IF: 7.479)
15. Y.-S. Lo, Y.-C. Chen, and J.-M. Yang*, "3D-interologs: An evolution database of physical protein-protein interactions across multiple genomes," BMC Genomics, (Suppl 3):S7, 2010. (IF: 3.76)
16. D. L. Clinciu, Y.-F. Chen, C.-N. Ko, C.-C. Lo, and J.-M. Yang*, "TSCC: Two-Stage Combinatorial Clustering for virtual screening using protein-ligand interactions and physicochemical features," BMC Genomics, (Suppl 4):S26, 2010. (IF: 3.76)
17. K.-P. Liu, K.-C. Hsu, J.-W. Huang, Y-S, Chang, and J.-M. Yang*, "ATRIPPI: An atom-residue preference scoring function for protein-protein interactions," International Journal on Artificial Intelligence Tools, pp. 251-266, 2010.
18. K.-C. Hsu, Y.-F. Chen, and J.-M. Yang*, "GemAffinity: A scoring function for predicting binding affinity and virtual screening, " International Journal on Data Mining and Bioinformatics, 2010, in press.
19. Chia-Han Chu, Wei-Cheng Lo, Hsin-Wei Wang, Yen-Chu Hsu, Jenn-Kang Hwang, Ping-Chiang Lyu, Tun-Wen Pai, Chuan Yi Tang. Detection and Alignment of 3D Domain Swapping Proteins Using Angle-Distance Image-Based Secondary Structural Matching Techniques." Plos One 5(10), e1336doi:10.1371 (2010) .

 

Research and Development - 2011

1. Reconstructing phylogeny from metabolic substrate-product relationships. Chang CW, Lyu PC, Arita M. BMC Bioinformatics. 2011. 15(12): Suppl 1:S27
2. Structural and functional comparison of cytokine interleukin-1 beta from chicken and human. Cheng CS, Chen WT, Lee LH, Chen YW, Chang SY, Lyu PC, Yin HS. Mol Immunol. 2011. 48(6-7): 947-955
3. Crystal structure and biophysical characterization of Helicobacter pylori phosphopantetheine adenylyltransferase. Cheng CS, Chen CH, Luo YC, Chen WT, Chang SY, Lyu PC, Kao MC, Yin HS. Biochem Bioph Res Co. 2011. 408(2): 356-361
4. Plasma proteomic analysis of the critical limb ischemia markers in diabetic patients with hemodialysis. Hung PH, Chen YW, Cheng KC, Chou HC, Lyu PC, Lu YC, Lee YR, Wu CT, Chan HL. Mol Biosyst. 2011. 1.7(6): 1990-1998
5. Mitochondrial proteomics analysis of tumorigenic and metastatic breast cancer markers. Chen YW, Chou HC, Lyu PC, Yin HS, Huang FL, Chang WS, Fan CY, Tu IF, Lai TC, Lin ST, Lu YC, Wu CL, Huang SH, Chan HL. Funct Integr Genomic. 2011. 11(2): 225-239
6. Comparative analysis of receptor binding by chicken and human interleukin-1beta Cheng CS, Lu WS, Tu IF, Lyu PC, Yin HS. J Mol Model. 2011. 17(6): 1283-1294
7. Proteomic analysis of gemcitabine-induced drug resistance in pancreatic cancer cells Chen YW, Liu JY, Lin ST, Li JM, Huang SH, Chen JY, Wu JY, Kuo CC, Wu CL, Lu YC, Chen YH, Fan CY, Huang PC, Law CH, Lyu PC, Chou HC, Chan HL. Mol Biosyst. 2011. 7(11) : 3065-3074.
8. Cytoskeleton network and cellular migration modulated by nuclear-localized receptor tyrosine kinase ROR1.Tseng HC, Kao HW, Ho MR, Chen YR, Lin TW, Lyu PC, Lin WC.Anticancer Res. 2011. 1 Dec;31(12):4239-49.
9. 1 Putative Canine Origin of Rotavirus Strain Detected in a Child with Diarrhea, Taiwan. Wu FT, Banyai K, Lin JS, Wu HS, Hsiung CA, Huang YC, Hwang KP, Jiang B, Gentsch JR. Vector-Borne and Zoonotic Diseases. 2011. 1.12(2):170-3
10. R432 is a key residue for the multiple functions of Ndt80p in Candida albicans. Yang YL, Wang CW, Leaw SN, Chang TP, Wang IC, Chen CG, Fan JC, Tseng KY, Huang SH, Chen CY, Hsiao TY, Hsiung CA, Chen CT, Hsiao CD, Lo HJ. Cellular and Molecular Life Sciences.2011. 69(6):1011-23
11. Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes. Lin CH, Hsiung CA, and Chen FC. BMC Bioinformatics. 2011. 12(Suppl 9):S19.
12. The genomic features that affect the lengths of 5’ untranslated regions in multicellular eukaryotes. Chen CH, Lin HY, Pan CL, and Chen FC. BMC Bioinformatics. 2011. 12(Suppl 9):S3
13. Exploring the selective constraint on the sizes of insertions and deletions in 5’ untranslated regions in mammals. Chen CH, Lin HY, Pan CL, and Chen FC. BMC Evolutionary Biology. 2011. 0.591667
14. An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL122Liao YC, Huang TW, Chen FC, Charusanti P, Hong JS, Chang HY, Tsai SF, Palsson BO, Hsiung CA. J Bacteriol. 2011. 193(7):1710-7.
15. Distribution of the number of false discoveries in large-scale family-based association testing with application to the association between PTPN1 and hypertension and obesity. Wang WC, Hsiung CA, Wang LC, Chuang LM, Quertermous T, Chang IS. Hum Genet. 2011. 129(4):425-32.
16. The plausible reason why the length of 5’ untranslated region is unrelated to organismal complexity. Chen CH, Lin HY, Pan CL, and Chen FC. BMC Research Notes. 2011. 0.383333
17. The Length Evolution of 5’ Untranslated Regions – the Stochastic Model Revisited. Chen CH, Lin HY, Pan CL, and Chen FC. Ieee Proceedings of Bioinformatics and Bioengineering. 2011. 24:162 - 166
18. MrBac: A web server for draft metabolic network reconstructions for bacteria. Liao YC, Chen JCY, Tsai MH, Tang YH, Chen FC*, and Hsiung CA. Bioengineered Bugs. 2011. 2(5): 284-287
19. A review of the major penaeid shrimp EST studies and the construction of a shrimp transcriptome database based on the ESTs from four penaeid shrimp. Leu JH, Chen SH, Wang YB, Chen YC, Su SY, Lin CY, Ho JM, Lo CF. Mar Biotechnol (NY). 2011. 13(4): 608-621.
20. DroPhEA: Drosophila phenotype enrichment analysis for insect functional genomics. Meng-Pin Weng and Ben-Yang Liao. Bioinformatics. 2011. 27: 3218-3219.
21. Arabidopsis Argonaute 2 Regulates Innate Immunity via miRNA393*-Mediated Silencing of a Golgi-Localized SNARE Gene, MEMB1X. Zhang, H. Zhao, S. Gao, W.C. Wang, S. Katiyar-Agarwal, H.D. Huang, N. Raikhel and H. Jin*. Molecular Cell. 2011. 42(3),356-366.
22. Characterization and prediction of mRNA polyadenylation sites in human genes. T.H. Chang, L.C. Wu, Y.T. Chen, H.D. Huang, B.J. Liu, K.F. Cheng, J.T. Horng. Medical & Biological Engineering & Computing. 2011. 49(4),463-472.
23. Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences. M. McDonald, W.C. Wang, H.D. Huang*, and J.Y. Leu*. PLoS Biology. 2011. 96(6),e1000622.
24. Flow-Dependent Regulation of Kruppel-Like Factor 2 Is Mediated by MicroRNA-92a. W. Wu, H. Xiao, A. Laguna-Fernandez, G. Villarreal, K.C. Wang, G.G. Geary, W.C. Wang, H.D. Huang, J. Zhou, Y.S. Li, S. Chien, G. Garcia-Cardena, J.Y-J. Shyy. Circulation. 2011. 124(5),633-641
25. Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. C.H. Chien, Y.M. Sun, W.C. Chang, P.Y. Chiang-Hsieh, T.Y. Lee, W.C. Tsai, J.T. Horng, A.P. Tsou, H.D. Huang . Nucleic Acids Research. 2011. 39(21),9345-9356.
26. Incorporating evolutionary information and functional domains for identifying RNA splicing factors in humans. J.B.K. Hsu, T.Y. Lee, N.A. Bretana, and H.D Huang. Plos One. 2011. 6(11),e27567.
27. miRTar: an integrated system for identifying miRNA-target interactions in human.. J.B.K. Hsu, C.M. Chiu, S.D. Hsu, W.Y. Huang, C.H. Chien, T.Y. Lee and H.D. Huang. BMC Bioinformatics. 2011. 12,300.
28. miRTarBase: a database curates experimentally validated microRNA-target interactions. S.D. Hsu, F.M. Lin, W.Y. Wu, C. Liang, C.J. Lee, C.Y. Huang, A.P. Tsou and H.D. Huang. Nucleic Acids Research. 2011. 39(Database issue),163-169.
29. RNAcentral: A vision for an international database of RNA sequences. Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright. AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C. RNA. 2011. 17(11),1941-1946.
30. Small molecule amiloride modulates oncogenic RNA alternative splicing to devitalize human cancer cells. J.G. Chang, D.M. Yang, W.H. Chang, L.P. Chow, W.L. Chan, H.H. Lin, H.D. Huang, Y.S. Chang, C.H. Hung, and W.K. Yang. Plos One. 2011. 6(6),e18643.
31. SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity. T.Z. Lee, Yi-Ju Chen, T.C. Lu, H.D. Huang, and Y.J. Chen. Plos One. 2011. 6(7),e21849.
32. RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans.
33. T.Y. Lee, J. B.K. Hsu, W.C. Chang and H.D. Huang. Nucleic Acids Research. 2011. 39(Database issue),777-787.
34. Analysis of Global Methylation during EBV Reactivation using a Zta-overexpressing NPC Cell Line. Ying-Fan Chen, Chao-Ling Tung , Wen-Chi Hsiao, Yao Chang, lh-Jen Su and H. Sunny Sun. Genomics. 2011. 97(4),205-213.
35. CCAAT/enhancer binding protein delta (CEBPD) elevating PTX3 expression inhibits macrophage-mediated phagocytosis of dying neuron cells. Ko CY, Chang LH, Lee YC, Sterneck E, Cheng CP, Chen SH, Huang AM, Tseng JT, Wang JM. Neurobiol Aging. 2011. 33(2),422.e11-425.e11.
36. Concurrent tumor suppressor gene methylation transforms mesenchymal stem cells into cancer stem/initiating cells. Teng IW, Hou PC, Lee KD, Chu PY, Yeh KT, Jin V, Tseng MJ, Tsai SJ, Chang YS, Wu CS, Sun HS, Tsai KD, Jeng LB, Nephew KP, Huang THM, Leu YW, Hsiao SH. Cancer Res. 2011. 71(13),4653-4663.
37. Differential expression of porcine testis proteins during postnatal development. San-Yuan Huang, Jyh-Hung Lin, Shih-Hua Teng, H. Sunny Sun, Yu-Hui Chen, Meng-Ting Chung, Chin-kai Chuang, En-Chung Lin, and Mu-Chiou Huang. Animal Reproduction Science. 2011. 123(3-4),221-233.
38. Interleukin-6 as an Early Chronic Inflammatory Marker in Polycystic Ovary Syndrome with Insulin Receptor Substrate-2 Polymorphism. Lin YS, Tsai SJ, Lin MW, Yang CT, Huang MF, Wu MH. Am J Reprod Immunol. 2011. 6(6),527-533.
39. Rapid whole-cell sensing chip for low-level arsenite detection. Chiou CH, Chien LJ, Chou TC, Lin JL, Tseng JT. Biosens Bioelectron. 2011. 26(5),2484-2488.
40. Suppression of dual specificity phosphatase-2 by hypoxia increases chemoresistance and malignancy in human cancer cells. Lin SC, Chien CW, Lee JC, Yeh YC, Hsu KF, Lai YY, Lin SC, and Tsai SJ. J Clin Invest. 2011. 121(5): 1905–1916.
41. Far upstream element-binding protein 3 (FUBP3) positively regulates FGF9 expression through TG microsatellite repeats on FGF9 3’- untranslated region. Bing-Huang Gau, Tsung-Ming Chen, Yu-Herg J. Shih, and H. Sunny Sun Nucleic Acids Research. 2011. 39(9):3582-93.
42. Hypoxia-inhibited dual specificity phosphatase-2 expression in endometriotic cells regulates cyclooxygenase-2 expression. Wu MH, Lin SC, Hsiao KY, Tsai SJ J Pathol. 2011. 10.1002/path.296225(3): 390-400.
43. The RNA-binding protein HuR stabilizes the cytosolic phospholipase A2{alpha} mRNA under interleukin-1{beta} treatment in non-small cell lung cancer A549 cells. Liao WL, Wang WC, Chang WC, Tseng JT. J Biol Chem. 2011. 286(41):35499-35508.
44. Overexpression of Pyruvate Dehydrogenase Kinase-3 Increases Drug Resistance and Early Recurrence in Colon Cancer. Lu CW, Lin SC, Chien CW, Lin SC, Lee CT, Lin BW, Lee JC, Tsai SJ. Am J Pathol. 2011. 179(3) DOI: 10.101179: 1405-11.
45. Inference of transcriptional regulatory network by bootstrapping patterns. Wang HC, Chen YS, Kao HY, Tsai SJ. Bioinformatics. 2011. 27(10):1422-1428.
46. Review on The Technologies And The Assessment Methods of Recommender. Li-Hua Li , Rong-Wang Hsu & Fu-Ming Lee. International Journal of Information System & Business Management (IJISBM). 2011. Vol.1, pp. 1-46.
47. The Node-Index-Matching Method for Ontology Structure Matching.Li-Hua Li, Rong-Wang Hsu, Fu-Ming Lee, and Yu-Chien Chou. International Journal of Information Technology and Network Application. (IJITNA). 2011. Vol. 1, No. 3, pp. 51-61.

 

Research and Development - 2012

1. A molten globule-to-ordered structure transition of Drosophila melanogaster crammer is required for its ability to inhibit cathepsin. Tseng TS, Cheng CS, Chen DJ, Shih MF, Liu YN, Hsu ST, Lyu PC .Biochem J .2012 . 442(3): 563-572.
2. An efficient RNA interference screening strategy for gene functional analysis. Chang CH, Wang HI, Lu HC, Chen CE, Chen HH, Yeh HH, Tang CY .BMC Genomics .2012 . 13(1): 491-.
3. Circular permutation of the starch-binding domain: inversion of ligand selectivity with increased affinity. Stephen P, Tseng KL, Liu YN, Lyu PC .Chem Commun .2012 . 48(20): 2612-2614.
4. Comparative transcriptomic and proteomic analyses of Trichomonas vaginalis following adherence to fibronectin. Huang KY, Huang PJ, Ku FM, Lin R, Alderete JF, Tang P .Infect Immun. .2012 . [Epub ahead of print].
5. Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB). Wang NJ, Lee CC, Cheng CS, Lo WC, Yang YF, Chen MN, Lyu PC .BMC Genomics .2012 . 13(Suppl 1): S9-.
6. CPred: a web server for predicting viable circular permutations in proteins. Lo WC, Wang LF, Liu YY, Dai T, Hwang JK, Lyu PC .Nucleic Acids Res .2012 . 40(): w232-237.
7. Crystal structure of the dopamine N-acetyltransferase-acetyl-CoA complex provides insights into the catalytic mechanism. Cheng KC, Liao JN, Lyu PC. .Biochem J .2012 . 446(3): 395-404.
8. Deciphering the preference and predicting the viability of circular permutations in proteins. Lo WC, Dai T, Liu YY, Wang LF, Hwang JK, Lyu PC .PLoS One .2012 . 7(2): e31791-.
9. Design of Novel FLT-3 Inhibitors Based on Dual-layer 3D-QSAR Model and Fragment-Based Compounds in Silico. Shih, Kuei-Chung, Lin, Chun-Yuan, Zhou, Jiayi, Chi, Hsiao-Chieh; Hwang, Chrong-Shiong, Chen, Ting-Shou, Tang, Chuan-Yi*, Hsiao, Nai-Wan .Journal of Chemical Information and Modeling .2012 . 52(1): 146-155.
10. FastAnnotator: an efficient transcript annotation web tool. Chen TW, Gan RCR, Wu TH, Huang PJ, Lee CY, Chen YYM, Chen CC and Tang P* .BMC Genomics .2012 . 13(Suppl 8): S9-.
11. Feature Identification of Compensatory Gene Pairs without Sequence Homology in Yeast. Peng CH, Lin SH, Peng SC, Lyu PC, Arita M, Tang CY .Comp Funct Genomics .2012 . 2012(): 653174-.
12. Functional profiling of the Tritrichomonas foetus transcriptome and proteome. Huang KY, Shin JW, Huang PJ, Ku FM, Lin WC, Lin R, Hsu WM, Tang P* .Mol Biochem Parasitol .2012 . 2012 Dec 17. pii: S0166-6851(12)00282-4. doi: 10.1016/j.molbiopara.2012.12.001.
13. Genome Sequence of Acinetobacter baumannii TYTH-1. Liou ML, Liu CC, Lu CW, Hsieh MF, Chang KC, Kuo HY, Lee CC, Chang CT, Yang CY, Tang CY .J Bacteriol. .2012 . 194(24): 6974-.
14. Identification of putative miRNAs from the deep-branching unicellular flagellates. Huang PJ, Lin WC, Chen SC, Lin YH, Sun CH, Lyu PC, Tang P. .Genomics .2012 . 99(2): 101-107.
15. Metabolic classification of microbial genomes using functional probes. Lee CC, Lo WC, Lai SM, Chen YP, Tang CY, Lyu PC .BMC Genomics .2012 . 13(): 157-.
16. Parallel Shellsort Algorithm for Many-Core GPUs with CUDA. Lin, Chun-Yuan, Lee, Wei-Sheng, Tang, Chuan-Yi .International Journal of Grid and High Performance Computing .2012 . 4(2): 1-16.
17. PreZon: prediction by zone and its application to egg productivity in chickens.. Lin YJ, Liou ML, Lee WC, Tang CY. .Scientific WorldJournal .2012 . 2012(): 785187-.
18. Proteome reference map of Drosophila melanogaster head. Lee TR, Huang SH, Lee CC, Lee HY, Chan HT, Lin KS, Chan HL, Lyu PC .Proteomics .2012 . 12(11): 1875-1878.
19. Proteomic analysis of a drosophila IBMPFD model reveals potential pathogenic mechanisms. Chan HT, Lee TR, Huang SH, Lee HY, Sang TK, Chan HL, Lyu PC .Mol Biosyst .2012 . 8(6): 1730-1741.
20. Transcriptomic identification of iron-regulated and iron-independent gene copies within the heavily duplicated Trichomonas vaginalis genome.. Horváthová L, Šafaříková L, Basler M, Hrdý I, Campo NB, Shin JW, Huang KY, Huang PJ, Lin R, Tang P*, Tachezy J* .Genome Biol. Evol. .2012 . 4(): 905-917.
21. VIP DB - A viral protein domain usage and distribution database. Chen TW, Gan RR, Wu TH, Lin WC, Tang P .Genomics .2012 . 100(3): 149-156.
22. A bean-free diet increases the risk of all-cause mortality among Taiwanese women: the role of the metabolic syndrome.. Chang WC, Wahlqvist ML, Chang HY, Hsu CC, Lee MS, Wang WS, Hsiung CA .Public health nutrition .2012 . 15(4): 663-672.
23. Assessing Determinants of Exonic Evolutionary Rates in Mammals.. Chen FC, Liao BY, Pan CL, Lin HY, Chang AY .Molecular biology and evolution .2012 . .
24. Determinants of exon-level evolutionary rates in Arabidopsis species.. Wu GC, Chen FC .Evolutionary bioinformatics online .2012 . 8(): 389-415.
25. DNA Methylation Rebalances Gene Dosage after Mammalian Gene Duplications.. Chang AY-F, Liao B-Y . Molecular biology and evolution .2012 . 29(1): 133-144.
26. GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization. Liao YC, Tsai MH, Chen FC, Hsiung CA .Bioinformatics .2012 . 28(13): 1752-1758.
27. Independent Effects of Alternative Splicing and Structural Constraint on the Evolution of Mammalian Coding Exons.. Chen F-C, Pan C-L, Lin H-Y .Molecular biology and evolution .2012 . 29(1): 187-193.
28. Mammalian genes preferentially co-retained in radiation hybrid panels tend to avoid coexpression.. Liao BY, Chang AY .PloS one .2012 . 7(2): e32284-.
29. Natural selection drives rapid evolution of mouse embryonic heart enhancers. Ben-Yang Liao and Meng-Pin Weng  .BMC Systems Biology .2012 . 6(Suppl 2): S1-.
30. Selective constraint on the upstream open reading frames that overlap with coding sequences in animals. Hsu, MK;Chen, FC .PLoS ONE .2012 . 7(11): e48413-.
31. Simultaneous detection of multiple fish pathogens using a naked-eye readable DNA microarray. . Chang CI, Hung PH, Wu CC, Cheng TC, Tsai JM, Lin KJ, Lin CY .Sensors (Basel)  .2012 . 12(3): 2710-2728.
32. Spotlight: Assembly of Protein Complexes by Integrating Graph Clustering Methods. Chia-Hao Chin, Shu-Hwa Chen, Chun-Yu Chen, Chao A Hsiung, Chin-Wen Ho, Ming-Tat Ko, Chung-Yen Lin .Gene .2012 . In Press.
33. The evolutionary landscape of the Mycobacterium tuberculosis genome. Tai-Chun Wang,Feng-Chi Chen .Gene .2012 . In Press.
34. dbSNO: a database of cysteine S-nitrosylation. Tzong-Yi Lee1,*, Yi-Ju Chen2, Cheng-Tsung Lu1, Wei-Chieh Ching2, Yu-Chuan Teng1, Hsien-Da Huang3,4 and Yu-Ju Chen2, .Bioinformatics .2012 . 28(17): 2293-2295.
35. ET1 Suppresses Cancer Invasion by Activating the Tissue Inhibitors of Metalloproteinases. C.H. Hsu, K.L. Peng, M.L. Kang, Y.R. Chen, Y.C. Yang, C.H. Tsai, C.S. Chu, Y.M. Jeng, Y.T. Chen, F.M. Lin, H.D. Huang, Y.Y. Lu, Y.C. Teng, S.T. Lin, R.K. Lin, F.M. Tang, S.B. Lee, H. M. Hsu, J.C. Yu *, P.W. Hsiao*, L.J. Juan* .Cell Reports, .2012 . 12(): 568-      579.
36. Functional Analyses of Endometriosis-Related Polymorphisms in the Estrogen Synthesis and Metabolism-Related Genes" PLoS One. H.S. Wang, H.M. Wu, B.H. Cheng, C.F. Yen, P.Y. Chang, A. Chao, Y.S. Lee, H.D. Huang*, T.H. Wang* .PLoS One .2012 . .
37. Identifying cancer highly-expressed membrane receptors for targeted drug delivery. W.C. Huang, F.M. Lin, T.H. Chang, K.W. Liao, H.D. Huang* .International Journal of Bioinformatics Research and Applications .2012 . (): 192-    209.
38. Let-7b is a novel regulator of hepatitis C virus replication. J.C. Cheng, Y.J. Yeh, C.P. Tseng, S.D. Hsu, Y.L. Chang, N. Sakamoto, H.D. Huang* .Cellular and Molecular Life Sciences .2012 . 12(): 2621-2633.
39. MicroRNA-122 plays a critical role in liver homeostasis and hepatocarcinogenesis" Journal of Clinical Investigation. W.C. Tsai, S.D. Hsu, C.S. Hsu, T.C. Lai, S.J. Chen, R. Shen, Yi Huang, H.C. Chen, C.H. Lee, T.F. Tsai, M.T. Hsu, J.C. Wu, H.D. Huang*, M.S. Shiao*, M. Hsiao*, A.P. Tsou* .Journal of Clinical Investigation .2012 . 13(): 2884-2897.
40. miR-103/107 promote metastasis of colorectal cancer by targeting the metastasis suppressors DAPK and KLF4. H.Y. Chen, Y.M. Lin, H.C. Chung, Y.D. Lang, C.J. Lin, J. Huang, W.C. Wang, F.M. Lin, Z. Chen, H.D. Huang, J. Y.J. Shyy, J.T. Liang, and R.H. Chen .Cancer Research .2012 . 10(): 3631-3641.
41. Phosphoproteome profiling of the sexually transmitted pathogen Trichomonas vaginalis. Yuan-Ming Yeha, b, Kuo-Yang Huanga, c, Ruei-Chi Richie Gand, e, Hsien-Da Huange, Tzu-Chien V. Wanga, b, Petrus Tanga, c, d, .Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi .2012 . (10.1016/j.jmii.2012.07.010) .
42. A miniature lighted stylet for fast oral endotracheal intubation in rabbits.. H.P. Su, C.J. Hou, W.H. Chen, K.J. Wang, Y.H. Chiu, H.S. Sun.  .The Veterinary Journal Jul 25. .2012 . [Epub ahead of print] http://dx.doi.org/10.1016/j.tvjl.2012.06.016.
43. Ectopic expression of T-Cell Lymphoma Invasion and Metastasis 2 Promotes Proliferation and Invasion in liver cancer Cells.. Jia–Shing Chen, Ih-Jen Su, Yu-Wei Leu, Kung-Chia Young, H. Sunny Sun*. .Int J Cancer  .2012 . 15;130(6): 1302-13.
44. Estrogen receptor expression affected by hypoxia inducible factor-1α in stromal cells from patients with endometriosis.. Wu MH, Lu CW, Chang FM, Tsai SJ* .Taiwan J Obstet Gynecol .2012 . 51: 50-54.
45. Hypoxia-induced microRNA-20a expression increases ERK phosphorylation and angiogenic gene expression in endometriotic stromal cells. . SC Lin, CC Wang, MH Wu, HS Yang, YH Lee, SJ Tsai* . J Clin Endocrinol Metab .2012 . 97: E1515–E1523.
46. "Hypoxia-induced tumor progression and drug resistance: from current understandings to future perspectives.. Chih-Chuan Wang；Shih-Chieh Lin；Yo-Hua Li；Shaw-Jenq Tsai .Adaptive Medicine .2012 . 4(3): 132-144."
47. Menstrual Cycle-dependent Febrile Episode Mediated by Sequence-specific Repression of Poly(ADP-ribose) Polymerase-1 on the Transcription of the Human Serotonin Receptor 1A Gene.. Yu-Chen Jiang, Hung-Ming Wu, Kai-Hsin Cheng and H. Sunny Sun*. .Human Mutation  .2012 . 33(1): 209-217.
48. Prediction of personalized microRNA activity.. Lee CC, Yen CJ, Liu T. .Gene .2012 . pii: S0378-1119(12)01517-X. doi: 10.1016/j.gene.2012.11.068. [Epub ahead of print].
49. Review of Recommender Systems and Their Application. Li-Hua Li , Rong-Wang Hsu & Fu-Ming Lee .International Journal of Advanced Information Technologies(IJAIT) .2012 . Vol. 6(No.1): 63-87.

 

Research and Development - 2013

1. "NMR assignments of a hypothetical pseudo-knotted protein HP0242 from Helicobacter pylori. Chien CT, Wang LW, Liu YN, Hsu BD, Lyu PC, Hsu ST. Biomol NMR Assign.. 2013.  10.1007/s12104-013-9502-6."
2. GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects. Lee CC, Chen YP, Yao TJ, Ma CY, Lo WC, Lyu PC * , Tang CY*. Gene. 2013. 518(1): 114-123.
3. Transcriptome profiling of the fifth-stage larvae of Angiostrongylus cantonensis by next-generation sequencing. Wang LC*, Chen KY, Chang SH, Chung LY, Gan RCR, Cheng CL, Tang P*. Parasitol Res.. 2013. doi:10.1007/s00436-013-3495-z.
4. Hydrated bovine serum albumin as the gate dielectric material for organic field-effect transistors. Chun-Yi Lee, Jenn-Chang Hwang*, Yu-Lun Chueh, Ting-Hao Chang, Yi-Yun Cheng, Ping-Chiang Lyu. Organic Electronics. 2013. 14(10): 2645-2651.
5. Residue-specific annotation of disorder-to-order transition and cathepsin inhibition of a propeptide-like crammer from D. melanogaster. Tseng TS, Cheng CS, Hsu ST, Shih MF, He PL, Lyu PC*. PLos One. 2013. 8(1): e54187-.
6. CPAP: Cancer Panel Analysis Pipeline. Huang PJ, Yeh YM, Gan RCR, Lee CC, Chen TW, Lee CY, Liu H, Chen SJ, Tang P*. Hum Mutat.. 2013. 34(10): 1340-1346.
7. Protein kinase inhibitor design by targeting the Asp-Phe-Gly (DFG) motif: the role of the DFG motif in the design of epidermal growth factor receptor inhibitors. Peng YH, Shiao HY, Tu CH, Liu PM, Hsu JT, Amancha PK, Wu JS, Coumar MS, Chen CH, Wang SY, Lin WH, Sun HY, Chao YS, Lyu PC, Hsieh HP, Wu SY.. J Med Chem. 2013. 56(10): 3889-3903."
8. Enzyme Reaction Annotation Using Cloud Techniques. Huang CC, Lin CY, Chang CW, Tang CY. Biomed Res Int.. 2013. doi: 10.1155/2013/140237.
9. Design checkpoint kinase 2 inhibitors by pharmacophore modeling and virtual screening techniques. Wang YL, Lin CY, Shih KC, Huang JW, Tang CY. Bioorg Med Chem Lett. 2013. doi: 10.1016/j.bmcl.2013.09.080.
10. Monitoring the antigenic evolution of human influenza A viruses to understand how and when viruses escape from existing immunity. Yu-Chieh Liao, Hsin-Hung Lin and Chieh-Hua Lin. BMC Research Notes. 2013. 6(): 227-.
11. CISA: Contig Integrator for Sequence Assembly of Bacterial Genomes. Shin-Hung Lin,Yu-Chieh Liao . PLoS ONE. 2013. 8(3): e60843-.
12. Flagellated algae protein evolution suggests the prevalence of lineage-specific rules governing evolutionary rates of eukaryotic proteins. Chang, TY;Liao, BY. Genome Biology and Evolution. 2013. 5(5): 913-.
13. Identification of cytotoxic T lymphocyte epitopes on swine viruses: multi-epitope design for universal T cell vaccine. Yu-Chieh Liao mail,Hsin-Hung Lin,Chieh-Hua Lin,Wen-Bin Chung. PLoS ONE. 2013. 8(12):  e84443-.
14. "Draft genome sequence of NDM-1-producing Klebsiella pneumoniae clinical isolate 303K. Yu-Chieh Liao, Ying-Hsiang Chen,  Hsin-Hung Lin, Jung-Jung Mu,  Ho-Sheng Wu, Feng-Chi Chen, Chao Agnes Hsiung. Genome Announc. . 2013. 1(5):  e01069-13 -."
15. A new method for post Genome-Wide-Association-Study (GWAS) analysis of colorectal cancer in Taiwan.  H.M. Wang, T.H. Chang, F.M. Lin, T.H. Chao, W.C. Huang, C. Liang, C.M. Chiu, W.Y. Wu, M.C. Chen, C.T. Weng, S.L. Weng, F.F. Chiang*, and H.D. Huang. Genes. 2013. 518(1): 107-113.
16. An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. T.H. Chang, H.Y. Huang, J. B.K. Hsu, S.L. Weng, J.T. Horng* and H.D. Huang* . BMC Bioinformatics . 2013. 14(Suppl 2): S4-.
17. pseudoMap: a novel method and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes.   W.L. Chan, W.K. Yang, H.D. Huang, and J.G. Chang*. Database. 2013. 2013(): bat001-.
18. EuLoc: a web-server for accurately predict protein subcellular localization in eukaryotes by incorporating various features of sequence segments into the general form of Chou’s PseAAC. T.H. Chang, L.C. Wu, T.Y. Lee, S.P. Chen, H.D. Huang, and J.T. Horng . Journal of Computer-Aided Molecular Design . 2013. 27(1): 91-103.
19. A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. C.H. Chou, F.M. Lin, M.T. Chou, S.D. Hsu, T.H. Chang, S.L. Weng, S. Shrestha, C.C. Hsiao, J.H. Hung* and H.D. Huang.  BMC Genomics . 2013. 14(Suppl 1): S2-.
20. The activation of directional stem cell motility by green light-emitting diode irradiation.  W.K. Ong, H.F. Chen, C.T. Tsai, Y.J. Fu, Y.S. Wong, D.J. Yen, T.H. Chang, H.D. Huang, O. K.S. Lee, S. Chien, and J. H.C. Ho*. Biomaterials. 2013. 34(8): 1911-1920.
21. dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. C.T. Lu, K.Y. Huang, M.G. Su, T.Y. Lee*, N. A. Bretaña, W.C. Chang, Y.J. Chen, and H.D. Huang*. Nucleic Acids Research. 2013. 41(database issue): D295-D305.
22. Transcribed pseudogene ψPPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma.  W.L. Chan, C.Y. Yuo, W.K. Yang, S.Y. Huang, Y.S. Chang, C.C. Chiu, K.T. Yeh, H.D. Huang, J.G. Chang. Nucleic Acids Research . 2013. 41(6): 3734-3747.
23. Angiogenesis Enhancement via MicroRNA Targeting of Argonaute 1: A Hypoxia-induced Translational De-suppression Mechanism.  Z. Chen, W.C. Wang, H. Xiao, Y.T. Wang, F.M. Lin, W. Sun, T.C. Lai, Y.H. Jan, Y.S. Li, X. Cui, T. Fang, H. Zhao, C. Padmanabhan, R. Sun, D.L. Wang, H. Jin, H.D. Huang, M. Hsiao and J. Y.J. Shyy1*. Journal of Clinical Investigation . 2013. 123(3): 1057-1067.
24. Using positive and negative patterns to extract information from journal articles regarding the regulation of a target gene by a transcription factor.. Hei Chia Wang, Tock-Kheng Kooi, Hung-Yu Kao, Shih Chieh Lin, Shaw-Jenq Tsai. Computers in Biology and Medicine. 2013. 43(12): 2214-2221.
25. Expression of EBV-encoded oncogenes and EBV-like virions in multiple canine tumors.. Chiu HC, Chow KC, Fan YH, Chang SC, Chiou SH*, Chiang SF, Chiou CH, Wu GH, Yang HC, Ho SP, Chen YK, Lee WC, Sun HS*.. Veterinary Microbiology. 2013. 163(1-2): 79-89.
26. Effects of GC bias in next-generation-sequencing data on de novo genome assembly. . Chen YC, Liu T (co-first author), Yu CH, Chiang TY, Hwang CC.. PLoS ONE. 2013. 8(4): e62856-.
27. Human DDX3 interacts with the HIV-1 Tat protein to facilitate viral mRNA translation.. Ming-Chih Lai, Shainn-Wei Wang, Lie Cheng, Woan-Yuh Tarn, Shaw-Jenq Tsai* and H. Sunny Sun*. . PLoS ONE. 2013. 8(7): e68665-.
28. Optimizing information in next-generation-sequencing (NGS) reads for improving de novo genome assembly.. Liu T, Tsai CH, Lee WB, Chiang JH*..  PLoS ONE. 2013. 8(7): e69503-e69503.
29. Suppression of annexin A2 by prostaglandin E2 impairs phagocytic ability of peritoneal macrophage in women with endometriosis. . MH Wu, PC Chuang, YJ Lin, SJ Tsai*. Human Reproduction. 2013. 28(4): 1045-1053.
30. In silico identification of oncogenic potential of fyn-related kinase in hepatocellular carcinoma.. Jia-Shing Chen, Wei-Shine Hong, Hsiang-Han Chan, Shaw-Jenq Tsai, and H. Sunny Sun*. Bioinformatics. 2013. 29(4): 420-427.
31. Overexpression of integrin-β1 promotes leiomyomal cell spreading and proliferation.. HM Chen, YH Lin, YM Cheng, LYC Wing, SJ Tsai*. J Clin Endocrinol Metab . 2013. 98(5): E837-E846.
32. Improving de novo assembly by pre-processing the next-generation-sequencing data.. Jeng SL*, Wu YH, Liu T. Journal of the Chinese Statistical Association. 2013. 51(3): 352-372.
33. Protein-protein interactions inferred from domain-domain interactions. Huang, Chuan-Ching and Tang, Chuan Yi*. International Journal of Genomics. 2013. doi:10.1155/2013/456356.

 

Research and Development - 2014

1. Downregulation of a putative tumor suppressor BMP4 by SOX2 promotes growth of lung squamous cell carcinoma. Fang WT, Fan CC, Li SM, Jang TH, Lin HP, Shih NY, Chen CH, Wang TY, Huang SF, Lee A YL, Liu YL, Tsai FY, Huang CT, Yang S J, Yen LJ, Chuu CP, Chen CY, Hsiung C A, Chang JY, Wang LH, Chang IS and Jiang S S.. International Journal of Cancer. 2014. 135(4): 809-819.
2. Development of a Human Dihydroorotate Dehydrogenase (hDHODH) Pharma-Similarity Index Approach with Scaffold-Hopping Strategy for the Design of Novel Potential Inhibitors. Shih, Kuei-Chung*, Lee, Chi-Ching, Tsai, Chi-Neu, Lin, Yu-Shan, Tang, Chuan-Yi* . PLOS one. 2014. DOI: 10.1371/journal.pone.0087960.
3. Adaptive responses to glucose restriction enhance cell survival, antioxidant capability, and autophagy of the protozoan parasite Trichomonas vaginalis.. Huang KY, Chen YYM, Fang YK, Cheng WH, Cheng CC, Chen YC, Wu TE, Ku FM, Chen SC, Lin R, Tang P*. BBA-Gen Subjects.. 2014. 1840(1):53–64.
4. ChIPseek, a web-based analysis tool for ChIP data.. Chen TW, Li HP, Lee CC, Gan RC, Huang PJ, Wu TH, Lee CY, Chang YF and Tang P*. BMC Genomics. 2014. (13): 159-.
5. Interference of Co-amplified Nuclear Mitochondrial DNA Sequences on the Determination of Human mtDNA Heteroplasmy by Using the SURVEYOR Nuclease and the WAVE HS System. Yen HC, Li SL, Hsu C, Tang P*. PLOS one. 2014. 9(3)e92817.
6. CMPD: Cancer Mutant Proteome Database. Huang PJ, Lee CC, Tan BCM, Yeh YM, Chu JLC, Chen TW, Chang KP, Gan RC, Liu H, Tang P.*.  Nucleic Acids Res.. 2014. doi: 10.1093/nar/gku1182.
7. Accumulation of CTCF-binding sites drives expression divergence between tandemly duplicated genes in humans. Liao, BY;Chang, AYF. BMC Genomics. 2014. 15(Suppl. 1): Article number S8-.
8. Sequencing and analysis of the transcriptome of the acorn worm Ptychodera flava, an indirect developing hemichordat. Shu-Hwa Chen, Kun-Lin Li, I-Hsuan Lu, Yu-Bin Wang,Che-Huang Tung, Hsiu-Chi Ting, Ching-Yi Lin, Chung-Yen Lin*, Yi-Hsien Su*, Jr-Kai Sky Yu. Marine Genomics. 2014. .
9. Draft genome sequence of the Mycobacterium tuberculosis clinical isolate C2, belonging to the Latin American–Mediterranean family. YC Liao, YY Chen, HH Lin, JR Chang, IJ Su, TS Huang, HY Dou. Genome Announcements. 2014. 2(3): e00536-14-.
10. DNA methylation is associated with an increased level of conservation at nondegenerate nucleotides in mammals. TJ Chuang, FC Chen*. Molecular biology and evolution. 2014. 31(2): 387-396.
11. Pros and cons of the tuberculosis drugome approach – An empirical analysis. Chen FC,Liao YC,Huang JM,Lin CH,Chen YY,Dou HY,Hsiung CA. PLoS ONE. 2014. 9(6): e100829-.
12. The evolution of the coding exome of the Arabidopsis species - the influences of DNA methylation, relative exon position, and exon length. Feng-Chi Chen,Trees-Juen Chuang,Hsuan-Yu Lin1,Min-Kung Hsu. BMC Evolutionary Biology. 2014. 14(): Article number 145-.
13. Draft Genome Sequences of the Mycobacterium tuberculosis Clinical Strains A2 and A4, Isolated from a Relapse Patient in Taiwan. Yu-Chieh Liao,Yih-Yuan Chen,Hsin-Hung Lin,Jia-Ru Chang,Ih-Jen Su,Tsi-Shu Huang,Horng-Yunn Dou. Genome Announcements. 2014. 2(5): e00672-14 -.
14. Are all of the human exons alternatively spliced?. Chen, FC. Briefings in Bioinformatics. 2014. 15(4): 542-551.
15. Functional implications of RNA splicing for human long intergenic noncoding RNAs. Chen, FC;Pan, CL;Lin, HY. Evolutionary Bioinformatics. 2014. 10(): 219-228.
16. Alternative RNA structure-coupled gene regulations in tumorigenesis. Chen, FC. International Journal of Molecular Sciences. 2014. 16(1): 452-475.
17. miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions.  S.D. Hsu, Y.T. Tseng, S. Shrestha, Y.L. Lin, A. Khaleel, C.H. Chou, C.F. Chu, H.Y. Huang, C.M. Lin, S.Y. Ho, T.Y. Jian, F.M. Lin, T.H. Chang, S.L. Weng, K.W. Liao, I.E. Liao, C.C. Liu*, H.D. Huang.  Nucleic Acids Research. 2014. 42(): D78-85.
18. Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing.  C.M. Chiu, F.M. Lin, T.H. Chang, W.C. Huang, C. Liang, T. Yang, W.Y. Wu, T.L. Yang, S.L. Weng, H.D. Huang.  Journal of Clinical Bioinformatics. 2014. 4(1): doi:10.1186/2043-9113-4-1-.
19. A systematic review of microRNA expression profiling studies in human gastric cancer.. S. Shrestha, S.D. Hsu, W.Y. Huang, H.Y. Huang, W. Chen, S.L. Weng, H.D. Huang*. Cancer Medicine. 2014. 3(4): 878-888.
20. Large-Scale Investigation of Human TF-miRNA Relations Based on Coexpression Profiles.. CH Chien, YF Chiang-Hsieh, AP Tsou, SL Weng, WC Chang, HD Huang*. Biomed Res Int.. 2014. 2014(): 623078-.
21. Bacterial communities in semen from men of infertile couples: metagenomic sequencing reveals relationships of seminal microbiota to semen quality.. S.L. Weng, C.M. Chiu, F.M Lin,W.C Huang, C. Liang, T. Yang, T.L. Yang, C.YC Liu, W.Y. Wu, Y.A. Chang, T.H. Chang*, H.D. Huang*. PLoS One. 2014. 9(10): e110152-.
22. Hypoxia-regulated gene network in drug resistance and cancer progression.. SC Lin, WL Liao, JC Lee, and SJ Tsai*. Experimental Biology and Medicine. 2014. (): doi:10.1177/1535370214532755-.
23. Hypoxia-induced tumor malignancy and drug resistance: The role of microRNAs.. WL Liao, SC Lin, HS Sun, and SJ Tsai*. Biomarkers and Genomic Medicine. 2014. 6:1-11.
24. Fibroblast growth factor 9 activates Akt and MAPK pathways to stimulate steroidogenesis in mouse Leydig cells.. MS Lai, YS Cheng, PR Chen, SJ Tsai, BM Huang. PLoS One. 2014. 9(3): e90243-.
25. Suppression of COUP-TFII by proinflammatory cytokines contributes to the pathogenesis of endometriosis.. SC Lin, YH Li, MH Wu, YF Chang, DK Lee, S Tsai, MJ Tsai, and SJ Tsai*. J Clin Endocrinol Metab. 2014. 99(3): E427-37-.
26. Comprehensive analysis of common coding sequence variants in Taiwanese Han population.. Ya-Chi Lin, Joseph T. Tseng, Shuen-Lin Jeng , H. Sunny Sun. Biomarkers and Genomic Medicine. 2014. DOI: 10.1016/j.bgm.2014.05.001.
27. Sequence variants of the HTR3A gene contribute to the genetic prediction of postoperative nausea in Taiwan. Yi-Mei Joy Lin, Cheng-Da Hsu, Hsiao-Yen Hsieh, Chia-Chih Alex Tseng, H. Sunny Sun*.. Journal of Human Genetics. 2014. 59(): 655-660.

 

Research and Development - 2015

1. Unraveling the association between mRNA expressions and mutant phenotypes in a genome-wide assessment of mice. Liao, Ben-Yang; Weng, Meng-Pin. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2015. 112(15): 4707-4712.
2. Completing bacterial genome assemblies: Strategy and performance comparisons. Liao, YC;Lin, SH;Lin, HH. Scientific Reports. 2015. 5(Article number 8747).
3. Emerging roles of frailty and inflammaging in risk assessment of age-related chronic diseases in older adults: The intersection between aging biology and personalized medicine. Wu, IC;Lin, CC;Hsiung, CA*. BioMedicine. 2015. 5(1): Article number 1.
4. Fluoroquinolone prescribing in Taiwan, 2000 to 2010. Kuo, SC;Shih, SM;Yang Lauderdale, TL;Chen, YC;Hsiung, CA*. Journal of Microbiology, Immunology and Infection. 2015. 48(2, Suppl.1): S103.
5. MethHC: a database of DNA methylation and gene expression in human cancer.. W.Y. Huang, S.D. Hsu, H.Y. Huang, Y.M. Sun, C.H. Chou, S.L. Weng, H.D. Huang*. Nucleic Acids Research . 2015. 43(Database issue): D856-D861.
6. GeNOSA: inferring and experimentally supporting quantitative gene regulatory networks in prokaryotes.. Y.H. Chen, C.D. Yang, C.P. Tseng, H.D. Huang, S.Y. Ho*. Bioinformatics. 2015. (): pii: btv075.
7. Characterization and distribution of repetitive elements in association with genes in the human genome.. Kai-Chiang Liang, Joseph T. Tseng1, Shaw-Jenq Tsai and H. Sunny Sun*. Computational Biology and Chemistry . 2015.  2015 Aug;57:29-38. Epub 2015 Feb 27.(): doi: 10.1016/j.compbiolchem.2015.02.007.
8. The non-canonical role of vascular endothelial growth factor-C axis in cancer progression.. Chu-An Wang and Shaw-Jenq Tsai. Exp Biol Med. 2015. 240(6): 718-724.

 

Collaborative Research - 2003

1. Computation of the Protein Structure Entrope and its Applications to Protein Folding Processes. Chen-hsiung Chan, Ping-Chiang Lyu and Jenn-Kang Hwang, J. Chin. Chem. Soc. 50, 677-684 (2003).
2. Relationship Between Protein Structures and Disulfide-Bonding Patterns. Chao-Chun Chuang, Chun-Yin Chen, Jinn-Moon Yang, Ping-Chiang Lyu and Jenn-Kang Hwang, Proteins: Structure, Function, Bioinformatics. 52, 1-5 (2003).
3. Fine-grained protein fold assignment by support vector machines using generalized n-peptide coding schemes and jury voting from multiple parameter sets. C.-H. Yu, J.-Y. Wang, J.-M. Yang, P.-C. Lyu, C.-J. Lin, J.-K. Hwang, Proteins: Structure, Function, Bioinformatics. 50, 531-536 (2003)

 

Collaborative Research - 2004

1. 1H, 13C, and 15N resonance assignments and secondary structure of human pancreatitis-associated protein (hPAP). M. R. Hoa, Y. C. Lou, W. C. Lin, P. C. Lyu, and C. P. Chen. J. Bio. NMR 30, 381-382 (2004). Relationship between local structural entropy and protein thermostabilty. C. H. Chan, H. K. Liang, N. W. Hsiao, M. T. Ko, P. C. Lyu, J. K. Hwang Proteins 57, 684-691 (2004).
2. Nonsteroidal anti-inflammatory drugs increase expression of inducible COX-2 isoform of cyclooxygenase in spinal cord of rats with adjuvant induced inflammation. S. F. Hsueh , C. Y. Lu , C. S. Chao , P. H. Tan , Y. W. Huang , S. W. Hsieh , H. T. Hsiao , N. C. Chung , S. H. Lin , P. L. Huang , P. C. Lyu, and L. C. Yang. Brain Res Mol Brain Res. 125, 113-9 (2004)
3. Jiang, S.S., Chen, T.C., Yang, J.Y., Hsiung, C. A. , Su, I.J., Liu, Y.L., Chen, P.C., Juang, J.L. 200Sensitive and quantitative detection of severe acute respiratory syndrome coronavirus infection by real-time nested polymerase chain reaction. Clinical Infectious Diseases. Jan 15;38(2):293-6.

 

Collaborative Research - 2005

1. Solution structure of a bacterial BolA-like protein XC975 from a plant pathogen Xanthomonas campestris pv. campestris. K. H. Chin, F. Y. Lin, Y. C. Hu, K. H. Sze, P. C. Lyu and S. H. Chou. J. Bio. NMR 31, 167-172 (2005).
2. Anti-phosphopeptide antibody, P-STM as a novel tool for detecting mitotic phosphoproteins: identification of lamins A and C as two major targets. I. C. Tsai, Y. J. Hsieh, P.C. Lyu and J. S. Yu, J Cell Biochem. 94, 967-981 (2005).
3. The Cloning, purification, crystallization, and preliminary X-ray crystallographic analysis of XC847, a 3'-5' oligoribonuclease from Xanthomonas campestris. Yan-You Wu, Ko-Hsin Chin, Chia-Cheng Chou, Cheng-Chung Lee, Hui-Lin Shr, Ping-Chiang Lyu, Andrew H.-J. Wang, & Shan-Ho Chou. Acta. Crystallogr. F61, 902-905 (2005).
4. The cloning, expression, crystallization, and preliminary X-ray analysis of a putative multiple antibiotic-resistance repressor protein (MarR) from Xanthomonas campestris. Z. L. Tu, J. N. Li, K. H. Chin, C. C. Chou, C. C.Lee, H. L. Shr, P. C. Lyu, F.P. Gao, H. J. Wang, & S. H. Chou. Acta. Crystallogr. F61, 706-708 (2005).
5. Cloning, purification, crystallization, and preliminary X-ray characterization of a conserved hypothetical protein XC6422 from Xanthomonas campestris. Chao-Yu Yang, Ko-Hsin Chin, Chia-Chen Chou, Hui-Lin Shr, Fei Philip Gao, Ping-Chiang Lyu, Andrew H.-J. Wang, & Shan-Ho Chou. Acta. Crystallogr. F61, 703-705 (2005).
6. In the preparation, crystallization, and preliminary X-ray analysis of XC2382, an ApaG protein of unknown structure from Xanthomonas campestris. Ko-Hsin Chin, Chia-Chen Chou, Cheng-Cheng Lee, Hui-Lin Shr, Ping-Chiang Lyu, Andrew H.-J. Wang, & Shan-Ho Chou. Acta. Crystallogr. F61, 700-702 (2005).
7. A putative polyketide synthesis protein XC5357 from Xanthomonas campestris: heterologous expression, crystallization, and preliminary X-ray analysis." Chyao-Li Chu, Ko-Hsin Chin, Fu-Yang Lin, Chia-Chen Chou, Cheng-Cheng Lee, Hui-Lin Shr, Ping-Chiang Lyu, Andrew H.-J. Wang, & Shan-Ho Chou. Acta. Crystallogr. F61, 697-699 (2005).
8. Cloning, purification, crystallization and preliminary X-ray analysis of XC229, a conserved hypothetical protein from Xanthomonas campestris. K. H. Chin, W. T. Kuo, C. C. Chou, H. L. Shr, P.C. Lyu, A. H. Wang, S. H. Chou . Acta Crystallograph Sect F Struct Biol Cryst Commun. 61, 694-696 (2005).
9. Preparation, crystallization, and preliminary X-ray characterization of a conserved hypothetical protein XC1692 from Xanthomonas campestris. Ko-Hsin Chin, Zhao-Wei Huang, Kun-Chou Wei, Chia-Chen Chou, Cheng-Cheng Lee, Hui-Lin Shr, Fei Philip Gao, Ping-Chiang Lyu, Andrew H.-J. Wang, & Shan-Ho Chou. Acta. Crystallogr. F61, 691-693 (2005).
10. An P, Freedman BI, Hanis CL, Chen YD, Weder AB, Schork NJ, Boerwinkle E, Province MA, Hsiung CA, Wu X, Quertermous T, Rao DC. “Genome-wide linkage scans for fasting glucose, insulin, and insulin resistance in the National Heart, Lung, and Blood Institute Family Blood Pressure Program: evidence of linkages to chromosome 7q36 and 19q13 from meta-analysis” Diabetes. 2005 Mar;54(3):909-14
11. Shih SR, Chen GW, Yang CC, Yang WZ, Liu DP, Lin JH, Chiu SC, Chen HY, Tsao KC, Huang CG, Huang YL, Mok CK, Chen CJ, Lin TY, Wang JR, Kao CL, Lin KH, Chen LK, Eng HL, Liu YC, Chen PY, Lin JS, Wang JH, Lin CW, Chan YJ, Lu JJ, Hsiung CA, Chen PJ, Su IJ. “Laboratory-Based Surveillance and Molecular Epidemiology of Influenza Virus in Taiwan” Journal of Clinical Microbiology, April 2005, 43(4):1651-1661
12. Lan YC, Liu TT, Yang JY, Lee CM, Chen YJ, Chan YJ, Lu JJ, Liu HF, Hsiung CA, Ho MS, Hsiao KJ, Chen HY, Chen YM. “Molecular Epidemiology of Severe Acute Respiratory Syndrome–Associated Coronavirus Infections in Taiwan” Journal of Infectious Diseases 2005 May, 191(9):1478-89
13. Huang, S. Y., J. H. Lin, Y. H. Chen, C.K. Chuang, E.-C. Lin, M. C. Huang, H. S. Sun and W. C. Lee*. 200A reference map and identification of porcine testis proteins using two-dimensional gel electrophoresis and mass spectrometry. Proteomics 5:4205-4212.

 

Collaborative Research - 2006

1. Jiang, SS, Chang, IS., Huang, LW., Chen, PC., Wen, CC., Liu, SC., Chien, LC., Lin, CY., Hsiung, CA., cJuang, JL. (2006) Temporal Transcription Program of Recombinant Autographa californica Multiple Nucleopolyhedrosis Virus. Journal of Virology. 80(18):8989-899IF: 5.178.
2. Crystallization and preliminary X-ray analysis of XC1015, a histidine triad-like protein from Xanthomonas campestris. W. T. Lo, K. H. Chin, H. L. Shr , F. P. Gao, P. C. Lyu, A. H. Wang, S. H. Chou. Acta Crystallograph Sect F Struct Biol Cryst Commun. 62, 1263-5 (2006).
3. Cloning, crystallization and preliminary X-ray studies of XC2981 from Xanthomonas campestris, a putative CutALin CH, K. H. Chin , F. P. Gao , P. C. Lyu , A. H. Wang , S. H. Chou. Acta Crystallograph Sect F Struct Biol Cryst Commun. 62, 1113-5 (2006).
4. Structural basis for the structure-activity relationships of peroxisome proliferator-activated receptor agonists. N. Mahindroo, Y. H. Peng, C. H. Lin, U. K. Tan, E. Prakash, T. W. Lien, I. L. Lu, H. J. Lee, J. T. Hsu, X. Chen, C. C. Liao, P. C. Lyu, Y. S. Chao, S. Y. Wu, H. P. Hsieh. J. Med. Chem. 49, 6421-4 (2006).
5. Human pancreatitis-associated protein forms fibrillar aggregates with a native-like conformation. M. R. Ho, Y. C. Lou, W. C. Lin, P. C. Lyu, W. N. Huang, C. Chen. J. Biol. Chem. 281, 33566-76 (2006).
6. Indol-1-yl acetic acids as peroxisome proliferator-activated receptor agonists: design, synthesis, structural biology, and molecular docking studies. N. Mahindroo , C. C. Wang, C. C. Liao, C. F. Huang, I. L. Lu, T. W. Lien, Y. H. Peng, W. J. Huang, Y. T. Lin, M. C. Hsu, C. H. Lin, C. H. Tsai, J. T. Hsu, X. Chen, P. C. Lyu, Y. S. Chao, S. Y. Wu, H.P. Hsieh. J Med Chem. 49, 1212-1216 (2006).
7. Japanese encephalitis virus NS2B-NS3 protease binding to phage-displayed human brain proteins with the domain of trypsin inhibitor and basic region leucine zipper. C.W. Lin, K.H. Lin, P.C. Lyu, W.J. Chen . Virus Res. 116, 106-113 (2006)
8. Wu, C.W., Chang, I.S., Lo, S.S., Hsieh, M.C., Chen, J.H., Lui, W.Y., Whang-Peng, J. Complications following D3 gastrectomy: Post Hoc analysis of a randomized trial. World J. Surg. 2006; 30:12-1
9. Jiang SS, Chang IS, Huang LW, Chen PC, Wen CC, Liu SC, Lin CY, Hsiung CA and Juang JL (2006) Temporal transcription program of recombinant Autographa californica multiple nucleopolyhedrosis virus. J Virol. 2006 Sep;80(18):8989-9
10. Tsan-Chi Chen, Guang-Wu Chen, Chao Agnes Hsiung, Jyh-Yuan Yang, Shin-Ru Shih, Yiu-Kay Lai, Jyh-Lyh Juang (2006) Combining Multiplex Reverse Transcription-PCR and a Diagnostic Microarray To Detect and Differentiate Enterovirus 71 and Coxsackievirus A1J Clin Microbiol. 2006 Jun ;44:2212-9
11. Luan-Yin Chang, Chao A. Hsiung, Chun-Yi Lu, Tzou-Yien Lin, Fu-Yuan Huang, Yu-Han Lai, Yu-Ping Chiang, Bor-Luen Chiang, Chin-Yun Lee, and Li-Min Hung. (2006) Status of Cellular Rather than Humoral Immunity is Correlated with Clinical Outcome of Enterovirus 71 Pediatr Res, DOI: 10.1203/01.pdr.0000238247.86041.19
12. Wang T.H., Wei K.C., Hsiung CA., Maloney S.A., Eidex R.B., Posey D.L., Chou W.H., Shih W.Y., Kuo H.S.Optimizing SARS response strategies—What have we learned from quarantine. American Journal of Public Health
13. Lin YS, Byrnes JK, Hwang JK, Li WH. Codon usage bias versus gene conversion in the evolution of yeast duplicate genes. Proc. Natl. Acad. Sci. USA. (2006) 103:14412-14416
14. Lin YS, Hwang JK, Li WH. Protein complexity, gene duplicability and gene dispensability in the yeast genome. Gene. (2006) [Epub ahead of print].
15. Chiu WC, You JY, Liu JS, Hsu SK, Hsu WH, Shih CH, Hwang JK, Wang WC, Structure-stability-activity relationship in covalently c 1 ross-linked N-carbamoyl D-amino acid amidohydrolase and N-acylamino acid racemase. J. Mol. Biol. (2006), 359: 741-753.
16. Hung SW, Hwang JK, Tseng F, Chang JM Chen CC, Chieng CC. Molecular dynamics simulation on enhancement of CTX and E6 protein binding on mixed SAMs molecules. Nanotechnology (2006), 17, S8-13
17. Yung-Hsian Hsu, Chaio-Wei Chen, H. S. Sun, Ruwen Jou, Jen-Jyh Lee and Ih-Jen Su. 200Association of NRAMP 1 Gene Polymorphisms with Susceptibility to Tuberculosis in Taiwanese Aboriginals. JFMA 105: 363-369.
18. Yen-Ni Teng, Yung-Ming Lin, H. Sunny Sun, Pei-Yang Hsu,Chia-Ling Chung, Pao-Lin Kuo, M.D. 200Association of DAZL Haplotypes with Spermatogenic Failure in Infertile Men. Fertility and Sterility 86:129-35
19. Shiang Ning Leaw, Hsien Chang Chang, H. S.Sun, Richard Barton, Jean-Philippe Bouchara, Tsung Chain Chang. 200 Identification of Medically Important Yeasts by Sequence Analysis of the Internal Transcribed Spacer Regions. Journal of Clinical Microbiology 44: 693–699.
20. Chen, C.H., Lin, E.C., Cheng, W.T.K., Sun, H.S., Mersmann, H.J., Ding, S. T. 200The abundantly expressed genes in pig adipose tissue: an expressed sequence tag approach. J. Animal Science 84:2673-83.
21. Shiang Ning Leaw, Hsien Chang Chang, Hsiao Fang Sun, Richard Barton, Jean-Philippe Bouchara, Tsung Chain Chang. 200 Identification of Medically Important Yeasts by Sequence Analysis of the Internal Transcribed Spacer Regions. Journal of Clinical Microbiology 44: 693–699.

 

Collaborative Research - 2007

1. Chiang, S. L., Jiang, S. S., Wang, Y. J., Chiang, H. C., Chen, P. H., Tu, H. P., Ho, K. Y., Tsai, Y. S., Chang, I. S., and Ko, Y. C. (2007) Characterization of arecoline-induced effects on cytotoxicity in normal human gingival fibroblasts by global gene expression profiling, Toxicol Sci 100, 66-74.
2. Hung, C. L., Liu, J. H., Chiu, W. C., Huang, S. W., Hwang, J. K., and Wang, W. C. (2007) Crystal structure of Helicobacter pylori formamidase AmiF reveals a cysteine-glutamate-lysine catalytic triad, J Biol Chem 282, 12220-12229.
3. Lin, S. C., Chueh, S. C., Hsiao, C. J., Li, T. K., Chen, T. H., Liao, C. H., Lyu, P. C., and Guh, J. H. (2007) Prazosin displays anticancer activity against human prostate cancers: targeting DNA and cell cycle, Neoplasia 9, 830-839.
4. Ruan, S. K., Chin, K. H., Shr, H. L., Lyu, P. C., Wang, A. H., and Chou, S. H. (2007) Preliminary X-ray analysis of XC5848, a hypothetical ORFan protein with an Sm-like motif from Xanthomonas campestris, Acta Crystallogr Sect F Struct Biol Cryst Commun 63, 30-33.
5. Lin, Y. S., Hsu, W. L., Hwang, J. K., and Li, W. H. (2007) Proportion of solvent-exposed amino acids in a protein and rate of protein evolution, Mol Biol Evol 24, 1005-1011.
6. Su, E. C., Chiu, H. S., Lo, A., Hwang, J. K., Sung, T. Y., and Hsu, W. L. (2007) Protein subcellular localization prediction based on compartment-specific features and structure conservation, BMC Bioinformatics 8, 330.

 

Collaborative Research - 2008

1. Cheng, M. C., Liao, D. L., Hsiung, C. A., Chen, C. Y., Liao, Y. C., and Chen, C. H. (2008) Chronic treatment with aripiprazole induces differential gene expression in the rat frontal cortex, Int J Neuropsychopharmacol 11, 207-216.
2. Huang, J. W., King, C. C., and Yang, J. M. (2009) Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses, BMC Bioinformatics 10 Suppl 1, S41.
3. Yang, M. C., Guan, H. H., Liu, M. Y., Lin, Y. H., Yang, J. M., Chen, W. L., Chen, C. J., and Mao, S. J. (2008) Crystal structure of a secondary vitamin D3 binding site of milk beta-lactoglobulin, Proteins 71, 1197-1210.
4. Liao, C. J., Chin, K. H., Lin, C. H., Tsai, P. S., Lyu, P. C., Young, C. C., Wang, A. H., and Chou, S. H. (2008) Crystal structure of DFA0005 complexed with alpha-ketoglutarate: a novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus, Proteins 73, 362-371.
5. Hwu, C. M., Hsiung, C. A., Wu, K. D., Lee, W. J., Shih, K. C., Grove, J., Chen, Y. D., Rodriguez, B. L., and Curb, J. D. (2008) Diagnosis of insulin resistance in hypertensive patients by the metabolic syndrome: AHA vs. IDF definitions, Int J Clin Pract 62, 1441-1446.
6. Lo, A., Chiu, H. S., Sung, T. Y., Lyu, P. C., and Hsu, W. L. (2008) Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function, J Proteome Res 7, 487-496.
7. Liang, H., Lin, Y. S., and Li, W. H. (2008) Fast evolution of core promoters in primate genomes, Mol Biol Evol 25, 1239-1244.
8. Liu, P. H., Jiang, Y. D., Chen, W. J., Chang, C. C., Lee, T. C., Sun, H. S., and Chuang, L. M. (2008) Genetic and environmental influences on adiponectin, leptin, and BMI among adolescents in Taiwan: a multivariate twin/sibling analysis, Twin Res Hum Genet 11, 495-504.
9. Hsu, S. D., Chu, C. H., Tsou, A. P., Chen, S. J., Chen, H. C., Hsu, P. W., Wong, Y. H., Chen, Y. H., Chen, G. H., and Huang, H. D. (2008) miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes, Nucleic Acids Res 36, D165-169.
10. Yang, Y. F., Chou, M. Y., Fan, C. Y., Chen, S. F., Lyu, P. C., Liu, C. C., and Tseng, T. L. (2008) The possible interaction of CDA14 and protein elongation factor 1alpha, Biochim Biophys Acta 1784, 312-318.
11. Cheng, C. W., Su, E. C., Hwang, J. K., Sung, T. Y., and Hsu, W. L. (2008) Predicting RNA-binding sites of proteins using support vector machines and evolutionary information, BMC Bioinformatics 9 Suppl 12, S6.
12. Hsu, C., Hsiung, C. A., Su, I. J., Hwang, W. S., Wang, M. C., Lin, S. F., Lin, T. H., Hsiao, H. H., Young, J. H., Chang, M. C., Liao, Y. M., Li, C. C., Wu, H. B., Tien, H. F., Chao, T. Y., Liu, T. W., Cheng, A. L., and Chen, P. J. (2008) A revisit of prophylactic lamivudine for chemotherapy-associated hepatitis B reactivation in non-Hodgkin's lymphoma: a randomized trial, Hepatology 47, 844-853.
13. Chang, T. H., Horng, J. T., and Huang, H. D. (2008) RNALogo: a new approach to display structural RNA alignment, Nucleic Acids Res 36, W91-96.
14. Hsiao, C. J., Li, T. K., Chan, Y. L., Hsin, L. W., Liao, C. H., Lee, C. H., Lyu, P. C., and Guh, J. H. (2008) WRC-213, an l-methionine-conjugated mitoxantrone derivative, displays anticancer activity with reduced cardiotoxicity and drug resistance: identification of topoisomerase II inhibition and apoptotic machinery in prostate cancers, Biochem Pharmacol 75, 847-856.
15. MC. Yang, HH. Guan, JM. Yang, CN. Ko, MY. Liu, YH. Lin, CJ. Chen, and Simon JT Mao. (2008) Rational Design for Crystallization of β-Lactoglobulin and Vitamin D3 Complex: Revealing a Secondary Binding Site, Cryst. Growth Des., 8(12):4268–4276.

 

Collaborative Research - 2009

1. Huang, J. W., King, C. C., and Yang, J. M. (2009) Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses, BMC Bioinformatics 10 Suppl 1, S41.
2. Liu, S. C., Jen, Y. M., Jiang, S. S., Chang, J. L., Hsiung, C. A., Wang, C. H., and Juang, J. L. (2009) G(alpha)12-mediated pathway promotes invasiveness of nasopharyngeal carcinoma by modulating actin cytoskeleton reorganization, Cancer Res 69, 6122-6130.
3. Chiang, Y. K., Kuo, C. C., Wu, Y. S., Chen, C. T., Coumar, M. S., Wu, J. S., Hsieh, H. P., Chang, C. Y., Jseng, H. Y., Wu, M. H., Leou, J. S., Song, J. S., Chang, J. Y., Lyu, P. C., Chao, Y. S., and Wu, S. Y. (2009) Generation of ligand-based pharmacophore model and virtual screening for identification of novel tubulin inhibitors with potent anticancer activity, J Med Chem 52, 4221-4233.
4. Chang, C. H., Hsiao, C. F., Chang, G. C., Tsai, Y. H., Chen, Y. M., Huang, M. S., Su, W. C., Hsieh, W. S., Yang, P. C., Chen, C. J., and Hsiung, C. A. (2009) Interactive effect of cigarette smoking with human 8-oxoguanine DNA N-glycosylase 1 (hOGG1) polymorphisms on the risk of lung cancer: a case-control study in Taiwan, Am J Epidemiol 170, 695-702.
5. Tsai, W. C., Hsu, P. W., Lai, T. C., Chau, G. Y., Lin, C. W., Chen, C. M., Lin, C. D., Liao, Y. L., Wang, J. L., Chau, Y. P., Hsu, M. T., Hsiao, M., Huang, H. D., and Tsou, A. P. (2009) MicroRNA-122, a tumor suppressor microRNA that regulates intrahepatic metastasis of hepatocellular carcinoma, Hepatology 49, 1571-1582.
6. Lo, A., Chiu, Y. Y., Rodland, E. A., Lyu, P. C., Sung, T. Y., and Hsu, W. L. (2009) Predicting helix-helix interactions from residue contacts in membrane proteins, Bioinformatics 25, 996-1003.
7. Ku, T., Lu, P., Chan, C., Wang, T., Lai, S., Lyu, P., and Hsiao, N. (2009) Predicting melting temperature directly from protein sequences, Comput Biol Chem 33, 445-450.

 

Collaborative Research - 2010

1. K.-H. Chin, Y.-C. Lee, Z.-L. Tu, C.-H. Chen, Y.-H. Tseng, J.-M. Yang, R. P. Ryan, Y. McCarthy, J. M. Dow, A. H.-J. Wang, and S.-H. Chou "The c-AMP receptor-like protein clp is a novel c-di-gmp receptor linking cell-cell signaling to virulence gene expression in xanthomonas campestris," Journal of Molecular Biology, pp. 646–662, 2010.(IF: 3.871)
2. Huang HL, Hsing HW, Lai TC, Chen YW, Lee TR, Chan HT, Lyu PC, Wu CL, Lu YC, Lin ST, Lin CW, Lai CH, Chang HT, Chou HC, Chan HL. Trypsin-induced proteome alteration during cell subculture in mammalian cells. J Biomed Sci. 2010 May 11;17:36.
3. Chen JC, Uang BJ, Lyu PC, Chang JY, Liu KJ, Kuo CC, Hsieh HP, Wang HC, Cheng CS, Chang YH, Chang MD, Chang WS, Lin CC. Design and Synthesis of alpha-Ketoamides as Cathepsin S Inhibitors with Potential Applications against Tumor Invasion and Angiogenesis. J Med Chem. 2010 Jun 10;53(11):4545-9.
4. Tseng HC, Lyu PC, Lin WC. Nuclear localization of orphan receptor protein kinase (Ror1) is mediated through the juxtamembrane domain. BMC Cell Biol. 2010 Jun 30;11:48.
5. Chen JC, Uang BJ, Lyu PC, Chang JY, Liu KJ, Kuo CC, Hsieh HP, Wang HC, Cheng CS, Chang YH, Chang MD, Chang WS, Lin CC. Design and synthesis of alpha-ketoamides as cathepsin S inhibitors with potential applications against tumor invasion and angiogenesis. J Med Chem. 2010 Jun 10;53(11):4545-9.
6. Chou HC, Chen YW, Lee TR, Wu FS, Chan HT, Lyu PC, Timms JF, Chan HL. Proteomics study of oxidative stress and Src kinase inhibition in H9C2 cardiomyocytes: a cell model of heart ischemia-reperfusion injury and treatment. Free Radic Biol Med. 2010 Jul 1;49(1):96-108.
7. Ho MR, Lou YC, Wei SY, Luo SC, Lin WC, Lyu PC, Chen C. Human RegIV protein adopts a typical C-type lectin fold but binds mannan with two calcium-independent sites. J Mol Biol. 2010 Oct 1;402(4):682-9Epub 2010 Aug 6.
8. Lee TS, Pan CC, Peng CC, Kou YR, Chen CY, Ching LC, Tsai TH, Chen SF, Lyu PC, Shyue SK. Anti-atherogenic effect of berberine on LXRalpha-ABCA1-dependent cholesterol efflux in macrophages. J Cell Biochem. 2010 Sep 1;111(1):104-10.
9. Peng YH, Coumar MS, Leou JS, Wu JS, Shiao HY, Lin CH, Lin WH, Lien TW, Chen X, Hsu JT, Chao YS, Huang CF, Lyu PC, Hsieh HP, Wu SY. Structural basis for the improved potency of peroxisome proliferator-activated receptor (PPAR) agonists. ChemMedChem. 2010 Oct 4;5(10):1707-16.
10. Chu CH, Lo WC, Wang HW, Hsu YC, Hwang JK, Lyu PC, Pai TW, Tang CY. Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques. PLoS One. 2010 Oct 14;5(10):e13361.
11. Lin CJ, Lai HC, Wang KH, Hsiung CA, Liu HW, Ding DC, Hsieh CY, Chu TY. “Testing for methylated PCDH10 or WT1 is superior to the HPV test in detecting severe neoplasms (CIN3 or greater) in the triage of ASC-US smear results.” Am J Obstet Gynecol. 2011 Jan;204(1):21.e1-Epub 2010 Sep 15.
12. Lin YM, Tsai CC, Chung CL, Chen PR, Sunny Sun H, Tsai SJ, Huang BM. 2010. Fibroblast growth factor 9 stimulates steroidogenesis in postnatal Leydig cells. Int J Androl. 33(3):545-53.
13. Tzu-Ling Tseng, Wei-Chung Lai, Ting Jian, Chuan Li, H. S. Sun, Tzong-Der Way, Jia-Ching Shieh, 2010. Affinity purification of Candida albicans CaCdc4-associated proteins reveals the presence of novel proteins involved in morphogenesis. Biochem Biophys Res Commun. 23;395(1):152-7..
14. Shu-Huei Hsiao; Kuan-Der Lee; Chia-Chen Hsu; Min-Jen Tseng; Victor Jin; Wei-Sheng Sun; Yi-Chen Hung; Kun-Tu Yeh; Pearlly Yan; Yen-Yu Lai; H. Sun; Yen-Jung Lu; Yu-Sun Chang; Shaw-Jenq Tsai; Tim Huang, and Yu-Wei Leu. 2010. DNA methylation of the Trip10 promoter accelerates mesenchymal stem cell lineage determination. Biochem Biophys Res Commun. 24;400(3):305-12

 

Collaborative Research - 2011

1. A proteome analysis of the tetracyanonickelate (II) responses in Klebsiella oxytoca. Chen WJ, Tang P, Hseu YC, Chen CC,Huang KY, Chen SC. Environmental Microbiology Reports. 2011. 3(1):106-111.
2. Antioxidant defense is one of the mechanisms by which mosquito cells survive dengue 2 viral infection. Chen TH, Tang P, Yang CF, Kao LH, Lo YP, Chuang CK, Shih YT, Chen WJ. Virology. 2011. 1.410(2):410-7.
3. Involvement of the GP63 protease in infection of Trichomonas vaginalis. Ma L, Meng Q, Cheng W, Sung Y, Tang P, Hu S, Yu J. Parasitol Res. 2011. 109(1):71-79.
4. A transcriptomic study on the pepsin-activated infective larvae of Angiostrongylus cantonensis. Chang SH, Tang P, Wang LC. Mol Biochem Parasitol. 2011. 179(1):47-50.
5. An evolutionary analysis of trypanosomatid GP63 proteases. Ma L, Chen K, Meng Q, Liu Q, Tang P, Hu S, Yu J. Parasitol Res. 2011. 109(4):1075-1084.
6. A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LTThiele I, Hyduke D, Steeb B, Fankam G, Douglas K. Allen, Susanna Bazzani, Pep Charusanti, Chen FC, Fleming RMT, Hsiung CA, De Keersmaecker SCJ, Liao YC, Marchal K, Mo ML, Ozdemir E, Raghunathan A, Reed JL, Shin SI, Sigurbjornsdottir S, Steinmann J, Sudarsan S, Swainston N, Thijs IM, Zengler K, Palsson BO, Adkins JN, and Bumann D. BMC Systems Biology 2011 05:08.
7. Prevalence and correlates of geriatric frailty in a northern Taiwan community. Chang CI, Chan DC, Kuo KN, Hsiung CA, Chen CY. J Formos Med Assoc. 2011. 110(4):247-57.
8. Testing for methylated PCDH10 or WT1 is superior to the HPV test in detecting severe neoplasms (CIN3 or greater) in the triage of ASC-US smear results. Lin CJ, Lai HC, Wang KH, Hsiung CA, Liu HW, Ding DC, Hsieh CY, Chu TY. Am J Obstet Gynecol. 2011. 204(1):21.e1-7.
9. Post-coital vaginal douching is risky for non-regression of low-grade squamous intraepithelial lesion of the cervix. Chu TY, Hsiung CA, Chen CA, Chou HH, Ho CM, Chien TY, Chang HJ, Chou CY, Liou JD, Kan YY, Hsieh CY. Gynecol Oncol. 2011. 120(3):449-53.
10. Epidermal growth factor receptor mutation status in stage I lung adenocarcinoma with different image patterns. Hsu KH, Chen KC, Yang TY, Yeh YC, Chou TY, Chen HY, Tsai CR, Chen CY, Hsu CP, Hsia JY, Chuang CY, Tsai YH, Chen KY, Huang MS, Su WC, Chen YM, Hsiung CA, Chang GC, Chen CJ, Yang PC. J Thorac Oncol. 2011. 6(6):1066-72.
11. EGFR L858R mutation and polymorphisms of genes related to estrogen biosynthesis and metabolism in never-smoking female lung adenocarcinoma patients. Yang SY, Yang TY, Chen KC, Li YJ, Hsu KH, Tsai CR, Chen CY, Hsu CP, Hsia JY, Chuang CY, Tsai YH, Chen KY, Huang MS, Su WC, Chen YM, Hsiung CA, Shen CY, Chang GC, Yang PC, Chen CJ. Cancer Res.2011. 17(8):2149-58.
12. Human infection with novel G3P[25] rotavirus strain in Taiwan. Wu FT, Banyai K, Huang JC, Wu HS, Chang FY, Hsiung CA, Huang YC, Lin JS, Hwang KP, Jiang B, Gentsch JR. Clinical Microbiology and Infection. 2011. 17(10):1570-73.
13. Diverse origin of P[19] rotaviruses in children with acute diarrhea in Taiwan: Detection of novel lineages of the G3, G5, and G9 VP7 genes. Wu FT, Banyai K, Huang JC, Wu HS, Chang FY, Yang JY, Hsiung CA, Huang YC, Lin JS, Hwang KP, Jiang B, Gentsch JR. Journal of Medical Virology. 2011. 83(7):1279-87.
14. Severe gastroenteritis associated with G3P[9] rotavirus in Taiwan. Hwang KP, Huang YC, Banyai K, Wu HS, Chang FY, Yang DC, Hsiung CA, Lin JS, Jiang B, Gentsch JR, Wu FT. Infection. 2011. 39(3):271-275.
15. A novel RING finger protein, Znf179, modulates cell cycle exit and neuronal differentiation of P19 embryonal carcinoma cells. Pao PC, Huang NK, Liu YW, Yeh SH, Lin ST, Hsieh CP, Huang AM, Huang HS, Tseng JT, Chang WC, Lee YC. Cell Death Differ. 2011. 18(11): 1791–1804.
16. Targeted methylation of two tumor suppressor genes is sufficient to transform mesenchymal stem cells into cancer stem/initiating cells. I-Wen Teng, Pei-Chi Hou, Kuan-Der Lee, Pei-Yi Chu, Kun-Tu Yeh, Victor Jin, Min-Jen Tseng, Shaw-Jenq Tsai, Yu-Sun Chang, Chi-Sheng Wu, H. Sunny Sun, Kuen-daw Tsai, Long-Bin Jeng, Kenneth Nephew, Tim Huang, Shu-Huei Hsiao, and Yu-Wei Leu. .Cancer Research. 2011. 71(13):4653-4663
17. Translational and transcriptional control of Sp1 against ischaemia through a hydrogen peroxide-activated internal ribosomal entry site pathway. Yeh SH, Yang WB, Gean PW, Hsu CY, Tseng JT, Su TP, Chang WC, Hung JJ. Nucleic Acids Res. 2011. 39(13),5412-5423.
18. CCAAT/enhancer binding protein delta mediates TNFalpha-induced aurora kinase C transcription and promotes genomic instability. Wu SR, Li CF, Hung LY, Huang AM, Tseng JT, Tsou JH, Wang JM.
19. J Biol Chem. 2011. 286(33),28662-28670.
20. Suppression of TG-interacting factor sensitizes arsenic trioxide-induced apoptosis in human hepatocellular carcinoma cells. Liu ZM, Tseng JT, Hong DY, Huang HS. Biochem J. 2011. 438(2),349-358.
21. Using unsupervised patterns toextract gene regulation relationships for network construction. Tang YT, Li SJ, Kao HY, Tsai SJ, Wang HC. Plos One. 2011. doi:10.1371/journal.pone.0019636(5):e19633.
22. HuR binding to AU-rich elements present in the 3' untranslated region of Classical swine fever virus.
23. Nadar M, Chan MY, Huang SW, Huang CC, Tseng JT, Tsai CH. Virol J. Jul 2011. 8(1):340.
24. Interleukin-6 as an Early Chronic Inflammatory Marker in Polycystic Ovary Syndrome with Insulin Receptor Substrate-2 Polymorphism. Lin YS, Tsai SJ, Lin MW, Yang CT, Huang MF, Wu MH. Am J Reprod Immunol. 2011. 0.1111/j.1600-0897.2011. 1.01059.x. 66(6): 527–533
25. A semi-supervised, weighted pattern-learning approach for extraction of gene regulation relationships from scientific literature. Tang YT, Kao HY, Tsai SJ, Wang HC. Int J Data Min Bioinform. 2011. (Accepted)
26. Caffeic Acid Phenethyl Ester Causes p21Cip induction, Akt signaling reduction, and growth inhibition in PC-3 Human Prostate Cancer Cells. Hui-Ping Lin, Shih Sheng Jiang, Chih-Pin Chuu. Plos One. 2011. 7(2):e31286.
27. Gene expression profiling suggests a pathological role of human bone marrow-derived mesenchymal stem cells in aging-related skeletal diseases. Jiang SS, Chen CH, Tseng KY, Tsai FY, Wang MJ, Chang IS, Lin JL, Lin S. Aging. 2011. 3(7),672-684.

 

Collaborative Research - 2012

1. "The database of chromosome imbalance regions and genes resided in. Lo, F.Y., Chang, J.W., Chang, I.S., Chen, Y.J., Hsu, H.S., Huang, S.F., Tsai, F.Y., Jiang, S.S., Kanteti, R., Nandi, S., Salgia, R., Wang, Y.C. BMC Cancer. 2012. 12(1): 235-.
2. Molecular profiling of prostatic acinar morphogenesis identifies PDCD4 and KLF6 as tissue architecture-specific prognostic markers in prostate cancer. Li, CR, Su, JJ, Wang, WY, Lee, MT, Wang, TY, Jiang, KY, Li, CF, Hsu, JM, Chen, CK, Chen, M, Jiang, SS, Weaver, VM, Tsai, KK. American Journal of Pathology. 2012. In press.
3. Proteomic analysis of proteins responsible for the development of doxorubicin resistance in human uterine cancer cells. Lin ST, Chou HC, Chang SJ, Chen YW, Lyu PC, Wang WC, Chang MD, Chan HL. J Proteomics. 2012. 75(18): 5822-5847.
4. Placenta proteome analysis from Down syndrome pregnancies for biomarker discovery. Chen CP, Chen YH, Chern SR, Chang SJ, Tsai TL, Li SH, Chou HC, Lo YW, Lyu PC, Chan HL. Mol Biosyst. 2012. 8(9): 2360-2372.
5. Photofrin binds to procaspase-3 and mediates photodynamic treatment-triggered methionine oxidation and inactivation of procaspase-3. Hsieh YJ, Chien KY, Lin SY, Sabu S, Hsu RM, Chi LM, Lyu PC, Yu JS. Cell Death Dis.. 2012. 3(): e347.
6. Proteomic and redox-proteomic analysis of berberine-induced cytotoxicity in breast cancer cells. Chou HC, Lu YC, Cheng CS, Chen YW, Lyu PC, Lin CW, Timms JF, Chan HL. J Proteomics. 2012. 75(11): 3158-3176.
7. Substitution of asparagine 76 by a tyrosine residue induces domain swapping in Helicobacter pylori phosphopantetheine adenylyltransferase. Cheng CS, Chen WT, Chen YW, Chen CH, Luo YC, Lyu PC, Yin HS. J Biomol Struct Dyn. 2012. 30(4): 488-502.
8. Acquisition of hydrogenosomal presequences: examples from Trichomonas vaginalis. Yu DL, Wang Y, Fang X, Hu SN, Tang P and Fu Y*. FEMS Microbiology Letters. 2012. 330(2): 127-131.
9. Complete genome and transcriptomes of Streptococcus parasanguinis FW213: phylogenic relations and potential virulence mechanisms.. Geng J, Chiu CH, Tang P, ChenY, Shieh HR, Hu SN, and Chen YM*. PLoS ONE. 2012. 7(4): e34769-.
10. Replication of Genome-Wide Association Signals of Type 2 Diabetes in Han Chinese in a Prospctive Cohort. Chang YC, Chiu YF, Liu PH, Shih KC, Lin MW, Sheu WH, Quertermous T, Curb JD, Hsiung CA, Lee WJ, Lee PC, Chen YT, Chuang LM. Clinical Endocrinology (Oxf). 2012. 76(3): 365-372.
11. A Bayesian measurement error model for two-channel cell-based RNAi data with replicates.. Chen CH, Su WC, Chen CY, Huang JY, Tsai FY, Wang WC, Hsiung CA, Jeng KS, Chang IS.. Annals of Applied Statistics. 2012. 6(1): 356-382.
12. R432 is a key residue for the multiple functions of Ndt80p in Candida albicans.. Yang YL, Wang CW, Leaw SN, Chang TP, Wang IC, Chen CG, Fan JC, Tseng KY, Huang SH, Chen CY, Hsiao TY, Hsiung CA, Chen CT, Hsiao CD, Lo HJ. . Cell Mol Life Sci.. 2012. 69(6): 1011-1023.
13. Putative Canine Origin of Rotavirus Strain Detected in a Child with Diarrhea, Taiwan.. Wu FT, Bányai K, Lin JS, Wu HS, Hsiung CA, Huang YC, Hwang KP, Jiang B, Gentsch JR.. Vector-Borne and Zoonotic Diseases. 2012. 12(2): 170-173.
14. Genetic variant in TP63 on locus 3q28 is associated with risk of lung adenocarcinoma among never-smoking females in Asia.. Hosgood HD 3rd, Wang WC, Hong YC, Wang JC, Chen K, Chang IS, Chen CJ, Lu D, Yin Z, Wu C, Zheng W, Qian B, Park JY, Kim YH, Chatterjee N, Chen Y, Chang GC, Hsiao CF, Yeager M, Tsai YH, Wei H, Kim YT, Wu W, Zhao Z, Chow WH, Zhu X, Lo YL, Sung SW, Chen KY, Yuenger J, Kim JH, Huang L, Chen YH, Gao YT, Kim JH, Huang MS, Jung TH, Caporaso N, Zhao X, Huan Z, Yu D, Kim CH, Su WC, Shu XO, Kim IS, Bassig B, Chen YM, Cha SI, Tan W, Chen H, Yang TY, Sung JS, Wang CL, Li X, Park KH, Yu CJ, Ryu JS, Xiang Y, Hutchinson A, Kim JS, Cai Q, Landi MT, Lee KM, Hung JY, Park JY, Tucker M, Lin CC, Ren Y, Perng RP, Chen CY, Jin L, Chen KC, Li YJ, Chiu YF, Tsai FY, Yang PC, Fraumeni JF Jr, Seow A, Lin D, Zhou B, Chanock S, Hsiung CA, Rothman N, Lan Q.. Hum Genet.. 2012. 131(7): 1197-1203.
15. Common ALDH2 genetic variants predict development of hypertension in the SAPPHIRe prospective cohort: Gene-environmental interaction with alcohol consumption.  Chang, YC;Chiu, YF;Lee, IT;Ho, LT;Hung, YJ;Hsiung, CA;Quertermous, T;Donlon, T;Lee, WJ;Lee, PC;Chen, CH;Mochly-Rosen, D;Chuang, LM. BMC Cardiovascular Disorders. 2012. 12(): 58.
16. EGFR exon 19 in-frame deletion and polymorphisms of DNA repair genes in never-smoking female lung adenocarcinoma patients. Yang, SY;Yang, TY;Li, YJ;Chen, KC;Liao, KM;Hsu, KH;Tsai, CR;Chen, CY;Hsu, CP;Hsia, JY;Chuang, CY;Tsai, YH;Chen, KY;Huang, MS;Su, WC;Chen, YM;Hsiung, CA;Shen, CY;Chang, GC;Yang, PC;Chen, CJ. International Journal of Cancer. 2012. 132(2): 449-458.
17. Identification of porcine rotavirus-like genotype P[6] strains in Taiwanese children. Hwang KP, Wu FT, Bányai K, Wu HS, Yang DC, Huang YC, Lin JS, Hsiung CA, Huang JC, Jiang B, Gentsch JR. Journal of Medical Microbiology. 2012. 61(PT7): 990-997.
18. Transcriptomes of mouse olfactory epithelium reveal sexual differences in odorant detection. Shiao, MS;Chang, YF;Liao, BY;Ching, YH;Jade Lu, MY;Chen, SM;Li, WH. Genome Biology and Evolution. 2012. 4(5): 703-712.
19. LDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs. Wang, MC;Chen, FC;Chen, YZ;Huang, YT;Chuang, TJ. BMC Research Notes. 2012. 5(1):212(1): 212-.
20. Involvement of transcriptional regulator Ndt80 in stress responses of Candida albicans. Yang, YL;Wu, SY;Hsiung, CA;Chen, CT;Hsiao, CD;Lo, HJ. Mycoses. 2012. 55(Suppl. S4): 131-132.
21. Metagenomic analysis reveals a functional signature for biomass degradation by cecal microbiota in the leaf-eating flying squirrel (Petaurista alborufus lena). Hsiao-Pei Lu, Yu-bin Wang, Shiao-Wei Huang, Chung-Yen Lin, Martin Wu, Chih-hao Hsieh and Hon-Tsen Yu. BMC Genomics. 2012. 13(): 466-.
22. Interplay of RsbM and RsbK controls the theta B activity of Bacillus cereus. Lei-Chin Chen, Jung-Chi Chen, Jwu-Ching Shu, Chien-Yen Chen, Ssu-Ching Chen, Shu-Hwa Chen, Chun-Yen-Lin, Chi-Yu Lu, and Chien-Cheng Chen. Environmental Microbiology. 2012. 14(10): 2788-2799.
23. EST and transcriptome analysis of cephalochordate amphioxus - past, present, and future. Wang, Y.B., Chen, S. H., Lin, C.Y. and Yu, J.K.. Brief in Functional Genomics. 2012. 11(2): 96-106.
24. Risk factors for salmonella gastroenteritis in children less than five years of age in taiwan. Chen CJ, Wu FT, Hsiung CA, Chang WC, Wu HS, Wu CY, Lin JS, Huang FC, Huang YC.. Pediatric Infectious Disease Journal. 2012. 31(12): E239-E243.
25. COUP-TFII inhibits TGF-β-induced growth barrier to promote prostate tumorigenesis. J Qin, SP Wu, F Dai, X Xie, CM Cheng, C J Creighton, A Frolov, Gustavo Ayala4, X Lin, XH Feng, MM Ittmann, SJ Tsai, MJ Tsai, S Y Tsai. Nature. 2012. doi:10.1038/nature11674.
26. A single-nucleotide polymorphism of the DAZL gene promoter confers susceptibility to spermatogenic failure in the Taiwanese Han.. Teng YN, Chang YP, Tseng JT, Kuo PH, Lee IW, Lee MS, Kuo PL..  Hum Reprod . 2012. 27(9): 2857-2865.

 

Collaborative Research - 2013

1. Disease-Related Growth Factor and Embryonic Signaling Pathways Modulate an Enhancer of TCF21 Expression at the 6q23.2 Coronary Heart Disease Locus. Clint L. Miller, D. Ryan Anderson, Ramendra K. Kundu, Azad Raiesdana, Sylvia T. Nürnberg, Roxanne Diaz, Karen Cheng, Nicholas J. Leeper, Chung-Hsing Chen, I-Shou Chang, Eric E. Schadt, Chao Agnes Hsiung, Themistocles L. Assimes, Thomas Quertermous. PLOS Genetics . 2013. 9(7): e1003652-e1003652.
2. Pentacene organic thin-film transistors with solution-based gelatin dielectric.. Lung-Kai Mao, Jenn-Chang Hwang, Ting-Hao Chang, Chao-Ying Hsieh, Li-Shiuan Tsai, Yu-Lun Chueh, Shawn S.H. Hsu, Ping-Chiang Lyu, Ta-Jo Liu. Organic Electronics. 2013. 14(): 1170-1176.
3. Redox-proteomic analysis of doxorubicin resistance-induced altered thiol activity in uterine carcinoma. Szu-Ting Lin, Yi-Wen Lo, Shing-Jyh Chang, Wen-Ching Wang, Margaret Dah-Tsyr Chang, Ping-Chiang Lyu, Yi-Wen Chen, Hsiu-Chuan Chou, Hong-Lin Chan. Journal of Pharmaceutical and Biomedical Analysis. 2013. 78-79(): 1-8.
4. COL11A1 Promotes Tumor Progression, and Predicts Poor Clinical Outcome in Ovarian Cancer.  Y.H. Wu, T.H. Chang, Y.F. Huang, H.D. Huang* and C.Y. Chou. Oncogene. 2013. doi: 10.1038/onc.2013.307.
5. Computational Analysis of KRAS Mutations: Implications for Different Effects on the KRAS p.G12D and p.G13D Mutations. Chen CC, Er TK, Liu YY, Hwang JK, Barrio MJ, Rodrigo M, Garcia-Toro E, Herreros-Villanueva M. PLoS One. 2013. 8(2): e55793-.
6. Fungal small RNAs as novel effectors to suppress plant immunity by hijacking the host RNAi machinery.  A. Weiberg, M. Wang, F.M. Lin, H.W. Zhao, Z.H. Zhang, I. Kaloshian, H.D. Huang, and H. Jin. Science. 2013. 342(6154): 118-123.
7. Histone Demethylase RBP2 Promotes Lung Tumorigenesis and Cancer Metastasis.  Y.C. Tseng, C.F. Lee, Y.S. Li, Y.R. Chen, P.W. Hsiao, M.Y. Chan, F.M. Lin, H.D. Huang, Y.T. Chen, Y.M. Jeng, C.H. Hsu, Q. Yan, M.D. Tsai, and L.J. Juan. Cancer Research. 2013. 73(15): 4711-4721.
8. Sterol Regulatory Element Binding Protein 2 Activation of NLRP3 Inflammasome in Endothelium Mediates Hemodynamic-Induced Atherosclerosis Susceptibility. H. Xiao, M. Lu, T.Y. Lin, Z. Chen, G. Chen, W.C. Wang, T. Marin, T.P. Shentu, L. Wen, B. Gongol, W. Sun, X. Liang, J. Chen, H.D. Huang, J.H. Pedra, D.A. Johnson, and J.Y. Shyy. Circulation. 2013. 128(6): 632-642.
9. YjcC, a c-di GMP phosphodiesterase protein, regulates the oxidative stress response and virulence of Klebsiella pneumoniae CG43.  C.J. Huang, Z.C. Wang, H.Y. Huang, H.D. Huang, and H.L. Peng. PLoS One. 2013. 8(7): e66740-.
10. AQU-1, a chromosomal class C β-lactamase, among clinical Aeromonas dhakensis isolates: distribution and clinical significance.. Chi-Jung Wua, Hsuan-Chen Wang, Po-Lin Chen, Ming-Chung Chang, H. Sunny Sun, Pei-Hsin Chou, Wen-Chien Ko.. International Journal of Antimicrobial Agents. 2013. 42(5): 456-461.
11. Association of aberrant expression of sex-determining gene fibroblast growth factor 9 with Sertoli cell-only syndrome.. Chia-Ling Chung, M.Sc., Chun-Wun Lu, Ph.D., Yu-Sheng Cheng, M.D., Ching-Yi Lin, M.Sc., H. Sunny Sun, Ph.D., Yung-Ming Lin, M.D.. Fertil Steril. 2013. S0015-0282(13): 02949-X-.
12. Atrial identity is determined by a COUP-TFII regulatory network.. SP Wu, CM Cheng, W Chen, T Wang, JL Respress, S Ather, RB Lanz, SJ Tsai, XHT Wehrens, MJ Tsai, and SY Tsai. Developmental Cell. 2013. 25(4): 417-426.
13. CCAAT/enhancer binding protein δ in macrophages contributes to immunosuppression and inhibits phagocytosis in nasopharyngeal carcinoma.. Hsiao YW, Li CF, Chi JY, Tseng JT, Chang Y, Hsu LJ, Lee CH, Chang TH, Wang SM, Wang DD, Cheng HC, Wang JM.. Sci Signal. 2013. 16(284): ra59-ra59.
14. miR-196a Ameliorates Phenotypes of Huntington Disease in Cell, Transgenic Mouse, and Induced Pluripotent Stem Cell Models.. Pei-Hsun Cheng, Chia-Ling Li, Yu-Fan Chang, Shaw-Jeng Tsai, Yen-Yu Lai, Anthony W.S. Chan, Chuan-Mu Chen, Shang-Hsun Yang. Am J Hum Genet. 2013. 93(2): 306-312.
15. MPT0B098: A Novel Microtubule Inhibitor that Destabilizes the HIF-1α mRNA through Decreasing Nuclear-cytoplasmic Translocation of RNA Binding Protein, HuR. Mol Cancer Ther.. Cheng YC, Liou JP, Kuo CC, Lai WY, Shih KH, Chang CY, Pan WY, Tseng JT, Chang JY. . Molecular Cancer Therapeutics. 2013. doi: 10.1158/1535-7163.MCT-12-0778(): doi: 10.1158/1535-7163.MCT-12-0778-doi: 10.1158/1535-7163.MCT-12-0778.
16. Non-mosaic uniparental trisomy 16 presenting with asplenia syndrome and placental abruption: a case report and literature review.. Mei-Tsz Su, Yu-Ling Liang, Jian-Chin Chen, H. Sunny Sun, Fong-Ming Chang, Pao-Lin Kuo. Eur J Med Genet. 2013. 56(4): 197-201.
17. Pb2+ induces gastrin gene expression by extracellular signal-regulated kinases 1/2 and transcription factor activator protein 1 in human gastric carcinoma cells.. Chan CP, Tsai YT, Chen YL, Hsu YW, Tseng JT, Chuang HY, Shiurba R, Lee MH, Wang JY, Chang WC.. Environmental Toxicology. 2013. DOI: 10.1002/tox.21878.

 

Collaborative Research - 2014

1. Prognostic CpG methylation biomarkers identified by methylation array in esophageal squamous cell carcinoma patients.. Kuo, I.Y., Chang, J.M., Jiang, S.S., Chen, C.H., Chang, I.S., Sheu, B.S., Lu, P.J., Chang, W.L., Lai, W.W., Wang, Y.C.. International Journal of Medical Sciences. 2014. 11(8): 779-787.
2. Downregulated miR-329 and miR-410 promote the proliferation and invasion of oral squamous cell carcinoma by targeting Wnt-7b. Shiah, SG;Hsiao, JR;Chang, WM;Chen, YW;Jin, YT;Wong, TY;Huang, JS;Tsai, ST;Hsu, YM;Chou, ST;Yen, YC;Jiang, SS;Shieh, YS;Chang, IS;Hsiao, M;Chang, JY. Cancer Research. 2014. 74(24): 7560-7572.
3. A quantitative high-resolution genetic profile rapidly identifies sequence determinants of viral fitness and drug sensitivity. Qi H, Olson CA, Wu NC, Ke R, Loverdo C, Chu V, Truong S, Remenyi R, Chen Z, Du Y, Su SY, Al-Mawsawi LQ, Wu TT, Chen SH, Lin CY, Zhong W, Lloyd-Smith JO, Sun R. PLoS Pathogens. 2014. 10(4): e1004064-.
4. High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution virus hemagglutinin gene at single-nucleotide resolution. Nicholas C. Wu, Arthur P. Young, Laith Q. Al-Mawsawi, C. Anders Olson, Jun Feng, Hangfei Qi, Shu-Hwa Chen, I.-Hsuan Lu, Chung-Yen Lin, Robert G. Chin, Harding H. Luan, Nguyen Nguyen, Stanley F. Nelson, Xinmin Li, Ting-Ting Wu & Ren Sun. Scientific Reports. 2014. 4(): 4942-."
5. Multiple nonglycemic genomic loci are newly associated with blood level of glycated hemoglobin in East Asians. Chen, P;Takeuchi, F;Lee, JY;Li, H;Wu, JY;Liang, J;Long, J;Tabara, Y;Goodarzi, MO;Pereira, MA;Kim, YJ;Go, MJ;Stram, DO;Vithana, E;Khor, CC;Liu, J;Liao, J;Ye, X;Wang, Y;Lu, L;Young, TL;Lee, J;Thai, AC;Cheng, CY;van Dam, RM;Friedlander, Y;Heng, CK;Koh, WP;Chen, CH;Chang, LC;Pan, WH;Qi, Q;Isono, M;Zheng, W;Cai, Q;Gao, Y;Yamamoto, K;Ohnaka, K;Takayanagi, R;Kita, Y;Ueshima, H;Hsiung, CA;Cui, J;Sheu, WH;Rotter, JI;Chen, YD;Hsu, C;Okada, Y;Kubo, M;Takahashi, A;Tanaka, T;van Rooij, FJ;Ganesh, SK;Huang, J;Huang, T;Yuan, J;Hwang, JY;Gross, MD;Assimes, TL;Miki, T;Shu, XO;Qi, L;Chen, YT;Lin, X;Aung, T;Wong, TY;Teo, YY;Kim, BJ;Kato, N;Tai, ES. Diabetes. 2014. 63(7): 2551-2562.
6. On the identification of potential regulatory variants within genome wide association candidate SNP sets. Chen, Cy;Chang, IS;Hsiung, CA;Wasserman, WW. BMC Medical Genomics. 2014. 7(): Article number 34-.
7. Attenuating the mortality risk of high serum uric acid: The role of physical activity underused. Chen, JH;Wen, CP;Wu, SB;Lan, JL;Tsai, MK;Tai, YP;Lee, JH;Hsu, CC;Tsao, CK;Wai, JP;Chiang, PH;Pan, WH;Hsiung, CA. Annals of the Rheumatic Diseases. 2014. Article in Press.
8. Assessing the relationship of evolutionary rates and functional variables by mixture estimating equations. Lin, PS;Chen, FC;Kuo, SF;Kung, YH. Statistics and Probability Letters. 2014. 94(): 248-256.
9. CloudDOE: A User-Friendly Tool for Deploying Hadoop Clouds and Analyzing High-Throughput Sequencing Data with MapReduce. Wei-Chun Chung, Chien-Chih Chen, Jan-Ming Ho, Chung-Yen Lin, Wen-Lian Hsu, Yu-Chun Wang, Der-Tsai Lee, Feipei Lai, Chih-Wei Huang and Yu-Jung Chang. PLoS One. 2014. 9(6): e98146-.
10. A Comprehensive Functional Map of the Hepatitis C Virus Genome Provides a Resource for Probing Viral Proteins). Roland Gilbert Remenyi , Hangfei Qi , Sheng-Yao Su , Zugen Chen , Nicholas C. Wu , Vaithilingaraja Arumugaswami , Shawna Truong , Virginia Chu , Tamar Stokelman , Hung-Hao Lo , C. Anders Olson ,Ting-Ting Wu , Shu-Hwa Chen , Chung-Yen Lin, Ren Sun. mBio. 2014. 5(5): e01469-14-.
11. cytoHubba: a Cytoscape Plug-in for Hub Object Analysis in Network Biology. Chia-Hao Chin, Shu-Hwa Chen, Hsin-Hung Wu, Chin-Wen Ho, Ming-Tat Ko *, and Chung-Yen Lin. BMC Systems Biology. 2014. 8(4): S11-.
12. Compartment-specific transcriptomics in a reef-building coral exposed to elevated temperatures. Mayfield, Anderson; Wang, Yu-Bin; Chen, Chii-Shiarng; Lin, Chung-Yen; Chen, Shu-Hwa. Molecular Ecology. 2014. 23(23): 5816-5830.
13. Meta-analysis of genome-wide association studies in East Asian-ancestry populations identifies four new loci for body mass index. Wen, W;Zheng, W;Okada, Y;Takeuchi, F;Tabara, Y;Hwang, JY;Dorajoo, R;Li, H;Tsai, FJ;Yang, X;He, J;Wu, Y;He, M;Zhang, Y;Liang, J;Guo, X;Sheu, WH;Delahanty, R;Kubo, M;Yamamoto, K;Ohkubo, T;Go, MJ;Liu, JJ;Gan, W;Chen, CC;Gao, Y;Li, S;Lee, NR;Wu, C;Zhou, X;Song, H;Yao, J;Lee, IT;Long, J;Tsunoda, T;Akiyama, K;Takashima, N;Cho, YS;Ong, RT;Lu, L;Chen, CH;Tan, A;Rice, TK;Adair, LS;Gui, L;Allison, M;Lee, WJ;Cai, Q;Isomura, M;Umemura, S;Kim, YJ;Seielstad, M;Hixson, J;Xiang, YB;Isono, M;Kim, BJ;Sim, X;Lu, W;Nabika, T;Lee, J;Lim, WY;Gao, YT;Takayanagi, R;Kang, DH;Wong, TY;Hsiung, CA;Wu, IC;Juang, JM;Shi, J;Choi, BY;Aung, T;Hu, F;Kim, MK;Wang, TD;Shin, MH;Ji, BT;Lee, YH;Young, TL;Shin, DH;Chun, BY;Cho, MC;Han, BG;Hwu, CM;Assimes, TL;Absher, D;Yan, X;Kim, E;Kuo, JZ;Kwon, S;Taylor, KD;Chen, YD;Rotter, JI;Qi, L;Zhu, D;Wu, T;Mohlke, KL;Gu, D, .;et al.. Human Molecular Genetics. 2014. 23(20): 5492-5504.
14. Molecular epidemiology of human G2P[4] rotaviruses in Taiwan, 2004-2011. Wu, FT;Banyai, K;Jiang, B;Wu, CY;Chen, HC;Feher, E;Huang, YC;Lin, JS;Huang, FC;Hsiung, CA;Huang, JC;Wu, HS. Infection, Genetics and Evolution. 2014. 2(28): 530-536.
15. High serum iron is associated with increased cancer risk. Wen, CP;Lee, JH;Tai, YP;Wen, C;Wu, SB;Tsai, MK;Hsieh, DP;Chiang, HC;Hsiung, CA;Hsu, CY;Wu, X. Cancer Research. 2014. 74(22): 6589-6597.
16. Analysis of non-separable spatiotemporal data with application to enterovirus study in Taiwan. Lin, PS;Hsiung, CA;Cheng, CW. Environmental and Ecological Statistics. 2014. 21(4): 733-750.
17. lncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome. W.L. Chan, H.D. Huang*, Chang JG. Comput Biol Chem.. 2014. In press.
18. The effects of actin cytoskeleton perturbation on keratin intermediate filament formation in mesenchymal stem/stromal cells.  T.H. Chang, H.D. Huang, W.K. Ong, Y.J. Fu, O.K. Lee, S. Chien, J.H. Ho. Biomaterials. 2014. 35(13): 3934-3944.
19. CRP represses the CRISPR/Cas system in Escherichia coli: evidence that endogenous CRISPR spacers impede phage P1 replication. C.D. Yang, Y.H. Chen, H.Y. Huang, H.D. Huang, C.P. Tseng*. Molecular Microbiology. 2014. 92(5): 1072-1091.
20. Investigating microRNA-target interaction-supported tissues in human cancer tissues based on miRNA and target gene expression profiling.. W.J. Hsieh, F.M. Lin, H.D. Huang*, H. Wang*. PLoS ONE. 2014. 9(7): e95697-.
21. RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals.. K.Y. Huang, H.Y. Wu, Y.J. Chen, C.T. Lu, M.G. Su, Y.C. Hsieh, C.M. Tsai, K.I. Lin, H.D. Huang, T.Y. Lee*, Y.J. Chen*. Database (Oxford). 2014. 2014(): bau034-.
22. Identification of Fungal Pathogens from 1 Clinical Specimens using Multi-locus PCR Coupled with Electrospray Ionization Mass Spectrometry.. Chi-Jung Wu, M.D.; Ya-Pin Chen; Hsuan-Chen Wang; Ih-Jen Su; Wen-Chien Ko; Jiann-Shiuh Chen; Chao-Neng Cheng; Nan-Yao Lee; H. Sunny Sun; Chia-Yu Chi; Tsai-Yun Chen.. Diagnostic Microbiology and Infectious Disease Diagn Microbiol Infect.. 2014. 78(2): 141-143.
23. Exploring the associations between genetic variants in genes encoding for subunits of calcium channel and subtypes of bipolar disorder.. Wen-Chi Jan, Shi-Yi Yang, Li-Chung Chuang, Ru-Band Lu, Ming-Kun Lu, H. S. Sun, Po-Hsiu Kuo.. J Affect Disord. 2014. 20(157): 80-6-.
24. Identification of novel loci for bipolar I disorder in a multi-stage genome-wide association study.. Kuo PH, Chuang LC, Liu JR, Liu CM, Huang MC, Lin SK, Sun HS, Hsieh MH, Hung H, Lu RB.. Progress in Neuro-Psychopharmacology & Biological Psychiatry.. 2014. (): 51:58-64-.
25. Rapid Identification of Bacteria and Candida Pathogens in Peritoneal Dialysis Effluent from Patients with Peritoneal Dialysis-Related Peritonitis Using Multilocus PCR Coupled with Electrospray Ionization Mass Spectrometry.. Yu-Tzu Chang, Hsuan-Chen Wang, Ming-Cheng Wang, An-Bang Wu, Junne-Ming Sung, H. Sunny Sun, Ih-Jen Su, Wei-Chih Kan, Chih-Chiang Chien, Jyh-Chang Hwang, Hsien-Yi Wang, Chin-Chung Tseng, and Chi-Jung Wu.. J Clin Microbiol. 2014. 52(4): 1217-1219.
26. Overexpression of Aurora-C interferes with the spindle checkpoint by promoting the degradation of Aurora-B.. Lin BW, Wang YC, Chang-Liao PY, Lin YJ, Yang ST, Tsou JH, Chang KC, Liu YW, Tseng JT, Lee CT, Lee JC, Hung LY.. Cell Death Dis.. 2014. 5:e1106..
27. Co-opting sulphur carrier proteins from primary pathways for 2-thiosugar biosynthesis.. Sasaki E, Zhang X, Sun HG, Lu MY, Liu T, Ou A, Li JY, Chen YH, Ealick SE, Liu HW.. Nature. 2014. (): doi:10.1038/nature13256-.
28. AlgaePath: comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae.. Zheng HQ, Chiang-Hsieh YF, Chien Chia-Hung, Hsu BK, Liu T, Chen CN, Chang WC.. BMC Genomics. 2014. Volume 15(): doi:10.1186/1471-2164-15-196-.
29. A semi–supervised, weighted pattern–learning approach for extraction of gene regulation relationships from scientific literature. Yi–Tsung Tang, Hung–Yu Kao, Shaw–Jenq Tsai, Hei–Chia Wang. International Journal of Data Mining and Bioinformatics. 2014. 9(4/2014): 401-416.

 

Collaborative Research - 2015

1. Prenatal exposure to phthalate ester and pubertal development in a birth cohort in central Taiwan: A 12-year follow-up study. Su, PH;Chang, CK;Lin, CY;Chen, HY;Liao, PC;Hsiung, CA;Chiang, HC;Wang, SL. Environmental Research. 2015. 136(): 324-330.
2. SeqSIMLA2: Simulating correlated quantitative traits accounting for shared environmental effects in user-specified pedigree structure. Chung, RH;Tsai, WY;Hsieh, CH;Hung, KY;Hsiung, CA;Hauser, ER. Genetic Epidemiology. 2015. 39(1): 20-24.
3. Identification of a Novel FN1-FGFR1 Genetic Fusion as a Frequent Event in Phosphaturic Mesenchymal Tumour. Jen-Chieh Lee,Yung-Ming Jeng, Sheng-Yao Su, Chen-Tu Wu, Keh-Sung Tsai, Cheng-Han Lee, Chung-Yen Lin, Jodi M. Carter, Jeng-Wen Huang, Shu-Hwa Chen, Shyang-Rong Shih, Adrián Mariño-Enríquez, Chih-Chih Chen, Andrew L. Folpe, Yih-Leong Chang and Cher-Wei Liang. The Journal of Pathology. 2015. 235(4): 539-545.
4. The novel white spot syndrome virus-induced gene, PmERP15, encodes an ER stress- responsive protein in black tiger shrimp, Penaeus monodon. Jiann-Horng Leu, Kuan-Fu Liu, Kuan-Yu Chen, Shu-Hwa Chen, Yu-Bin Wang, Chung-Yen Lin, Chu-Fang Lo. Developmental & Comparative Immunology. 2015. 49(2): 239-248.
5. The ability of bilirubin in identifying smokers with higher risk of lung cancer: A large cohort study in conjunction with global metabolomic profiling. Wen, CP;Zhang, F;Liang, D;Wen, C;Gu, J;Skinner, H;Chow, WH;Ye, Y;Pu, X;Hildebrandt, MAT;Huang, M;Chen, CH;Hsiung, CA;Tsai, MK;Tsao, CK;Lippman, SM;Wu, X. Clinical Cancer Research. 2015. 21(1): 193-200.
6. Combined association of chronic disease and low skeletal muscle mass with physical performance in older adults in the Sarcopenia and Translational Aging Research in Taiwan (START) study.  Li, CI;Li, TC;Lin, WY;Liu, CS;Hsu, CC;Hsiung, CA;Chen, CY;Huang, KC;Wu, CH;Wang, CY;Lin, CC;the Sarcopenia and Translational Aging Research in Taiwan (START) Team. BMC Geriatrics. 2015. 15(): Article number 11-.
7. Interactions between household air pollution and GWAS-identified lung cancer susceptibility markers in the Female Lung Cancer Consortium in Asia (FLCCA). Hosgood, HD;Song, MS;Hsiung, CA;Yin, ZH;Shu, XO;Wang, ZM;Chatterjee, N;Zheng, W;Caporaso, N;Burdette, L;Yeager, M;Berndt, SI;Landi, MT;Chen, CJ;Chang, GC;Hsiao, CF;Tsai, YH;Chien, LH;Chen, KY;Huang, MS;Su, WC;Chen, YM;Chen, CH;Yang, TY;Wang, CL;Hung, JY;Lin, CC;Perng, RP;Chen, CY;Chen, KC;Li, YJ;Yu, CJ;Chen, YS;Chen, YH;Tsai, FY;Kim, C;Seow, WJ;Bassig, BA;Wu, W;Guan, P;He, QC;Gao, YT;Cai, QY;Chow, WH;Xiang, YB;Lin, DX;Wu, C;Wu, YL;Shin, MH;Hong, YC;Matsuo, K;Chen, KX;Wong, MP;Lu, DR;Jin, L;Wang, JC;Seow, A;Wu, TC;Shen, HB;Fraumeni, JF;Yang, PC;Chang, IS;Zhou, BS;Chanock, SJ;Rothman, N;Lan, Q. Human Genetics. 2015. 134(3): 333-341.
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15. Genome Sequences of Three Helicobacter pylori Strains from Patients with Gastric Mucosa-Associated Lymphoid Tissue Lymphoma. Hsuan-Chen Wang, Feng-Chi Cheng, Ming-Shiang Wu, Hung-Yu Shu, H. Sunny Sun, Yu-Chun Wang, Ih-Jen Su, Chi-Jung Wu . Genome Announc. . 2015. 3(2): 2 e00229-15-.