Year Graduated: 2012

Student's Name Thesis Advisor(s) List of Published Papers During Study Time
**Equally Contributing Authors
* Corresponding Author(s)
Edward Hsuan-Cheng Shih
Dr. Ming-Jing Hwang
  1. Shih, E. S., Hwang, M. J., (2012). On the use of distance constraints in protein-protein docking computations. Proteins. 80, 194-205.
  2. Shaw, G. T. W., Shih, E. S. C., Chen, C.-H., Hwang, M.-J., (2011). Preservation of Ranking Order in the Expression of Human Housekeeping Genes. PLoS One. 6, e29314.
  3. Shih, E.S., Hwang, M.J., (2010). Non-sequential protein structure comparisons. Chapter 4, Sequence and Genome Analysis: Methods and Applications, edited by Zhongming Zhao, iConcept Press (invited review).
  4. Shih, E. S., Gan, R. C., Hwang, M. J., (2006). OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures. Nucleic Acids Res. 34, W95-8.
  5. Shih, E. S., Hwang, M. J., (2004). Alternative alignments from comparison of protein structures. Proteins. 56, 519-27.
  6. Shih, E. S., Hwang, M. J., (2003). Protein structure comparison by probability-based matching of secondary structure elements. Bioinformatics. 19, 735-41.
  7. Chen, L. Y., Lu, S. H., Shih, E. S., Hwang, M. J., (2002). Single nucleotide polymorphism mapping using genome-wide unique sequences. Genome Res. 12, 1106-11.
Mahalingam Rajasekaran
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Dr. Chinpan Chen
  1. M. Rajasekaran, Chen C. Structural Effect of the L16Q, K50E, and R53P Mutations on Homeodomain of Pituitary Homeobox Protein 2 Int. J. Biol. Macromol. (2012), doi:10.1016/j.ijbiomac.2012.05.008.
  2. M. Rajasekaran, Abirami S, Chen C. Effects of single nucleotide polymorphisms on human N-acetyltransferase 2 structure and dynamics by molecular dynamics simulation. PLoS One. 2011;6(9):e25801.
  3. Wei SY, Lou YC, Tsai JY, Ho MR, Chou CC, Rajasekaran M, Hsu HM, Tai JH, Hsiao CD, Chen C. Structure of the Trichomonas vaginalis Myb3 DNA-binding domain bound to a promoter sequence reveals a unique C-terminal {beta}-hairpin conformation. Nucleic Acids Res. 2011 Sep 8.
  4. Chou CC, Rajasekaran M**, Chen C. An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking. BMC Bioinformatics. 2010 Jun 18;11:334.
  5. Elumalai P, Rajasekaran M**, Liu HL, Chen C. Investigation of cation-k interactions in sugar-binding proteins. Protoplasma. 2010 Nov;247(1-2):13-24.
  6. Lou YC, Wei SY, Rajasekaran M, Chou CC, Hsu HM, Tai JH, Chen C. NMR structural analysis of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan parasite Trichomonas vaginalis. Nucleic Acids Res. 2009 Apr;37(7):2381-94.
Santhanam Abirami
Dr. Tzu-Ching Meng
Dr. Guang-Chao Chen
  1. Santhanam A, Liang SY, Chen GC, Meng TC. Midgut-enriched receptor protein tyrosine phosphatase PTP52F regulates Drosophila development during larva-pupa transition. FEBS J. 2012 ; PMID:22780963
  2. Rajasekaran M, Santhanam A, Chen C. Effects of single nucleotide polymorphisms on human N-acetyltransferase 2 structure and dynamics by molecular dynamics simulation. PLoS One. 2011;6(9):e25801.
Chia-Chi Flora Huang
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Dr. Ming-Daw Tsai
  1. Huang. C.C., Weng, J.H., Wei, T.Y., Wu, P Y., Hsu, P.H., Chen, Y.H., Wang, S.C., Qin, D., Hung, C.C., Chen, S.T., Wang, A.H., Shyy, J.Y., Tsai, M.D. lntermolecular binding between TIFA-FHA and TIFA-pT mediates tumor necrosis factor alpha stimulation and NF-KB activation. Mol Cell Biol. 2012 Jul; 32(14):2664-7.
  2. Li, Y.S., Ho, J.Y., Huang. C.C., Lyu, S.Y., Lee, C.Y., Huang, Y.T., Wu, C.J., Chan, H.C., Huang, C.J., Hsu, N.S., Tsai, M.D., Li, T.L. A unique flavin mononucleotide-Iinked primary alcohol oxidase for glycopeptide A40926 maturation. J Am Chem Soc. 2007 Nov 7;129(44): 13384-5
Alan Chuan-Ying Lai
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Dr. Yu-Ju Chen
Dr. Alice Lin-Tsing Yu
  1. Lai AC, Tsai CF, Hsu CC, Sun YN, Chen YJ. Complementary Fe3+- and Ti4+-immobilized metal ion affinity chromatography for purification of acidic and basic phosphopeptides. Rapid Commun Mass Spectrom. 2012 Sep 30;26(18):2186-94.
  2. Chou PH, Chen SH, Liao HK, Lin PC, Her GR, Lai AC, Chen JH, Lin CC, Chen YJ. Nanoprobe-based affinity mass spectrometry for selected protein profiling in human plasma. Anal Chem. 2005 Sep 15;77(18):5990-7.
Zhi-Qiang Wesley You
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Dr. Chao-Ping Hsu
  1. Hung-Cheng Chen, Zhi-Qiang You, and Chao-Ping Hsu. The mediated excitation energy transfer: Effects of bridge polarizability. The Journal of Chemical Physics, 129(8):084708, 2008.
  2. Chao-Ping Hsu, Zhi-Qiang You, and Hung-Cheng Chen. Characterization of the shortrange couplings in excitation energy transfer. The Journal of Physical Chemistry C, 112(4):1204V1212, 2008.
  3. Sheng-Jui Lee, Hung-Cheng Chen, Zhi-Qiang You, Kuan-Lin Liu, Tahsin J. Chow, IChia Chen, and Chao-Ping Hsu. Theoretical characterization of photoinduced electron transfer in rigidly linked donorVacceptor molecules: the fragment charge difference and the generalized mullikenVhush schemes. Molecular Physics, 108(19):2775V2789, 2010.
  4. Zhi-Qiang You and Chao-Ping Hsu. The fragment spin difference scheme for triplettriplet energy transfer coupling. The Journal of Chemical Physics, 133(7):074105, 2010.
  5. Zhi-Qiang You and Chao-Ping Hsu. Ab inito study on triplet excitation energy transfer in photosynthetic light-harvesting complexes. The Journal of Physical Chemistry A,115(16):4092V4100, 2011