Graduate Student Publications
- Bammes, B., & Olafsen, J.S. Polymerlike folding of a two-dimensional granular chain in water. Chaos, 14: S9. (2004)
- Bammes, B. Model system to study polymer folding in poor solvents. American Physical Society, 58th Annual Meeting of the Division of Fluid Dynamics, Abstract #NJ.009. (2005)
- DA Wheeler et al. The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008 Apr 17;452(7189):872-6.
- B. K. Muralidhara, Mingzhi Chen, Jianpeng Ma and Pernilla Wittung-Stafshede, Effect of Inorganic Phosphate on FMN Binding and Loop Flexibilit in Desulfovibrio desulfuricans. J. Mol. Biol. (2005) 349, 87-97
- Yinghao Wu, Mingzhi Chen, Mingyang Lu, Qinghua Wang and Jianpeng Ma, Determining Protein Topology from Skeletons of Secondary Structures. J. Mol. Biol. (2005) 350, 571-586
- Yinghao Wu, Xia Tian, Mingyang Lu, Mingzhi Chen Qinghua Wang and Jianpeng Ma, Folding of Small Helical Proteins Assisted by Small-Angle X-Ray Scattering Profiles. Structure (2005) 13, 1587-1597.
- Michael Perham, Mingzhi Chen, Jianpeng Ma, and Pernilla Wittung-Stafshede, Unfolding of Heptameric Co-chaperonin Protein Follows "Fly Casting" Mechanism: Observation of Transient Nonnative Heptamer. J. AM. CHEM. SOC. (2005) 127, 16402-16403
- Rajesh R. Singh, Kumaralal Kaluarachchi, Mingzhi Chen, Suresh K,Rayala, Seetharaman Balasenthil, Jianpeng Ma, and Rakesh Kumar, Solution Structure and Antiestrogenic Activity of the Unique C-terminal, NR-box Motif-containing Region of MTA1S. J. Biol. Chem. (2006) 281, 25612-25621
- Mingzhi Chen, Corey J. Wilson, Yinghao Wu, Pernilla Wittung-Stafshede, and Jianpeng Ma, Correlation between Protein Stability Cores and Protein Folding Kinetics: A Case Study on Pseudomonas aeruginosa Apo-Azurin. Structure (2006) 14, 1401-1410
- Yinghao Wu, Mingyang Lu, Mingzhi Chen, Jialin Li, and Jianpeng Ma, OPUS-Ca: a knowledge-based potential function requiring only Calpha positions. Protein Sci. (2007) 16, 1449-63
- Feng Cheng, Qinghua Wang, Mingzhi Chen, Florante A. Quiocho, and Jianpeng Ma, Molecular docking study of the interactions between the thioesterase domain of human fatty acid synthase and its ligands. Proteins. (2007)
- Chuan Hong, Stephen G. Bell, Wen Yang, Hui Wang, Yiming Hao, Xin Li, Weihong Zhou, Mark Bartlama, and Luet-Lok Wong (2009) Purification, crystallization and preliminary X-ray analysis of cytochrome P450 219A1 from Novosphingobium aromaticivorans DSM 12444, Acta Crystallographica Section F, 2009 Apr 1;65(Pt4):364-7.Epub 2009 Mar 25.
- Hudson, T.W., S. Zawko, C. Deister, S. Lundy, C.Y. Hu, K. Lee, C.E. Schmidt (2004). Optimized Acellular Nerve Graft is Immunologically Tolerated and Supports Regeneration. Tissue Engineering. 10(11/12): 1641-1651.
- Hu C.Y., Pettitt BM and Roesgen J. Osmolyte solutions and protein folding. F1000 Biology Reports 2009, 1:41.
- Hu, C.Y., Rosgen, J., Pettitt, B.M. Modeling of Solvent Environments. Wiley-VCH. "Osmolyte influence on protein stability: perspectives from theory and experiments." in press.
- Hu, C.Y., Lynch, G.C., Kokubo, H., Pettitt, B.M. TMAO's influence on the backbone of proteins. Proteins: Structure, Function, Bioinformatics. in press.
- Lopez MA, Pardo PS, Cox GA, Boriek AM. Early mechanical dysfunction of the diaphragm in the muscular dystrophy with myositis (Ttnmdm) model. Am J Physiol Cell Physiol. 2008 Nov;295(5):C1092-102.
- Pardo PS, Lopez MA, Boriek AM. The FOXO Transcription Factors Are Mechanosensitive And Their Regulation Is Altered With Aging In The Respiratory Pump. Am J Physiol Cell Physiol 294:1056-1066, 2008.
- M. A. Lopez, U. Mayer, W. Hwang, T. Taylor, M. A. Hashmi, S. R. Jannapureddy, and Aladin M. Boriek. Force transmission, compliance, and viscoelasticity are altered in the alpha7-integrin-null mouse diaphragm. Am J Physiol Cell Physiol, Feb 2005; 288: C282 - C289.
- Letarte M, McDonald M, Li M, Kathirkamathamby K, Vera S, Pece-Barbara N, Kumar S.(2005) Reduced endothelial secretion and plasma levels of TGF-þ1 in Hemorrhagic patients with Hereditary Telangiectasia type 1. Cardiovascular Research.
- Bourdeau A, Faughnan ME, McDonald ML, Paterson AD, Wanless IR and Letarte M. (2001) Potential Role of Modifier Genes Influencing Transforming Growth Factor-B1 Levels in the Development of Vascular Defects in Endoglin Heterozygous Mice with Hereditary Hemorrhagic Telangiectasia. American Journal of Pathology, 158(6):2011-2020.
- A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome.
Hampton OA, Den Hollander P, Miller CA, Delgado DA, Li J, Coarfa C, Harris RA, Richards S, Scherer SE, Muzny DM, Gibbs RA, Lee AV, Milosavljevic, A. Genome Res. Advance Online Publication, December 3, 2008. doi:10.1101/gr.080259.108
- Comprehensive genomic characterization defines human glioblastoma genes and core pathways.
The Cancer Genome Atlas Research Network. Nature 455, 1061-1068 (23 October 2008) doi:10.1038/nature07385
- Evolutionary Trace Annotation (ETA) Server: Automated Enzyme Function Prediction in Protein Structures Using 3D Templates R. Matthew Ward 1,2,5, Eric Venner 1,2, Bryce Daines 1, Stephen Murray 1, Serkan Erdin 1,5, David M. Kristensen 1,2,5, and Olivier Lichtarge 1,2,3,4,5,*
1 Departments of Molecular and Human Genetics, 2 Program in Structural and Computational Biology and Molecular Biophysics,
3 Department of Biochemistry and Molecular Biology, 4 Department of Pharmacology, One Baylor Plaza, Houston, TX 77030, 5W. M. Keck Center for Interdisciplinary Bioscience Training, Houston, TX 77005
- Little JB, Ortiz D, Ortiz-Rosado R, Pablo R, Rios-Soto K. Some remarks on Fitzpatrick and Flynn's Grobner basis technique for Pade approximation. J. Symb. Comput. 35(4): 451-461 (2003)
- Parikh A and Miranda E, Katoh K, Fuller D, Rot G, Zagar L, Curk T, Chen R, Zupan B, Loomis W, Kuspa A and Shaulsky G (2009). High Conservation of Developmental Transcriptional Programs in Divergent Social Amoebae. (In Preparation for Nature).
- Parikh A, Huang E, Dinh C, Zupan B, Kuspa A, Subramanian D and Shaulsky G (2009). New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of transcriptional profiling data. (Submitted Bioinformatics)
- Parikh A and Rot G, Curk T, Kuspa A, Shaulsky G, Zupan B (2009). dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface. BMC Bioinformatics 2009, 10:265.
- Santorelli LA, Thompson CRL, Villegas E, Svetz J, Dinh C, Parikh A, Sucgang R, Kuspa A, Strassmann JE, Queller DC, Shaulsky G (2008). Facultative cheater mutants reveal the genetic complexity of cooperation in social amoebae. Nature 451: 1107-1110.
- Rees I, Lee S, Kim H, Tsai FT. (2006). The E3 ubiquitin ligase CHIP binds the androgen receptor in a phosphorylation-dependent manner. Biochim Biophys Acta. Jun;1764(6):1073-9.
- Shigaki T, Rees I, Nakhleh L, and Hirschi KD. (2006). Identification of Three Distinct Phylogenetic Groups of CAX Cation/Proton Antiporters. Journal of Molecular Evolution, In Press.
- Fogg JM, Kolmakova N, Rees I, Magonov S, Hansma H, Perona JJ, Zechiedrich EL. (2006). Exploring writhe in supercoiled minicircle DNA. J. Phys.: Condens. Matter 18 S145-S159
- Tang G, Peng L, Baldwin PR, Mann DS, Jiang W, Rees I, Ludtke SJ. (2006). EMAN2: An extensible image processing suite for electron microscopy. J Struct Biol. Jun 8;
- Zhang R, Hu X, Khant H, Ludtke SJ, Chiu W, Schmid MF, Frieden C & Lee JM (2009). Interprotofilament interactions between Alzheimer's Abeta1-42 peptides in amyloid fibrils revealed by cryoEM. Proc Natl Acad Sci U S A
2009 vol. 106 (12) pp. 4653-8
- Parmenter, CD, Cane, MC, Zhang, R & Stoilova-McPhie, S (2008).
- Cryo-electron microscopy of coagulation Factor VIII bound to lipid nanotubes. Biochem Biophys Res Commun 366, 288-93
- Hall D, Bhandarkar SM, Wang J. (2001) ODS2: a multiplatform software application for creating integrated physical and genetic maps. Genetics. 157(3):1045-56.
- Kraemer E, Wang J, Guo J, Hopkins S, Arnold J. (2001) An analysis of gene-finding programs for Neurospora crassa. Bioinformatics. 17(10):901-12.
- Wang J, Kraemer E. (2003) GFPE: gene-finding program evaluation. Bioinformatics. 19(13):1712-3.
- Jian Wang, Tsz-Kwong Man, Kwong Kwok Wong, Pulivarthi H. Rao, Hon-Chiu Eastwood Leung, Rudy Guerra, Ching C. Lau. Genome-Wide Analysis of Copy Number Variations in Normal Population Identified by SNP Arrays. (2009) The Open Biology Journal. Volume 2:54-65.
- David C. Marciano, Jeanine M. Pennington, Xiaohu Wang, Jian Wang et al. Genetic and Structural Characterization of an L201P Global Suppressor Substitution in TEM-1 ß-Lactamase. Journal of Molecular Biology. 2008. 384(1): 151-64.
- Ching C. Lau and Jian Wang. Genomic Profiling and Personalized Medicine. Enterprise Imaging and Therapeutic Radiology Management. 2008. 18(3): 32
- Jian Wang and Eileen Kraemer. GFPE: gene-finding program evaluation. Bioinformatics. 2003. 19(13): 1712-13.
- Eileen Kraemer, Jian Wang, Jinhua Guo et al. An analysis of gene-finding programs for Neurospora crassa. Bioinformatics. 2001. 7(10): 901-12.
- David Hall, Suchendra M. Bhandarkar, and Jian Wang. ODS2: A Multiplatform Software Application for Creating Integrated Physical and Genetic Maps. Genetics. 2001. 157(3): 1045-56.
- Kristensen, D.M., B. Chen, V. Fofanov, R.M. Ward, A.M. Lisewski, M. Kimmel, L. Kavraki, and O. Lichtarge (2006). "Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity." Protein Science: In Press.
Former Student Publications:
- Adams GJ, Greene J, Vick III GW, Karmonik C, Ballantyne CM, Insull Jr. W, Morrisett JD (2003) Tracking Regression and Progression of Atherosclerosis in Carotid Arteries using High Resolution Magnetic Resonance Imaging. Submitted.
- Adams GJ, Simoni D, Bordelon Jr. CB, Vick III GW, Kimball KT, Insull Jr. W, Morrisett JD (2002) Bilateral Symmetry of Human Carotid Artery Atherosclerosis. Stroke, 2002;33:2575-2580.
- Adams GJ, Vick III GW, Insull Jr. W, Morrisett JD (2002) Estimation of Carotid Atherosclerotic Plaque Volume from In Vivo Magnetic Resonance Images. Proceedings of the Second Joint Meeting of the IEEE Engineering in Medicine and Biology Society and the Biomedical Engineering Society, Houston, TX. Oct. 23-26, 2002, 1072-1073.
- Adams GJ, Bordelon Jr. CB, Vick III GW, Insull Jr. W, Morrisett JD (2002) An Algorithm for Quantifying Advanced Carotid Artery Atherosclerosis using MRI and Active Contours. Proceedings of the SPIE Medical Imaging 2002, San Diego, CA. Feb. 23-28, 2002, 1448-1458.
- I.I. Serysheva,S. J. Ludtke, M. R. Baker, W. Chiu, and S. L. Hamilton (2002) Structure of the voltage-gated L-type Ca2+ channel by electron cryomicroscopy. PNAS, 99: 10370-10375
- Lu, G.Y., Zhou, Z.H., Baker, M.L., Jakana, J., Cai, D.Y., Wei, X.C., Chen, S.X., Gu, X.C., Chiu, W. (1998) Structure of the Double-Shelled Rice Dwarf Virus. J Virol (72), p 8541-8549.
- Petrosino, J., Baker, M.L., Palzkill, T. (1999) Tolerance of Amino Acid Substitutions at Beta-Lactamase Core Positions as Determined by Site Directed Mutagenesis. Protein Eng (9), p 761-769.
- Jiang, W.*, Baker M.L.*, Ludtke, S.J., Chiu, W. (2001) Bridging the Information Gap: Computational Tools for Intermediate Resolution Structure Interpretation. J Mol Biol (308), p 1033-1044. *contributed equally
- Zhou, Z.H., Baker, M.L., Jiang, W., Dougherty, M., Jakana, J., Dong, G., Lu, G., Chiu, W. (2001) Protein Folds of the Rice Dwarf Virus Revealed by Electron Cryomicroscopy. Nat Struct Biol (8), p 868-873.
- Jiang, W., Li, Z., Zhang, Z., Booth, C. R., Baker, M. L., Chiu, W. (2001) Semi-Automated Icosahedral Particle Reconstruction at Sub-nanometer Resolution. J Struct Biol (3), p214-225.
- Chiu, W., Baker, M.L., Jiang, W., Zhou, Z.H. (2002) Deriving the Folds of Macromolecular Complexes Through Electron Cryomicroscopy and Bioinformatics Approaches. Curr Opin Struct Biol (2), p 263-269.
- Baker, M.L., Serysheva, I.I., Sencer, S., Ludtke, S.J., Jiang, W., Chiu, W., Hamilton, S.L. (Accepted) The Skeletal Muscle Ca2+ Release Channel has an Oxidoreductase-like Domain.
- Bowman, B.R., Baker, M.L., Rixon, F, Chiu. W., Quiocho, F. (Submitted) X-ray Structure of the Upper Domain of the Herpes Simplex Virus-1 Major Capsid Protein: Identification of a Novel Fold and its Functional Implications.
- Baker, M.L., Jiang, W., Zhou, Z.H., Rixon, F., Chiu, W. (manuscript in preparation) Architecture of the Herpes Simplex Virus Major Capsid Protein Derived from Electron Cryomicroscopy and Bioinformatics
- Jiang, W., Li, Z., Zhang, Z., Baker, M.L., Prevelige, P.E., Chiu, W. (manuscript in preparation) Structural Transformations of Bacteriophage P22 Seen at Sub-nanometer Resolutions.
- Booth EO, Van Driessche N, Zhuchenko O, Kuspa A, Shaulsky Gad (2005) Microarray phenotyping in Dictyostelium reveals a regulon of chemotaxis genes. Bioinformatics, 21(24):4371-7.
- Van Driessche N, Demsar J, Booth EO, Hill P, Juvan P, Zupan B, Kuspa A, Shaulsk G (2005) Epistasis analysis with global transcriptional phenotypes.
Nature Genetics, 37(5):471-7.
- Jiang W, Li Z, Zhang Z, Booth CR, Baker ML, Chiu W. (2001) Semi-automated icosahedral particle reconstruction at sub-nanometer resolution. J Struct Biol. 136(3):214-25
- Flynn TC, Swint-Kruse L, Kong Y, Booth C, Matthews KS, Ma J. (2003) Allosteric transition pathways in the lactose repressor protein core domains: asymmetric motions in a homodimer. Protein Sci. 12(11):2523-41.
- Booth CR, Jiang W, Baker ML, Zhou ZH, Ludtke SJ, Chiu W. (2004) A 9 Å Single Particle Reconstruction from CCD Captured Images on a 200 kV Electron Cryomicroscope. J Struct Biol. 147:116-127
- Passmore LA, Booth CR, Venien-Bryan C, Ludtke SJ, Fioretto C, Johnson LN, Chiu W, Barford D. (2005) Structural analysis of the anaphase-promoting complex reveals multiple active sites and insights into polyubiquitylation. Mol. Cell. 20(6):855-66
- Yu X, Acehan D, Menetret JF, Booth CR, Ludtke SJ, Riedl SJ, Shi Y, Wang X, Akey CW. (2005) A structure of the human apoptosome at 12.8 A resolution provides insights into this cell death platform. Structure. 13(11):1725-35
- Callaway, C., Wang, J.-P., Slavik, K., Needleman, D., Seryshev, A., Cantu, C. III, Wu, Y., Jayaraman, T., Marks, A., and Hamilton, S.L. (1994). Localization of the High and Low Affinity [3H]-Ryanodine Binding Sites on the Skeletal Muscle Ca2+ Release Channel. J. Biol. Chem. 269: 15876-15884.
- Cantu, C. III, Huang, W., and Palzkill, T. (1996). Selection and Characterization of Amino Acid Substitutions at Residues 237-240 of TEM-1 Beta-lactamase with Altered Substrate Specificity for Aztreonam and Ceftazidime. J. Biol. Chem. 271: 22538-22545.
- Cantu, C. III, Huang, W., and Palzkill, T. (1997). Cephalosporin Substrate Specificity Determinants of TEM-1 Beta-lactamase. J. Biol. Chemi. 272: 29144-29150.
- Cantu, C. III, and Palzkill, T. (1998). The role of residue 238 of Beta-lactamase in the hydrolysis of extended-spectrum Beta-lactam antibiotics. J. Biol. Chem. 273: 26603-26609.
- Petrosino, J., Cantu, C. III, and Palzkill, T. (1998). Beta-lactamases: Protein evolution in real time. Trends Microbiol. 6: 323-327.
- Cantu, C. III, Benlagha, K., Savage, P.B., Bendelac, A. and Teyton, L. (2003). The paradox of immune molecular recognition of alpha-galactosylceramide: low affinity, low specificity for CD1d, high affinity for alpha beta TCRs. J. Immunol. 170(9): 4673-4682.
- Zhou, D.*, Cantu, C. III*, Sagiv, Y., Schrantz, N., Kulkarni, A.B., Qi, X., Mahuran, D.J., Morales, C.R., Grabowski, G.A., Benlagha, K., Savage, P., Bendelac, A. and Teyton, L. (2004). Editing of CD1d-bound lipid antigens by endosomal lipid transfer proteins.
Science. 303(5657): 523-527.
*co-first author
- Goff, R.D., Gao, Y., Mattner, J., Zhou, D., Yin, N., Cantu, C. III, Teyton, L., Bendelac, A. and Savage, P.B. (2004). Effects of lipid chain lengths in alpha-galactosylceramides on cytokine release by natural killer T cells. J. Am. Chem. Soc. 126(42): 13602-13603.
- Zhou, D., Mattner, J., Cantu, C. III, Schrantz, N., Yin, N., Gao, Y., Sagiv, Y., Hudspeth, K., Wu, Y.P., Yamashita, T., Teneberg, S., Wang, D., Proia, R.L., Levery, S.B., Savage, P.B., Teyton, L. and Bendelac, A. (2004). Lysosomal glycosphingolipid recognition by NKT cells. Science 306(5702): 1786-1789.
- Mattner, J., Debord, K.L., Ismail, N., Goff, R.D., Cantu, C. III, Zhou, D., Saint-Mezard, P., Wang, V., Gao, Y., Yin, N., Hoebe, K., Schneewind, O., Walker, D., Beutler, B., Teyton, L., Savage, P.B. and Bendelac, A. (2005). Exogenous and endogenous glycolipid antigens activate NKT cells during microbial infections.
Nature 434(7032): 525-529.
- Zajonc, D.M., Cantu, C. III, Mattner, J., Zhou, D., Savage, P.B., Bendelac, A., Wilson, I.A., Teyton, L. (2005). Structure and function of a potent agonist for the semi-invariant natural killer T cell receptor.
Nat Immunol. 2005 Aug;6(8):810-8.
- Carson JP, Eichele G, Chiu W. (2005). A method for automated detection of gene expression required for the establishment of a digital transcriptome-wide gene expression atlas.
J. Microsc. 217: 275-281.
- Tao Ju, Joe Warren, Gregor Eichele, Christina Thaller, Wah Chiu, James Carson (2003). A Geometric Database for Gene Expression Data. Eurographics Symposium on Geometry Processing.
- Zangwill KM, Greenberg DP, Chiu CY, Mendelman P, Wong VK, Chang SJ, Partridge S, Ward JI. (2003). Safety and immunogenicity of a heptavalent pneumococcal conjugate vaccine in infants.
Vaccine. 21(17-18): 1894-1900.
- James Carson, Christina Thaller, Gregor Eichele (2002). A Transcriptome Atlas of the Mouse Brain at Cellular Resolution. Curr. Opin. Neurobiol. 12(5): 562-565.
- Abstracts
- Chang JT, Marsh M, Rixon F, Chiu W. (2005)
Mr T: Automated Electron Cryotomography for JEOL 2010F TEM
Microscopy and Microanalysis 11 (Suppl 2): 308-309
[link]
- Marsh M, Chang J, Chen J, Lopez J, Chiu W. (2005)
Three-Dimensional Architecture of Platelets in its Native State by Electron Cryotomography
Blood (ASH Annual Meeting Abstracts) 106(11): 1658
[link]
[Also in 45th Meeting of the American Society for Cell Biology]
- Marsh MP, Chang J, Chen J, Lopez J, Chiu w. (2007)
Electron Cryo-tomography of Human Platelets Captures Exocytosis Pathway of Diverse Secretory Granules.
Biophysical J Suppl: 389-Pos.
- Schmid MF, Khant H, Chang J, Marsh M, Cruciano A, Chiu W. (2007)
Aligning and averaging subvolumes extracted from an electron cryo-tomogram.
Biophysical J Suppl: 2423-Pos.
- Schmid MF, Marsh M, Cruciano A, Chang J, Khant H, Chiu W. (2006)
Aligning and averaging single particles from a tomogram.
American Chemical Society 62nd Southwest Regional Meeting
Articles
- Jiang W, Chang J, Jakana J, Weigele P, King J, Chiu W. (2006)
Structure of Epsilon 15 Bacteriophage Reveals Genome Organization and DNA Packaging/Injection Apparatus.
Nature 439(7076): 612-616
[link]
- Chang J, Weigele P, King J, Chiu W, Jiang W. (2006)
Cryo-EM Asymmetric Reconstruction of Bacteriophage P22 Reveals Organization of its DNA Packaging and Infecting Machinery.
Structure 14(6): 1073-1082
[link]
- Chang JT, Schmid MF, Rixon FJ, Chiu W. (2007)
Electron Cryo-Tomography Reveals the Portal in the Herpesvirus Capsid.
Journal of Virology 81(4): 2065-2068
[Pubmed]
- Pope WH, Weigele PR, Chang J, Pedulla ML, Ford ME, Houtz JM, Jiang W, Chiu W, Hatfull GF, Hendrix RW, King JA. (2007)
Genome Sequence, Structural Proteins, and Capsid Organization of the Cyanophage Syn5: A "Horned" Bacteriophage of Marine Synechococcus.
Journal of Molecular Biology 368(4): 966-981
[Pubmed]
- Marsh MP, Chang JT, Booth CR, Liang N, Schmid MF, Chiu W. (2007)
Modular Software Platform for Low-Dose Elecron Microscopy and Tomography
Journal of Microscopy 228(3): 384-389. [link]
- Chiu W, Chen D, Jakana J, Chang J, Jiang W, Ludtke SJ, Baker ML. (2006) Visualization of Biological Nano-Machines at Subnanometer Resolutions JEOL News 41(1): 12-17. [website]
- Vidakovic M, Crossnoe CR, Neidre C, Kim K, Krause KL, Germanas JP. (2003). Reactivity of reduced [2Fe-2S] ferredoxins parallels host susceptibility to nitroimidazoles. Antimicrob. Agents Chemother. 47(1): 302-308.
- Crossnoe CR, Germanas JP, LeMagueres P, Mustata G, Krause KL. (2002). The crystal structure of Trichomonas vaginalis Ferredoxin provides insight into Metronidazole activation. J. Mol. Biol. 318: 503-518.
- Cui, X., Jeter, C.B., Yang, D., Montague, P.R., and Eagleman, D.M. (2007) Vividness of mental imagery: individual variability can be measured objectively. Vision Research 47, 474-478
- Fisher, R.E., Harvey, A.H., Li, J., Cui, X., McClure, S.M., and Montague, P.R. (2007) Comparing Pepsi and Picasso: Neural responses underlying preference and familiarity of diverse rewarding stimuli. In submission
- Stetson, C., Cui, X.*, Montague, P.R., and Eagleman, D.M. (2006). Motor-sensory recalibration leads to an illusory reversal of action and sensation. Neuron 5, 651-659.
*parallel first author
- Li, D.H., Yang, X., Cui, X., Cui, K.M., Li, Z.L., and Lee, C.L. (2002). Early development of pollen chamber in Ginkgo biloba ovule. Acta Bot. Sin. 7, 757-763.
- Cui, X, 2002, Master thesis: Time series analysis of bat ultrasound signals
- Cui, X, 2000, B.S. thesis: Cellular mechanism underlying the formation of pollen chamber in ginkgo biloba
- Pajukanta P, Lilja HE, Sinsheimer JS, Cantor RM, Lusis AJ, Gentile M, Duan XJ, Soro-Paavonen A, Naukkarinen J, Saarela J, Laakso M, Ehnholm C, Taskinen MR, Peltonen L. (2004). Familial combined hyperlipidemia is associated with upstream transcription factor 1 (USF1).
Nat Genet. 36(4): 371-376.
- Duan XJ, Xenarios I, Eisenberg D. (2002). Describing biological protein interactions in terms of protein states and state transitions: the LiveDIP database. Mol. Cell Proteomics. 1(2): 104-116.
- Duan X, Quiocho FA. (2002). Structural evidence for a dominant role of nonpolar interactions in the binding of a transport/chemosensory receptor to its highly polar ligands. Biochemistry. 41(3): 706-712.
- Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, Eisenberg D. (2002). DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30(1): 303-305.
- Gonzalez AL, Gobin AS, West JL, McIntire LV, Smith CW. (2004). Integrin interactions with immobilized peptides in polyethylene glycol diacrylate hydrogels. Tissue Eng. 10(11-12): 1775-1786.
- He J, Schmid MF, Zhou ZH, Rixon F, Chiu W.(2001) Finding and using local symmetry in identifying lower domain movements in hexon subunits of the herpes simplex virus type 1 B capsid. J Mol Biol, 309(4):903-14
- Zhou ZH, Dougherty M, Jakana J, He J, Rixon FJ, Chiu W.(2000) Seeing the herpesvirus capsid at 8.5 A.Science,288(5467):877-80
- Zhou ZH, He J, Jakana J, Tatman JD, Rixon FJ, Chiu W.(1995) Assembly of VP26 in herpes simplex virus-1 inferred from structures of wild-type and recombinant capsids.Nat Struct Biol,2(11):1026-30
- Hayakawa K, He J.(1998) Maximum hydrostress response charts for drying or hydrating elastic, cylindrical food with finite Biot number. Food Science Technology International, Tokyo, 4(2), 130-5
- Hu G, Jain K, Hurle M (2005). Revealing transforming growth factor – beta signaling transduction in human kidney by gene expression data mining (Submitted).
- Wang SW, Oh CK, Cho SH, Hu G, Martin R, Demissie-Sanders S, Li K, Moyle M, Yao Z. (2005). Amphiregulin expression in human mast cells and its effect on the primary human lung fibroblasts.
J. Allergy Clin. Immunol. 115(2): 287-294.
- Hu G, Tsai AL, Quiocho FA. (2003). Insertion of an N7-methylguanine mRNA cap between two coplanar aromatic residues of a cap-binding protein is fast and selective for a positively charged cap. J. Biol. Chem. 278(51): 51515-51520.
- Yang J, Hu G, Wang SW, Li Y, Martin R, Li K, Yao Z. (2003). Calcineurin/nuclear factors of activated T cells (NFAT)-activating and immunoreceptor tyrosine-based activation motif (ITAM)-containing protein (CNAIP), a novel ITAM-containing protein that activates the calcineurin/NFAT-signaling pathway. J. Biol. Chem. 278(19): 16797-16801.
- Hu G, Modrek B, Stensland H, Saarela J, Pajukanta P, Kustanovich V, Peltonen L, Nelson S, Lee C (2002). Efficient identification of single-nucleotide polymorphisms in coding regions of human genes. Pharmacogenomics J. 2: 236.
- Hu G, Oguro A, Li C, Gershon PD, Quiocho FA. (2002). The "cap-binding slot" of an mRNA cap-binding protein: quantitative effects of aromatic side chain choice in the double-stacking sandwich with cap. Biochemistry. 41(24): 7677-7687.
- Irizarry K, Hu G, Wong ML, Licinio J, Lee C (2001). Single nucleotide polymorphism identification in candidate gene systems of obesity. Pharmacogenomics J 1: 193.
- Quiocho FA, Hu G, Gershon PD. (2000). Structural basis of mRNA cap recognition by proteins. Curr. Opin. Struct. Biol. 10: 78.
- Hu G, Gershon PD, Hodel A, Quiocho FA. (1999). mRNA cap recognition: dominant role of enhanced stacking interactions between methylated bases and protein aromatic sidechains. Proc. Natl. Acad. Sci. U.S.A. 96: 7149.
- Eryong Huang, Simone L. Blagg, Thomas Keller, Gad Shaulsky and Christopher R. L.Thompson.(2005) bZIP Transcription Factor Interactions Regulate DIF Responses in Dictyostelium. Development, In Press
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