Publications Made Using UMBC Resources
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Cao, Song & ShiJie Chen, "Biphasic folding kinetics of RNA pseudoknots and human telomerase RNA activity". Journal of Molecular Biology, Vol. 367, pp. 909-924, 2007.
Tan, Zhijie & ShiJie Chen, "RNA helix stability in mixed Na+/Mg2+ solution", Biophysical Journal, Vol 92, pp. 3615-3632, 2007.
Zhi-Jie Tan and Shi-Jie Chen. "Ion-mediated nucleic acid helix-helix interactions". Biophysical Journal, 91: 518-536, 2006.
Shi-Jie Chen (invited). "RNA and Macromolecular Folding", Annual Review of Biophysics & Biomolecular Structure, Volume 37, 2008. in press
Tan, Zhijie & ShiJie Chen, "Electrostatic free energy landscapes for DNA helix bending," Biophysical Journal, in press, 2007.
A. Randall, J. Cheng, M. Sweredoski, and P. Baldi. TMBpro: Secondary Structure, Beta-Contact, and Tertiary Structure Prediction of Transmembrane Beta-Barrel Proteins. Bioinformatics, in press, 2007.
J. Dai and J. Cheng. HMMEditor: a visual editing tool for profile hidden Markov model. BMC Genomics, in press, 2007.
J. Buban, K. Matsunaga, J. Chen, N. Shibata, W.Y. Ching, T. Yamamoto, Y. Ikuhara, "Grain Boundary Strengthening in Alumina by Rare Earth Impurities", Science, 311, 212-215 (2006).
W.Y Ching and Paul Rulis, "Ab-initio calculation of the electronic and spectroscopic properties of spinel γ-Sn3N4", Phys. Rev. B73, 045202-1-9 (2006).
W.Y. Ching, Paul Rulis, Yong-Nian Xu and L. Ouyang, "The electronic structure and spectroscopic properties of 3C, 2H, 4H, 6H, 15R, 21R polymorphs of SiC", Materials Science and Engineering A, 422 C1-2, 147-156 (2006).
W. Y. Ching, Jun Chen, Paul Rulis, Lizhi Ouyang, and Anil Misra, "Ab initio Modeling of Clean and Y-doped Grain Boundaries in Alumina and Intergranular Glassy Films (IGF) in β-Si3N4", J. Materials Science, 41 (16) 5061-5067, (2006).
J.B. MacNaughton, A. Mowes, J.S. Lee, S.D. Wetting, H.-B. Kraatz, L. Ouyang, W.Y. Ching and E.Z. Kurmaev, "Dependence of the DNA Electronic structure on environmental and structural variations", J. Phys. Chem. 110(32), 15742-748 (2006).
Jun Chen, Paul Rulis, Lizhi Ouyang, S. Satpathy, and W.Y. Ching,, "Vacancy enhanced ferromagnetism in Fe-doped rutile TiO2", Phys. Rev. B74, 235207-1-5 (2006).
A. Misra, L. Ouyang, J. Chen and W.Y. Ching, "Ab initio calculations of strain field and failure pattern in silicon nitride intergranular glassy films", Philosophical Magazine A. 87(25), 3839-3852 (2007).
Hongzhi Yao, L. Ouyang and W.Y. Ching, "Ab initio Calculation of the elastic constants of ceramic crystals", J. Am. Ceram. Soc. 90  3194-3204 (2007).
P. Rulis, Hongzhi Yao, L. Ouyang, and W.Y. Ching, "Electronic structure, bonding, charge distribution and X-ray absorption spectra of the (001) surfaces of fluorapatite and hydroxyapatite", Phys. Rev. B76, 245410-1-15, (2007).
Sitaram Aryal, Paul Rulis and W. Y. Ching, "Density functional calculation of the electronic structure and optical properties of Aluminosilicate polymorphs (Al2SiO5)", American Mineralogy (accepted, in press 2007).
W.Y. Ching, and P. Rulis, "Ab initio calculation of the O-K, N-K, Si-K, Si-L3, Y-K, Y-L3 edges in the Y-Si-O-N system: A new strategy for ELNES/XANES spectral modeling in complex materials", Phys. Rev. B. (accepted).
Legarsky, J., E. Loehr, C. Davis, B. Rosenblad, B. Bloomfield, A. Hedrick, R. Coffman, and D. Manjunath (2007), "Scatterer informatics using NASA JPL Polarimetric Airsar Imagery", EOS Transactions, accepted.
M. Klaric, G. Scott, C.R. Shyu, C. Davis, K. Palaniappan, "A framework for geospatial satellite imagery retrieval systems", IEEE Int. Geoscience and Remote Sensing Symposium, Denver, CO, Jul 31- Aug 4, 2006, Accepted.
TOXICOLOGY (for details, see http://web.missouri.edu/~glaserr/vitpub/RG_Publications.html)
"Ammonia Elimination from Protonated Nucleobases and Related Synthetic Substrates", Ming Qian, Shuo Yang, Hong Wu, Papiya Majumdar, Nathan Leigh, and Rainer Glaser. Article, J. Am. Soc. Mass Spectrometry (JASMS) 2007, 18 (11), 2040-2057. PDF DOI (Online: Sept. 1, 2007. In Print: Nov. 2007 Issue) Supporting Information
"Adenine Synthesis in Interstellar Space: Mechanisms of Prebiotic Pyrimidine Ring-Formation in Monocyclic HCN-Pentamers", Rainer Glaser, Brian Hodgen, Dean Farrelly, and Elliot McKee. Article, Astrobiology 2007, 7, 455-470. PDF. (Publication in Print: June 2007). Online Visualization: Chime Displays and Reaction Animations
Electronic Structures and Spin Topologies of γ-Picoliniumyl Radicals. A Study of the Homolysis of N-Methyl-γ-Picolinium and of Benzo-, Dibenzo-, and Naphthoannulated Analogs. Rainer Glaser, Yongqiang Sui, Ujjal Sarkar, and Kent Gates. Article, submitted.
Stabilities and Spin Density Distributions of Benzannulated Benzyl Radicals. Yongqiang Sui, Rainer Glaser, Ujjal Sarkar, and Kent Gates. Article, J. Chem. Theory Comput. 2007, 3, 1091-1099. PDF. (Web Release Date: April 20, 2007. Published in Issue 3, May 2007.)
MATERIALS (for details, see http://web.missouri.edu/~glaserr/vitpub/RG_Publications.html)
What's in a name? Noncovalent Ar-Cl...(H-Ar')n interactions and terminology based on structure and nature of the bonding. Rainer Glaser and Richard F. Murphy. Letter, CrystEngComm 2006, 8, 948-951. PDF. (Web Release Date: October 12, 2006 )
Multifurcated halogen bonding involving Ph-Cl---H-CPh=N-R' interactions and its relation to idioteloamphiphile layer architecture. Rainer Glaser, Richard F. Murphy, Yongqiang Sui, Charles L. Barnes, and Sung Hoon Kim, Communication, CrystEngComm 2006, 8, 372-376. PDF. (Web Release Date: April 26, 2006.)
Helically Annelated and Cross-Conjugated β-Oligothiophenes: An FT-Raman Spectroscopic and Quantum Chemical DFT Study. Reyes Malavé Osuna, Rocío Ponce Ortiz, Victor Hernández, Juan Teodomiro López Navarrete,* Makoto Miyasaka, Suchada Rajca, Andrzej Rajca,* and Rainer Glaser. Article, J. Phys. Chem. C 2007, 1, 4854-4860. PDF. (Web Release: January 18, 2007; Publication in Print: March 29, 2007.) Online Visualization: Strong Raman Modes of beta-Oligothiophenes
THESES (for details, see http://web.missouri.edu/~glaserr/vitpub/RG_Publications.html#dissertations)
NMR and Ab Initio Study of Structure and Dynamics. Yang Liu, M.S. Dissertation, University of Missouri-Columbia, 2008.
Anisotropic Organic Materials: Ferroelectric Crystals and Spin-Polarized Radicals. Yongqiang Sui, Ph.D. Dissertation, University of Missouri-Columbia, 2007.
Ammonia Elimination from Protonated Nucleobases. Proton Mobility, Ammonium Ion Formation, and Fragmentation Paths. Shuo Yang, M.S. Dissertation, University of Missouri-Columbia, 2007.
Nitrosative Guanine Deamination: Pyrimidine Ring-Opening - Implications of Effects in Homogeneous Solution as well as Anisotropic Environments. Papiya Majumdar, Ph.D. Dissertation, University of Missouri-Columbia, 2007.
Aza-Analogues of Distyrylbenzene (DSB). Synthesis, Structures, and Properties of 1,4- Phenylenediamine Bisimines (PDABI). Richard F. Murphy, M.S. Dissertation, University of Missouri-Columbia, 2006.
P. Prayongpan, D. S. Stripe, and C. M. Greenlief, "Cycloaddition-Like Reactions at Germanium (100) Surfaces: Adsorption and Reaction of 1,5-Cyclooctadiene", Surface Science (in press).
Ioan Kosztin and Klaus Schulten, "Molecular dynamics methods for bioelectronic systems in photosynthesis", in Thijs Aartsma and Joerg Matysik, editors, Biophysical Techniques in Photosynthesis, 2nd Ed., (Kluwer Academic Publishers, New York, 2008)
Bogdan Barz, Tuck C. Wong and Ioan Kosztin, "The Conformation and Oligomeric State of the HIV-1 gp41 Fusion Peptide in Membrane are Determined by the Membrane Surface Area per Lipid", Biochimica et Biophysica Acta - Biomembranes, (2008) [in press]
Francoise Marga, Adrian Neagu, Ioan Kosztin and Gabor Forgacs, "Developmental biology and tissue engineering", Birth Defects Research Part C: Embryo Today: Reviews, (2007)
Elijah Flenner, Francoise Marga, A. Neagu, Ioan Kosztin and Gabor Forgacs, "Relating Biophysical Properties Across Scales", Current Topics in Developmental Biology 81, 461 (2007)
L. Janosi and I. Kosztin, Free energy profile of glycerol transport through GlpF, Biophys. J., 119A (2007).
J. Das, L. Janosi and I. Kosztin, Free energy profile of water transport through GlpF, Biophys. J., 119A (2007).
E. Flenner, B. Barz, L. Janosi, A. Neagu and I. Kosztin, Monte Carlo and particle dynamics simulations of cellular aggregates: a comparative study, Biophys. J., 153A (2007).
B. Barz, T. C. Wong and I. Kosztin, Conformation and oligomeric state of the HIV-1 Gp41 fusion peptide in membranes: a combined FITR and MD simulation study, Biophys. J., 208A (2007).
B. Barz, J. Hammel, D. Saenz, C. Norotte, F. Marga, A. Neagu, I. Kosztin and G. Forgacs, In vitro and in silico design of branched tubular structures from cellular aggregates, Biophys. J., 487A (2007).
M. Forney, L. Janosi and I. Kosztin, Reconstruction of free energy profiles from fast non-equilibrium processes, Biophys. J., 642A (2007).
L. Janosi "Multiscale Modeling of Biomolecular Systems" (Aug., 2007)
Chung F. Wong:
C.F. Wong, "Flexible ligand-flexible protein docking in protein kinase systems", Biochim. Biophys. Acta., in press.
Z. Huang, C.F. Wong & R. Wheeler, "Flexible Protein-Flexible Ligand Docking with Disrupted Velocity imulated Annealing", Proteins: Structure, Function, Bioinformatics, in press.
Z. Huang & C.F. Wong, "A Mining-Minima Approach to Exploring the Docking Pathways of p-Nitrocatechol Sulfate to YopH", Biophys. J., 93 (2007) 4141-4150.
M. Wang, C. F. Wong, J. Liu & P. Zhang, "Efficient Quantum Mechanical Calculation of Solvation Free Energies Based on Density Functional Theory, Numerical Atomic Orbitals and Poisson-Boltzmann Equation", Chem. Phys. Lett., 442 (2007) 464-467.
M. Wang & C.F. Wong, "Rank-ordering Protein-Ligand Binding Affinity by a QM/MM/PBSA Model", J. Chem. Phys., 126 (2007) 026101.
M. Wang & C.F. Wong, "Calculation of Solvation Energy from Quantum Mechanical Charge Density and Continuum Dielectric Theory", J. Phys. Chem. A, 110 (2006) 4873-4879.
An iterative knowledge-based scoring function for protein-protein recognition. Sheng-You Huang, and Xiaoqin Zou. Proteins (in press). (The computer resources are acknowledged.)
Xiaomeng Wu, Xiu-Feng Wan, Gang Wu, Dong Xu, and Guohui Lin. Phylogenetic Analysis Using Complete Signature Information of Whole Genomes and Clustered Neighbor-Joining Method. International Journal of Bioinformatics Research and Applications. 2:219-248, 2006.
Monir Shababi, Karuppaiah Palanichelvam, Anthony B. Cole, Dong Xu, Xiu-Feng Wan, and James E. Schoelz. The ribosomal shunt translation strategy of Cauliflower mosaic virus has evolved from ancient long terminal repeats. Journal of Virology. 80:3811-3822, 2006.
Pin-Hao Chi, Chi-Ren Shyu, Dong Xu. A fast SCOP fold classification system using content-based E-Predict algorithm. BMC Bioinformatics. 7:362, 2006 (http://www.biomedcentral.com/1471-2105/7/362).
Xiufeng Wan, Guohui Lin and Dong Xu. Rnall: An Efficient Algorithm for Predicting RNA Local Secondary Structural Landscape in Genomes. Journal of Bioinformatics and Computational Biology. 4:1015-1031, 2006.
Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, Luonan Chen. Inferring Gene Regulatory Networks from Multiple Microarray Datasets. Bioinformatics. 22:2413-2420, 2006.
Andrew Nunberg, Joseph A. Bedell, Mohammad A. Budiman, Robert W. Citek, Sandra W. Clifton, Lucinda Fulton, Deana Pape, Zheng Cai, Trupti Joshi, Henry Nguyen, Dong Xu and Gary Stacey. Survey sequencing of soybean elucidates the genome structure and composition. Functional Plant Biology. 33(8):765-773, 2006.
Rajkumar Bondugula and Dong Xu. MUPRED: A Tool for Bridging the Gap between Template Based Methods and Sequence Profile Based Methods for Protein Secondary Structure Prediction. Proteins. 66(3):664-670, 2007.
Zhao Song, Luonan Chen, Ashwin Ganapathy, Xiu-Feng Wan, Laurent Brechenmacher, Nengbing Tao, David Emerich, Gary Stacey, Dong Xu. Development and Assessment of Scoring Functions for Protein Identification Using Peptide Mass Fingerprinting Data. Electrophoresis. 28:864-870, 2007.
Predrag S Krstić, Jack C. Wells, Miguel Fuentes-Cabrera, Dong Xu, and James W. Lee. Toward electronic conductance characterization of DNA nucleotide bases. Solid State Phenomena. Vols 121-123, pages 1387-1390, 2007.
Rajesh Kumar, Jing Qiu, Trupti Joshi, Babu Valliyodan, Dong Xu, Henry T. Nguyen. Single Feature Polymorphism Discovery in Rice. PLoS ONE 2(3): e284. doi:10.1371/journal.pone.0000284, 2007
Robin Kramer and Dong Xu. Projecting Gene Expression Trajectories through Inducing Differential Equations from Microarray Time Series Experiments. Journal of VLSI Signal Processing Systems. In press.
Trupti Joshi and Dong Xu. Quantitative Assessment for Relationship between Sequence Similarity and Function Similarity. BMC Genomics. 8:222, doi:10.1186/1471-2164-8-222, 2007.
Kristen H. Taylor, Robin S. Kramer, J. Wade Davis, Dong Xu, Charles W. Caldwell, and Huidong Shi. Ultra-Deep Bisulfite Sequencing Analysis of DNA Methylation Patterns in Multiple Gene Promoters by 454-Sequencing. Cancer Research. 67(18):8511-8518, 2007.
James O. Allen, Christiane M. Fauron, Patrick Minx, Leah Westgate, Swetha Oddiraju, Guan Ning Lin, Louis Meyer, Hui Sun, Kyung Kim, Chunyan Wang, Feiyu Du, Dong Xu, Michael Gibson, Jill Cifrese, Sandra W. Clifton, and Kathleen J. Newton. Comparisons among Two Fertile and Three Male-Sterile Mitochondrial Genomes of Maize. Genetics. 2007 Jul 29.
Dong Xu, Ognen Duzlevski, and Xiu-Feng Wan. In search of remote homolog. In Handbook of Computational Molecular Biology, edited by Srinivas Aluru, CRC Press. 33:1-33:27, 2006.
Ying Xu, Zhijie Liu, Liming Cai, Dong Xu. Protein Structure Prediction by Protein Threading. In, Computational Methods for Protein Structure Prediction and Modeling, edited by Ying Xu, Dong Xu, and Jie Liang. Springer-Verlag. Vol. 2. Pages 1-42, 2007.
Dong Xu and Ying Xu. Protein Structure Prediction as a Systems Problem. In, Computational Methods for Protein Structure Prediction and Modeling, edited by Ying Xu, Dong Xu, and Jie Liang. Springer-Verlag. Vol. 2. Pages 177-206, 2007.
Dong Xu, Jie Liang, and Ying Xu. Resources and Infrastructure for Structural Bioinformatics. In Computational Methods for Protein Structure Prediction and Modeling, edited by Ying Xu, Dong Xu, and Jie Liang. Springer-Verlag. Vol. 2. Pages 207-227, 2007.
Guohui Lin, Dong Xu, Ying Xu. Computer Science for Structural Bioinformatics. In, Computational Methods for Protein Structure Prediction and Modeling, edited by Ying Xu, Dong Xu, and Jie Liang. Springer-Verlag. Vol. 2. Pages 241-266, 2007.
Hui Lu, Ognjen Perisic, and Dong Xu. Physical and Chemical Basis for Structural Bioinformatics. In, Computational Methods for Protein Structure Prediction and Modeling, edited by Ying Xu, Dong Xu, and Jie Liang. Springer-Verlag. Vol. 2. Pages 267-297, 2007.
Gyan Prakash Srivastava and Dong Xu. Genome-Scale Probe and Primer Design with PRIMEGENS. In, Methods in Molecular Biology, vol 402: PCR Primer Design, edited by Anton Yuryev, Humana Press, Totowa, New Jersey. Pages 159-175, 2007.
Trupti Joshi, Jinrong Wan, Curtis J. Palm, Kara Juneau, Ron Davis, Audrey Southwick, Katrina M. Ramonell, Gary Stacey, Dong Xu. Bioinformatics Analyses of Arabidopsis thaliana Tiling Array Expression Data In Knowledge Discovery in Bioinformatics: techniques, Methods and Applications" edited by Yi Pan and Xiaohua (Tony) Hu, John Wiley and Sons, New York. In press.
Trupti Joshi, Chao Zhang, Guan Ning Lin, Zhao Song, Dong Xu. GeneFAS: A tool for prediction of gene function using multiple sources of data. In "Genomics Protocols" volume of "Methods in Molecular Biology", the second edition, edited by Ramnath Elaswarapu and Michael P. Starkey. Humana Press, Totowa, New Jersey. In press.
Rajkumar Bondugula, Ognen Duzlevski, Dong Xu. "Profiles and fuzzy K-nearest neighbor algorithm for protein secondary structure prediction". Pages 85-94. Yi-Ping Phoebe Chen and Limsoon Wong, editors. Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore. Imperial College Press, London.
Robin Kramer, Victor Olman, Ying Xu, and Dong Xu. "DigitalTree: A Tool for Displaying Biological Data in Tree Structure". Lecture Notes in Computer Science, 3992, 855-862. 2006. (Also in Proceeding of International Conference on Computational Science 2006 (ICCS 2006), University of Reading, UK).
Yong Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, and Luonan Chen. "Supervised Inference of Gene Regulatory Networks by Linear Programming". Lecture Notes in Computer Science, 4115, 551-561, 2006. (Also in Proceeding of the 2006 International Conference on Intelligent Computing (ICIC 2006), Kunming, China).
Dong Xu, Rajkumar Bondugula, Mihail Popescu, James M Keller. "Bioinformatics and Fuzzy Logic". Proceeding of 15th IEEE International Conference on Fuzzy Systems, Vancouver, BC, Canada, July 2006, pp. 4208-4215.
Rajkumar Bondugula, Dong Xu, and Yi Shang. "A Fast Algorithm for Low-Resolution Protein Structure Prediction". Proceeding of the 28th International Conference of the IEEE Engineering in Medicine and Biology Society, New York. 2006.
Zhao Song, Luonan Chen, Chao Zhang, Dong Xu. "Design and Implementation of Probability-Based Scoring Function for Peptide Mass Fingerprinting Protein Identification". Proceeding of the 28th International Conference of the IEEE Engineering in Medicine and Biology Society, New York. 2006.
Mihail Popescu, Dong Xu, Erik Taylor. GoFuzzKegg: Mapping Genes to KEGG Pathways Using an Ontological Fuzzy Rule System. Proc. of the 2007 IEEE Symposium on Comp. Intell. in Bioinf. and Comp. Biology (CIBCB 2007), Hawaii, USA, pp. 298-303, 2007.
Mihail Popescu, Dong Xu. Mapping Genes to Pathways Using Ontological Fuzzy Rule Systems. Fuzzy Systems Conference, FUZZIEEE2007, London, UK, July 23-26, pp. 1-6, 2007.
Sum Kim, Meng Li, Henry H. Paik, Kenneth P. Nephew, Huidong Shi, Robin Kramer, Dong Xu, Tim H.-M. Huang. Predicting DNA Methylation Susceptibility Using CpG Flanking Sequences. Pacific Symposium on Biocomputing, the Big Island of Hawaii, 13:315-326, January, 2008.
H. K. Ching and J. K. Chen, "Thermal Stress Analysis of Functionally Graded Composites with Temperature-dependent Material Properties", Journal of Mechanics of Materials and Structures. Vol. 2, No. 4, pp. 633-654, 2007.
X. Song and J. K. Chen, "A Comparative Study on Poiseuille Flow of Simple Fluids through Cylindrical and Slit-like Nanochannels", International Journal of Heat and Mass Transfer (in press).
Crosslinking prediction tool, (detailed in: Nadeau OW, Anderson DW, Yang Q, Artigues A, Paschall JE, Wyckoff GJ, McClintock JL, Carlson GM. Evidence for the location of the allosteric activation switch in the multisubunit phosphorylase kinase complex from mass spectrometric identification of chemically crosslinked peptides. J Mol Biol. 2007 Feb 2; 365(5):1429-45. Epub 2006 Oct 21.)
Evolutionary database: Vallender EJ, Paschall JE, Malcom CM, Lahn BT, Wyckoff GJ. SPEED: a molecular-evolution-based database of mammalian orthologous groups. Bioinformatics. 2006 Nov 15; 22(22):2835-7. Epub 2006 Sep 11.
Mass Spec analysis tool: Starkweather R, Barnes CS, Wyckoff GJ, Keightley JA. Virtual polymorphism: finding divergent peptide matches in mass spectrometry data. Anal Chem. 2007 Jul 1; 79(13):5030-9. Epub 2007 May 24.