ICBR: Research Publications

Search Publications by Year and Division

2007 » Bioinformatics | Cellomics | Genomics | Proteomics
2006 » Bioinformatics | Cellomics | Genomics | Proteomics
2005 » Bioinformatics | Cellomics | Genomics | Proteomics
2004 » Bioinformatics | Cellomics | Genomics | Proteomics
2003 » Bioinformatics | Cellomics | Genomics | Proteomics


2007
Bioinformatics

  1. Popp MP, Liu L, Timmers A, Esson DW, Shiroma L, Meyers C, Berceli S, Tao M, Wistow G, Schultz GS, Sherwood MB. "Development of a Microarray Chip for Rabbit Ocular Research". Molecular Vision. 2007, 13:.
  2. Sun Y, Goodison S, Li J, Liu L, Farmerie WG "Improved breast cancer prognosis through the combination of clinical and genetic markers" Bioinformatics. 2007, 23(1), 30-37
  3. Sun Y, "Iterative RELIEF for Feature Weighting: Algorithms, Theories, and Applications", IEEE Transactions on Pattern Analysis and Machine Intelligence. 2007, in press.
  4. Sun Y, Todorovic S, Li J, "Unifying Multi-Class AdaBoost Algorithms with Binary Base Learners under the Margin Framework", Pattern Recognition Letters, vo. 28, no. 5, pp. 631-643, April 2007.
  5. Sun Y, Todorovic S, Li J, "Increasing the Robustness of Boosting Algorithms within the Linear-Programming Framework", Journal of VLSI Signal Processing Systems, 2007, in press.
  6. Yu FR, Yu FH, Li R., Wang R. "The Effect of Hydrocotyle Sibthorpioides extract on transplanted tumor and the immune function of mice. Phytomedicine, 2007, in press.

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2006
Bioinformatics
  1. Chao EM, Liu L, Farmerie WG, Keyhani NO "EST analysis of cDNA libraries from the entomopathogenic fungus Beauveria (Cordyceps) bassiana. I. Evidence for stage-specific gene expression in aerial conidia, in vitro blastospores and submerged conidia." Microbiology. 2006 Sep;152(Pt 9):2843-54.
  2. Ding X, Richter T, Chen M, Fujii H, Xie M, Zheng X, Kanrar S, Stevenson B, Dardick C, Li Y, Jiang H, Zhang Y, Yu FH, Zhu L, Farmerie WG, Gribskov M, Zh J, Fromm M, Ronald PC, Song W. "A rice kinase-protein interaction map". 2006 Plant Cell
  3. Gabriel DW, Allen C, Schell M, Denny TP, Greenberg JT, Duan Y, Flores-Cruz Z, Huang Q, Clifford JM, Presting G, Gonzalez ET, Reddy J, Elphinstone J, Swanson J, Yao J, Mulholland V, Liu L, Farmerie WG, Patnaikuni M, Balogh B, Norman D, Alvarez A, Castillo JA, Jones J, Saddler G, Walunas T, Zhukov A, Mikhailova N "Identification of open reading frames unique to a Select Agent: Ralstonia solanacearum race 3 biovar 2", Molecular Plant-Microbe Interactions, 2006 Jan; 19(1):69-79
  4. Moroz LL, Edwards JR, Puthanveettil SV, Kohn A, Ha T, Heyland A, Knudsen B, Sahni A, Yu F, Liu L, Jezzini S, Sadreyev R, Lovell P, Iannucculli W, Chen M, Nguyen T, Sheng H, Shaw R, Kalachikov S, Panchin Y, Farmerie WG, Russo JJ, Ju J, Kandel ER "The Neuronal Transcriptome of Aplysia californica: A Platform for the Neurogenomics of Defined Neurons, Neuronal Compartments and Neuronal Circuitry", Cell. 2006 Dec 29;127(7):1453-1467
  5. Sun Y, Liu L, Popp M, Farmerie W. "Estimation of Cross-hybridization Signals Using Support Vector Regression." in Proc. IEEE Symp. of Computations in Bioinformatics and Bioscience (SCBB'06), 2006, June. pp. 17-21, Hangzhou, China
  6. Sun Y, Todorovic S, Li J, "Reducing the Overfitting of AdaBoost by Controlling its Data Distribution Skewness." International Journal of Pattern Recognition and Artificial Intelligence, vol. 20, no. 7, pp. 1093-1116, November 2006.
  7. Sun Y, Li J. "Iterative RELIEF for Feature Weighting", in Proc. International Conference on Machine Learning (ICML'06), pp. 913 - 920, Pittsburgh, PA, June 2006
  8. Xu CJ, Xu LZ, Yu FH, Tan WH, Moroz LL, Li J. "Nonparametric estimation of the number of unique mRNA transcripts expressed in a biological tissue." 2006 IEEE Transactions on Signal Processing 54 (10), 3759-3767.
  9. Yu FR, Lu SQ, Yu FH, Feng ST, McGuire PM, Li R, Wang R. "Protective effects of the polysaccharide from Euphorbia Kansui (Euphorbiaceae) on the swimming exercise-induced oxidative stress in mice" 2006 Canadian Journal of Physiology and Pharmacology 84: 1071-1079.
  10. Yu, FH, P. M. McGuire, W. C. Kilpatrick, and C. A. Woods "Phylogeography of the Giant Flying Squirrel (Petaurista) (Rodentia, Sciuridae), Inferred from Molecular and Morphological Analyses." 2006 Molecular Phylogenetics and Evolution 38:755-766.
Cellomics
  1. M. Palazuelos, D. A. Moraga; G. Erdos, K. Powers, B. Moudgil. 2006 In Vitro Toxicity of Nanosized Aluminum. J. Nanotoxicology (In Press)
Genomics
  1. Baco, AR, AM Clark, TM Shank. 2006. Six microsatellite loci from the deep-sea coral Corallium lauuense (Octocorallia: Coralliidae) from the island and seamonts of the Hawaiian archipelago. Molecular Ecology Notes, 6: 147-149.
  2. Clark, AM. 2006. Using microsatellite loci to determine the fine scale genetic structure of a complex of timber rattlesnake (Crotalus horridus) dens in northeastern New York. Masters Thesis, University of Florida, Gainesville, FL.
  3. Holbrook, KM, BA Loiselle, and AM Clark. 2006. Eight Polymorphic microsatellite loci for a neotropical nutmeg, Virola flexuosa. Molecular Ecology Notes 1-3.
  4. Moroz, L.L., Edwards, J.R., Puthanveettil, S.V., Kohn, A., Ha, T., Heyland, A., Knudsen, B., Sahni, A., Yu, F., Liu, L., Jezzini, S., Sadreyev, R., Lovell, P., Iannucculli, W., Chen, M., Nguyen, T., Sheng, H., Shaw, R., Kalachikov, S., Panchin, Y., Farmerie, W., Russo, J.J., Ju, J., and Kandel, E.R. (2006) "The Neuronal Transcriptome of Aplysia californica: A Platform for the Neurogenomics of Defined Neurons, Neuronal Compartments and Neuronal Circuitry" Cell 127: 1453-1467
  5. Moore, M.J., Dhingra, A., Soltis, P.S., Shaw, R., Farmerie, W.G., Folta, K.M., and Soltis, D.E. (2006) "Rapid and accurate pyrosequencing of angiosperm plastid genomes." BMC Plant Biol. 6:17
Proteomics
  1. Fuller, B. F.; Stevens Jr., S. M.; Sehnke, P. C.; Ferl, R. J.; "A Proteomics Analysis of Arabidopsis 14-3-3s"; Proteomics, 6, 3050-3059.
  2. Liu, L. C.; Cui, Y. H.; Chung, A. Y.; Shitara, Y.; Sugiyama, Y.; Keppler, D.; Pang, K. S.; "Vectorial transport of enalapril by Oatp1a1/Mrp2 and OATP1B1 and OATP1B3/MRP2 in rat and human livers" J. Pharmacol. Exp. Ther., 318, 395-402 .

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2005
Bioinformatics
  1. Farmerie WG, Hammer J, Liu L, Sahni A, Schneider M. "Biological Workflow with BlastQuest", Data & Knowledge Engineering, Volume 53, Issue 1, April 2005, Pages 75-97
  2. Kornberg LJ, Villaret D, Popp MP, Liu L, McLaren R, Brown H, and McFadden M. "Gene Expression Profiling in Squamous Cell Carcinoma of the Oral Cavity Shows Abnormalities in Several Signaling Pathways". Laryngoscope, 2005 Apr;115(4):690-8
  3. Yu FR, Lian XZ, Guo HY, McGuire PM, Li R., Wang R., Yu FH. "Isolation and characterization of methyl esters and derivatives from Euphorbia kansui (Euphorbiaceae) and their inhibitory effects on the human SGC-7901 cells." 2005 Journal of Pharmacy and Pharmaceutical Science 8: 528-535.
Genomics
  1. Ernst, J.A., M.S. Ascunce, A.M. Clark, and H.N. Nigg. 2005. Polymorphic microsatellite loci for Diaprepes root weevil (Diaprepes abbreviatus L.) Molecular Ecology Notes, 6:1-4.
  2. Leonard, D. 2005. The White-Breasted Nuthatch in Florida: history, limiting factors, and phylogeography. Ph.D. Dissertation, University of Florida, Gainesville, FL.
Proteomics
  1. Stevens Jr., S. M.; Chung, A. Y.; Chow, M. C.; McClung, S. H.; Strachan, C. N.; Harmon, A. C.; Denslow, N. D.; Prokai, L.; "Enhancement of Phosphoprotein Analysis Using a Fluorescent Affinity Tag and Mass Spectrometry"; Rapid Commun. Mass Spectrom., 19, 2157-2162.
  2. Beyer, B. B.; Johnson, J. V.; Chung, A. Y.; Li, T.; Madabushi, A.; Agbandje-Mckenna, M.; Mckenna, R.; Dame, J. B.; Dunn, B. M.; "Active-site specificity of digestive aspartic peptidases from the four species of Plasmodium that infect humans using chromogenic combinatorial peptide libraries"; Biochemistry, 44, 1768-1779 (2005).
  3. Haskins, W. E.; Kobeissy, F. H.; Wolper, R. A.; Ottens, A. K.; Kitlen, J. W.; McClung, S. H.; O'Steen, B. E.; Chow, M. C.; Pineda, J. A.; Denslow, N. D.; Hayes, R. L.; Wang, KKW; "Rapid discovery of putative protein biomarkers of traumatic brain injury by SDS-PAGE-capillary liquid chromatography-tandem mass spectrometry"; J. Neurotrauma, 22, 629-644 (2005).

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2004
Bioinformatics
  1. Esson DW, Popp MP, Liu L, Schultz GS, Sherwood MB. "Microarray analysis of the failure of filtering blebs in a rat model of glaucoma filtering surgery", Invest Ophthalmol Vis Sci. 2004 Dec;45(12):4450-62.
  2. Lu, S. Q., Z. G. Yuan, J. F. Pang, D. T. Yang, Yu FH, P. M. McGuire, F. Xie, and Y. P. Zhang "Molecular Phylogeny of the Genus Paramesotriton (Caudata: Salamandridae)." 2004 Biochemical Genetics, 42:139-148.
  3. Yu, FH., F. R. Yu, P. M. McGuire, C. W. Kilpatrick, and C. A. Woods "Phylogeography of Woolly Flying Squirrel (Eupetaurus): Implications for Development of Mitochondrial Cytochrome b Gene Sequences." 2004 Molecular Phylogenetics and Evolution 33:735-744.
  4. Yu FR, Yu FH, Li R., Wang R. "Toxic effect of chloromycetin on the ultrastructures of the motor neurons of the Chinese tree shrew." 2004, Canadian Journal of Physiology and Pharmacology 82: 276-281.
  5. Yu FR. Yu FH, Li R., Wang R. "Inhibitory effects of the Gentiana macrophylla extract on rheumatoid arthritis of rats" 2004, Journal of Ethnopharmacology 95(1): 77-81.
Genomics
  1. Ernst, JA, LC Branch, AM Clark, and G Hokit. 2004. Polymorphic microsatellite markers for the Florida scrub lizard (Sceloporus woodi). Molecular Ecology Notes 4:364-365.


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2003
Bioinformatics
  1. Cousins RJ, Blanchard RK, Popp MP, Liu L, Cao J, Moore JB and Green CL. "A Global View of the Selectivity of Zinc Deprivation and Excess on Genes Expressed in Human THP-1 Mononuclear Cells", PNAS, 2003 100:6952-6957
  2. Liu, Y. Z.; Yu FH, S. T. Su, and H. Lam "A cost-benefit evaluation server for supporting e-business decision-making." 2003 Decision Support Systems, 36(1):81-97.
Cellomics
  1. Metcalf T, Kelley KL, Erdos GW, Kaplan L and West CM. 2003 Formation of the outer layer of the Dictyostelium spore coat depends on the inner-layer protein SP85/PsB. Microbiology: 305-317
  2. Rivera RM, Kelley, KL, Erdos, GW and Hansen, PJ 2003. Alterations in ultrastructural morphology of two-cell bovine embryos produced in vitro and in vivo following physiologically relevant heat shock. Biol. Repro. 69:2068-2077
Genomics
  1. Allsteadt, J. 2003. Geographic variation in the morphology of Crotalus horridus (Serpentes: Viperidae). Ph.D. Dissertation, Old Dominion University, Norfolk, VA.
  2. Zhong, CK, JS Puhr, SS Wu, MM Goodenow, and JW Sleasman. 2003. Combination antiretroviral therapy results in a rapid increase in T Cell receptor variable region ß repertoire diversity within CD45RA CD8 T Cells in human immunodeficiency virus-infected children. Journal of Infectious Diseases 187:385-397.


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