Publications
Only select publications, beginning January 2009, are available online. Please contact ICBR if you are searching for a specific citation. Please note that the publications listed are the result of data generated by one or more ICBR cores.
| Select Publications |
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| Anderson C., Kubisiak, T., Nelson, C., Smith, J., & Davis, J. (2010, Nov). Genome size variationin the pine fusiform rust pathogen Cronartium quercuum f.sp. fusiforme as determined by flow cytometry. Mycologia, 102(6), 1295-1302. |
| Aydemir, T., Liuzzi, J., McClellan, S., & Cousins, R. (2009, Aug). Zinc transporter ZIP8 (SLC39A8) and zinc influence IFN-gamma expression in activated human T cells. Journal of Leukocyte Biology, 86(2), 337-348. |
| Bae, K., Su, Z., Frye, C., McClellan, S., Allan, R., Andrejewski, J., Kelley, V., Jorgensen, M., Steindler, D., Vieweg, J., & Siemann, D. (2010, May). Expression of pluripotent stem cell reprogramming factors by prostate tumor initiating cells. Journal of Urology, 183(5), 2045-2053. |
| Beem, J., Lee, P., & Segal, M. (2009, Jul) Lambda chops: creation of site-directed mutants in insertable fragments utilizing Gateway technology. Molecular Biotechnology, 42(3), 275-281. |
| Benskin, J., & Chen, S. (2011). Proteomics in the classroom: an investigative study of proteins in microorganisms. The American Biology Teacher, 74(4), 237-243. |
| Bhatwadekar, A., Guerin, E., Jarajapu, Y., Caballero, S., Sheridan, C., Kent, D., Kennedy, L., Lansang, M., Ruscetti, F., Pepine, C., Higgins, P., Bartelmez, S., & Grant, M. (2010, Aug). Transient inhibition of transforming growth factor-beta1 in human diabetic CD34+ cells enhances vascular reparative functions. Diabetes, 59(8), 2010-2019. |
| Brown, D., Farmerie, W., May, M., Benders, G., Durkin, A., Hlavinka, K., Hostetler, J., Jackson, J., Johnson, J., Miller, R., Paralanov, V., Radune, D., Szczypinski, B., & Glass, J. (2011). Genome sequences of Mycoplasma alligatoris A21JP2T and Mycoplasma crocodyli MP145T. Journal of Bacteriology, 193(11), 2892-2893. |
| Cabrera, R., Ararat, M., Cao, M., Xu, Y., Wasserfall, C., Atkinson, M., Liu, C., & Nelson, D. (2010, Feb). Hepatocellular carcinoma immunopathogenesis: clinical evidence for global T cell defects and an immunomodulatory role for soluble CD25 (sCD25). Digestive Diseases and Sciences, 55(2), 484-495. |
| Cai, Y., & Sun, Y. (2011). ESPRIT-Tree: taxonomy independent analysis of millions of pyrosequences in quasilinear computational time. Nucleic Acids Research, 39, e95. |
| Cao, M., Cabrera, R., Xu, Y., Liu, C., & Nelson, D. (2009, May). Gamma irradiation alters the phenotype and function of CD4+CD25+ regulatory T cells. Cell Biology International, 33(5), 565-571. |
| Carpentino, J., Hynes, M., Appelman, H., Zheng, T., Steindler, D., Scott, E., & Huang, E. (2009, Oct 15). Aldehyde dehydrogenase-expressing colon stem cells contribute to tumorigenesis in the transition from colitis to cancer. Cancer Researchearch, 69(20), 8208-8215. |
| Chen, Y., Pang, Q., Dai, S., Wang, Y., Chen, S., & Yan, X. (2011). Proteomic identification of differentially expressed proteins in Arabidopsis in response to methyl jasmonate. Journal of Plant Physiology, 168, 995-1008. |
| Cho, E., Yuen, C., Kang, B., Ondzighi, C., Staehelin, L., & Christopher, D. (2011). Protein disulfide isomerase-2 of Arabidopsis mediates protein folding and localizes to both the secretory pathway and nucleus, where it interacts with maternal effect embryo arrest factor. Molecules and Cells, 32, 459-475. |
| Choi, K., & Harfe, B. (2011) Hedgehog signaling is required for formation of the notochord sheath and patterning of nuclei pulposi within the intervertebral discs. Proceedings of the National Academy of Sciences of the United States of America, 108, 9484-9489. |
| Chourey, P., Li, Q., & Kumar, D. (2010). Sugar-hormone cross-talk in seed development: Two redundant pathways of IAA biosynthesis are regulated differentially in the invertase-deficient miniature1 (mns1) seed mutant in maize. Molecular Plant, 3, 1026-1036. |
| Dai, S., & Chen, S. (2011). Information processing at the proteomics level. In Kasabov, N. (Eds.), Springer Handbook of Bio-/Neuro-Informatics (Ch. 4). New York, NY: Springer |
| Garcia-Reyero, N., Lavelle, C., Escalon, B., Martinović, D., Kroll, K., Sorensen, P., & Denslow, N. (2010, Sep 29). Behavioral and genomic impacts of a wastewater effluent on the fathead minnow. Aquatic Toxicology, 101(1), 38-48. |
| Goodison, S., Sun, Y., & Urquidi, V. (2010). Review: Derivation of cancer diagnostic and prognostic signatures from gene expression data. Bioanalysis, 2, 855-862. |
| Hansen, P., Block, J., Loureiro, B., Bonilla, L., & Hendricks, K. (2010). Effects of gamete source and culture conditions on the competence of in vitro-produced embryos for post-transfer survival in cattle. Reproduction, Fertility and Development, 22(1), 59-66. |
| Harris J., Fisher, R., Jorgensen, M., Kaushal, S., & Scott, E. (2009, Feb). CD133 progenitor cells from the bone marrow contribute to retinal pigment epithelium repair. Stem Cells, 27(2), 457-466. |
| Havre, P., Abe, M., Urasaki, Y., Ohnuma, K., Morimoto, C., & Dang, N. (2009, Sep 15) CD26 expression on T cell lines increases SDF-1-alpha-mediated invasion. British Journal of Cancer, 101(6), 983-991. |
| He, Y., Chen, L., Zhou, Y., Mawhinney, T., Chen, B., Kang, B., Hauser, B., & Chen, S. (2011). Functional characterization of Arabidopsis thaliana isopropylmalate dehydrogenases reveals their important roles in gametophyte development. New Phytol, 189, 160-175. |
| Humbard, M., Miranda, H., Lim, J., Krause, D., Pritz, J., Zhou, G., Chen, S., Wells, L., & Maupin-Furlow, J. (2010) Ubiquitin-like Small Archaeal Modifier Proteins (SAMPs) and their conjugation to proteins in Haloferax volcanii. Nature, 463, 54-60. |
| Jaiswal, A., Aneja, R., Connors, S., Joshi, H., Multani, A., Pathak, S., & Narayan, S. (2009, Apr 15). 9-bromonoscapine-induced mitotic arrest of cigarette smoke condensate-transformed breast epithelial cells. Journal of Cellular Biochemistry, 106(6), 1146-1156. |
| Jeyaprakash, A., & Hoy, M. (2009, Apr). The nuclear genome of the phytoseiid Metaseiulus occidentalis (Acari: Phytoseiidae) is among the smallest known in arthropods. Experimental and Applied Acarology, 47(4), 263-273. |
| Jungke, P., Ostrow, G., Li, J., Norton, S., Nieber, K., Kelber, O., & Butterweck, V. (2011, Feb). Profiling of hypothalamic and hippocampal gene expression in chronically stressed rats treated with St. John’s wort extract (STW 3-VI) and fluoxetine. Psychopharmacology, 213(4), 757-772. |
| Kang, B. (2011). Shrinkage and fragmentation of the trans-Golgi network in non-meristematic plant cells. Plant Signaling & Behavior, 6, 884-886. |
| Kang, B., Nielsen, E., Preuss, M., Mastronarde, D., & Staehelin, L. (2011). Electron Tomography of RabA4b- and PI-4Kbeta1-Labeled Trans Golgi Network Compartments in Arabidopsis. Traffic, 12, 313-329. |
| Kang, S., Chen, S., & Dai, S. (2010) Proteomics characteristics of rice leaves in response to environmental factors. Frontiers in Biology, 5, 246-254. |
| Knoll, J., Ramos, M., Zeng, Y., Holbrook, C., Chow, M., Chen, S., Maleki, S., Bhattacharya, A., & Ozias-Akins, P. (2011). TILLING for allergen reduction and improvement of quality traits in peanut (Arachis hypogaea L.). BMC Plant Biology, 11, 81. |
| Koh, E., Zhou, L., Williams, D., Park, J., Ding, N., Duan, Y., & Kang, B. (2011). Callose deposition in the phloem plasmodesmata and inhibition of phloem transport in citrus leaves infected with “Candidatus Liberibacter asiaticus”. Protoplasma, 249(3), 687-697. |
| Levings, P., McGarry, S., Currie, T., Nickerson, D., McClellan, S., Ghivizzani, S., Steindler, A., & Gibbs, C. (2009, Jul 15). Expression of an exogenous human Oct-4 promoter identifies tumor-initiating cells in osteosarcoma. Cancer Research, 69(14), 5648-5655. |
| Li, X., Hu, Z., Jorgenson, M., & Slayton, W. (2009, Nov 10). High levels of acetylated low-density lipoprotein uptake and low tyrosine kinase with immunoglobulin and epidermal growth factor homology domains-2 (Tie2) promoter activity distinguish sinusoids from other vessel types in murine bone marrow. Circulation, 120(19), 1910-1918. |
| Li, Y., Lee, P., Kellner, E., Paulus, M., Switanek, J., Xu, Y., Zhuang, H., Sobel, E., Segal, M., Satoh, M., & Reeves, W. (2010). Monocyte surface expression of Fcgamma receptor RI (CD64), a biomarker reflecting type-I interferon levels in systemic lupus erythematosus. Arthritis Research & Therapy, 12(3), R90. |
| Li, Y., Lee, P., Sobel, E., Narain, S., Satoh, M., Segal, M., Reeves, W., & Richards, H. (2009). Increased expression of FcgammaRI/CD64 on circulating monocytes parallels ongoing inflammation and nephritis in lupus. Arthritis Research & Therapy, 11(1), R6. |
| Mai, V., Young, C., Ukhanova, M., Wang, X., Sun, Y., Shuster, J., Theriaque, D., Li, N., Sharma, R., Hudak, M., & Neu, J. (2011). Fecal microbiota in premature infants prior to necrotizing enterocolitis. PLoS ONE, 6, e20647. |
| Martyniuk, C., Feswick, A., Spade, D., Kroll, K., Barber, D., & Denslow, N. (2010). Effects of acute dieldrin exposure on neurotransmitters and global gene transcription in largemouth bass (Micropterus salmoides) hypothalamus. Neurotoxicology, 31(4), 356-366. |
| Mohandas, R., & Segal, M. (2010). Endothelial progenitor cells and endothelial vesicles – what is the significance for patients with chronic kidney disease? Blood Purif, 29(2), 158-162. |
| Muthukrishnan, G., Quinn, G., Lamers, R., Diaz, C., Cole, A., Chen, S., & Cole, A. (2011). Exoproteome of Staphylococcus aureus Reveals Putative Determinants of Nasal Carriage. J. Proteome Res., 10(4), 2064-2078. |
| Nirmala, X., Schetelig, M.F., Yu, F.H., Handler, A.M. (2013). An EST database of the Caribbean fruit fly, Anastrepha suspense (Diptera: Tephritidae). Gene, 517:212-217. |
| Ozawa, M., Sakatani, M., Yao, J., Shanker, S., Yu, F., Yamashita, R., Wakabayashi, S., Nakai, K., Dobbs, K., Sudano, M., Farmerie, W., & Hansen, P. (2012). Global gene expression of the inner cell mass and trophectoderm of the bovine blastocyst. BMC Developmental Biology, 12, 33. |
| Paul, A., Amalfitano, C., & Ferl, R. (2012). Plant growth strategies are remodeled by spaceflight. BMC Plant Biology, 12, 232. |
| Paul, A., Zupanska, A., Ostrow, D., Zhang, Y., Sun, Y., Li, J., Shanker, S., Farmerie, W., Amalfitano, C., & Ferl, R. (2011). Spaceflight transcriptomes: unique responses to a novel environment. Astrobiology, 12(1), 40-56. |
| Pennington, K., Oliveira, L., Yang, Q., Ealy, A. (2010, Aug). The enrichment of trophoblast giant cells from mid-gestation bovine placentae using fluorescence-activated cell sorting. Placenta, 31(8):738-740. |
| Popesku, J., Martyniuk, C., Denslow, N., & Trudeau, V. (2010, Aug 20). Rapid dopaminergic modulation of the fish hypothalamic transcriptome and proteome. PLoS One, 5(8), e12338. |
| Saldana, Z., Sanchez, E., Cortes, J., Peunte, J., & Giron, J. (2011). Surface structures involved in plant stomata and leaf colonization by Shiga-toxigenic Escherichia coli O157:H7. Frontiers in Microbiology, 2, 119. |
| Sandhu, S., Blount, A., Quesenberry, K., & Altpeter, F. (2010, Sep) Apomixis and ploidy barrier suppress pollen-mediated gene flow in field grown transgenic turf and forage grass (Paspalum notatum Flüggé). Theoretical and Applied Genetics, 121(5), 919-929. |
| Sandhu, S., James, V., Quesenberry, K., & Altpeter, F. (2009, Nov) Risk assessment of transgenicapomictic tetraploid bahiagrass, cytogenetics, breeding behavior and performance of intra-specific hybrids. Theoretical and Applied Genetics, 119(8), 1383-1395. |
| Schmidt, L., Hewlett, T., Green, A., Simmons, L., Kelley, K., Doroh, M., & Stetina, S. (2010) Molecular and morphological characterization and biological control capabilities of a Pasteuria ssp: Parasitizing Rotylenchulus reniformis, the Reniform Nematode. Journal of Nematology 42(3), 207-217. |
| Sefah, K., Shangguan, D., Xiong, X., O’Donoghue, M., & Tan, W. (2010). Development of DNA aptamers using Cell-SELEX. Nat Protoc, 5(6), 1169-1185. |
| Shupe, T., Piscaglia, A., Oh, S., Gasbarrini, A., & Petersen, B. (2009). Isolation and characterization of hepatic stem cells, or “oval cells,” from rat livers. Methods in Molecular Biology, 482, 387-405. |
| Simpson, A., Maeda, S., & Marsella, R. (2009, Sep). Temporal dynamic changes of phenotypic expression of peripheral CD4 cells during environmental allergen challenge in an experimental model of canine atopic dermatitis: A pilot study. Journal of Veterinary Medical Science, 71(9), 1177-1181. |
| Skinner, R., Trujillo, A., Ma, X., & Beierle, E. (2009, Jan). Ketone bodies inhibit the viability of human neuroblastoma cells. Journal of Pediatric Surgery, 44(1), 212-216. |
| Spade, D., Griffitt, R., Liu, L., Brown-Peterson, N., Kroll, K., Feswick, A., Glazer, R., Barber, D., & Denslow N. (2012, Sep 15). Queen conch (Strombus gigas) testis regresses during the reproductive season at nearshore sites in the Florida Keys. PLoS One, 5(9), e12737. |
| Sun, Y., Cai, Y., Huse, S., Farmerie, W., Knight, R., Wang, X., & Mai, V. (2011). A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. Briefings in Bioinformatics, 13(1), 107-121. |
| Sun, Y., Cai, Y., Mai, V., Farmerie, W., Yu, F., Li, J., & Goodison, S. (2010). Advanced computational algorithms for microbial community analysis using mass 16S rRNA sequence data. Nucleic Acid Research, 38, e205. |
| Sun, Y., Todorovic, S., & Goodison, S. (2010). Local learning based feature selection for high dimensional data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence, 32, 1610-1626. |
| Sun, Y., Urquidi, V., & Goodison S. (2010). Derivation of molecular signatures for breast cancer recurrence prediction using a two-way validation approach. Breast Cancer Researchearch and Treatment, 119, 593-599. |
| Ucar, D., Cogle, C., Zucali, J., Ostmark, B., Scott, E., Zori, R., Gray, B., & Moreb, J. (2009, Mar 16). Aldehyde dehydrogenase activity as a functional marker for lung cancer. Chemico-Biological Interactions, 178(1-3), 48-55. |
| Wallet, M., Rodriguez, C., Yin, L., Saporta, S., Chinratanapisit, S., Hou, W., Sleasman, J., & Goodenow, M. (2010, Jun 1). Microbial translocation induces persistent macrophage activation unrelated to HIV-1 levels or T-cell activation following therapy. AIDS, 24(9), 1281-1290. |
| Walton, N., Snyder, G., Park, D., Kobeissy, F., Scheffler, B., & Steindler, D. (2009, Feb). Gliotypic neural stem cells transiently adopt tumorigenic properties during normal differentiation. Stem Cells, 27(2), 280-289. |
| Wanchoo, A., Lewis, M., & Keyhani, N. (2009, Sep). Lectin mapping reveals stage-specific display of surface carbohydrates in in vitro and haemolymph-derived cells of the entomopathogenic fungus Beauveria bassiana. Microbiology, 155(9), 3121-3133. |
| Wang, B., Han, S., Lien, L., & Chang, L. (2009, Sep). Lentiviral calnexin-modified dendritic cells promote expansion of high-avidity effector T cells with central memory phenotype. Immunology, 128(1), 43-57. |
| Wang, Q., Gao, F., Wang, T., Flagg, T., & Deng, X. (2009, Oct). A nonhomologous end-joining pathway is required for protein phosphatase 2A promotion of DNA double-strand break repair. Neoplasia, 11(10), 1012-1021. |
| Wang, X., Chen, S., Zhang, H., Shi, L., Cao, F., Guo, L., Xie, Y., Wang, T., Yan, X., & Dai, S. (2010) Desiccation tolerance mechanism in resurrection fern-ally Selaginella tamariscina revealed by physiological and proteomic analysis. Journal of Proteome Research, 9, 6561-6577. |
| Wellehan, J., Yu, F., Venn-Watson, S., Jensen, E., Smith, C., Farmerie, W., & Nollens, H. (2010). Characterization of San Migue sea lion virus populations using pyrosequencing based methods. Infection, Genetics and Evolution, 10, 254-260. |
| Wilson, K., Proneth, B., Luesch, H., Litherland, S., & Haskell-Luevano, C. (2009) Construction and characterization of melanocortin-2 and -4 receptor chimeras. Advances in Experimental Medicine and Biology, 611, 301-302. |
| Wurm, Y., Wang, J., Riba-Grognuz, O., Corona, M., Nygaard, S., Hunt, B., Ingram, K., Falquet, L., Nipitwattanaphon, M., Gotzekk, D., Dijkstra, M., Oettler, J., Comtesse, F., Shih, C., Wu, W., Yang, C., Thomas, J., Beaudoing, E., Pradervand, S., Flegel, V., Cook, E., Fabbretti, R., Stockinger, H., Long, L., Farmerie, W., Oakey, J., Boomsma, J., Pamilo, P., Yi, S., Heinze, J., Goodisman, M., Farinelli, L., Harshman, K., Hulo, N., Cerutti, L., Xenarios, I., Shoemaker, D., & Keller, L. (2011). The genome of the fire ant Solenopsis invicta. Proceedings Of The National Academy Of Sciences Of The United States Of America, 108(14), 5679-5684. |
| Xiang, Z., Proneth, B., Dirain, M., Litherland, S., & Haskell-Luevano, C. (2010, Jun 8). Pharmacological characterization of 30 human melanocortin-4 receptor polymorphisms with the endogenous proopiomelanocortin-derived agonists, synthetic agonists, and the endogenous agouti-related protein antagonist. Biochemistry, 49(22), 4583-4600. |
| Xiong, Y., Li, Q., Kang, B., & Chourey, P. (2011). Discovery of Genes Expressed in Basal Endosperm Transfer Cells in Maize Using 454 Transcriptome Sequencing. Plant Molecular Biology Reporter, 29, 835-847. |
| Yao, J., & Yu, F. (2011). DEB: A web interface for RNA-seq digital gene expression analysis. Bioinformation, 7(1), 44-45. |
| Yin L., Liu L., Sun Y., Hou W., Lowe A., Gardner B., Salemi M., Williams W., Farmerie W., Sleasman J., Goodenow M. (2012). High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems. Retrovirology, 9, 108. |
| Yu, F., Liu, Y., Cui, Y., Chan, E., Xie, M., McGuire, P., & Yu, F. (2010). Effect of a flavonoid extract from Cynomorium songaricum on the swimming endurance of rats. The American Journal of Chinese Medicines, 38, 65-73. |
| Yu, J., Chen, S., Zhao, Q., Wang, T., Yang, C., Diaz, C., Sun, G., & Dai, S. (2011). Physiological and proteomic analysis of salinity tolerance in Puccinellia tenuiflora. Journal of Proteome Research, 10, 3852-3870. |
| Yuan, Q., Zhang, Y., Chen, Y., Wang, R., Du, C., Yasun, E., & Tan, W. (2011). Using silver nanowire antennas to enhance the conversion efficiency of photoresponsive DNA nanomotors. Proceedings of the National Academy of Sciences of the United States of America, 108, 9331-9336. |
| Valladares, R., Bojilova, L., Potts, A.H., Cameron, E., Gardner, C., Lorca, G., & Gonzalez, C.F. (2013). Lactobacillus johnsonii inhibits indoleamine 2,3-dioxygenase and alters tryptophan metabolite levels in BioBreeding rats. FASEB Journal, 27, 1711-1720. |
| Zhang, S., Flores-Cruz, Z., Zhou, L., Kang, B., Fleites, L., Gooch, M., Wulff, N., Davis, M., Duan, Y., & Gabriel, D. (2011). ‘Ca. Liberibacter asiaticus’ carries an excision plasmid prophage and a chromosomally integrated prophage that becomes lytic in plant infections. Molecular Plant-Microbe Interactions, 24, 458-468. |
| Zhu, M., Dai, S., & Chen, S. (2011). The stomata frontline of plant interaction with the environment-perspectives from hormone regulation. Frontiers in Biology, 7(2), 96-112. |
| Zhu, M., Simons, B., Ning, Z., Oppenheimer, D., & Chen, S. (2010). Analysis of abscisic acid responsive proteins in Brassica napus guard cells by multiplexed isobaric tagging. Journal of Proteomics, 73, 790-805. |
