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
Agrawal, G., Sarkar, A., Agrawal, R., Ndimba, B., Tanou, G., Dunn, M., Kieselbach, T., Cramer, R., Wienkoop, S., Chen, S., Rafudeen, M., Deswal, R., Barkla, B., Weckwerth, W., Heazlewood, J., Renaut, J., Job, D., & Rakwal, R. (2012). Boosting the globalization of plant proteomics through INPPO: current developments and future prospects. Proteomics, 12(3), 359-368.
Al-Khedery, B., Barbet, A.F. (2014). Comparative Genomics Identifies a Potential Marker of Human-Virulent Anaplasma phagocytophilum. Pathogens, 3(1):25-35.
Anderson C., Kubisiak, T., Nelson, C., Smith, J., & Davis, J. (2010). Genome size variation in the pine fusiform rust pathogen Cronartium quercuum f.sp. fusiforme as determined by flow cytometry. Mycologia, 102(6), 1295-1302.
Ashrafi H., Hill T., Stoffel K., Kozik A., Yao J., Chin-Wo S., & Van Deynze A. (2012). De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes. BMC Genomics, 13, 571.
Aydemir, T., Liuzzi, J., McClellan, S., & Cousins, R. (2009). Zinc transporter ZIP8 (SLC39A8) and zinc influence IFN-gamma expression in activated human T cells. Journal of Leukocyte Biology, 86(2), 337-348.
Azari H., Sharififar S., Fortin J., & Reynolds B. (2012). The neuroblast assay: an assay for the generation and enrichment of neuronal progenitor cells from differentiating neural stem cell progeny using flow cytometry. J Vis Exp.
Bae, K., Su, Z., Frye, C., McClellan, S., Allan, R., Andrejewski, J., Kelley, V., Jorgensen, M., Steindler, D., Vieweg, J., & Siemann, D. (2010). 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) 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.
Bergeron, R.J.,Bharti, N., Singh, S., McManis, J.S., Wiegand, J. & Green, L.G. (2009). Vibriobactin Antibodies: A Vaccine Strategy. J. Med. Chem, 52, 3801–3813.
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). Transient inhibition of transforming growth factor-beta1 in human diabetic CD34+ cells enhances vascular reparative functions. Diabetes, 59(8), 2010-2019.
Bocsanczy, A. M., Achenbach, U. C., Mangravita-Novo, A., Chow, M., & Norman, D. J. (2014). Proteomic comparison of Ralstonia solanacearum strains reveals temperature dependent virulence factors. BMC genomics, 15(1), 280.
Boucias, D., Cai, Y., Sun, Y., Lietze, V.U., Sen, R., Raychoudhury, R., and Sharf, M.E. (2013). The hindgut lumen prokaryotic microbiota of the termite Reticulitermes flavipes and its responses to dietary lignocellulose composition. Molecular Ecology, 22, 1836-1853.
Boucias, D., Kariithi, H., Bourtzis, K., Schneider, D., Kelley, K., Miller, W., Parker, A., & Adb-Alla, A. (2013). Transgenerational Transmission of the Glossina pallidipes Hytrosavirus Depends on the Presence of a Functional Symbiome. PLoS ONE, 8(4), e61150.
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). 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.
Cabrera R., Ararat M., Xu Y., Brusko T., Wasserfall C., Atkinson M., Chang L., Liu C., & Nelson D. (2013). Immune modulation of effector CD4+ and regulatory T cell function by sorafenib in patients with hepatocellular carcinoma. Cancer Immunol Immunother, 62(4), 737-46.
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). 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). Aldehyde dehydrogenase-expressing colon stem cells contribute to tumorigenesis in the transition from colitis to cancer. Cancer Researchearch, 69(20), 8208-8215.
Chen, S. (2012). Proteomic characterization of stomatal movement. Plant Science J., 30, 12.
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
Dai, S., & Chen, S. (2012). Single-cell-type proteomics toward a holistic understanding of plant functions. Molecular and Cellular Proteomics, 11(12), 1622-30.
Darst, R. , Pardo, C., Ai, L., Brown, K., & Kladde, M. (2010). Bisulfite Sequencing of DNA. In Current Protocols in Molecular Biology (91:7.9.1–7.9.17). John Wiley & Sons, Inc.
DeFraia, C., Wang, Y., Yao, J., & Mou, Z. (2013). Elongator subunit 3 positively regulates plant immunity through its histone acetyltransferase and radical S-adenosylmethionine domains. BMC Plant Biology, 13:102 doi:10.1186/1471-2229-13-102.
Donohoe, B., Kang, B., Gerl, M., Gergely, Z., McMichael, C., Bednarek, S., Staehelin, L. (2013). Cis-Golgi Cisternal Assembly and Biosynthetic Activation Occur Sequentially in Plants and Algae. TRAFFIC, 14(5), 551-567.
Garcia-Reyero, N., Lavelle, C., Escalon, B., Martinović, D., Kroll, K., Sorensen, P., & Denslow, N. (2010). Behavioral and genomic impacts of a wastewater effluent on the fathead minnow. Aquatic Toxicology, 101(1), 38-48.
Goncalves, E., Johnson, J., & Rathinasabapthi, B. (2013). Conversion of membrane lipid acyl groups to triacylglycerol and formation of lipid bodies upon nitrogen starvation in biofuel green algae Chlorella UTEX29. Planta, doi:10.1007/s00425-013-1946-5.
Goodison, S., Sun, Y., & Urquidi, V. (2010). Review: Derivation of cancer diagnostic and prognostic signatures from gene expression data. Bioanalysis, 2, 855-862.
Gray, J., Dittrich, A., Chen, S., Avila, J., Giavalisco, P., & Devarenne, T. (2013). Two Pdk1 phosphorylation sites on the plant cell death suppressor Adi3 contribute to substrate phosphorylation. BBA - Proteins and Proteomics, 1834, 1099-1106.
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). 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). 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.
He, Y., Dai, S., Dufresne, C., Zhu, N., Pang, Q., & Chen, S. (2012). Integrated proteomics and metabolomics of Arabidopsis acclimation to gene-dosage dependent perturbation of isopropylmalate dehydrogenases. PLoS ONE, 8(3): e57118. doi:10.1371/journal.pone.0057118.
Hepowit, N., Uthandi, S., Miranda, H., Toniutti, M., Olivarez, O., De Vera, S.., Fanucci, G., Chen, S., & Maupin-Furlow, J. (2012). Archaeal JAB1/MPN/MOV34 metalloenzyme (HvJAMM1) cleaves ubiquitin-like small archaeal modifier proteins (SAMPs) from protein-conjugates. Molecular Microbiology, 86, 971-987.
Hill T., Ashrafi H., Reyes-Chin-Wo S., Yao J., Stoffel K., Truco M., Kozik L., & Michelmore R. (2013). Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene pepper GeneChip. PLoS ONE, 8(2), e56200.
Hoy M., Yu F., Meyer J., Tarazona O., Jeyaprakash A., & Wu K. (2012). Transcriptome sequencing and annotation of the predatory mite Metaseiulus occidentalis (Acari: Phytoseiidae): a cautionary tale about possible contamination by prey sequences. Experimental and Applied Acarology, 59(3), 283-296.
Hu, G., Koh, J., Yoo, M., Grupp, K., Chen, S., & Wendel, J. (2013). Proteomic profiling of developing cotton fibers from wild and domesticated Gossypium barbadense. New Phytologist, doi: 10.1111/nph.12381.
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.
Jadhao C., Bhatwadekar A., Jiang Y., Boulton M., Steinle J., & Grant M. (2012). Nerve growth factor promotes endothelial progenitor cell-mediated angiogenic responses. Invest Ophthalmol Vis Sci, 53(4), 2030-7.
Jaiswal, A., Aneja, R., Connors, S., Joshi, H., Multani, A., Pathak, S., & Narayan, S. (2009). 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). 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.
Jubair, M., Morris, J., & Ali, A. (2012). Survival of Vibrio cholera in Nutrient-Poor Environments Is Associated with Novel “Persister” Phenotype. PLoS ONE, 7(9), e45187. doi:10.1371.
Jungke, P., Ostrow, G., Li, J., Norton, S., Nieber, K., Kelber, O., & Butterweck, V. (2011). 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.
Koh, J., Chen, S., Zhu, N., Yu, F., Soltis, P., & Soltis, D. (2012). Comparative proteomics of the recently and recurrently formed natural allopolyploid Tragopogon mirus (Asteraceae) and its parents. New Phytologist, 196, 292-305.
Law, L., Corsino, P., Jahn, S., Davis, B., Chen, S., Patel, B., Pham, K., Lu, J., Sheppard, B., Nørgaard, P., Hong, J., Luesch, H., & Law, B. (2013). Glucocorticoids and histone deacetylase inhibitors cooperate to block the invasiveness of basal-like breast cancer cells through novel mechanisms. Oncogene, 32(10), 1316-29.
Lee, K., Park, J., Williams, D., Xiong, Y., Hwang, I., Kang, B. (2013). Defective chloroplast development inhibits maintenance of normal levels of abscisic acid in a mutant of the Arabidopsis RH3 DEAD-box protein during early post-germination growth. Plant Journal, 73(5), pgs, 720-732. .
Levings, P., McGarry, S., Currie, T., Nickerson, D., McClellan, S., Ghivizzani, S., Steindler, A., & Gibbs, C. (2009). Expression of an exogenous human Oct-4 promoter identifies tumor-initiating cells in osteosarcoma. Cancer Research, 69(14), 5648-5655.
Li S., & Yu F. (2012). Cranial morphometric study of four giant flying squirrels (Petaurista) (Rodentia: Sciuridae) from China. Zoological Research, 33, 119-126.
Li, X., Hu, Z., Jorgenson, M., & Slayton, W. (2009). 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.
Li Y., Yao J., Garden B., Chang K., Yu F., & Goodenow, M. (2012). HPV-QUEST: a highly customized system for automated HPV sequence analysis capable of processing Next Generation Sequencing data set. Bioinformation, 8(8), 388-90.
Lovett D., Shekhar N, Nickerson J., Roux K., & Lele T. (2013). Modulation of Nuclear Shape by Substrate Rigidity. Cell Mol Bioeng, 6(2), 230-238.
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.
Moreb, J., Ucar, D., Han, S., Amory, J., Goldstein, A., Ostmark, B., & Chang, L. (2012). The enzymatic activity of human aldehyde dehydrogenases 1A2 and 2 (ALDH1A2 and ALDH2) is detected by Aldefluor, inhibited by diethylaminobenzaldehyde and has significant effects on cell proliferation and drug resistance. Chem Biol Interact, 195(1), 52-60.
Moroz, L. L., Kocot, K. M., Citarella, M. R., Dosung, S., Norekian, T. P., Povolotskaya, I. S., Fahong, Y, & Kohn, A. B. (2014). The ctenophore genome and the evolutionary origins of neural systems. Nature.
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.
Nicholson, W., Leonard, M., Fajardo-Cavazos, P., Panayotova, N., Farmerie, W., Triplett, E. & Schuerger, A. (2013). Complete Genome Sequence of Serratia liquefaciens Strain ATCC 27592. Genome Announcements, 1(4), e00548-13. doi:10.1128/genomeA.00548-13.
Nirmala, X., Schetelig, M., Yu, F., Handler, A. (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.
Parker, J., Koh, J., Yoo, M., Zhu, N., Feole, M., Yi, S., & Chen, S. (2013) Quantitative proteomics of tomato defense against Pseudomonas syringae infection. Proteomics 13, 1934-1946.
Parker, J., Zhu, N., Zhu, M., & Chen, S. (2012). Profiling thiol redox proteome using isotope tagging mass spectrometry. Journal of Visual Experiments, 61, e3766. doi:10.3791/3766.
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). 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). Rapid dopaminergic modulation of the fish hypothalamic transcriptome and proteome. PLoS One, 5(8), e12338.
Raychoudhury, R., Sen, R., Cai, Y., Sun, Y., Lietze, V., Boucias, D., & Sharf, M. (2012). Comparative metatranscriptomic signatures of wood and paper feeding in the gut of the termite Reticulitermes flavipes (Isoptera: Rhinotermitidae). Insect Molecular Biology, 22(2), 155-171.
Rice, L., Lepler, S., Pampo, C., & Siemann, D. (2012). Impact of the SRC inhibitor dasatinib on the metastatic phenotype of human prostate cancer cells. Clin Exp Metastasis, 2, 133-42.
Ruiz, C., Nollens, H., Venn-Watson, S., Green, L., Wells, R., Walsh, M., Nolan, E., McBain, J., & Jacobson, E. (2009). Baseline circulating immunoglobulin G levels in managed collection and free-ranging bottlenose dolphins (Tursiops truncates). Developmental and Comparative Immunology, 33, 449–455.
Sakatani, M., Bonilla, L., Dobbs, K., Block, J., Ozawa, M., Shanker, S., Yao, J., & Hansen, P. (2013). Changes in the transcriptome of morula-stage bovine embryos caused by heat shock: relationship to developmental acquisition of thermotolerance. Reproductive Biology and Endocrinology, doi: 10.1186/1477-7827-11-3.
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). 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). Risk assessment of transgenicapomictic tetraploid bahiagrass, cytogenetics, breeding behavior and performance of intra-specific hybrids. Theoretical and Applied Genetics, 119(8), 1383-1395.
Satoh, M., Chan, J., Ross, S., Li, Y., Yamasaki, Y., Yamada, H., Vazquez-del, M., Petri, M., Jara, L., Saavedra, M., Cruz-Reyes, C., Sobel, E., Reeves, W., Ceribelli, A., & Chan, E. (2012). Autoantibodies to transcription intermediary factor (TIF)1β associated with dermatomyositis. Arthritis Research & Therapy, 14(2), R79.
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.
Sefah, K., Yang, Z., Bradley, K.M., Hoshika, S., Jiménez, E., Zhang, L., Zhu, G., Shanker, S., Yu, F., Turek, D., Tan, W., Benner, S.A. (Dec., 30 2013). In vitro selection with artificial expanded genetic information systems. Proc. Natl. Acad. Sci. USA, 10.1073/pnas.010123497
Shenoy, A., Butterworth, E., & Huang, E. (2012). ALDH as a marker for enriching tumorigenic human colonic stem cells. Methods Mol Biol, 916, 373-85.
Shenoy, A., Fisher, R., Butterworth, E., Pi, L., Chang, L,. Appelman, H., Chang, M., Scott, E., & Huang, E. (2012). Transition from colitis to cancer: high Wnt activity sustains the tumor-initiating potential of colon cancer stem cell precursors. Cancer Res, 72(19), 5091-100.
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.
Silva-Sanchez, C., Chen, S., Zhu, N., Li, Q., Chourey, P. (2013). Proteomic comparison of basal endosperm in Maize miniature1 mutant and its wild-type Mn1. Frontiers in Plant Physiology, 4, 210.
Simpson, A., Maeda, S., & Marsella, R. (2009). 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). 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). Queen conch (Strombus gigas) testis regresses during the reproductive season at nearshore sites in the Florida Keys. PLoS One, 5(9), e12737.
Sriwanayos, P., Francis-Floyd, R., Stidworthy, M., Petty, B., Kelley, K., & Waltzek, T. (2013). Megalocytivirus infection in orbiculate batfish Platax orbicularis. Diseases of Aquatic Organisms, 105, 1-8.
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). Aldehyde dehydrogenase activity as a functional marker for lung cancer. Chemico-Biological Interactions, 178(1-3), 48-55.
Ucar, D., Kurenova, E., Garrett, T., Cance, W., Nyberg, C., Cox, A., Massoll, N., Ostrov, D., Lawrence, N., Sebti, S., Zajac-Kaye, M., & Hochwald, S. (2012). Disruption of the protein interaction between FAK and IGF-1R inhibits melanoma tumor growth. Cell Cycle, 11(17), 3250-9.
Valladares, R., Bojilova, L., Potts, A., Cameron, E., Gardner, C., Lorca, G., & Gonzalez, C. (2013). Lactobacillus johnsonii inhibits indoleamine 2,3-dioxygenase and alters tryptophan metabolite levels in BioBreeding rats. FASEB Journal, 27, 1711-1720.
Valles, S., Oi, D., Yu, F., Tan, X., & Buss, E. (2012). Application of metagenomics and pyrosequencing to facilitate discovery of potential viral natural enemies of the invasive Caribbean crazy ant, Nylanderia pubens (Forel). PLoS ONE, 7, e31828.
Wallet, M., Rodriguez, C., Yin, L., Saporta, S., Chinratanapisit, S., Hou, W., Sleasman, J., & Goodenow, M. (2010). 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). Gliotypic neural stem cells transiently adopt tumorigenic properties during normal differentiation. Stem Cells, 27(2), 280-289.
Wanchoo, A., Lewis, M., & Keyhani, N. (2009). 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). 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). 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.
Wang, Y., An, C., DeFraia, C., Yao, J., Zhang, X., Zhang, Y., Sun, Y., Yu, F., Amador, A., & Mou Z. (2013). The Arabidopsis elongator complex subunit2 epigenetically regulates plant immune responses. Plant Cell, 25(2), 762-776.
Wellehan, J.F., Green, L.G., Duke, D.G., Bootorabi, S., Heard, D.J., Klein, P.A., & Jacobson, E.R. (2009). Detection of specific antibody responses to vaccination in variable flying foxes (Pteropus hypomelanus).Comp Immunol Microbiol Infect Dis., 32, 379-394.
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). 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.
Xu, G., Stevens, S., Moore, B., McClung, S., Borchelt, D. (2013). Cytosolic proteins lose solubility as amyloid deposits in a transgenic mouse model of Alzheimer-amyloidosis. Human Molecular Genetics, 22(14), 2765-74.
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.
You, J., Lee, E., Bonilla, L., Francis, J., Koh, J., Block, J., Chen, S., & Hansen, P. (2012) Treatment with the proteasome inhibitor MG132 during the end of oocyte maturation improves oocyte competence for development after fertilization in cattle. Plos One, 7(11): e48613. doi:10.1371.
Yu, F., Li, S., Kilpatrick, C., McGuire, P., He, K., & Wei W. (2012). Biogeographical study of plateau pika Ochotona curzoniae (Lagomorpha, Ochotona). Zoological Sciences, 29(8), 518-526.
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.
Zhalnina, K. V., Dias, R., Leonard, M. T., de Quadros, P. D., Camargo, F. A., Drew, J. C., Farmerie, W, Daroub, S, & Triplett, E. W. (2014). Genome Sequence of Candidatus Nitrososphaera evergladensis from Group I. 1b Enriched from Everglades Soil Reveals Novel Genomic Features of the Ammonia-Oxidizing Archaea. PloS one, 9(7), e101648.
Zhang, H., Han, B., Wang, T., Chen, S., Li, H., Zhang, Y., & Dai, S. (2012) Mechanisms of plant salt response: insights from proteomics. Journal of Proteome Research, 11, 49-67.
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.
Zhang, X., Wang, C., Zhang, Y., Sun, Y., & Mou, Z. (2012). The Arabidopsis mediator complex subunit16 positively regulates salicylate-mediated systemic acquired resistance and jasmonate/ethylene-induced defense pathways. Plant Cell, 24(10), 4294-309.
Zhang X., Yao J., Zhang Y., Sun Y., & Mou Z. (2013). The Arabidopsis Mediator complex subunits MED14/SWP and MED16/SFR6/IEN1 differentially regulate defense gene expression in plant immune responses. Plant Journal, 75(3), 484-97.
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.