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 PublicationsAssociated Cores
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.Proteomics & Mass Spectrometry
Al-Khedery, B., Barbet, A.F. (2014). Comparative Genomics Identifies a Potential Marker of Human-Virulent Anaplasma phagocytophilum. Pathogens, 3(1):25-35.NextGen DNA Sequencing
Amador, David Moraga, et al. "Library Construction for Genome-wide Bisulfite Sequencing in Plants." (2013).NextGen DNA Sequencing
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.Cytometry
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.Bioinformatics
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.Cytometry
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.Cytometry
Badylak, S., Phlips, E. J., Mathews, A. L., & Kelley, K. (2014). Akashiwo sanguinea (Dinophyceae) extruding mucous from pores on the cell surface. Algae, 29(3), 197-201.Electron Microscopy
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.Cytometry
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.Proteomics & Mass Spectrometry
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.Monoclonal Antibodies
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.Proteomics & Mass Spectrometry
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.Electron Microcospy
Brant, J. O., Riva, A., Resnick, J. L., & Yang, T. P. (2014). Influence of the Prader-Willi syndrome imprinting center on the DNA methylation landscape in the mouse brain. Epigenetics, 9(11), 1540-1556.Bioinformatics
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.Bioinformatics
Brockmeier, E. K., Yu, F., Amador, D. M., Bargar, T. A., & Denslow, N. D. (2013). Custom microarray construction and analysis for determining potential biomarkers of subchronic androgen exposure in the Eastern Mosquitofish (Gambusia holbrooki). BMC genomics, 14(1), 660.NextGen DNA Sequencing
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.
Chakraborty, P. K., Zhang, Y., Coomes, A. S., Kim, W. J., Stupay, R., Lynch, L. D., ... & Daaka, Y. (2014). G Protein–Coupled Receptor Kinase GRK5 Phosphorylates Moesin and Regulates Metastasis in Prostate Cancer. Cancer research, 74(13), 3489-3500.Gene Expression & Genotyping, Proteomics & Mass Spectrometry
Chang, L.W., Fu, A, Wozniak, E., Chow, M., Duke, D.G., Green, L., Kelley, K., Hernandez, J.A., Jacobson, E.R. (2013, Dec). Immunohistochemical detection of a unique protein within cells of snakes having inclusion body disease, a world-wide disease seen in members of the families Boidae and Pythonidae, Plos One, 8(12), article e82916.Monoclonal Antibody
Chen, S. (2012). Proteomic characterization of stomatal movement. Plant Science J., 30, 12.Proteomics & Mass Spectrometry
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.Proteomics & Mass Spectrometry
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.Electron Microcopy
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.
Christiansen H.E., Mehinto A.C., Yu F.H., Perry R.W., Denslow N.D., Maule A.G., Mesa M.G. 2014. Correlation of gene expression and contaminant concentrations in wild largescale suckers: A field-based study. Science of The Total Environment. 484: 379-389.Bioinformatics
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: SpringerProteomics & Mass Spectrometry
Dai, S., & Chen, S. (2012). Single-cell-type proteomics toward a holistic understanding of plant functions. Molecular and Cellular Proteomics, 11(12), 1622-30.Proteomics & Mass Spectrometry
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.Sanger Sequencing
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.Bioinformatics
Denison, Fiona C., Tufan Gökirmak, and Robert J. Ferl. "Phosphorylation-related modification at the dimer interface of 14-3-3ω dramatically alters monomer interaction dynamics." Archives of biochemistry and biophysics 541 (2014): 1-12.Sanger Sequencing
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.
Dyka, F. M., Boye, S. L., Chiodo, V. A., Hauswirth, W. W., & Boye, S. E. (2014). Dual adeno-associated virus vectors result in efficient in vitro and in vivo expression of an oversized gene, MYO7A. Human gene therapy methods, 25(2), 166-177.Sanger Sequencing
Gao, C., Cai, Y., Wang, Y., Kang, B. H., Aniento, F., Robinson, D. G., & Jiang, L. (2014). Retention mechanisms for ER and Golgi membrane proteins. Trends in plant science, 19(8), 508-515.Electron Microscopy
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.Electron Microscopy
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.Proteomics & Mass Spectrometry
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.Cytometry
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.Electron Microscopy
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.Proteomics & Mass Spectrometry
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.Proteomics & Mass Spectrometry
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. Bioinformatics
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.NextGen DNA Sequnecing, Bioinformatics
Hu G, Koh J, Yoo MJ, Pathak D, Chen S, Wendel JF. 2014 Proteomics profiling of fiber development and domestication in upland cotton (Gossypium hirsutum L.). Planta. DOI: 10.1007/s00425-014-2146-7Bioinformatics, Proteomics & Mass Spectrometry
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.Proteomics & Mass Spectrometry
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.Proteomics & Mass Spectrometry
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.Cytometry
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.Electron Microscopy
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.Gene Expression & Genotyping
Kang, B. (2011). Shrinkage and fragmentation of the trans-Golgi network in non-meristematic plant cells. Plant Signaling & Behavior, 6, 884-886.Electron Microscopy
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.Electron Microscopy
Kang, S., Chen, S., & Dai, S. (2010) Proteomics characteristics of rice leaves in response to environmental factors. Frontiers in Biology, 5, 246-254.Proteomics & Mass Spectrometry
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.Proteomics & Mass Spectrometry
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.Electron Microscopy
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.Proteomics & Mass Spectrometry, Bioinformatics
Laurence Prunetti, Christopher J. Reuter, Nathaniel L. Hepowit, Yifei Wu, Luisa Barrueto, Hugo V. Miranda, Karen Kelley, Julie A. Maupin-Furlow. (2013) Structural and biochemical properties of an extreme ‘salt-loving’ proteasome activating nucleotidase from archaeon Haloferax volcanii. Extremophiles, 18(2), pp 283-293. Electron Microscopy
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.Proteomics & Mass Spectrometry
Lednicky, J. A., Waltzek, T. B., McGeehan, E., Loeb, J. C., Hamilton, S. B., & Luetke, M. C. (2013). Isolation and genetic characterization of human coronavirus NL63 in primary human renal proximal tubular epithelial cells obtained from a commercial supplier, and confirmation of its replication in two different types of human primary kidney cells. Virology Journal, 10, 213. doi:10.1186/1743-422X-10-213Electron Microscopy
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. .Electron Microscopy
Leem, G., Morseth, Z. A., Puodziukynaite, E., Jiang, J., Fang, Z., Gilligan, A. T., ... & Schanze, K. S. (2014). Light-Harvesting and Charge Separation in a π-Conjugated Antenna Polymer Bound to TiO2. The Journal of Physical Chemistry C. Electron Microscopy
Leonard, M.T., Panayotova, N., Farmerie, W.G., Triplett, E.W., Nicholson, W.L. (2013). Complete Genome Sequence of Carnobacterium gilichinskyi Strain WN1359T (DSM 27470T). Genome Announc, 1(6), e00985-13, doi: 10.1128/genomeA.00985-13.Bioinformatics
Leonard, M. T., Davis-Richardson, A. G., Ardissone, A. N., Kemppainen, K. M., Drew, J. C., Ilonen, J., ... & Triplett, E. W. (2014). The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei. Frontiers in microbiology, 5.
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., He K., Yu F.H., Yang Q.S. 2013. Molecular Phylogeny and Biogeography of Petaurist Inferred from the Cytochrome b Gene, with Implications for the Taxonomic Status of P. caniceps, P. marica and P. sybilla. Plos One 8:e70461.Bioinformatics
Li S., Yu F.H. 2013. Differentiation in cranial variables among six species of Hylopetes (Sciurinae: Pteromyini). Zoological Research, 34: E120-E127.Bioinformatics
Li S., & Yu F. (2012). Cranial morphometric study of four giant flying squirrels (Petaurista) (Rodentia: Sciuridae) from China. Zoological Research, 33, 119-126.Bioinformatics
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.Bioinformatics
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.Bioinformatics
Li-Wen Chang, Ann Fu, Edward Wozniak, Marjorie Chow, Diane G. Duke, Linda Green, Karen Kelley, Jorge A. Hernandes, Elliot R. Jacobson. (2013) Immunohistochemical Detection of a Unique Protein within Cells of Snakes Having Inclusion Body Disease, a World-Wide Disease Seen in Members of the Families Boidae and Pythonidae. PLoS ONE 8(12): e82916. (Press release Vet School, featured ICBR web)Electron Microscopy
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.
Lu, S., Zeumer, L., Sorensen, H., Yang, H., Ng, Y., Yu, F., ... & Morel, L. (2015). The Murine Pbx1-d Lupus Susceptibility Allele Accelerates Mesenchymal Stem Cell Differentiation and Impairs Their Immunosuppressive Function. The Journal of Immunology, 194(1), 43-55.Bioinformatics
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.Proteomics & Mass Spectrometry
Nabilsi, N. H., Deleyrolle, L. P., Darst, R. P., Riva, A., Reynolds, B. A., & Kladde, M. P. (2014). Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma. Genome research, 24(2), 329-339.Bioinformatics, NextGen DNA Sequencing
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.Bioinformatics
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.Bioinformatics
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.Bioinformatics
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. Proteomics & Mass Spectrometry
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.Proteomics & Mass Spectrometry
Paul, A., Amalfitano, C., & Ferl, R. (2012). Plant growth strategies are remodeled by spaceflight. BMC Plant Biology, 12, 232.Director
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.Bioinformatics
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.Cytometry
Popesku, J., Martyniuk, C., Denslow, N., & Trudeau, V. (2010). Rapid dopaminergic modulation of the fish hypothalamic transcriptome and proteome. PLoS One, 5(8), e12338.
Puthanveettil S.V., Antonov I., Kalachikod S., Rajasethupathy P., Choi Y.B., Koh, A.B., Citarella M., Yu F.H., Karl K.A., Kinet,M., Morozova I., Russo J.J., Ju J.Y., Moroz L.L., Kandel E.R. 2013. A strategy to capture and characterize the synaptic transcriptome. PNAS, 110, 7464-7469.Bioinformatics
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.
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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.Electron Microscopy
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.Bioinformatics
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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.Sanger Sequencing
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.Gene Expression & Genotyping
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. Gene Expression & Genotyping
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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.Proteomics & Mass Spectrometry