Publications

The following publications feature data analyzed using Rosetta Biosoftware products. To learn how to cite the use of Rosetta Biosoftware products, see Citation Guidelines.

Transcriptional profiling of Wnt4 mutant mouse kidneys identifies genes expressed during nephron formation

Valerius, M.T., McMahon, AP.Gene Expr Patterns (2008) vol. 8 (5) pp. 297-306.

 

Label-Free Detection of Differential Protein Expression by LC/MALDI Mass Spectrometry

Hendrik Neubert, Timothy P. Bonnert, Klaus Rumpel, Brandon T. Hunt, Ernst S. Henle, and Ian T. James. Web Release Date: April 16, 2008.

Genomic and functional profiling of human Down syndrome neural progenitors implicates S100B and aquaporin 4 in cell injury

Giuseppe Esposito, Jaime Imitola, Jie Lu, Daniele De Filippis, Caterina Scuderi, Vijay S. Ganesh, Rebecca Folkerth, Jonathan Hecht, Soojung Shin, Teresa Iuvone, Jonathan Chesnut, Luca Steardo and Volney Sheen. Human Molecular Genetics, 2008 17(3):440-457.

Aberrant innate immune response in lethal infection of macaques

Kobasa D., Jones S.M., Shinya K., Kash J.C., Copps J., Ebihara H., Hatta Y., Kim J.H., Halfmann P., Hatta M., Feldmann F., Alimonti J.B., Fernando L., Li Y., Katze M.G., Feldmann H., Kawaoka Y. Nature. 2007 Jan 18;445(7125):319-23.

Genomic analysis of increased host immune and cell death responses by 1918 influenza virus

Kash, J.C., Tumpey, T.M., Proll, S.C., Carter, V., Perwitasari, O., Thomas, M.J., Basler, C.F., Palese, P., Taubenberger, J.K., Garcia-Sastre, A., Swayne, D.E., Katze, M.G. Nature. 2006 Oct 5;443(7111):578-81. Epub 2006 Sep 27.

Altered hippocampal gene expression 2 days after general anesthesia in rats.

Culley, D.J., Yukhananov, R.Y., Xie, Z., Gali, R.R., Tanzi, R.E., Crosby, G. European Journal of Pharmacology.2006 Nov 7;549(1-3):71-8. Epub 2006 Aug 26.

Molecular characterization of adult mouse subventricular zone progenitor cells during the onset of differentiation.

Bonnert, T.P., Bilsland, J.G., Guest, P.C., Heavens, R., McLaren, D., Dale, C., Thakur, M., McAllister, G., Munoz-Sanjuan, I. (2006), European Journal of Neuroscience. 2006 Aug;24(3):661-75.

Profiling the hepatic effects of flutamide in rats: a microarray comparison with classical aryl hydrocarbon receptor ligands and atypical CYP1A inducers.

Coe, K. J., Nelson, S. D., Ulrich, R. G., He, Y., Dai, X., Cheng, O., Caguyong, M., Roberts, C. J., and Slatter, J. G. (2006), Drug Metabolism and Disposition., (34) 1266-1275.

Host-specific response to HCV infection in the chimeric SCID-beige/Alb-uPA mouse model: role of the innate antiviral immune response

Walters, K.A., Joyce, M.A., Thompson, J.C., Smith, M.W., Yeh, M.M., Proll, S., Zhu, L.F., Gao, T.J., Kneteman, N.M., Tyrrell, D.L., Katze, M.G. Public Library of Science Pathogens. 2006 Jun;2(6):e59. Epub 2006 Jun 23.

Agonists of the peroxisome proliferator-activated receptor alpha induce a fiber-type-selective transcriptional response in rat skeletal muscle.

De Souza, A.T., Cornwell, P.D., Dai, X., Caguyong, M.J., Ulrich, R.G. Toxicological Sciences 2006 Aug;92(2):578-86. Epub 2006 May 17.

Gene expression profiling of primary cutaneous melanoma and clinical outcome.

Winnepenninckx, V., Lazar, V., Michiels, S., Dessen, P., Stas, M., Alonso, S.R., Avril, M.F., Ortiz, Romero P.L., Robert, T., Balacescu, O., Eggermont, A.M., Lenoir, G., Sarasin, A., Tursz, T., van den Oord, J.J., Spatz, A. Journal of the National Cancer Institute. 2006 Apr 5;98(7):472-82.

Life Science Technologies: Proteomics - Interacting Instruments

May, M., Heebner, G. Science. 2006 April. Special Advertising Section.

Influence of sex on gene expression in the mouse lacrimal gland.

Richards, S.M., Jensen, R.V., Liu, M., Sullivan, B.D., Lombardi, M.J., Rowley, P., Schirra, F., Treister, N.S., Suzuki, T., Steagall, R.J., Yamagami, H., Sullivan, D.A. Experimental Eye Research. 2006 Jan;82(1):13-23. Epub 2005 Jun 24.

Hepatic gene expression changes throughout the day in the Fischer rat: implications for toxicogenomic experiments.

Boorman G.A., Blackshear P.E., Parker J.S., Lobenhofer E.K., Malarkey D.E., Vallant M.K., Gerken D.K., Irwin R.D. Toxicological Sciences. 2005 Jul;86(1):185-93. Epub 2005 Apr 6.

Toxicogenomic analysis methods for predictive toxicology.
 

Maggioli, J., Hoover, A., Weng, L. Journal of Pharmacological and Toxicological Methods. 2006 Jan-Feb;53(1):31-7. Epub 2005 Oct 19.

Gene expression profiling of the PPAR-alpha agonist ciprofibrate in the cynomolgus monkey liver

Cariello, N.F., Romach, E.H., Colton, H.M., Ni, H., Yoon, L., Falls, J.G., Casey, W., Creech, D., Anderson, S.P., Benavides, G.R., Hoivik, D.J., Brown, R., Miller, R.T. Toxicological Sciences. 2005 Nov;88(1):250-64. Epub 2005 Aug 4. 

Comparison of the chondrosarcoma cell line SW1353 with primary human adult articular chondrocytes with regard to their gene expression profile and reactivity to IL-1b1

Gebauer, M., Saas, J., Sohler, F., Haag, J., Soder, S., Pieper, M., Bartnik, E., Beninga, J., Zimmer, R., Aigner, T. Osteoarthritis Cartilage. 2005 Aug;13(8):697-708.

Gene expression profiling in the hippocampus of learned helpless and nonhelpless rats

Kohen, R., Kirov, S., Navaja, G.P., Happe, H.K., Hamblin, M.W., Snoddy, J.R., Neumaier, J.F., Petty, F. The Pharmacogenomics Journal. 2005;5(5):278-91.

Repression of anti-proliferative factor Tob1 in osteoarthritic cartilage

Gebauer, M., Saas, J., Haag, J., Dietz, U., Takigawa, M., Bartnik, E., Aigner, T. Arthritis Research & Therapy. 2005;7(2):R274-84. Epub 2005 Jan 11. 

Multifunctionality of PAI-1 in fibrogenesis: Evidence from obstructive nephropathy in PAI-1overexpressing mice

Matsuo, S., Lopez-Guisa, J.M., Cai, X., Okamura, D.M., Alpers, C.E., Bumgarner, R.E., Peters, M.A., Zhang, G., Eddy, A.A. Kidney International. 2005 Jun;67(6):2221-38.

Developmentally induced changes in transcriptional program alter spatial organization across chromosomes

Casolari, J.M., Brown, C.R., Drubin, D.A., Rando, O.J., Silver, P.A. Genes and Development. 2005 May 15;19(10):1188-98.

The HEAT repeat protein Blm10 regulates the yeast proteasome by capping the core particle.

Schmidt, M., Haas, W., Crosas, B., Santamaria, P.G., Gygi, S.P., Walz, T., Finley, D. Nature Structural & Molecular Biology. 2005 Apr;12(4):294-303. Epub 2005 Mar 20.

Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo.

Arlotta P., Molyneaux B.J., Chen J., Inoue J., Kominami R., and Macklis J. Neuron. 2005 Jan 20;45(2):207-21.

Transcriptional profiling of the left and median liver lobes of male f344/n rats following exposure to acetaminophen.

Irwin R.D., Parker J.S., Lobenhofer E.K., Burka L.T., Blackshear P.E., Vallant M.K., Lebetkin E.H., Gerken D.F., Boorman G.A. Toxicologic Pathology. 2005;33(1):111-7. 

Transcription profiling analysis of the mechanisms of vaccine-induced protection against H. pylori.

Walduck, A., Schmitt, A., Lucas, B., Aebischer, T., Meyer, T.F. Federation of American Societies for Experimental Biology Journal. 2004 Dec;18(15):1955-7. Epub 2004 Sep 28.

Bcl-2 Overexpression Leads to Increases in Suppressor of Cytokine Signaling-3 Expression in B Cells and De novo Follicular Lymphoma
 

Vanasse, G.J., Winn, R.K., Rodov, S., Zieske, A.W., Li, J.T., Tupper, J.C., Tang, J., Raines, E.W., Peters, M.A., Yeung, K.Y., Harlan, J.M. Molecular Cancer Research. 2004 Nov;2(11):620-31. 

Arginine methyltransferase affects interactions and recruitment of mRNA processing and export factors.

Yu, M.C., Bachand, F., McBride, A.E., Komili, S., Casolari, J.M., Silver, P.A. Genes & Development. 2004 Aug 15;18(16):2024-35.

The host response to West Nile Virus infection limits viral spread through the activation of the interferon regulatory factor 3 pathway.

Fredericksen, B.L., Smith, M., Katze, M.G., Shi, P.Y., Gale, M. Jr. Journal of Virology. 2004 Jul;78(14):7737-47.

Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. 

Casolari, J.M., Brown, C.R., Komili, S., West, J., Hieronymus, H., Silver, P.A. Cell. 2004 May 14;117(4):427-39

PDGF C is a selective alpha platelet-derived growth factor receptor agonist that is highly expressed in platelet alpha granules and vascular smooth muscle.

Fang, L., Yan, Y., Komuves, L.G., Yonkovich, S., Sullivan, C.M., Stringer, B., Galbraith, S., Lokker, N.A., Hwang, S.S., Nurden, P., Phillips, D.R., Giese, N.A. Arteriosclerosis, Thrombosis, and Vascular Biology. 2004 Apr;24(4):787-92. 

Bioinformatics Moves into the Mainstream 

Ouellette, J. The Industrial Physicist. 2003. Oct;14-19(9)

Using gene expression profiling to identify the molecular basis of the synergistic actions of hepatocyte growth factor and vascular endothelial growth factor in human endothelial cells
 

Gerritsen, M.E., Tomlinson, J.E., Zlot, C., Ziman, M., Hwang, S. British Journal of Pharmacology. 2003 Oct;140(4):595-610. Epub 2003 Sep 22. 

A comparison of statistical methods for analysis of high density oligonucleotide array data

Rajagopalan, D. Bioinformatics. 2003 Aug 12;19(12):1469-76. 

Induction of endogenous genes by peroxisome proliferator activated receptor alpha ligands in a human kidney cell line and in vivo
 

Liu, P.C., Huber, R., Stow, M.D., Schlingmann, K.L., Collier, P., Liao, B., Link, J., Burn, T.C., Hollis, G., Young, P.R., Mukherjee, R. The Journal of Steroid Biochemistry and Molecular Biology. 2003 May;85(1):71-9.

In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling
 

Carter, M.G., Hamatani. T., Sharov, A.A., Carmack, C.E., Qian, Y., Aiba, K., Ko, N.T., Dudekula, D.B., Brzoska, P.M., Hwang, S.S., Ko, M.S. Genome Research. 2003 May;13(5):1011-21.

Microarray analyses of the metabolic responses of Saccharomyces cerevisiae to organic solvent dimethyl sulfoxide

Zhang, W., Needham, D.L., Coffin, M., Rooker, A., Hurban, P., Tanzer, M.M., Shuster, J.R. Journal of Industrial Microbiology & Biotechnology. 2003 Jan;30(1):57-69. Epub 2003 Jan 3. 

Gene-microarray analysis of multiple sclerosis lesions yields new targets validated in autoimmune encephalomyelitis

Lock, C., Hermans, G., Pedotti, R., Brendolan, A., Schadt, E., Garren, H., Langer-Gould, A., Strober, S., Cannella, B., Allard, J., Klonowski, P., Austin, A., Lad, N., Kaminski, N., Galli, S.J., Oksenberg, J.R., Raine, C.S., Heller, R., Steinman, L. Nature Medicine 2002 May;8(5):500-8. 

Gene expression profiling predicts clinical outcome of breast cancer

van 't Veer, L.J., Dai, H., van de Vijver, M.J., He, Y.D., Hart, A.A., Mao, M., Peterse, H.L., van der Kooy, K., Marton, M.J., Witteveen, A.T., Schreiber, G.J., Kerkhoven, R.M., Roberts, C., Linsley, P.S., Bernards, R., Friend, S.H. Nature. 2002 Jan 31;415(6871):530-6. 

Clustering of hepatotoxins based on mechanism of toxicity using gene expression profiles

Waring, J.F., Jolly, R.A., Ciurlionis, R., Lum, P.Y., Praestgaard, J.T., Morfitt, D.C., Buratto, B., Roberts, C., Schadt, E., Ulrich, R.G. Toxicology and Applied Pharmacology. 2001 Aug 15;175(1):28-42. 

Functional discovery via a compendium of expression profiles

Hughes, T.R., Marton, M.J., Jones, A.R., Roberts, C.J., Stoughton, R., Armour, C.D., Bennett, H.A., Coffey, E., Dai, H., He, Y.D., Kidd, M.J., King, A.M., Meyer, M.R., Slade, D., Lum, P.Y., Stepaniants, S.B., Shoemaker, D.D., Gachotte, D., Chakraburtty, K., Simon, J., Bard, M., Friend, S.H. Cell. 2000 Jul 7;102(1):109-26