Center for Cancer Nanotechnology Excellence Focused on Therapy Response

1. S. J. Osterfeld and S. X. Wang, MagArray Biochips for Protein and DNA Detection with Magnetic Nanotags: Design, Experiment, and Signal to Noise Ratio, book chapter to appear in Microarrays: New Development Towards Recognition of Nucleic Acid and Protein Signatures, edited by Kilian Dill, Robin Liu, and Piotr Grodzinski, Springer Verlag/Kluwer, in press, 2008.
2. S. X. Wang and G. Li, Advances in GMR Biosensors with Magnetic Nanoparticle Tags: Review and Outlook, Invited Review for Advances in Magnetics of IEEE Trans. Magn., in press, 2008.
3. H.Y. Lee, S. H. Lee, J.H. Lee, B. Wu, A. L. Koh, X. Wang, S. X. Wang, D.G. Nishimura, S. Biswal, S. H. Cho, and X. Chen, "In Vitro and In Vivo Test of PVP-coated Large Core Iron Oxide Nanoparticles as Macrophage Specific MRI Contrast Agent," Nanotechnology, in press, 2008.
4. W. Hu, R.J. Wilson, A. Koh, A. Fu, A.Z. Faranesh, C.M. Earhart, S.J. Osterfeld, S.-J. Han, L. Xu, S. Guccione, R. Sinclair, and S.X. Wang, "High-moment antiferromagnetic nanoparticles with tunable magnetic properties," Advanced Materials, in press, 2008.
5. A. Koh, W. Hu, R.J. Wilson, S. X. Wang, R. Sinclair, "TEM studies of synthetic antiferromagnetic (SAF) nanoparticles," Microsc. Microanal. 13 (Suppl. 2), 66CD (2007).
6. S. X. Wang, "Giant magnetoresistive biochips for biomarker detection and genotyping: an overview (invited)," AIP Conference Proceedings, European Symposium on Biomagnetism and Magnetic Biosystems Based on Molecular Recognition Processes (ESF-EMBO Symposium), Sant Feliu de Guixols, Spain, Sept 22-27, 2007.
7. L. Xu, H. Yu, M. S. Akhrasb, S.-J. Han, S. J. Osterfeld, R. L. White, N. Pourmand, S. X. Wang, "Giant magnetoresistive biochip for DNA detection and HPV genotyping," Under review at Biosensors and Bioelectronics.
8. L. Xu, H. Yu, S.-J. Han, S. J. Osterfeld, R. L. White, N. Pourmand, and S. X. Wang, "Giant magneto- resistive sensors for DNA microarray," Under review at IEEE Trans. Magn.
9. W. Hu, R. J. Wilson, C. M. Earhart, A.-L. Koh, A. Z. Faranesh, R. Sinclair, S. Guccione, and S. X. Wang, "High moment synthetic magnetic nanoparticles for biomedical applications," Under review at IEEE Trans. Magn.

1. Earhart, W. Hu, R. J. Wilson, S. X. Wang, "Self-assembled template for high throughput nanoimprint lithography," Digests of the 5th International Conference on Nanoimprint and Nanoprint Technology, San Francisco, CA, USA, Nov. 15-17, 2006.
2. W. Hu, R. J. Wilson, L. Xu, S.-J. Han, and S. X. Wang, "High density gigabit patterning of magnetic nanodot arrays by nanoimprint lithography," J. Vacuum Sci.Tech. A, July/Aug 2007.
3. S-J Han, H. Yu, B. Murmann, N. Pourmand, and S. X. Wang, "A high density magnetoresistive biosensor array with drift compensation mechanism," Proceedings of IEEE International Solid-State Circuits Conference (ISSCC), San Francisco Marriott, CA, USA, February 11-15, 2007.
4. S.-J. Han, H. Yu, L. Xu, R. J. Wilson, N. Pourmand, and S. X. Wang, "CMOS integrated DNA microarray based on GMR sensors," Proceedings of International Electron Device Meeting (IEDM), Paper #28.2, San Francisco, CA, USA, December 11-13, 2006.
5. N. Pourmand, S. Caramuta, A. Villablanca, S. Mori, M. Karhanek, S. X. Wang and R. W. Davis, Branch migration displacement assay with automated heuristic analysis for discrete DNA length measurement using DNA microarrays, PNAS, vol. 104, no. 15, 6146ˆ6151, 2007.
6. W. Hu, R. J. Wilson, A. Koh, A. Fu, A. Z. Faranesh, C. M. Earhart, S. J. Osterfeld, S.-J. Han, L. Xu, S. Guccione, R. Sinclair & S. X. Wang, "Nanoimprinted high-moment antiferromagnetic nanoparticles with multiplex functionality," Under review by Nature Materials.

1. Welsher, K.; Liu, Z.; Daranciang, D.; Dai, H. "Selective Probing and Imaging of Cells with Single Walled Carbon Nanotubes as Near-Infrared Fluorescent Molecules" Nano Lett.;8(2); 586-590, 2008.
2. Zhuang L., Davis, C., Cai W., He, L., Chen X., and Dai H. "Circulation and long-term fate of functionalized, biocompatible single-walled carbon nanotubes in mice probed by Raman spectroscopy" PNAS, Vol. 105, No. 5, 1410-1415, 2008.
3. Z. Liu, X. Sun, N. Nakayama-Ratchford, and H. Dai. "Supramolecular Chemistry on Water-Soluble Carbon Nanotubes for Drug Loading and Delivery" ACS NANO, Vol. 1, No. 1, 50-56, 2007.
4. Chen, Z, Tabakman, S.M., Goodwin, A.P., Daranciang, D., Wang, X, Zhang, G, Dai, H. "Carbon Nanotubes as Raman Labels for Femtomolar Protein Detection on Surface Enhanced Raman Scattering Substrates" Submitted to J.Am.Chem.Soc., 2008.
5. Liu Z, Chen K, Davis C, Sherlock S, Cao Q, Chen X, Hongjie Dai. "Drug delivery with carbon nanotubes for in vivo cancer treatment." Submitted to Nature Nanotechnology., 2008.
6. Schipper, M. Nakayama-Ratchford, N. Davis, C. Kam, N. W. S. Chu, P. Liu, Z. Sun, X. Cork, L. Dai, H. Gambhir, S. "Initial Toxicology Studies of Single Walled Carbon Nanotubes in Mice." Nature Nanotechnology, in press, 2008.

1. Seo WS, Hyung Lee JH, Sun X, Suzuki Y, Mann D, Liu Z, Terashima M, Yang PC, McConnell MV, Nishimura DG, and Dai H. FeCo/graphitic-shell nanocrystals as advancedmagnetic-resonance-imaging and near-infrared agents. Nature Materials 2006; 5: 971-976, Suppl. S1-S3.
2. Liu Z, Winters M, Holodniy M, Dai H. siRNA Delivery into Human T Cells and Primary Cells with Carbon-Nanotube Transporters. Agnew. Chem. Int. Ed. 2007; 46: 2023-2027.
3. Liu Z, Cai W, He L, Nakayama N, Chen K, Sun X, Chen X, Dai H. In vivo biodistribution and highly efficient tumour targeting of carbon nanotubes in mice. Nature Nanotechnology 2007; 2: 47-52.
4. Nakayama-Ratchford N, Bangsaruntip S, Sun X, Welsher K, Dai H. Noncovalent Functionalization of Carbon Nanotubes by Fluorescein-Polyethylene Glycol: Supramolecular Conjugates with pH-Dependent Absorbance and Fluorescence. J. Am Chem Society. 2007; 129: 2448-2449.

1. Shachaf CM, Perez OD, Youssef S, Fan AC, Elchuri S, Goldstein MJ, Shirer AE, Sharpe O, Chen J, Mitchell DJ, Chang M, Nolan GP, Steinman L and Felsher DW. (2007). Inhibition of HMGcoA reductase by atorvastatin prevents and reverses MYC-induced lymphomagenesis. Blood. Oct 1;110(7):2674-84. Epub 2007 Jul 10.
2. Perez OD, Mitchell D and Nolan GP. (2007) Differential role of ICAM ligands in determination of human memory T cell differentiation. BMC Immunol. Jan 18;8:2.
3. Perez O.D. and Nolan G.P. (2006). Phospho-proteomic immune analysis by flow cytometry: from mechanism to translational medicine at the single-cell level. Immunological Reviews. Apr;210:208-28.
4. Schulz K.R., Danna E.A., Krutzik P.O, and Nolan G.P. (2007). Single-Cell Phospho-Protein Analysis by Flow Cytometry. Current Protocols in Immunology. Aug;8(17):1-20.
5. Krutzik PO, Crane JM, Clutter MR, Nolan GP. (2008). High-content single-cell drug screening with phosphospecific flow cytometry. Nat Chem Biol. Feb;4(2):132-42. Epub 2007 Dec 23.
6. Nolan GP. (2007) Visualizing Inside the Cell. Biology of Blood and Marrow Transplantation. January Vol 13: 120-123.
7. Lee AW, Sharp ER, O'Mahony A, Rosenberg MG, Israelski DM, Nolan GP, Nixon DF. (2008). Single cell, phosphoepitope-specific analysis demonstrates cell type- and pathway-specific dysregulation of Jak/STAT and MAPK signaling associated with in vivo HIV-1 infection. J Virol. 2008 Jan 23.
8. Shachaf, C.M., Elchuri, E., Koh, A.L., Mitchell, D. , Zhu J., Nguyen, L., Zhang, J., Sun, L., Chan, S., Sinclair, R. and Nolan, G.P. Under submission Detection of surface molecules and phosphorylation events by Surface Enhanced Raman Scattering (SERS) using Composite Organic-Inorganic Nanoparticles COINs in single cells.
9. Koh, A.L., Shachaf, C.M., Elchuri, S., Mitchell, D.M., Nolan, G.P., and Sinclair,R., Under submission. Localization of Functionalized SERS Nanoparticles on Cells Using Scanning Electron Microscopy Techniques.
10. Itani, S., Ohannessian, M.I., Sachs, K. , Nolan, G.P., Dahleh, M.A. Submitted to The 24th Conference on Uncertainty in Artificial Intelligence (UAI 2008). Formalism and Structure Learning for Cyclic Networks.

1. Irish, J.M., D.K. Czerwinski, G.P. Nolan, and R. Levy, Kinetics of B cell receptor signaling in human B cell subsets mapped by phosphospecific flow cytometry. J Immunol, 2006. 177(3): p. 1581-9.
2. Irish, J.M., D.K. Czerwinski, G.P. Nolan, and R. Levy, Altered B-cell receptor signaling kinetics distinguish human follicular lymphoma B cells from tumor-infiltrating nonmalignant B cells. Blood, 2006. 108(9): p. 3135-42.
3. Irish, J.M., N. Anensen, R. Hovland, J. Skavland, A.L. Borresen-Dale, O. Bruserud, G.P. Nolan, and B.T. Gjertsen, Flt3 Y591 duplication and Bcl-2 overexpression are detected in acute myeloid leukemia cells with high levels of phosphorylated wild-type p53. Blood, 2007. 109(6): p. 2589-96.
4. Van Meter, M.E., E. Diaz-Flores, J.A. Archard, E. Passegue, J.M. Irish, N. Kotecha, G.P. Nolan, K. Shannon, and B.S. Braun, K-RasG12D expression induces hyperproliferation and aberrant signaling in primary hematopoietic stem/progenitor cells. Blood, 2006.
5. Irish, J.M., N. Kotecha, and G.P. Nolan, Mapping normal and cancer cell signaling networks: towards single-cell proteomics. Nat Rev Cancer, 2006. 6(2): p. 146-55.
6. Nolan, G.P., Deeper Insights into Hematological Oncology Disorders via Single-Cell Phospho-Signaling Analysis. Hematology Am Soc Hematol Educ Program, 2006: p. 123-7.
7. Krutzik, P.O. and G.P. Nolan, Fluorescent cell barcoding in flow cytometry allows high-throughput drug screening and signaling profiling. Nat Methods, 2006. 3(5): p. 361-8.

1. Kuick R, Misek DE, Monsma DJ, Webb CP, Wang H, Peterson KJ, Pisano M, Omenn GS, Hanash SM Discovery of cancer biomarkers through the use of mouse models. Cancer Lett. 2007 Feb 21.
2. TGF-_ Induced Protein dynamics in Hepatoma Cells B Deng, H Wang, L Beretta, S Hanash (submitted).
3. Chu, T., Ebright, J., and A.D. Ellington (2007). Using aptamers to identify and enter cells. Curr Opin Mol Ther, 9(2):137-44. Review.
4. Pai, S.S., and A.D. Ellington (2007). Using RNA aptamers and the proximity ligation assay (PLA) for the detection of cell surface antigens. Methods in Biotechnology.
5. Hanash, S., Pitteri, S., Faca, V. Mining the plasma proteome for cancer Biomarkers. Nature in press.
6. Madoz-Gurpide J, Rork K, Misek DE, Hanash S. Integral protein microarrays for the identification of lung cancer antigens in sera that induce a humoral immune response. Molecular Cellular Proteomics 2007, Oct 4.
7. Pitteri S, Hanash S, Proteomic approaches for cancer biomarker discovery in plasma. Expert Review 2007, Oct. in press.
8. Faca V, Pitteri S, Newcomb L, Glukhova V, Phanstiel D, Krasnoselsky A, Zhang Q, Struthers J, Wang H, Eng J, Fitzgibbon M, McIntosh M, Hanash S. Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes. Journal of Proteome Research 2007, 6, (9), 3558-65.
9. Kuick R, Misek DE, Monsma DJ, Webb CP, Wang H, Peterson KJ, Pisano M, Omenn GS, Hanash SM Discovery of cancer biomarkers through the use of mouse models. Cancer Lett. 2007 Apr 28;249(1):40-8.
10. Prenosil E, Shahbaba B, Mizutani J, Ryvkin A, Komisopoulou E, Plevritis, S, Graeber T, Agus D, Jain A. "Global Tyrosine phosphorylation patterns upon EGFR stimulation and inhibition with distinct anti-EGFR therapeutics" In progress.
11. Jain A, Zhang W, Schmidt J, Hodge A, Curran J, Huang G, Agus D. In vivo derivation and characterization of acquired resistance to reversible EGFR-TKIs. In progress.
12. Kani K., Faca V., Hughes L., Shahbaba B., Zhang W, Schmidt J, Katz J., Plevritis S., Tibshirani R., Jain A., Hanash S., Mallick P., Agus D. Quantitative proteomic profiling identifies a panel of proteins indicative of response to geftinib both in vitro and in vivo. In progress.

1. Chu, T.C., Marks III, J.W., Lavery, L.A., Faulkner, S., Rosenblum, M.G., Ellington, A.D, and M. Levy (2006). Aptamer: toxin conjugates that specifically target prostate tumor cells. Cancer Res, 66(12):5989-92.
2. Chu, T.C., Shieh, F., Lavery, L.A., Levy, M., Richards-Kortum, R., Korgel, B.A., and A.D. Ellington (2006). Labeling tumor cells with fluorescent nanocrystal-aptamer bioconjugates. Biosens Bioelectron, 21(10):1859-66.
3. Chu, T.C., Twu, K.Y., Ellington, A.D., and M. Levy (2006). Aptamer mediated siRNA delivery. Nucleic Acids Res, 34(10):e73.
4. Chu, T.C., Pai, S.S., Levy, M., and Ellington, A.D. (2007). Cell-specific aptamers and the proximity ligation assay for sensitively typing cells. Tumor Biology, in press.
5. Davidson, E.A., and A.D. Ellington (2007). Synthetic RNA circuits. Nat Chem Biol, 3(1):23-28.
6. Soper, S.A., Brown, K., Ellington, A.D., Frazier, B., Garcia-Manero, G., Gau, V., Gutman, S.I., Hayes, D.F., Korte, B., Landers, J.L., Larson, D., Ligler, F., Majumdar, A., Mascini, M., Nolte, D., Rosenzweig, Z., Wang, J., and D. Wilson. (2006). Point-of-care biosensor systems for cancer diagnostics/prognostics. Biosens Bioelectron, 21(10):1932-42.
7. Agus DB, Sweeney CJ, Morris MJ, Mendelson DS, McNeel DG, Ahmann FR, Wang J, Derynck MK, Ng K, Lyons B, Allison DE, Kattan MW, Scher HI. Efficacy and safety of single-agent pertuzumab (rhuMAb 2C4), a human epidermal growth factor receptor dimerization inhibitor, in castration-resistant prostate cancer after progression from taxane-based therapy. J Clin Oncol. 2007 Feb 20;25(6):675-81.
8. deVera IE, Katz JE, Agus DB. Clinical proteomics: the promises and challenges of mass spectrometry-based biomarker discovery. Clin Adv Hematol Oncol. 2006 Jul;4(7):541-9.
9. Laux I, Jain A, Singh S, Agus DB. Epidermal growth factor receptor dimerization status determines skin toxicity to HER-kinase targeted therapies. Br J Cancer. 2006 Jan 16;94(1):85-92.
10. Shazer, R. L., Jain, A., Galkin, A. V., Cinman, N., Nguyen, K. N., Natale, R. B., Gross, M., Green, L., Bender, L. I., Holden, S., Kaplan, L., and Agus, D. B. (2006). Raloxifene, an ER Targeted Therapy, Inhibits Androgen Independent Prostate Cancer Growth: Results from Preclinical Studies and a Pilot Phase II Clinical Trial. BJU International, 97, 691-697.
11. Jain, A., Vashistha, S. Gross, M. E., and Agus, D. B. (2006). Models for Prostate Cancer. Cancer Handbook, 2nd Edition, (Wiley&Son, UK). (In Press).
12. Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T, Kuster B, Aebersold R. Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol. 2007 Jan;25(1):125-31. Epub 2006 Dec 31.
13. Flory MR, Lee H, Bonneau R, Mallick P, Serikawa K, Morris DR, Aebersold R. Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotope-coded affinity tag reagents. Proteomics. 2006 Dec;6(23):6146-57.
14. Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R. The PeptideAtlas project. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D655-8.
15. Rauch A, Bellew M, Eng J, Fitzgibbon M, Holzman T, Hussey P, Igra M, Maclean B, Lin CW, Detter A, Fang R, Faca V, Gafken P, Zhang H, Whiteaker J, States D, Hanash S, Paulovich A, McIntosh MW. Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J Proteome Res. 2006;5(1):112-21.
16. Faca V, Coram M, Phanstiel D, Glukhova V, Zhang Q, Fitzgibbon M, McIntosh M, Hanash S Quantitative analysis of acrylamide labeled serum proteins by LC-MS/MS. J Proteome Res. 2006 Aug;5(8):2009-18.
17. B Deng, H Wang, L Beretta, S Hanash, TGF-_ Induced Protein dynamics in Hepatoma Cells, 2007, Submitted.

1. Cai, W., Olafsen, T., Zhang, X., Cao, Q., Gambhir, S.S., Williams, L.E., Wu, A.M. and Chen, X. (2007) PET imaging of colorectal cancer in xenograft-bearing mice by use of an 18F-labeled T84.66 anti-carcinoembryonic antigen diabody. J. Nucl. Med. 48:304-310.
2. Olafsen, T., Gu, Z., Sherman, M.A., Leyton, J.V., Witkosky, M.E., Shively, J.E.., Raubitschek, A.A., Morrison, S.L., Wu, A.M. and Reiter, R.E. (2007) Targeting, imaging, and therapy using a humanized anti-prostate stem cell antigen (PSCA) antibody. J. Immunotherapy, 30:396-405.
3. Barat, B. and Wu, A.M. (2007) Metabolic biotinyation of recombinant antibody by biotin ligase retained in endoplasmic reticulum. Biomolec. Eng. 24:283-291.
4. Venisnik, K.M., Olafsen, T., Gambhir, S.S., and Wu, A.M. (2007) Fusion of Gaussia luciferase to an engineered anti-carcinoembryonic antigen (CEA) antibody for in vivo optical imaging. Mol. Imaging Biol., 9:267-277.
5. Loening, A.M., Wu, A.M., and Gambhir, S.S. (2007) Red-shifted Renilla reniformis luciferase variants for imaging in living subjects. Nat. Methods. 4:641-643.
6. Schipper, M.L., Cheng, Z., Lee, S.-W., Bentolila, L.A., Iyer, G., Rao, J., Chen, X., Wu, A.M., Weiss, S., and Gambhir, S.S. (2007) MicroPET-based biodistribution of quantum dots in living mice. J. Nuc. Med. 48:1511-1518.
7. Olafsen, T., Betting, D., Kenanova, V.E., Raubitschek, A.A., Timmerman, J.M. and Wu, A.M. An engineered anti-CD20 antibody fragment (minibody) for PET imaging of B-cell lymphoma xenografts. Submitted, under revision.
8. Leyton, J.V., Olafsen, T., Lepin, E.J., Hahm, S., Bauer, K., Reiter, R.E., and Wu, A.M. A humanized radioiodinated minibody as an imaging agent for the detection of prostate stem cell antigen (PSCA)-expressing tumors by microPET. Submitted, under revision.
9. Shimazaki, K., Lepin, E.J., Wei, B., Nagy, A., Coulum, P., Mareninov, S., Fu, M., Wu, A.M., Marks, J.D., Braun, J., Gordon, L.K., and Wadehra, M. Bivalent biospecific diabodies targeting epithelial membrane protein 2 decrease tumorigenicity in human endometrial cancer cell lines. Submitted.
10. Sirk, S., Olafsen, T., Barat, B., Bauer, K. B., McCabe, K.E., and Wu, A.M. Site-specific thiol-mediated conjugation of fluorescent probes to cysteine-modifided diabodies targeting CD20 r HER2. Submitted.
11. Barat, B., Sirk, S., McCabe, K., Li, J., Koh, A.L., Lepin, E., Olafsen, T., Weiss, S. and Wu, A.M. Engineered antibody-quantum dot conjugates (immunoQdots) for cancer marker detection. Submitted.
12. Gratton, S.E.A., Williams, S.S., Napier, M., Pohlhaus, P.D., Olafsen, T., Shen, C., Samulski, E.T., and DeSimone, J.M. The pursuit of a scalable nanofabrication platform for use in material and life science applications. (review; submitted) (Dr. Olafsen, from A. Wu's lab, contributed key in vivo data for this three-way collaborative publication from the North Carolina CCNE, Stanford CCNE-TR and Caltech/UCLA NSBCC).
13. Cai W, Chen X. Preparation of peptide-conjugated quantum dots for tumor vasculature-targeted imaging. Nat Protoc. 2008;3(1):89-96.
14. Cai W, Chen X. Nanoplatforms for targeted molecular imaging in living subjects. Small. 2007 Nov;3(11):1840-54.
15. Chen K, Li Z-B, Wang H, Cai W, Chen X. Modification of Quantum Dot for Dual Modality Imaging of Tumor Vascular VEGFR. Eur J Nucl Med Mol Imaging, submitted.
16. Zavaleta C, Keren S, Cheng Z, Schipper M, Liu Z, Chen X, Dai H, Gambhir SS. Use of Non-invasive Raman Spectroscopy in Living Mice for Evaluation of Tumor Targeting with Carbon Nanotubes. Nat Nanotechnol, submitted.
17. de la Zerda A, Zavaleta C, Keren S, Vaithilingam S, Bodapati S, Liu Z, Levi J, Ma T-J, Oralkan O, Cheng Z, Chen X, Dai H, Khuri-Yakub BP, Gambhir SS. Photoacoustic Molecular Imaging in Living Mice Utilizing Targeted Carbon Nanotubes. Nat Methods, submitted.
18. Liu Z, Chen K, Davis C, Sherlock S, Cao Q, Chen X, Dai H. Drug delivery with carbon nanotubes for in vivo cancer treatment. Nat Nanotechol, revised.
19. Liu Z, Davis C, Cai W, He L, Chen X, Dai H. Circulation and Long-Term Fate of Functionalized, Biocompatible Single-Walled Carbon Nanotubes in Mice Probed by Raman Spectroscopy. PNAS, 2008;105:1410-1415.
20. Lee H-Y, Lee, S-H, Xu C, Xie J, Lee J-H, Wu B, Koh AL, Wang X, Wang SX, Nishimura DG, Biswal S, Sun S, Cho SH, Chen X. Synthesis and Characterization of PVP-Coated Large Core Iron Oxide Nanoparticles as MRI Contrast Agent. Nanotechnology, in press.
21. Lee H-Y, Li Z-B, Chen K, Hsu AR, Xu C, Xie J, Sun S, Chen X. PET/MRI Dual Modality Tumor Imaging Using Conjugated Radiolabeled Iron Oxide Nanoparticles. J Nucl Med, revised.
22. Xie J, Chen K, Lee H-Y, Xu C, Hsu AR, Peng S, Chen X, Sun S. Ultra-Small c(RGDyK)-Fe3O4 Nanoparticles and Their Specific Targeting to Integrin _v_3-rich Tumor Cells. J Am Chem Soc, submitted.
23. Lin S, Xie X, Yang Y, Li Z, Cao F, Patel MR, Gheysens O, Zhang Y, Gambhir SS, Rao J, Wu J. Quantum dots imaging for embryonic stem cells. BMC Biotechnology; 2007; 7: 67.
24. Xing Y, So MK, Rao J. Improving the in vivo stability of self-illuminating quantum dot conjugates for in vivo imaging. Biomaterials, Submitted.
25. Xing Y, Rao J. Semiconductor quantum dot bioconjugates for in vivo imaging. Invited submission to Disease Markers and Cancer Biomarkers.
26. So MK, Yao H, Rao J. HaloTag protein-mediated specific labeling of live cells with quantum dots. Biochemical and Biophysical Research Communications, Submitted.

1. Zhang Y, So M-K, Rao J. Protease-modulated cellular uptake of quantum dots. Nano Letters. 2006; 6: 1988-1992.
2. So M-K, Xu C, Loening AM, Gambhir SS, Rao J. Self-illuminating quantum dot conjugates for in vivo imaging. Nature Biotechnology. 2006; 24: 339-343.
3. So M-K, Loening AM, Gambhir SS, Rao, J. Creating self-illuminating quantum dot conjugates. Nature Protocols. 2006; 3: 1160-1164. (Invited).
4. Sui, G., Wang, J., Lee, C.-C., Lu, W., Lee, S.P., Leyton, J.V., Wu, A.M., and Tseng, H.-R. (2006) Solution-phase surface modification in intact poly(dimethylsiloxane) microfluidic channels. Anal. Chem. 78:5543-5551.
5. Xu C, Xing B, Rao J. A self-assembled quantum dot probe for detecting B-lactamase activity. Biochemical & Biophysical Research Communications 2006; 344: 931-935.
6. Zhang Y, So M-K, Loening AM, Yao H, Gambhir SS, Rao J. HaloTag protein-mediated site-specific conjugation of bioluminescent proteins to quantum dots. Angew Chem Intl Ed 2006; 45: 4936-4940. Angew Chem 2006; 118: 5058-5062.
7. Rao J, Dragulescu-Andrasi A, Yao H. Fluorescence imaging in vivo: recent advances. Current Opinion in Biotechnology 2007; 18:17-15. (Invited).
8. Yao H, Zhang Y, Xiao F, Xia Z, Rao J. QD BRET-based highly sensitive detection of proteases. Angewandte Chemie 2007 In press.
9. Cai W, Shin D-W, Wu Y, Cao Q, Gheysens O, Gambhir SS, Wang SX, Chen. Peptide-labeled near-infrared quantum dots for imaging tumor vasculature in living subjects. Nano Letters. 2006;6:669-676.
10. Cai W, Rao J, Gambhir SS, Chen X Molecular Imaging in Anti-Angiogenic Drug Development Mol Cancer Ther. 2006;5(11): 2624-33.
11. Li Z, Cai W, Chen X Biocompatible Quantum Dots for In Vivo Imaging J Nanosci Nanotechnol. 2007, In press.
12. Hsu AR, Chen X Biomedical applications of quantum dot semiconductor nanoparticles Encyclopedia of Nanoscience and Nanotechnology (Editor, HS Nalwa), 2007.
13. Cai W, Chen K, Li Z-B, Gambhir SS, Chen X. Dual Functional Quantum Dot-Based Probe for Near-Infrared Fluorescence and Positron Emission Tomography Imaging of Cancer Nano Letters, 2007, submitted.
14. Cai W, Hsu AR, Li Z-B, Chen X. Are Quantum Dots Ready for In Vivo Imaging in Human Subjects Nanoscale Research Letters, 2007 to be submitted.

1. Keren, S., Gheysens, O., Levin, C. S., Gambhir, S. S. A comparison between a time domain and continuous wave small animal optical imaging system. Medical Imaging, IEEE Transactions on 27, 58-63 (2008).
2. Cai, W., Olafsen, T., Zhang, X., Cao, Q., Gambhir, S.S., Williams, L.E., Wu, A.M. and Chen, X. (2007) PET imaging of colorectal cancer in xenograft-bearing mice by use of an 18F-labeled T84.66 anti-carcinoembryonic antigen diabody. J. Nucl. Med. 48:304-310.
3. Venisnik, K.M., Olafsen, T., Gambhir, S.S., and Wu, A.M. (2007) Fusion of Gaussia luciferase to an engineered anti-carcinoembryonic antigen (CEA) antibody for in vivo optical imaging. Mol. Imaging Biol., 9:267-277.
4. Lin S, Xie X, Yang Y, Li Z, Cao F, Patel MR, Gheysens O, Zhang Y, Gambhir SS, Rao J, Wu J. Quantum dots imaging for embryonic stem cells. BMC Biotechnology; 2007; 7: 67.
5. M. Schipper, Z. Cheng, S. Lee, L. Bentolila, G. Iyer, J. Rao, X. Chen, A. Wu, S. Weiss, S.S. Gambhir. MicroPET-Based Biodistribution of Quantum Dots in Living Mice. Journal of Nuclear Medicine, 48(9): 1511-1518, 2007.
6. A. Loening, A. Wu, S.S. Gambhir. Red-shifted Renilla Reniformis Luciferase Variants for Imaging in Living Subjects. Nature Methods, 4(8): 641-643, 2007.
7. Keren S*, Zavaleta C*, Cheng Z., de la Zerda A, Gheysens O., Gambhir S.S. Noninvasive Molecular Imaging of Small Living Subjects Using Raman Spectroscopy. PNAS, in-press. *Co-first authors.
8. Meike L. Schipper, Nozomi Nakayama-Ratchford, Corrine R. Davis, Nadine Wong Shi Kam, Pauline Chu, Zhuang Li, Xiaoming Sun, Hongjie Dai, and Sanjiv S. Gambhir. Preliminary Toxicology Studies of Single Walled Carbon Nanotubes in Mice. Nature Nanotechnology, In-press.
9. Bryan Ronain Smith, Zhen Cheng, Abhijit De, Ai Leen Koh, Sanjiv Sam Gambhir/. Real-time intravital imaging of RGD-quantum dot binding to luminal endothelium in mouse tumor neovasculature. Nano Letters, in-press.
10. Meike L. Schipper, Gopal Iyer, Ai Leen Koh, Zhen Cheng, Yuval Ebenstein, Shay Keren, Laurent A. Bentolila, Adam de la Zerda, Jianquing Li, Bryan R. Smith, Jianghong Rao, Xiaoyuan Chen, Anna M. Wu, Robert Sinclair, Shimon S. Weiss, and Sanjiv S. Gambhir. Particle Size, Surface Coating, and Pegylation Influence the Biodistribution of Quantum Dots in Living Mice. Small, under final-review.
11. Adam de la Zerda, Cristina Zavaleta, Shay Keren, Srikant Vaithilingam, Sunil Bodapati, Zhuang Liu, Jelena Levi, Te-Jen Ma, Omer Oralkan, Zhen Cheng, Xiaoyuan Chen, Hongjie Dai, Butrus T. Khuri-Yakub, Sanjiv S. Gambhir. Carbon Nanotubes as Photoacoustic Molecular Imaging Agents in Living Mice. Nature Nanotechnology, under final review.
12. Zavaleta C, de la Zerda A, Keren S, Cheng Z, Schipper M, Chen X, Liu Z, Dai H., Gambhir S.S. Non-invasive Raman Spectroscopy in Living Mice for Evaluation of Tumor Targeting with Carbon Nanotubes. Nature Nanotechnology, submitted.
13. Adam de la Zerda, Sunil Bodapati, Meike L. Schipper, Shay Keren, Bryan R. Smith, Johnny S.T. Ng, Sanjiv Sam Gambhir. A Comparison between Spectral and Time Domain Imaging Systems for Imaging Quantum Dots in Small Living Animals. Journal of Biomedical Optics, Submitted.
14. BR Smith and SS Gambhir. Nanoparticle-Based Molecular Imaging in Living Subjects, in Molecular Imaging in Oncology. M. Pomper and J. Gelovani, eds. Expected publication date: August 2008.

1. S. Keren, O. Gheysens, C.S. Levin and S.S. Gambhir. A comparison between a time domain and continuous wave small animal optical imaging system. IEEE (in-press).
2. A.M. Loening, A.M. Wu, S.S. Gambhir. Red Shifted Renilla Luciferase Variants for Improved Imaging in Living Subjects. Nature Methods (Under Final Revision).
3. S. Keren, C. Zaveleta, Z. Cheng, O. Gheysens, S.S. Gambhir. Noninvasive Molecular Imaging of Small Living Subjects Using Raman Spectroscopy. Submitted to Nature Medicine.

1. "TEM Observations of Bio-Conjugated Streptavidin Gold Nanoparticles", A.L. Koh and R. Sinclair, in Engineered Nanoscale Materials for the Diagnosis and Treatment of Disease, edited by V.A. Hackley, A.K. Patri, J. Stein, B.M. Moudgil (Mater. Res. Soc. Symp. Proc. Volume 1019E, Warrendale, PA, 2007) 1019-FF05-01.
2. "TEM Studies of Iron Oxide Nanoparticles for Cell Labeling and Magnetic Separation", A. L. Koh and R. Sinclair, Technical Proceedings of the 2007 Nanotechnology Conference and Trade Show, 4, pp. 101-104 (2007).
3. "Characterization of Magnetic Nanoparticles by High Resolution TEM Methods", R. Sinclair, H. Li, and A. L. Koh, Proc. Microscopy and Microanalysis, 13, Supplement 2, p. 622CD (2007).
4. "TEM Studies of Synthetic Anti-ferromagnetic (SAF) Nanoparticles", A. L. Koh, W. Hu, R. Wilson, S. X. Wang, and R. Sinclair, Proc. Microscopy and Microanalysis, 13, Supplement 2, p. 66CD (2007).
5. A.L. Koh, W. Hu, R.J. Wilson, S.X. Wang and R. Sinclair, "TEM Analyses of Synthetic Anti-Ferromagnetic (SAF) Nanoparticles Fabricated Using Different Release Layers" (2007), submitted to Ultramicroscopy.
6. A.L. Koh, C.M. Shachaf, S. Elchuri, G.P. Nolan and R. Sinclair, "Electron Microscopy Characterization of Composite Organic-Inorganic Nanoparticles (COINs) as Raman Labels for Extra-cellular Analyses" submitted to Microscopy and Microanalysis 2008 meeting.
7. Shachaf, C.M., Elchuri, E., Koh, A.L., Mitchell, D.J., Zhu J., Nguyen, L., Zhang, J., Sun, L., Chan, S., Sinclair, R., and Nolan, G.P., "Detection of surface molecules and phosphorylation events by Surface Enhanced Raman Scattering (SERS) using Composite Organic-Inorganic Nanoparticles (COINs) in single cells", Nature Nanotechnology, in preparation.
8. A.L. Koh, C.M. Shachaf, S. Elchuri, G.P. Nolan and R. Sinclair, "Scanning Electron Microscopy Localization of Functionalized Composite Organic-Inorganic SERS Nanoparticles on Cells", Nature Methods, in preparation.
9. A.L. Koh, W. Hu, R.J. Wilson, S.X. Wang and R. Sinclair, "Structural and Magnetic Characterization of Synthetic Anti-ferromagnetic (SAF) Nanoparticles", Microscopy and Microanalysis, in preparation.

1. "TEM Observations of Bio-conjugated Streptavidin-Gold Nanoparticles", A. L. Koh and R. Sinclair, 2007 MRS Spring Meeting Symposium FF Proceedings, in-press.

1. "High-moment antiferromagnetic nanoparticles with tunable magnetic properties," W. Hu, R. J. Wilson, A. Koh, A. Fu, A. Z. Faranesh, C. M. Earhart, S. J. Osterfeld, S. Han, L. Xu, S. Guccione, R. Sinclair, S. X. Wang, Adv. Mater., accepted, (2008).
2. "High density gigabit patterning of magnetic nanodot arrays by nanoimprint lithography," W. Hu, R. J. Wilson, L. Xu, S.-J. Han, and S. X. Wang, J. Vac. Sci. Technol. A. 25, 1294 (2007).
3. "TEM studies of synthetic antiferromagnetic (SAF) nanoparticles," A. Koh, W. Hu, R.J. Wilson, S. X. Wang, R. Sinclair, Microsc. Microanal. 13 (Suppl. 2), 66CD (2007).

1. C. Earhart, W. Hu, R. J. Wilson, S. X. Wang, "Self-assembled template for high throughput nanoimprint lithography," Digests of the 5th International Conference on Nanoimprint and Nanoprint Technology, San Francisco, CA, USA, Nov. 15-17, 2006.
2. W. Hu, R. J. Wilson, L. Xu, S.-J. Han, and S. X. Wang, "Patterning of high density magnetic nanodot arrays by nanoimprint lithography," J. Vacuum Sci.Tech., Jul/Aug, 2007.

1. Shahbaba B, Tibshirani R, Plevritis S, Bayesian gene set enrichment analysis: Submitted to The Annals of Applied Statistics, 2008.
2. Shahbaba B., Prenosil E., Jain A., and Plevritis S., "A modified Dirichlet process mixture model for clustering proteins based on their response to anti-cancer drug perturbation," Submitted to BIIOCOMP'08, 2008.
3. Plevritis S, "Identification of Biomarkers from High Throughput Data" (chapter), Molecular Imaging (book), Principles and Practice, submitted.
4. Shahbaba, B., Gentles A.J., Beyene, J., Plevritis, S.K., and Greenwood, C.M.T. (2008), A Bayesian nonparametric method for model evaluation: Application to gene-disease studies, Submitted to Statistical Applications in Genetics and Molecular Biology, 2008.
5. Prenosil, E., Shahbaba, B., Mizutani, J., Ryvkin, A., Komisopoulou, E., Graeber, T., Plevritis, S. Agus, D., Jain, A, "Global Tyrosine phosphorylation patterns upon EGFR stimulation and inhibition with distinct anti-EGFR therapeutics", in preparation.
6. Kani K., Faca V., Shahbaba B., Hughes L., Wu H., Katz J., Plevritis S., Tibshirani R., Jain A., Hanash S., Mallick P., Agus D., Quantitative proteomic profiling of A431 identifies a panel of proteins indicative of response to gefitinib both in vitro and in vivo, in preparation.