MIPS Molecular Imaging Program at Stanford
Center for Cancer Nanotechnology Excellence Focused on Therapy Response

CCNE-TR Scientific Papers

NCI Alliance's Scientific Bibliography

Project 1: 2009-2010

  • W. Hu, R. J. Wilson, C. M. Earhart, A. L. Koh, S. X. Wang, "Synthetic Antiferromagnetic Nanoparticles with Tunable Susceptibilities", online at J. Appl. Physics 105, 07b508 (2009) DOI:10 1063/1.3072028
  • C. Earhart, R. J. Wilson, R. L. White, N. Pourmand, S.X. Wang, "Microfabricated magnetic sifter for high-throughput and high-gradient magnetic separation", J Magn Magn Mat 9, 321: 1436 (2009).
  • W. Hu, A. Koh, R. J. Wilson, S. X. Wang, Novel Synthetic Magnetic Nanoparticles for Biomedical Applications, VDM Verlag Dr. Müller Aktiengesellschaft & Co. kG, Germany, 2009.
  • R. J. Wilson, W. Hu, C. Wong Po Fu, A. L. Koh, R. Gaster, C. M. Earhart, A. Fu, S. C. Heilshorn, R. Sinclair, S. X. Wang, "Formation and properties of magnetic chains for 100 nm nanoparticles used in separations of molecules and cells", J Magn Magn Mat, 321(10):1452 (2009).
  • C. M. Earhart, E. M. Nguyen, R. J. Wilson, Y. A. Wang, and Shan X. Wang. "Designs for a Micro-fabricated Magnetic Sifter", IEEE Trans. Magn., 45 (10): 4884 (2009).
  • R. S. Gaster, D. A. Hall, C. H. Nielsen, S. J. Osterfeld, H. Yu, K. E.Mach, R. J. Wilson, B. Murmann, J. C. Liao, S. S. Gambhir, and S. X. Wang, "Matrix-insensitive femtomolar-level multiplex protein detection", Nature Medicine online at doi:10.1038/nm.2032
  • M. R. Benoit, D. Mayer, Y. Barak, I. Y. Chen, Z. Cheng, W. Hu, S. X. Wang, S. S. Gambhir, A. Matin, "Visualizing implanted tumors in mice with MRI using magnetotactic bacteria," Clin. Cancer Res., 15(16), 5170-7, 2009.
  • M. Donolato, M. Gobbi, P. Vavassori, M. Leone, M. Cantoni, V. Metlushko, B. Ilic, M. Zhang, S. X.Wang and R. Bertacco, "Nanosized corners for trapping and detecting magnetic nanoparticles," Nanotechnology, 20, 385501 (6pp), 2009.
  • A. L. Koh, W. Hu, R. J. Wilson, C. M. Earhart, S. X. Wang and R. Sinclair. "Structural and Magnetic Characterization of High Moment Synthetic Antiferromagnetic Nanoparticles Fabricated Using Self-Assembled Stamps", submitted to J Appl Phys.
  • R. S. Gaster, D. A. Hall, and S. X. Wang, "NanoLab - Auto-assembly immunoassay and portable electronics for individualized molecular diagnostics," submitted to PNAS
  • D. A. Hall, R. S. Gaster, S. J. Osterfeld, B. Murmann, and S. X. Wang, "GMR biosensor arrays: correction techniques for reproducibility and enhanced sensitivity," submitted to Biosensors and Bioelectronics.
  • D. A. Hall, R. S. Gaster, T. Lin, S. J. Osterfeld, S. Han, B. Murmann, and S. X. Wang, "GMR biosensor arrays: a system perspective," Biosensors and Bioelectronics, in press.
  • M. Zhang, W. Hu, C. M. Earhart, M. Tang, R. J. Wilson, S. X. Wang. "Silane-based functionalization of synthetic antiferromagnetic nanoparticles for biomedical applications". submitted to J Appl Phys.
  • W. Hu, M. Zhang, R. J. Wilson, A. L. Koh, and S. X. Wang."Fabrication of Aqueous Stable Synthetic Magnetic Nanoparticles with Tri-layer Resist Lift-off and Release", in preparation.

Project 1: 2008-2009

  • A. Fu, W. Hu, L. Xu, R. J. Wilson, H. Yu, S. J. Osterfeld, S. S. Gambhir, S. X. Wang, Protein Functionalized Antiferromagnetic Nanoparticles for Biomolecule Detection and Magnetic Manipulation, Angewandte Chemie 2009, 121(9): 1648-52.
  • W. Hu, R. J. Wilson, C. M. Earhart, A. L. Koh, S. X. Wang, Synthetic Antiferromagnetic Nanoparticles with Tunable Susceptibilities, online at J. Appl. Physics 105, 07b508 (2009) DOI:10 1063/1.3072028
  • C. Earhart, R. J. Wilson, R. L. White, N. Pourmand, S.X. Wang, Microfabricated magnetic sifter for high-throughput and high-gradient magnetic separation, J. of Magnetism and Magnetic Materials, in press, 2009.
  • A. L. Koh, W. Hu, R. J. Wilson, S. X. Wang, R. Sinclair, Preparation, Structural and Magnetic Characterization of Synthetic Anti-ferromagnetic (SAF) Nanoparticles, Philosophical Magazine 2008 88(36): 4225-41.
  • A. Fu, S. Kim, Y. Li, A. Z. Faranesh, B. Smith, W. Hu, B. Bales, D. L. Petko, R. J. Wilson, R. Tsien, R. N. Zare, S. S. Gambhir, S. X. Wang, Highly Fluorescent Magnetic Nanoprobes for Advanced Magnetic Resonance and Single Molecule Fluorescence Imaging, in revision.
  • R. J. Wilson, W. Hu, C. Wong Po Fu, A. L. Koh, R. Gaster, C. M. Earhart, A. Fu, S. C. Heilshorn, R. Sinclair, S. X. Wang, Formation and properties of magnetic chains for 100 nm nanoparticles used in separations of molecules and cells, J. of Magnetism and Magnetic Materials, in press, 2009.
  • W. Hu, R.J. Wilson, A.L. Koh, A. Fu, A. Z. Faranesh, C. M. Earhart, S. J. Osterfeld, S. J. Han, L. Xu, S. Guccione, R. Sinclair, S. X. Wang, High-Moment Antiferromagnetic Nanoparticles with Tunable Magnetic Properties, Adv. Mat. 2008, 20(7): 1479.
  • S. X. Wang, G. Li, Advances in GMR biosensors with magnetic nanoparticle tags: review and outlook. IEEE Trans. Magn. 2008, 44(7): 1687-1702.
  • S. J. Osterfeld, H. Yu H, R. Gaster et al., Multiplex Protein Assays Based on Real-Time Magnetic Nanotag Sensing. PNAS 2008, 105(52): 20637-40.
  • S. J. Osterfeld, S. X. Wang, Book Chapter in Microarrays: New Development Towards Recognition of Nucleic Acid and Protein Signatures (edited by Kilian Dill, Robin Liu and Piotr Grodzinski) 2009.
  • R. S. Gaster, D. A. Hall, C. H. Nielsen, S. J. Osterfeld, H. Yu, K. E.Mach, R. J. Wilson, B. Murmann, J. C. Liao, S. S. Gambhir, and S. X. Wang, "Matrix-insensitive femtomolar-level multiplex protein detection", submitted.
  • L. Xu, H. Yu, S.-J. Han, S. J. Osterfeld, R. L. White, N. Pourmand and S. X. Wang, Giant magnetoresistive sensors for DNA microarray, IEEE Trans. Mag., 44, 3989-91, 2008.
  • L. Xu, H. Yu, M. S. Akhras, S.-J. Han, S. J. Osterfeld, R. L. White, N. Pourmand, S. X. Wang, Giant magnetoresistive biochip for DNA detection and HPV genotyping, Biosensors and Bioelectronics, 24, 99–103, 2008.

Project 1: 2007-2008

  • 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.
  • 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.
  • 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.
  • 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.
  • 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).
  • 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.
  • 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.
  • 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.
  • 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.

Project 1 2006-2007

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

Project 2: 2009-2010

  • Zhuang Liu, Scott Takabman, Sarah Sherlock, Xiaolin Li, Zhuo Chen, Kaili Jiang, Shoushan Fan, Hongjie Dai. "Multiplexed Five-Color Molecular Imaging of Cancer Cells and Tumor Tissues with Carbon Nanotube Raman Tags in the Near-Infrared," J. Am. Chem. Soc. Submitted October 2009.
  • Kevin Welsher, Zhuang Liu, Sarah P. Sherlock, Joshua Tucker Robinson, Zhuo Chen, Dan Daranciang & Hongjie Dai. "A route to brightly fluorescent carbon nanotubes for near-infrared imaging in mice," Nature Nanotechnology, adv. online publication – 11 October, 2009. doi:10.1038/nnano.2009.294.
  • Zhuang Liu, Alice C. Fan, Kavya Rakhr, Sarah Sherlock, Andrew Goodwin, Xiaoyuan Chen, Qiwei Yang, Dean W. Felsher, Hongjie Dai. "Supramolecular Stacking of Doxorubicin on Carbon Nanotubes for In Vivo Cancer Therapy," Angew. Chem. Int. Ed. 48(41), 7668-7672, 2009.
  • Zhuang Liu, Scott M Tabakman, Zhuo Chen, Hongjie Dai. "Preparation of Carbon Nanotube Bioconjugates for Biomedical Applications," Nature Protocols 4(9), 1372-1382, 2009.
  • Giuseppe Prencipe, Scott M. Tabakman, Kevin Welsher, Zhuang Liu, Andrew P. Goodwin, Li Zhang, Joy Henry, and Hongjie Dai. "PEG Branched Polymer for Functionalization of Nanomaterials with Ultralong Blood Circulation," J. Am. Chem. Soc. 131, 4783–4787, 2009.
  • Li Zhang, Xiaomin Tu, Kevin Welsher, Xinran Wang, Ming Zheng, Hongjie Dai. "Optical Characterizations and Electronic Devices of Nearly Pure (10,5) Single-Walled Carbon Nanotubes," J. Am. Chem. Soc. 131(7), 2454–2455, 2009.
  • Zhuang Liu, Scott Tabakman, Kevin Welsher, Hongjie Dai. "Carbon Nanotubes in Biology and Medicine: In vitro and in vivo Detection, Imaging and Drug Delivery," Nano Res. 2(85), 120, 2009.

Project 2: 2008-2009

  • Z Liu, SM Tabakman, K Welsher, H Dai. "Carbon Nanotubes in Biology and Medicine: in vitro and in vivo Detection, Imaging and Drug Delivery," Nano Research In Press, 2009.
  • G Prencipe, SM Tabakman, K Welsher, Z Liu, AP Goodwin, L Zhang, J Henry, H Dai. "PEG Branched Polymer for Functionalization of Nanomaterials with Ultralong Blood Circulation," J. Am. Chem. Soc. 2009 Advance Online Publication.
  • A P Goodwin, S M Tabakman, K Welsher, S P Sherlock, G Prencipe, H Dai. "Phospholipid-Dextran with a Single Coupling Point: A Useful Amphiphile for Functionalization of Nanomaterials," J. Am. Chem. Soc. 131(1), 289 -296, 2009.
  • Z Chen, S M Tabakman, A P Goodwin, M G Kattah, D Daranciang, X Wang, G Zhang, X Li, Z Liu, P J Utz, K Jiang, S Fan, H Dai. "Protein microarrays with carbon nanotubes as multicolor Raman labels," Nature Biotechnology 26(11), 1285-1292, 2008.
  • Z Liu, X Li, S M Tabakman, K Jiang, S Fan, H Dai. "Multiplexed Multicolor Raman Imaging of Live Cells with Isotopically Modified Single Walled Carbon Nanotubes," J. Am. Chem. Soc. 130, 13540–13541, 2008.
  • X Sun, Z Liu, K Welsher, J T Robinson, A P Goodwin, S Zaric, H Dai. "Nano-Graphene Oxide for Cellular Imaging and Drug Delivery," Nano Res. 1, 203-212, 2008.
  • A de La Zerda, C Zavaleta, S Keren, S Vaithilingam, S Bodapati, Z Liu, J Levi, B R Smith, T Ma, O Oralkan, Z Cheng, X Chen, H Dai, B T Khuri-Yakub, S S Gambhir. "Carbon Nanotubes As Photoacoustic Molecular Imaging Agents In Living Mice," Nature Nanotechnology 3, 556-562, 2008.
  • S Dhar, Z Liu, J Thomale, H Dai, S J Lippard. "Targeted Single-Wall Carbon Nanotube-Mediated Pt(IV) Prodrug Delivery Using Folate as a Homing Device," J. Am. Chem. Soc. 130, 11467–11476, 2008.
  • KA Drouvalakis, S Bangasruntip, H Wolfgang, LG Kozar, PJ Utz, H Dai. "Peptide-coated nanotube-based biosensor for the detection of disease-specific autoantibodies in human serum," Biosensors & Bioelectronics 23(10), 1413-1421, 2008.
  • Z Liu, J T Robinson, X Sun, H Dai. "PEGylated Nanographene Oxide for Delivery of Water-Insoluble Cancer Drugs," J. Am. Chem. Soc. 130, 10876–10877, 2008.
  • Z Liu, K Chen, C Davis, S Sherlock, Q Cao, X Chen, H Dai. "Drug Delivery with Carbon Nanotubes for In vivo Cancer Treatment," Cancer Res. 68(16), 6652-6660, 2008.
  • I Hamad, A C Hunter, K J Rutt, Z Liu, H Dai, S M Moghimi "Complement activation by PEGylated single-walled carbon nanotubes is independent of C1q and alternative pathway turnover," Molecular Immunology 45, 3797–3803, 2008.
  • X Sun, S Zaric, D Daranciang, K Welsher, Y Lu, X Li, H Dai. "Optical Properties of Ultrashort Semiconducting Single-Walled Carbon Nanotube Capsules Down to Sub-10 nm," J. Am. Chem. Soc. 130, 6551–6555, 2008.
  • M L Schipper, N Nakayama-Ratchford, C R Davis, N W Sh Kam, P Chu, Z Liu, X Sun, H Dai, S S. Gambhir. "A pilot toxicology study of single-walled carbon nanotubes in a small sample of mice," Nature Nanotechnology 3, 216-221, 2008.
  • K Welsher, Z Liu, D Daranciang, H Dai. "Selective Probing and Imaging of Cells with Single Walled Carbon Nanotubes as Near-Infrared Fluorescent Molecules," Nano Lett. 8(2), 586-590, 2008.
  • Z Liu, C Davis, W Cai, L He, X Chen, H Dai. "Circulation and long-term fate of functionalized, biocompatible single-walled carbon nanotubes in mice probed by Raman spectroscopy," PNAS 105(5), 1410–1415, 2008.

Project 2: 2007-2008

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

Project 2: 2006-2007

  • 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.
  • 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.
  • 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.
  • 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.

Project 3: 2008-2009

Project 3 evolved into other areas and is no longer continuing with the CCNE-TR grant
  • C. M. Shachaf, S. V. Elchuri, A. L. Koh, J. Zhu, L. N. Nguyen, D. J. Mitchell, J. Zhang, K. B. Swartz, , L. Sun, S. Chan, R. Sinclair, and G. P. Nolan. A novel method for detection of phosphorylation in single cells by Surface Enhanced Raman Scattering (SERS) using Composite Organic-Inorganic Nanoparticles (COINs). PLoS ONE in press.
  • C. M. Shachaf, S. V. Elchuri, D. J. Mitchell, and G. P. Nolan. Uses of COIN SERS particles to monitor dynamic signaling. In preparation.
  • S. Itani, K. Sachs (co-first author), G.P. Nolan and M.A. Dahleh, "Adapting cyclic structure learning to biological networks", IEEE BIBE conference on Systems Biology, Oct. 8-10, 2008 (Best paper award).
  • K. Sachs, S. Itani, J. Carlisle, G. P. Nolan, D. Pe'er and Douglas A.Lauffenburger, "Learning signaling network structures from sparsely distributed data", s 2009 Feb;16(2):201-12.
  • K. Sachs, S. Itani, J. Fitzgerald, L. Wille, B. Schoeberl, M.A. Dahleh and G.P. Nolan, "Learning cyclic signaling pathway structures while minimizing data requirements", Proceedings of the Pacific Symposium on Biocomputing, 2009.
  • S. Itani, M. Ohannessian (co-first), K. Sachs (co-first), G. P. Nolan and M. A. Dahleh, "Formalism and structure learning for cyclic networks", Journal of Machine Learning Research (JMLR), submitted.
  • S. Itani, K. Sachs, G.P. Nolan and M.A. Dahleh, "Single time point models of dynamic systems", in preparation.

Project 3: 2007-2008

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Nolan GP. (2007) Visualizing Inside the Cell. Biology of Blood and Marrow Transplantation. January Vol 13: 120-123.
  • 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.
  • 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.
  • 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.
  • 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.

Project 3: 2006-2007

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

Project 4: 2009-2010

  • Jeong SK, Kwon MS, Lee EY, Lee HJ, Cho SY, Kim H, Yoo JS, Omenn GS, Aebersold R, Hanash S, Paik YK. BiomarkerDigger: a versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers. Proteomics. 2009 Jul;9(14):3729-40.
  • Taylor AD, Hancock WS, Hincapie M, Taniguchi N, Hanash SM. Towards an integrated proteomic and glycomic approach to finding cancer biomarkers. Genome Med. 2009 Jun 4;1(6):57.
  • Vaisocherová H, Faca VM, Taylor AD, Hanash S, Jiang S. Comparative study of SPR and ELISA methods based on analysis of CD166/ALCAM levels in cancer and control human sera. Biosens Bioelectron. 2009 Mar 15;24(7):2143-8. Epub 2008 Nov 27.
  • Faça VM, Hanash SM. In-depth proteomics to define the cell surface and secretome of ovarian cancer cells and processes of protein shedding. Cancer Res. 2009 Feb 1;69(3):728-30.
  • Faca V, Wang H, Hanash S. Proteomic global profiling for cancer biomarker discovery. Methods Mol Biol. 2009;492:309-20. PubMed PMID: 19241042.
  • Hall B, Cater S, Levy M, Ellington AD. Kinetic optimization of a protein-responsive aptamer beacon. Biotechnol Bioeng. 2009 Aug 15;103(6):1049-59.
  • Li N, Ebright JN, Stovall GM, Chen X, Nguyen HH, Singh A, Syrett A, Ellington AD. Technical and biological issues relevant to cell typing with aptamers. J Proteome Res. 2009 May;8(5):2438-48.
  • Pai SS, Ellington AD. Using RNA aptamers and the proximity ligation assay for the detection of cell surface antigens. Methods Mol Biol. 2009;504:385-98.
  • McIntosh M, Fitzgibbon M. Biomarker validation by targeted mass spectrometry. Nat Biotechnol. 2009 Jul;27(7):622-3.
  • May D, Law W, Fitzgibbon M, Fang Q, McIntosh M. Software platform for rapidly creating computational tools for mass spectrometry-based proteomics. J Proteome Res. 2009 Jun;8(6):3212-7.
  • Kani et al. Quantitative proteomic profiling identifies a panel of proteins indicative of EGFR kinase inhibition response in vitro and in vivo.
  • Kani et al. Quantitative Proteomics Evidence that Acquisition of Resistance Leads to Massive Alterations in Cellular Physiology.

Project 4: 2008-2009

  • "Platform for visual curation of quantitative mass spectrometry experiments to support biomarker discovery", D. May, Q. Fang, M. Fitzgibbon, W. Law, M. Mcintosh, Journal of Proteome Research, Submitted Feb 2009.
  • Li, N., Ebright, J.N., Stovall, G.M., Chen, X., Nguyen, H.H., Singh, A., Syrett, A., and A.D. Ellington. (2009) Technical and Biological Issues Relevant to Cell Typing by Aptamers. J Proteome Res, in process.
  • "A development platform for rapidly creating mass spectrometry proteomics computational tools", May, Fang, Law, Fitzgibbon, McIntosh, Journal of Proteomics Research, Submitted February 19, 2009.
  • "Platform for visual curation of quantitative mass spectrometry experiments to support biomarker discovery", D. May, Q. Fang, M. Fitzgibbon, W. Law, M. Mcintosh, Journal of Proteome Research, Submitted Feb 2009.
  • 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.
  • 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.
  • 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.
  • 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.
  • Vaisocherová H, Faca VM, Taylor AD, Hanash S, Jiang S. Biosens Bioelectron. Comparative study of SPR and ELISA methods based on analysis of CD166/ALCAM levels in cancer and control human sera. 2008 Nov 27.
  • Faça VM, Hanash SM. In-depth proteomics to define the cell surface and secretome of ovarian cancer cells and processes of protein shedding. Cancer Res. 2009 Feb 1;69(3):728-30. Epub 2009 Jan 20.
  • Menon R, Zhang Q, Zhang Y, Fermin D, Bardeesy N, DePinho RA, Lu C, Hanash SM, Omenn GS, States DJ. Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer. Cancer Res. 2009 Jan 1;69(1):300.
  • May D, Liu Y, Law W, Fitzgibbon M, Wang H, Hanash S, McIntosh M. Peptide Sequence Confidence in Accurate Mass and Time Analysis and Its Use in Complex Proteomics Experiments. J Proteome Res. 2008 Oct 28.
  • Shedden K, Taylor JM, Enkemann SA, Tsao MS, Yeatman TJ, Gerald WL, Eschrich S, Jurisica I, Giordano TJ, Misek DE, Chang 10. AC, Zhu CQ, Strumpf D, Hanash S, Shepherd FA, Ding K, Seymour L, Naoki K, Pennell N, Weir B, Verhaak R, Ladd-Acosta C, Golub T, Gruidl M, Sharma A, Szoke J, Zakowski M, Rusch V, Kris M, Viale A, Motoi N, Travis W, Conley B, Seshan VE, Meyerson M, Kuick R, Dobbin KK, Lively T, Jacobson JW, Beer DG. Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Director's Challenge Consortium for the Molecular Classification of Lung Adenocarcinoma, Nat Med. 2008 Aug;14(8):822-7. Epub 2008 Jul 20.
  • Kim YS, Son OL, Lee JY, Kim SH, Oh S, Lee YS, Kim CH, Yoo JS, Lee JH, Miyoshi E, Taniguchi N, Hanash SM, Yoo HS, Ko JH. Lectin precipitation using phytohemagglutinin-L(4) coupled to avidin-agarose for serological biomarker discovery in colorectal cancer. Proteomics. 2008 Aug;8(16):3229-35.
  • Faça VM, Ventura AP, Fitzgibbon MP, Pereira-Faça SR, Pitteri SJ, Green AE, Ireton RC, Zhang Q, Wang H, O'Briant KC, Drescher CW, Schummer M, McIntosh MW, Knudsen BS, Hanash SM. Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extra-cellular domains. PLoS ONE. 2008 Jun 18;3(6):e2425.
  • Faca VM, Song KS, Wang H, Zhang Q, Krasnoselsky AL, Newcomb LF, Plentz RR, Gurumurthy S, Redston MS, Pitteri SJ, Pereira-Faca SR, Ireton RC, Katayama H, Glukhova V, Phanstiel D, Brenner DE, Anderson MA, Misek D, Scholler N, Urban ND, Barnett MJ, Edelstein C, Goodman GE, Thornquist MD, McIntosh MW, DePinho RA, Bardeesy N, Hanash SM. A mouse to human search for plasma proteome changes associated with pancreatic tumor development. PLoS Med. 2008 Jun 10;5(6):e123.
  • Zhang Q, Menon R, Deutsch EW, Pitteri SJ, Faca VM, Wang H, Newcomb LF, Depinho RA, Bardeesy N, Dinulescu D, Hung KE, Kucherlapati R, Jacks T, Politi K, Aebersold R, Omenn GS, States DJ, Hanash SM. A mouse plasma peptide atlas as a resource for disease proteomics. Genome Biol. 2008;9(6):R93. Epub 2008 Jun 3.
  • Wang H, Hanash SM. Increased throughput and reduced carryover of mass spectrometry-based proteomics using a high-efficiency nonsplit nanoflow parallel dual-column capillary HPLC system. J. Proteome Res. 2008 Jul;7(7):2743-55. Epub 2008 May 31.
  • Krasnoselsky AL, Faca VM, Pitteri SJ, Zhang Q, Hanash SM. Isoform analysis of LC-MS/MS data from multidimensional fractionation of the serum proteome. J Proteome Res. 2008 Jun;7(6):2546-52. Epub 2008 Apr 18.
  • Hanash SM, Pitteri SJ, Faca VM. Mining the plasma proteome for cancer biomarkers. Nature. 2008 Apr 3;452(7187):571-9.
  • Javier, D.J., Nitin, N., Levy, M., Ellington, A., and R. Richards-Kortum. (2008) Aptamer-targeted gold nanoparticles as molecular-specific contrast agents for reflectance imaging. Bioconjugate Chemistry, 19:1309–12.
  • B Deng, H Wang, L Beretta, S Hanash. TGF-β Induced Protein dynamics in Hepatoma Cells (submitted).
  • Kani K, Faca V, Hughes L, Zhang W, Fang Q, Shahbaba B, Katz J, Luethy R, Erde J, Schmidt J, Pitteri S, Zhang Q, Tibshirani R, Plevritis S, McIntosh M, Jain A, Hanash S, Agus D, Mallick P. Quantitative proteomic profiling identifies a panel of proteins indicative of EGFR kinase inhibition in vitro and in vivo. (in prep)
  • May D, Law W, Fitzgibbon M, Fang Q, and McIntosh M. A development platform for rapidly creating mass spectrometry proteomics computational tools. J. of Proteome Research. 2009 Feb: submitted.

Project 4: 2007-2008

  • 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.
  • TGF-_ Induced Protein dynamics in Hepatoma Cells B Deng, H Wang, L Beretta, S Hanash (submitted).
  • 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.
  • 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.
  • Hanash, S., Pitteri, S., Faca, V. Mining the plasma proteome for cancer Biomarkers. Nature in press.
  • 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.
  • Pitteri S, Hanash S, Proteomic approaches for cancer biomarker discovery in plasma. Expert Review 2007, Oct. in press.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

Project 4: 2006-2007

  • 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.
  • 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.
  • Chu, T.C., Twu, K.Y., Ellington, A.D., and M. Levy (2006). Aptamer mediated siRNA delivery. Nucleic Acids Res, 34(10):e73.
  • 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.
  • Davidson, E.A., and A.D. Ellington (2007). Synthetic RNA circuits. Nat Chem Biol, 3(1):23-28.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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).
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • B Deng, H Wang, L Beretta, S Hanash, TGF-_ Induced Protein dynamics in Hepatoma Cells, 2007, Submitted.

Project 5: 2009-2010

  • Barat, B., Sirk, S., McCabe, K., Li, J., Koh, A.L., Lepin, E., Olafsen, T., Gambhir, S.S., Weiss, S., and Wu, A.M. Cys-diabody quantum dot conjugates (immunoQdots) for cancer marker detection, Bioconj. Chem.,20:1474-1481.
  • McCabe, K., Liu, B., Marks, J.D., Wu, H., and Wu, A.M. An engineered antibody fragment for PET imaging of ALCAM-positive tumors. World Molecular Imaging Congress, 2009, Montreal, Quebec, Canada.
  • Gao, J., Chen, K., Xie R., Xie, J., Yan, Y., Cheng, Z., Peng, X., and Chen, X. In vivo Tumor-targeted Fluorescence Imaging Using Near-infrared Non-cadmium Quantum Dots. Bioconj. Chem. Accepted.
  • Dragulescu-Andrasi A, Liang GL, Rao J. In vivo bioluminescence imaging of furin activity in breast cancer cells using luminogenic substrates. Bioconjugate Chemistry 2009; 20: 1660-1666.
  • Kim Y-P, Daniel WL, Xia Z, Xie H, Mirkin CA, Rao J. Bioluminescent nanosensors for protease detection based upon gold nanopartice-luciferase conjugates. Chemical Communications (London) 2009; ASAP.
  • Liang G, Ren H, Rao J. A biocompatible condensation reaction for controlled assembly of nanostructures in cells. Nature Chemistry 2009; Accepted.
  • Ren H, Xiao F, Zhan K, Kim Y-P, Xie H, Xia Z, Rao J. A biocompatible condensation reaction for labeling of terminal cysteine on proteins. Angewandte Chemie International Edition 2009; Accepted.
  • Xia Z, Xing Y, Dragulescu-Andrasi A, Gambhir SS, Rao J. In vivo mapping extracellular MMP-2 activity with an immobilized, activatable bioluminescent reporter. Submitted.

Project 5: 2008-2009

  • 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.
  • Wu, A.M. and Olafsen, T. (2008) Cancer Journal 14:191-197.
  • 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. (2008) Diabodies targeting epithelial membrane protein 2 reduce tumorigenicity of human endometrial cancer cell lines. Clin. Cancer Res., 14:7367-7377.
  • Leyton, J.V., Olafsen, T., Lepin, E.J., Hahm, S., Bauer, K., Reiter, R.E., and Wu, A.M. (2008) A humanized radioiodinated minibody as an imaging agent for the detection of prostate stem cell antigen (PSCA)-expressing tumors by microPET. Clin. Canc. Res., 14:7488-7496.
  • Sirk, S., Olafsen, T., Barat, B., Bauer, K. B., McCabe, K.E., and Wu, A.M. (2008) Site-specific thiol-mediated conjugation of fluorescent probes to cysteine-modified diabodies targeting CD20 or HER2. Bioconj. Chem., 19:2527-2534.
  • Wu, A.M. (2009) Antibodies and Antimatter: The resurgence of immunoPET. J. Nuc. Med. 50:2-5.
  • Schipper, M.L., Iyer, G., Koh, A.L., Cheng, Z, Ebenstein, Y., Ahroni, A., Keren, S., Bentolilla, L., Li, J., Rao, J., Chen, X., Banin, U., Wu, A.M., Sinclair, R., Weiss, S., and Gambhir, S.S. (2009) Particle size, surface coating, and PEGylation influence the biodistribution of quantum dots in living mice. Small, 5:126-134.
  • Leyton, J.V., Olafsen, T., Sherman, M.A., Bauer, K.B., Aghajanian, P., Reiter, R.E., and Wu, A.M. (2009) Engineered humanized diabodies for microPET imaging of prostate stem cell antigen (PSCA)-expressing tumors. Prot. Eng. Des. Select., ePub ahead of print.
  • Shimazaki, K., Chan, A.M., Moniz, R.J., Wadehra, M., Nagy, A., Coulam, C.P., Mareninov, S., Lepin, E.M., Wu, A.M., Kelly, K.A., Braun, J., and Gordon, L.K. (2009) Blockade of epithelial membrane protein 2 (EMP2) abrogates infection of Chlamydia muridarum murine genital infection model. FEMS Immunology and Medical Microbiology, ePub ahead of print.
  • 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.
  • Xing Y, So M-K, Koh AL, Sinclair R, Rao J. Improved QD-BRET conjugates for detection and imaging. Biochemical & Biophysical Research Communications 2008; 372:388-394.
  • Xing Y, Rao J. Quantum dot bioconjugates for in vitro diagnostics and in vivo imaging. Cancer Biomarkers 2008; 4:307-319 (Invited).
  • So M-K, Yao H, Rao J. HaloTag protein-mediated specific labeling of living cells with quantum dots. Biochemical & Biophysical Research Communications 2008; 374:419-423.
  • Xia Z, Xing Y, So M-K, Koh AL, Sinclair R, Rao J. Multiplex detection of protease activity with nanosensors prepared by intein-mediated specific bioconjugation. Analytical Chemistry 2008; 80:8649-8655.
  • Rao J. Shedding light on tumors using nanoparticles. ACS Nano 2008; 2:1984-1986 (Invited).
  • Schipper ML, Iyer G, Koh AL, Cheng Z, Ebenstein Y, Aharoni A, Keren S, Bentolila LA, Li J, Rao J, Chen X, Banin U, Wu AM, Sinclair R, Weiss SS, Gambhir SS. Particle size, surface coating, and PEGylation influence the biodistribution of quantum dots in living mice. Small 2009; 5:126-134.
  • Xing Y, Xia Z, Rao J. Semiconductor quantum dots for biosensing and in vivo imaging. IEEE Transactions on NanoBioscience 2009; In press (Invited).
  • Xia Z, Rao J. Biosensing and imaging based on bioluminescence resonance energy transfer. Current Opinion in Biotechnology 2009; In press (Invited).

Project 5<: 2007-2008

  • 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.
  • 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.
  • Barat, B. and Wu, A.M. (2007) Metabolic biotinyation of recombinant antibody by biotin ligase retained in endoplasmic reticulum. Biomolec. Eng. 24:283-291.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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).
  • Cai W, Chen X. Preparation of peptide-conjugated quantum dots for tumor vasculature-targeted imaging. Nat Protoc. 2008;3(1):89-96.
  • Cai W, Chen X. Nanoplatforms for targeted molecular imaging in living subjects. Small. 2007 Nov;3(11):1840-54.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Xing Y, So MK, Rao J. Improving the in vivo stability of self-illuminating quantum dot conjugates for in vivo imaging. Biomaterials, Submitted.
  • Xing Y, Rao J. Semiconductor quantum dot bioconjugates for in vivo imaging. Invited submission to Disease Markers and Cancer Biomarkers.
  • So MK, Yao H, Rao J. HaloTag protein-mediated specific labeling of live cells with quantum dots. Biochemical and Biophysical Research Communications, Submitted.

Project 5: 2006-2007

  • Zhang Y, So M-K, Rao J. Protease-modulated cellular uptake of quantum dots. Nano Letters. 2006; 6: 1988-1992.
  • 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.
  • So M-K, Loening AM, Gambhir SS, Rao, J. Creating self-illuminating quantum dot conjugates. Nature Protocols. 2006; 3: 1160-1164. (Invited).
  • 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.
  • 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.
  • 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.
  • Rao J, Dragulescu-Andrasi A, Yao H. Fluorescence imaging in vivo: recent advances. Current Opinion in Biotechnology 2007; 18:17-15. (Invited).
  • Yao H, Zhang Y, Xiao F, Xia Z, Rao J. QD BRET-based highly sensitive detection of proteases. Angewandte Chemie 2007 In press.
  • 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.
  • Cai W, Rao J, Gambhir SS, Chen X Molecular Imaging in Anti-Angiogenic Drug Development Mol Cancer Ther. 2006;5(11): 2624-33.
  • Li Z, Cai W, Chen X Biocompatible Quantum Dots for In Vivo Imaging J Nanosci Nanotechnol. 2007, In press.
  • Hsu AR, Chen X Biomedical applications of quantum dot semiconductor nanoparticles Encyclopedia of Nanoscience and Nanotechnology (Editor, HS Nalwa), 2007.
  • 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.
  • 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.

Project 6: 2009-2010

  • De la Zerda A, Liu Z, Zavaleta C, Srikant V, Bodapati S, Teed R, Ma TJ, Oralkan O, Chen X, Khuri-Yakub BT, Dai H, Gambhir SS. Enhanced Carbon Nanotubes for Photoacoustic Molecular Imaging in Living Mice. Nat Nanotechnol, Submitted Febuary 2009.
  • De la Zerda A, Zavaleta C, Keren S, Vaithilingam S, Bodapati S, Liu Z, Levi J, Smith BR, Ma TJ, Oralkan O, Cheng Z, Chen X, Dai H, Khuri-Yakub BT, Gambhir SS. Carbon nanotubes as photoacoustic molecular imaging agents in living mice. Nat Nanotechnol 3 (9): 557-62, 2008.
  • Keren S, Zavaleta C, Cheng Z, de la Zerda A, Gheysens O, Gambhir SS. Noninvasive molecular imaging of small living subjects using Raman spectroscopy. Proc Natl Acad Sci U S A 105 (15): 5844-9, 2008.
  • Schipper ML, Nakayama-Ratchford N, Davis CR, Kam NW, Chu P, Liu Z, Sun X, Dai H, Gambhir SS. A pilot toxicology study of single-walled carbon nanotubes in a small sample of mice. Nat Nanotechnol 3 (4): 216-21, 2008.
  • Smith BR, Cheng Z, De A, Koh AL, Sinclair R, Gambhir SS. Real-time intravital imaging of RGD-quantum dot binding to luminal endothelium in mouse tumor neovasculature. Nano Lett 8 (9): 2599-606, 2008.
  • Smith BR, Cheng Z, de la Zerda A, Koh AL, Sinclair R, Gambhir SS. Real-time visualization of RGD-quantum dot binding in tumor neovasculature using intravital microscopy in multiple living mouse models. Proc SPIE In Press, 2009.
  • Zavaleta C, de la Zerda A, Liu Z, Keren S, Cheng Z, Schipper M, Chen X, Dai H, Gambhir SS. Noninvasive Raman spectroscopy in living mice for evaluation of tumor targeting with carbon nanotubes. Nano Lett 8 (9): 2800-5, 2008.
  • Zavaleta CL, Smith BR, Walton I, Doering W, Davis G, Shojaei B, Natan MJ, Gambhir SS. Multiplexed imaging of surface enhanced Raman scattering nanotags in living mice using noninvasive Raman spectroscopy. Proc Natl Acad Sci U S A 106 (32): 13511-6, 2009.

Project 6: 2008-2009

  • De la Zerda A, Liu Z, Zavaleta C, Srikant V, Bodapati S, Teed R, Ma TJ, Oralkan O, Chen X, Khuri-Yakub BT, Dai H, Gambhir SS. Enhanced Carbon Nanotubes for Photoacoustic Molecular Imaging in Living Mice. Nat Nanotechnol, Submitted Febuary 2009.
  • De la Zerda A, Zavaleta C, Keren S, Vaithilingam S, Bodapati S, Liu Z, Levi J, Smith BR, Ma TJ, Oralkan O, Cheng Z, Chen X, Dai H, Khuri-Yakub BT, Gambhir SS. Carbon nanotubes as photoacoustic molecular imaging agents in living mice. Nat Nanotechnol 3 (9): 557-62, 2008.
  • Keren S, Zavaleta C, Cheng Z, de la Zerda A, Gheysens O, Gambhir SS. Noninvasive molecular imaging of small living subjects using Raman spectroscopy. Proc Natl Acad Sci U S A 105 (15): 5844-9, 2008.
  • Schipper ML, Nakayama-Ratchford N, Davis CR, Kam NW, Chu P, Liu Z, Sun X, Dai H, Gambhir SS. A pilot toxicology study of single-walled carbon nanotubes in a small sample of mice. Nat Nanotechnol 3 (4): 216-21, 2008.
  • Smith BR, Cheng Z, De A, Koh AL, Sinclair R, Gambhir SS. Real-time intravital imaging of RGD-quantum dot binding to luminal endothelium in mouse tumor neovasculature. Nano Lett 8 (9): 2599-606, 2008 (Cover Article).
  • Smith BR, Cheng Z, de la Zerda A, Koh AL, Sinclair R, Gambhir SS. Real-time visualization of RGD-quantum dot binding in tumor neovasculature using intravital microscopy in multiple living mouse models. Proc SPIE In Press, 2009.
  • Zavaleta C, de la Zerda A, Liu Z, Keren S, Cheng Z, Schipper M, Chen X, Dai H, Gambhir SS. Noninvasive Raman spectroscopy in living mice for evaluation of tumor targeting with carbon nanotubes. Nano Lett 8 (9): 2800-5, 2008.
  • Zavaleta C, Walton I, Doering WE, Shojaei B, Davis G, Natan MJ, Gambhir SS. Multiplexed Imaging of SERS Nanotags in Living Mice Using Non-invasive Raman Spectroscopy. Proc Natl Acad Sci U S A, Submitted December 2008.
  • Adam de la Zerda, Sunil Bodapati, Robert Teed, Meike L. Schipper, Shay Keren, Bryan R. Smith, Johnny S.T. Ng, Sanjiv Sam Gambhir. A Comparison between Time Domain and Spectral Imaging Systems for Imaging Quantum Dots in Small Living Animals. Submitted, March 2009.

Project 6: 2007-2008

  • 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).
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

Project 6: 2006-2007

  • 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).
  • 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).
  • 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.

Core 1: 2009-2010

  • Hu W, Wilson RJ, Earhart CM, Koh AL, Sinclair R, Wang SX. Synthetic Antiferromagnetic Nanoparticles with Tunable Susceptibilities. J. Appl. Phys. 2009; 105:07B508 1-3.
  • Sinclair R, Chin R, Koh AL, Solorzano G. "No Titan, No Excuse" (T. J. Konno, 1 April 2008) A Report on an International Workshop on Remote Electron Microscopy for In Situ Studies. Acta Microscopica 2009; 18 (1):33–38.
  • Koh AL, Watanabe M, Sinclair R. Electron Energy-Loss Spectrometry (EELS) and Energy-Filtered TEM (EFTEM) Analyses of Organic-Inorganic Nanoparticles. Microsc. Microanal. 2009; 15 (Suppl 2): 432CD.
  • Sinclair R, Koh AL, Kempen PJ, Jung HJ. In Situ and High Resolution TEM Studies of Nano-scale Materials. Microsc. Microanal. 2009; 15 (Suppl 2): 1200CD.
  • Barat B, Sirk S, McCabe K, Li J, Lepin EJ, Remenyi R, Koh AL., Olafsen T, Gambhir SS, Weiss S. and Wu AM. Cys-diabody Quantum Dot Conjugates (immunoQdots) for Cancer Marker Detection. Bioconjugate Chemistry 2009, in-press
  • Koh AL, Sinclair R. Scanning Electron Microscopy and Surface Enhanced Raman Spectroscopy Correlation Studies of Functionalized Composite Organic-Inorganic SERS Nanoparticles on Cancer Cells", under review.
  • Koh AL, Sinclair R. Composite Organic-Inorganic SERS Nanoparticles as Labels to Detect Phosphorylation Events in cells", in-preparation.

Core 1: 2008-2009<

  • Hu. W, Wilson RJ, Koh AL, Fu A, Faranesh AZ, Earhart CM, Osterfeld SJ, Han S-J, Xu L, Guccione S, Sinclair R, Wang SX. High-Moment Antiferromagnetic Nanoparticles with Tunable Magnetic Properties. Advanced Materials 2008; 20:1479–1483.
  • Smith BR, Cheng Z, De A, Koh AL, Sinclair R, Gambhir SS. Real-Time Intravital Imaging of RGD-Quantum Dot Binding to Luminal Endothelium in Mouse Tumor Neovasculature. Nano Letters 2008; 8 (9):2599–2606.
  • Lee H-Y, Lee S-H, Xu C, Xie J, Lee J-H, We B, Koh AL, Wang X, Sinclair R, Wang SX, Nishimura DG, Biswal S, Sun S, Cho SH, Chen X. Synthesis and characterization of PVP-coated large core iron oxide nanoparticles as an MRI contrast agent. Nanotechnology 2008; 19:165101.
  • Koh AL, Hu W, Wilson RJ, Wang SX, Sinclair R. TEM Analyses of Synthetic Anti-Ferromagnetic (SAF) Nanoparticles Fabricated Using Different Release Layers. Ultramicroscopy 2008; 108:1490–1494.
  • Xing Y, So M-K, Koh AL, Sinclair R, Rao J. Improved QD-BRET Conjugates for Detection and Imaging. Biochemical and Biophysical Research Communications 2008; 372:388–394.
  • Koh AL, Shachaf CM, Elchuri S, Nolan GP, Sinclair R. Electron Microscopy Localization and Characterization of Functionalized Composite Organic-Inorganic SERS Nanoparticles on Leukemia Cells. Ultramicroscopy 2008; 109:111–121.
  • Koh AL, Hu W, Wilson RJ, Wang SX, Sinclair R. Preparation, Structural and Magnetic Characterization of Synthetic Anti-ferromagnetic (SAF) Nanoparticles. Philosophical Magazine 2008; 88 (36):4225–4241.
  • Xia Z, Xing Y, So M-K, Koh AL, Sinclair R, Rao J. Multiplex detection of protease activity with quantum dot nanosensors prepared by intein-mediated specific bioconjugation. Anal. Chem. 2008; 80:8649–8655.

Core 1: 2007-2008<

  • "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.
  • "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).
  • "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).
  • "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).
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

Core 1: 2006-2007

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

Core 2: 2008-2009

  • Fu, W. Hu , L.Xu, R. J. Wilson, H.Yu, S.J. Osterfeld, S. S. Gambhir, S.X.Wang. "Protein-Functionalized Synthetic Antiferromagnetic Nanoparticles for Biomolecule Detection and Magnetic Manipulation." Angewandte Chemie, 48, 1620. (2009).
  • E.S. Barnard, J.S. White, A. Chandran, M.L. Brongersma. "Spectral properties of plasmonic resonator antennas." Optics Express, 16, 16529 (2008).
  • Ching-Mei Hsu, Stephen T. Connor, Mary X. Tang, and Yi Cui. "Wafer-scale silicon nanopillars and nanocones by Langmuir-Blodgett assembly and etching." Appl. Phys. Lett. 93, 133109 (2008).

Core 2: 2007-2008

  • "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).
  • "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).
  • "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).

Core 2: 2006-2007

  • 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.
  • 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.

Core 3: 2009-2010

  • Baker NA, Fritts M, Guccione S, Paik DS, Pappu RV, Patri A, Rubin D, Shaw SY, Thomas DG, "Nanotechnology Informatics White Paper," white paper commissioned by NCI caBIG, February 2009.
  • Baker NA, Fritts M, Guccione S, Paik DS, Pappu RV, Rubin D, Shaw SY, Thomas DG, "The need for minimum information standards for development and advancement of nanomaterials as cancer diagnostics and therapeutics," white paper commissioned by NCI caBIG, February 2009.
  • Baker NA, Fritts M, Guccione S, Paik DS, Pappu RV, Rubin D, Shaw SY, Thomas DG, "Ontologies in cancer nanotechnology research," white paper commissioned by NCI caBIG, January 2009.
  • Kode KK, Shachaf C, Elchuri S, Nolan G, Paik DS. "Quantitative Unmixing of Raman Spectra for Flow Cytometry." In preparation, November 2009.

Core 3: 2008-2009

  • Paik DS, Guccione S, Baker NA, Pan S, Gaheen S, Molnar L, Kode K, Thomas D, Pappu R, Jones P, Wang M, "An Informatics Perspective on the Experience of Developing and Populating a Database of Cancer-related Nanotechnology." accepted to Radiological Society of North America 94th Scientific Sessions, November 2008.
  • Paik DS, Kode K, Guccione S, Baker NA, Thomas D, Pappu R, Jones P, Wang M, Molnar L, Pan S, Gaheen S, "Experience Developing and Populating a Database of Cancer-related Nanotechnology." caBIG 2008 Annual Meeting, Washington, DC, June 2008.

Core 3: 2007-2008

  • Shahbaba B, Tibshirani R, Plevritis S, Bayesian gene set enrichment analysis: Submitted to The Annals of Applied Statistics, 2008.
  • 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.
  • Plevritis S, "Identification of Biomarkers from High Throughput Data" (chapter), Molecular Imaging (book), Principles and Practice, submitted.
  • 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.
  • 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.
  • 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.

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