Publications and Reports
The following is a selected list of published papers and reports by KGI faculty. For more information about individual faculty members, visit the KGI Faculty Directory or contact Noel Brinkerhoff, Director of Donor and Media Relations, at 909-607-0135 or nbrinker@kgi.edu. In addition, by clicking on each individual faculty member, the full profile can be viewed. Adami, Christoph
Professor
Areas of Expertise: Computational Biology, Artificial Life, Evolutionary Biology Adami, C. Digital genetics: unravelling the genetic basis of evolution. Nature Reviews Genetics 7, 109-118 (February 2006). D.A. Drummond, J.D. Bloom, C. Adami, C.O. Wilke, and F.H. Arnold, (2005) Why highly expressed proteins evolve slowly, Proc. Natl. Acad. Sci. U.S.A. 102, 14338-14343. C. Adami: Information Theory in Molecular Biology; Physics of Life Reviews 1 (2004) 3-22. Aufderheide, Brian
Assistant Professor
Areas of Expertise: Bioengineering, Optimization of Fermenters, Physiological Control R. Entus and B. Aufderheide, (2005) Bacterial Decisions: Chemotaxis And Multiple Attractants", in Foundations of Systems Biology in Engineering Conference: Santa Barbara, CA. B. Aufderheide and B.W. Bequette, (2003) Extension of dynamic matrix control to multiple models, Computers & Chemical Engineering, 27, 1079-1096. R. R. Rao, B. Aufderheide, and B.W. Bequette, (2003) Experimental studies on multiple-model predictive control for automated regulation of hemodynamic variables, IEEE Transactions Biomedical Engineering, 50, 277-288. Baura, Gail D.
Professor
Areas of Expertise: Medical Devices, System Theory, Engineering Ethics Baura, G.D. System Theory and Practical Applications of Biomedical Signals (Wiley-IEEE Press, Hoboken, NJ, 2002). Baura, G.D., Foster, D.M., Porte, Jr., D., Kahn, S.E., Bergman, R.N., Cobelli, C. & Schwartz, M.W. Saturable transport of insulin from plasma into the central nervous system of dogs in vivo. J. Clinical Investigation 92, 1824-1830 (1993). Baura, G.D., Malecha, J.R., and Bradley, P.W. Apparatus And Method For Defibrillation Of A Living Subject, U.S. Patent 7,149,576. December 12, 2006. Casper, Steven
Associate Professor, Director of the MBS Program
Areas of Expertise: Management, Biotechnology Clusters, Corporate Governance Creating Silicon Valley in Europe: Technology Policy Towards New Technology Industries, Oxford University Press, 2007. "How Do Technology Clusters Emerge and Become Sustainable? Social Network Formation and Inter-firm Mobility within San Diego Biotechnology," Research Policy, v. 36, 2007, pp. 438-455. Co-authored with Richard Whitley, "Managing competences in entrepreneurial technology firms: a comparative institutional analysis of Germany, Sweden and the UK." Research Policy, v. 33, 2004, pp. 89-106. Chakravarti, Bulbul
Research Associate Professor
Areas of Expertise: Proteomics, Immunobiology of Aging B. Chakravarti and D.N. Chakravarti; "Oxidative modification of proteins: age-related changes": Gerontology53, 128-139 (2007). B. Chakravarti and D.N. Chakravarti; "Protein phosphorylation in T-cell signaling: effect of age": Advances in Cell Aging and Gerontology, Ed. M. Mattson, pp35-56, Volume 16, Elsevier, (2004). D.N. Chakravarti, S. Gallagher and B. Chakravarti; "Difference gel electrophoresis: Application in quantitative proteomics research": Current Proteomics 1, 261-271 (2004). Chakravarti, Deb N.
Arnold and Mabel Beckman Professor, Director of Proteomics
Areas of Expertise: Proteomics, Protein Biochemistry, Vaccine Discovery and Development N. Gupta, A. Law, R. Poddar, M. Louie, A. Ray and D.N. Chakravarti. Toxicoproteomics: Applications in drug development. Current Proteomics 2, 97-101 (2005). A. Rajan, J. Mullen, N. Bhatnagar, A. Dubey, A. Niemz, B. Chakravarti and D.N. Chakravarti. Micro-parallel liquid chromatography for analysis of peptides and proteins. JALA 9, 312-317 (2004). D.N. Chakravarti, M.J. Fiske, L.D. Fletcher and R.J. Zagursky. Application of genomics and proteomics for identification of bacterial gene products as potential vaccine candidates. Vaccine 19, 601-612 (2001). Cregg, James M.
Professor
Areas of Expertise: Recombinant Protein Expression, Peroxisome Biogenesis, Molecular Biology, Pichia pastoris D. Esposito, W. K. Gillette, D. A. Miller, T. E. Taylor, P. H. Frank, R. Hu, J. Bekisz, J. Hernandez, J.M. Cregg, Pichia pastoris,Prot. Exp. Purif. 40, 424-428. C. Ilgen, J.L. Cereghino, and J.M. Cregg,< Chapter 7: Pichia pastoris. In: Production of recombinant proteins: microbial and eukaryotic expression systems. Gellissen, G. (ed.) Wiley-VCH Verlag, Weinheim, Germany, pp.143-162 (2005). A.J. Sunga, and J.M. Cregg, <(2004) The Pichia pastoris formaldehyde dehydrogenase gene (FLD1) as a marker for selection of multicopy expression strains of P. pastoris. Gene 330, 39-47. Croughan, Matthew S.
George B. and Joy Rathmann Professor, Director of the Amgen Bioprocessing Center
Area of Expertise: Bioprocessing Croughan, M.S., Hu, W.S. (2006) "From Microcarriers to Hydrodynamics: Introducing Engineering Science into Animal Cell Culture," Biotechnol. Bioeng. 95, 220-225. Croughan, M.S., Hamel, J.F., Wang, D.I.C. (2006) "Hydrodynamic Effects on Animal Cells Grown in Microcarrier Cultures," Biotechnol. Bioeng. 95, 295-305. Croughan, M.S., Chiou, T-W., Wang, D.I.C. "Immobilized Animal Cell Bioreactors in Bioreactor System Design," J.A. Asenjo and J.C. Merchuk, eds., Marcel Dekker, N.Y., 1995. Dewey, T. Gregory
Vice President for Academic Affairs, Dean of Faculty, Robert E. Finnigan Professor
Areas of Expertise: Systems Biology, Protein Structure, Computational Biology Streicher, K., Willmorth, N., Gracia, J., Boerner, J., Dewey, T.G., Ethier, S. (2007) "Activation of an NF-Kb/ IL-1 Positive Feedback by Amphiregulin in Human Breast Cancer Cells," Mol. Cancer Res. in press Chang, P. L., Rinne, A.W. & Dewey, T. G. (2006) "Structure Alignment Based on coding of Local Geometric Measures," BMC Bioinformatics 7, 346-348 Wu, X., Dewey, T.G "From Microarray to Biological Networks: Analysis of Gene Expression Profiles," Bioinformatics and Drug Discovery, ed. Larson, R.S. pp. 35-48 Humana Press, Totowa, NJ (2006) Kan, Chen-Chen
Research Professor
Areas of Expertise: Drug Discovery, Genomics, Proteomics T.J. Cheng, A. Brik, C.H.. Wong, C.-C. Kan (2004) Model system for high-throughput screening of human immunodeficiency virus protease inhibitors in Escherichia coli, Antimicrobial Agents and Chemotherapy 48, 2437-2447. T.J. Cheng, P.G. Rey, T. Poon, C.-C. Kan et al. (2002) Kinetic studies of human tyrosyl-DNA phosphodiesterase, an enzyme in the topoisomerase I Dnase repair pathway, Eur. J. Biochem. 269, 3697-3704. Molecular Analysis and Genome Discovery, Chapter 14: Structure-based Drug Discovery (Chen-Chen Kan, Kevin Hambly and Derek A. Debe). April 2004, John Wiley & Sons. Moynihan, Karen
Associate Professor
Areas of Expertise: Drug Delivery, Liposomes, Business Development Liposomal camptothecin formulations
U.S. patent 6,740,335, issued May 25, 2004
Karen L. Moynihan, David L. Emerson, Su-Ming Chiang and Ning Hu, inventors
http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-%20bool.html&r=18&f=G&l=50&co1=AND&d=PTXT&s1=moynihan.INNM.&OS=IN/moynihan&RS=IN/moynihan G.M. Jensen, C.R. Skenes, T.H. Bunch, C.A. Weissman, N. Amirghahari, A. Satorius, K.L. Moynihan and C.G.S. Eley, "Determination of Relative Toxicity of Amphotericin B Formulations: A Red Blood Cell Potassium Release Assay " (1999) Drug Delivery 68 81-88. Emerson DL, Bendele R, Brown E, Chiang SM, Desjardins JP, Dihel LC, Gill SC, Hamilton M, LeRay JD, Moon-McDermott L, Moynihan K, Richardson FC, Tomkinson B, Luzzio MJ, Baccanari D., "Antitumor efficacy, pharmacokinetics, and biodistribution of NX 211: a low-clearance liposomal formulation of lurtotecan" (2000) Clinical Cancer Research, 6 2903-12. Nadim, Ali
Professor
Areas of Expertise: Microfluidics, Fluid Mechanics, Bioengineering E. F. Fabrizio, A. Nadim and J. D. Sterling, "Resolution of Multiple ssDNA Structures in Free Solution Electrophoresis," Anal. Chem.,75, 5012-5021 (2003). M. S. Olufsen and A. Nadim, "On Deriving Lumped Models for Blood Flow and Pressure in the Systemic Arteries," Mathematical Biosciences and Engineering, 1, 61-80 (2004). C. G. Cooney, C.-Y. Chen, M. R. Emerling, A. Nadim and J. D. Sterling, "Electrowetting Droplet Microfluidics on a Single Planar Surface," Microfluidics and Nanofluidics, 2, 435-446 (2006). Niemz, Angelika
Assistant Professor
Areas of Expertise: Nanotechnology, Biosensors "Fabrication of nanoporous templates from diblock copolymer thin films on alkylchlorosilane-neutralized surfaces" Niemz, A.; Bandyopadhyay, K.; Tan, E., Cha, K.; Baker, S.M.; Langmuir 2006, 22, 11092-11096 "Deposition of DNA-functionalized Gold Nanospheres into Nanoporous Surfaces" Krisanu Bandyopadhyay, Eric Tan, Lin Ho, Sara Bundick, Shenda M. Baker, Angelika Niemz; Langmuir, 2006, 22, 4978-4984 "Isothermal DNA Amplification Coupled with DNA Nanosphere-Based Colorimetric Detection" Tan, E.; Wong,J.; Nguyen, D.; Zhang, Y.; Erwin, B.; Van Ness, L.K.; Baker, S.M.; Galas, D.J.; Niemz, A.; Anal. Chem. 2005, 77,7984-7992 Phillips, M. Ian
Norris Professor of Applied Life Sciences
Areas of Expertise: Biology of Stem Cells, Gene Regulatory Networks Phillips MI. Passage to global stem cells. Science ,317:322, 2007. Phillips MI and Tang YL Gene modification of stem cells . Advances in Drug Delivery Review 2007 ( in Press). Tang YL, Shen l, Qian K, Phillips MI a novel two-step procedure to expand cardiac Sca-1+stem cells clonally. BiochemBiophys Res Comm . 359,877-883 2007. Arnold AS, Tang YL, Qian K, Shen L, Valencia V, Phillips MI, Zhang YC. Specific beta1-adrenergic receptor silencing with small interfering RNA lowers high blood pressure and improves cardiac function in myocardial schemia. J Hypertens 25:197-205 (2007). Raval, Alpan
Assistant Professor
Areas of Expertise: Computational Biology, Systems Biology Raval, A. (2007) "Molecular Clock on a Neutral Network," Physical Review Letters (in press). Drummond, D.A., Raval, A., Wilke, C. O. (2006) "A Single Determinant for the Rate of Yeast Protein Evolution," Mol. Biol. Evolution 23:327-337. Parker, L. and Raval, A. (2001) "A New Look at the Accelerating Universe," Physical Review Letters 86:749-752. Ray, Animesh
Professor, director of the MBS-PhD Program
Areas of Expertise: Gene Regulatory Networks, MicroRNA, Plant Development, Gene Function, Homologous Recombination M. Langer, L. F. Snyderhan, U. Grossniklaus, and A. Ray. "Transposon excision from an atypical site: A mechanism of evolution of novel transposable elements" PLoS One (in press) (2007) R. J. Perera, and A. Ray. "MicroRNAs in the search for understanding human diseases" J. BioDrugs 21:97-104 (2007) V. Chickarmane, Ray, A., Sauro, H., and Nadim, A. "A model for p53 dynamics triggered by DNA damage" SIAM J. Applied Dynamical Systems 6: 61-78 (2007). Schmid, Molly B.
Professor, Entrepreneur-in-Residence, Director of Research
Areas of Expertise: Antimicrobial Drug Discovery, Pharmaceutical Development Schmid, M.B. Crystallizing new approaches for antimicrobial drug discovery. Biochemical Pharmacology 7, 1048-1056 (2006). Schmid, M.B. Do targets limit antibiotic discovery? Nature Biotechnology 24, 419-420 (2006). Kimber MS, Martin F, Lu Y, Houston, S, Vedadi, M, Dharamsi, A, Fiebig KM, Schmid M, Rock CO. (2004) The Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Pseudomonas aeruginosa. J. Biol. Chem. 279: 52593-52602. Schrick, Kathrin
Research Assistant Professor
Areas of Expertise: Molecular Biology, Genomics, Plant Steroids Venkata, B.P., and Schrick, K. 2006. START domains in lipid/sterol transfer and signaling in plants. In C. Benning and J. Ohlrogge (eds.) Current Advances in the Biochemistry and Cell Biology of Plant Lipids: Proceedings of the 17th International Symposium on Plant Lipids, Michigan State University, East Lansing, Michigan. ISPL2006, pp. 57-61. Schrick, K., Nguyen, D., Karlowski, W.M., and Mayer, K.F.X. 2004. START lipid/sterol binding domains are amplified in plants and are predominately associated with homeodomain transcription factors. Genome Biology 5: R41. Schrick, K., Fujioka, S., Takatsuto, S., Stierhof, Y.-D., Stransky, H., Yoshida, S., and Jürgens, G. 2004. A link between sterol biosynthesis, the cell wall and cellulose in Arabidopsis. Plant J. 38: 227-243. Schuster, Sheldon
President and Professor
Areas of Expertise: Molecular Biology, Protein Biochemistry, DNA Protein Biosensors Li, J. J., Fang, X., Schuster, S. M., and Tan, W., "Molecular beacons: a novel approach to detect protein -- DNA interactions," Angewandte Chemie Int. Ed.(2000) 39 (6): 1049-1052 Fang, X., Liu, X., Schuster, S., and Tan, W., "Designing a Novel Molecular Beacon for Surface-Immobilized DNA Hybridization Studies," J. Am. Chem. Soc. (1999), 121 (12) 2921-2922 Sterling, James D.
Associate Professor, Director of the Team Masters Program
Areas of Expertise: Bioengineering, Electrowetting, Microfluidics C. G. Cooney, C.-Y. Chen, M. R. Emerling, A. Nadim and J. D. Sterling, Electrowetting Droplet Microfluidics on a Single Planar Surface, Microfluidics and Nanofluidics, 2:435-446, 2006. J. Dai, J. D. Sterling and A. Nadim, Numerical Simulation of Air Bubbles Rising in Water Using an Axisymmetric VOF Method, in Computational Methods in Multiphase Flow II, A. A. Mammoli and C. A. Brebbia, Editors, pp. 343-351, WIT Press, Southampton, 2004. Eve F. Fabrizio, Ali Nadim, and James D. Sterling, Resolution of Multiple ssDNA Structures in Free Solution Electrophoresis, Anal. Chem., 75, pp. 5012-5021, 2003. Tang, Yao Liang
Research Assistant Professor
Areas of Expertise: Gene Regulatory Networks and Biology of Stem Cells Tang YL, Shen L, Qian K, Phillips MI. A novel two-step procedure to expand cardiac Sca-1+ cells clonally. Biochem Biophys Res Commun. 2007 Aug 10;359(4):877-83. Tang YL, Tang Y, Zhang YC, Qian K, Shen L, Phillips MI. Improved graft mesenchymal stem cell survival in ischemic heart with a hypoxia-regulated heme oxygenase-1 vector. J Am Coll Cardiol. 2005 Oct 4;46(7):1339-50. Tang YL, Zhao Q, Qin X, Shen L, Cheng L, Ge J, Phillips MI. Paracrine action enhances the effects of autologous mesenchymal stem cell transplantation on vascular regeneration in rat model of myocardial infarction. Ann Thorac Surg. 2005 Jul;80(1):229-36; discussion 236-7.
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