Robert D. Phair, Ph.D.

BioInformatics Services
Integrative BioInformatics, Inc.

301.437.0601
http://www.BioInformaticsServices.com
www.integrativebioinformatics.com
rphair "at" bioinformaticsservices.com
rphair "at" integrativebioinformatics.com

PUBLICATIONS

ARTICLES

Liu, W., R. Duden, R.D. Phair, and J. Lippincott-Schwartz. ArfGAP1 dynamics and its role in COPI coat assembly on Golgi membranes of living cells. Journal of Cell Biology 168: 1053-1063, 2005.

Lin, Y., S.R. Dueker, J.R. Follet, J.G. Fadel, A. Arjomand, P.D. Schneider, J.W. Miller, R. Green, B.A. Bucholz, J.S. Vogel, R.D. Phair, A.J. Clifford. Quantitation of in vivo human folate metabolism. American Journal of Clinical Nutrition 80: 680-691, 2004.

Phair, R.D., S.A. Gorski, and T. Misteli. Measurement of dynamic protein binding to chromatin in vivo, using photobleaching microscopy. Methods in Enzymology 375: 385 - 406, 2004.

Phair, R.D., P. Scaffidi, C. Elbi, J. Vecerova, A. Dey, K. Okato, D.T. Brown, G. Hager, M. Bustin, and T. Misteli. Global nature of dynamic protein-chromatin interactions in vivo: three dimensional genome scanning and dynamic interaction networks of chromatin proteins. Molecular Cell Biology 24:6393-6402, 2004.

Altan-Bonnet, N., R.D. Phair, R.S. Polishchuk, R. Weigert, and J. Lippincott-Schwartz. A role for Arf1 in mitotic Golgi disassembly, chromasome segregation, and cytokinesis. Proceedings of the National Academy of Sciences USA 100: 13314-13319, 2003.

Dundr, M., U. Hoffmann-Rohrer, Q. Hu, I. Grummt, L.I. Rothblum, R.D. Phair, and T. Misteli. A kinetic framework for a mammalian RNA polymerase in vivo. Science 298: 1623 - 1626, 2002.

Presley, J.F., T.H. Ward, A.C. Pfeifer, E.D. Siggia, R.D. Phair and J. Lippincott-Schwartz. Dissection of COPI and Arf1 dynamics in vivo and role in Golgi membrane transport. Nature 417: 187-193, 2002.

Phair, R.D. and T. Misteli. Kinetic modeling approaches to in vivo imaging. Nature Reviews Molecular Cell Biology 2: 898-907, 2001.

Nichols, B.J., A.K. Kenworthy, R.S. Polishchuk, R. Lodge, T.H. Roberts, K. Hirschberg, R.D. Phair and J. Lippincott-Schwartz. Rapid cycling of lipid raft markers between the cell surface and Golgi complex. Journal of Cell Biology, 153: 529-541, 2001.

Phair, R.D. and T. Misteli. High mobility of proteins in the mammalian cell nucleus. Nature, 404: 604-609, 2000.

Hirschberg, K, R.D. Phair and J. Lippincott-Schwartz. Kinetic analysis of intracellular trafficking in single living cells with vesicular stomatitis virus protein G-green fluorescent protein hybrids. Methods in Enzymology 327:69-89, 2000.

Zaal, K.J.M., C.L. Smith, R.S. Polishchuk, N. Altan, N.B. Cole, J. Ellenberg, K. Hirschberg, J.F. Presley, T.H. Roberts, E. Siggia, R.D. Phair, and J. Lippincott-Schwartz. Golgi membranes are absorbed into and reemerge from the ER during mitosis. Cell 99: 589-601, 1999. Abstract

Hirschberg K., J. Presley, R. Phair, J. Lippincott-Schwartz. Analysis of secretory protein trafficking within living cells. Journal of Histochemistry and Cytochemistry 47(12):1644, 1999.

Hirschberg, K, C.M. Miller, J. Ellenberg, J.F. Presley, E.D. Siggia, R.D. Phair and J. Lippincott-Schwartz. Kinetic analysis of secretory protein traffic and characterization of Golgi to plasma membrane transport intermediates in living cells. Journal of Cell Biology, 143 (6) 1485-1503, 1998. Abstract QuickTime Sequences (a must-see)

Phair, R.D. Development of kinetic models in the nonlinear world of molecular cell biology. Metabolism 46: 1489-1495, 1997. Abstract

Shamburek, R.D., P.G. Pentchev, L.A. Zech, J. Blanchette-Mackie, E.D. Carstea, J.M. VandenBroek, P.S. Cooper, E.B. Neufeld, R.D. Phair, H.B. Brewer, Jr., R.O. Brady, and C.C. Schwartz. Intracellular trafficking of the free cholesterol derived from LDL cholesteryl ester is defective in vivo in Niemann-Pick C disease: insights on normal metabolism of HDL and LDL gained from the NP-C mutation. Journal of Lipid Research 38: 2422-2435, 1997.

Lapidot, S.A., B.K. Huang, L.N. Russek, A.E. Brooks, A. Fayazi and R.D. Phair. Mechanisms for Ca signaling in vascular smooth muscle: resolved from 45Ca uptake and efflux experiments. Cell Calcium 19: 167-184, 1996.

Allaf, M., E. Halsey, G. Shechter and R.D. Phair. An algorithm for computer-assisted selection of effective antisense oligonucleotides targeting specific genes. In Preparation for Antisense Research and Development.

Fayazi, A., S.A. Lapidot, B.K. Huang, R.W. Tucker and R.D. Phair. Resolution of the basal plasma membrane calcium flux in vascular smooth muscle cells. American Journal of Physiology (Heart and Circulatory Physiology) 270: H1972-H1978, 1996.

Applebaum-Bowden, D., B.J. Auerbach, J.D. Neff, and R.D. Phair. Identification of a putative lipid transfer zone in the intermediate density lipoproteins of human plasma. In revision for Arteriosclerosis, Thrombosis and Vascular Biology.

Fayazi, A., C.D. Ferris and R.D. Phair. Incremental model for quantal calcium release by the inositol 1,4,5-trisphosphate receptor. In preparation.

Lapidot, S.A., and R.D. Phair. Platelet derived growth factor causes sustained depletion of both InsP3 -sensitive and ryanodine-sensitive intracellular Ca2+ stores in vascular smooth muscle cells. Arteriosclerosis, Thrombosis, and Vascular Biology 15: 44-51, 1995.

Foster, D.M., P.H.R. Barrett, W.F. Beltz, C. Cobelli, H. Golde, J.A. Jacquez, R.D. Phair, A. Ruggeri, M.P. Saccomani, A. Schumitzky, G. Toffolo. Using SAAM II to model kinetic and pharmacokinetic data. Proc. Simulation in Health Sci. Conf., Society for Computer Simulation, San Diego, pp. 87-90, 1994.

Foster, D.M., P.H.R. Barrett, W.F. Beltz, C. Cobelli, H. Golde, J.A. Jacquez, R.D. Phair, A. Ruggeri, M.P. Saccomani, D.M. Shames, G. Toffolo. SAAM II: A reengineered, menu-driven SAAM for enhancing biokinetic applications. Proc. Soc. Comput. Simulation, 1992.

Georgopoulos, A., and R.D. Phair. Abnormal clearance of postprandial Sf 100-400 plasma lipoproteins in insulin dependent diabetes mellitus (IDDM). Journal of Lipid Research 32: 1133-1141, 1991.

Phair, R.D., W.R. Hazzard and D. Applebaum-Bowden. Theoretical consequences of hypotheses concerning reverse cholesterol transport. In: High Density Lipoproteins and Atherosclerosis II, N.E. Miller (Ed.), Excerpta Medica, Amsterdam, 1989.

Hai, C.M. and R.D. Phair. Forskolin and caffeine induce calcium release from intracellular stores in rabbit aorta. American Journal of Physiology (Cell Physiology) 257: C413-C418, 1989.

Phair, R.D. Cellular calcium and atherosclerosis: A brief review. Cell Calcium 9: 275 - 284, 1988.

National Research Network Review Committee, CSTB, CPSMR, NRC. Toward a national research network. National Academy Press, Washington, D.C., 1988.

Strickberger, S.A., L.N. Russek and R.D. Phair.  Evidence for increased aortic plasma membrane calcium transport caused by experimental atherosclerosis in rabbits. Circulation Research 62: 75-80, 1988.

Howell, S., R.S. Fitzgerald and R.D. Phair. Long term calcium-45 efflux kinetics from rat diaphragm. In Proceedings of Respiratory Muscles and their Neuromotor Control, G.C. Sieck, S.C. Gandevia and W.E. Cameron, eds., pp. 301-6, Alan R. Liss, New York, 1987.

Hai, C.M. and R.D. Phair. Kinetic identification of an intracellular calcium compartment sensitive to phosphate and dinitrophenol in intact rabbit aorta.  Circulation Research 59:85-92, 1986.

Phair, R.D. and C.M. Hai. Resolution of intracellular calcium metabolism in intact aortic segments. Circulation Research 59:74-84, 1986.

Gonen, B., W. Patsch, I. Kuisk, A. Goldberg, R. Phair and G. Schonfeld. Altered HDL subclasses in endogenous hypertriglyceridemia are not altered by weight reduction. Metabolism 34:494-501, 1985.

Phair, R.D., S.B. Pek and W.E.M. Lands. Arachadonic acid induced release of insulin and glucagon: role of endogenous prostaglandins in pancreatic hormone secretion. Diabete et Metabolisme (Paris) 10:71-77, 1984.

Dempsher, D.P., D.S. Gann and R.D. Phair. A mechanistic model of ACTH - stimulated cortisol secretion. American Journal of Physiology 246:R587-R596, 1984.

Sparks, H.V., J.P. Manfredi, and R.D. Phair. A compartmental model of changes in interstitial adenosine associated with increased myocardial adenosine. In: Calcium Entry Blockers, Adenosine and Neurohumors, G.F. Merril and H.R. Weiss (Eds.), Urban and Schwarzenberg, Baltimore, 1983.

Phair, R.D. Models of plasma lipoprotein triglyceride kinetics - a critical review. In: Lipoprotein Kinetics and Modeling, M. Berman, S.M. Grundy and B.V. Howard (Eds.), Academic Press, New York, 1982.

Phair, R.D. The role of kinetic modeling in physiology. In: Lipoprotein Kinetics and Modeling, M. Berman, S.M. Grundy and B.V. Howard (Eds.), Academic Press, New York, 1982.

Belloni, F.L., R.D. Phair and H.V. Sparks. The role of adenosine in prolonged vasodilation following flow-restricted exercise of canine skeletal muscle. Circulation Research 44:767-780, 1979.

Phair, R.D. and H.V. Sparks. Adenosine content of skeletal muscle during active hyperemia and ischemic contraction. American Journal of Physiology 237:H1-H9, 1979.

Berman, M., M. Hall III, R.I. Levy, D.W. Bilheimer, R.D. Phair and R.H. Goebel. Metabolism of apoB and apoC lipoproteins in man: kinetic studies in normal and hyperlipoproteinemic subjects. Journal of Lipid Research 19:38-56, 1978.

Sparks, H.V. and R.D. Phair. Myogenic responses in exercise hyperemia. In: Mechanisms of Vasodilation, P.M. Vanhoutte (Ed.), S.Karger, Basel, 1978.

Phair, R.D., M. Hall III, D.W. Bilheimer, R.I. Levy, R.H. Goebel and M. Berman. Modeling lipoprotein metabolism in man. In: Proceedings of the 1976 Summer Simulation Conference, Simulation Councils Inc, La Jolla, California, 1976.

Eckman, W.W., R.D. Phair, J.D. Fenstermacher, C.S. Patlak, D. Kennedy and L. Sokoloff. Permeability limitation in estimation of local brain blood flow with C-14 antipyrine. American Journal of Physiology 229:215-221, 1975.

Phair, R.D., M.G. Hammond, J.A. Bowden, M. Fried, W.R. Fisher, and M. Berman. A preliminary model for human lipoprotein metabolism in hyperlipoproteinemia. Federation Proceedings 34:2263-2270, 1975.

Eckman, W.W., R.D. Phair, J.D. Fenstermacher and L. Sokoloff. The influence of capillary permeability limitations on the measurement of regional blood flow. In: Capillary Permeability. Springer-Verlag, New York, 1975.

Fried, M., W.R. Fisher, M.G. Hammond, J.A. Bowden, M. Berman and R.D. Phair. Computer model of lipoprotein metabolism in hyperlipoproteinemia. In: Protides of the Biological Fluids 22nd Colloquium. Pergamon Press, Oxford, 1975.

DeGroot, L.J., P. DeCostre and R.D. Phair. A mathematical model of human iodine metabolism. Journal of Clinical Endocrinology and Metabolism 32:757-762, 1971.

DeCostre, P., R.D. Phair, I.W. Dingwell, and L.J. DeGroot. A thyroid model and its analysis by computer. In: Endemic Goiter, J.B. Stanbury (Ed.), Pan American Health Organization, Washington, DC, 1969.

ELECTRONIC PUBLICATIONS

Phair, R.D. Integrative Bioinformatics: Practical Kinetic Modeling of Biological Systems, a textbook published on the World Wide Web, 1995 - date

Phair, R.D. Computational Biology Frequently Asked Questions, a FAQ available on the World Wide Web, 1996 - date

SELECTED ABSTRACTS

Chasson, A. K., M. Dundr, T. Misteli, and R. D. Phair. Database support for managing and testing complex theories of nuclear function. Dynamic Organization of Nuclear Function, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 2002.

Chasson, A. K. and R. D. Phair. ProcessDB: A cellular process database supporting large-scale iterative kinetic modeling in cell biology. 2nd International Conference on Systems Biology (ICSB2001), Pasadena, CA, 2001.

Lapidot, S. A., B. K. Huang, and R. D. Phair. Mechanisms for calcium signaling in vascular smooth muscle resolved from 45Ca uptake and efflux experiments. Biophysical Journal 68: A276, 1995.

Phair, R.D. and A. Fayazi. A three-state ion channel model for quantal Ca2+ release by the inositol trisphosphate receptor. Biophysical Journal 68:A122, 1995

Fayazi, A.H. and R.D. Phair. Calcium release by the InsP3 receptor is incremental, not quantal. Circulation, 1994.

Foster, D.M., P.H.R. Barrett, B.M. Bell, W.F. Beltz, C. Cobelli, H. Golde, J.A. Jacquez and R.D. Phair. SAAM II: Simulation, Analysis and Modeling Software. Biomedical Engineering Society Bulletin 18, 19-21, 1994.

Lapidot, S.A. and R.D. Phair. PDGF-BB activates calcium release from intracellular stores continuously not transiently. FASEB J. 8:A49, 1994.

Phair, R.D., D. Applebaum-Bowden, R. Abrol, P.L. Colvin, W.H. Ettinger, and W.R. Hazzard. Modulation by estrogen of plasma apolipoprotein B kinetics in postmenopausal women. Arteriosclerosis Council Abstracts, American Heart Association, 1992.

Applebaum-Bowden, D., and R.D. Phair. Small IDLs contain more cholesteryl ester molecules per particle than large IDLs or LDLs. Arteriosclerosis 11: 1417a, 1991.

Phair, R.D., J.D. Neff, and D. Applebaum-Bowden. Kinetics of cholesteryl ester transfer to human plasma ApoB-containing Lipoproteins. Arteriosclerosis 11:1399a, 1991.

Phair, R.D., and D. Applebaum-Bowden. Kinetics of cholesteryl ester transport in the putative lipid transfer zone. 9th International Atherosclerosis Symposium, Chicago, IL, p. 283, 1991.

Applebaum-Bowden, D., and R.D. Phair. Identification of a putative lipid transfer zone in human plasma apolipoprotein B containing lipoproteins. FASEB J. 4: A1747, 1990

Applebaum-Bowden, D., and R.D. Phair. Quantitation of reverse cholesterol transport in human subjects. Circulation 80: II-330, 1989 or Arteriosclerosis 9: 723a, 1989.

Phair, R.D., and D. Applebaum-Bowden. Measurement of reverse cholesterol transport in human subjects based on biochemical and kinetic analysis of single plasma samples. FASEB J. 3: A1243, 1989.

Phair, R.D., D. Applebaum-Bowden, and W.R. Hazzard. Modulation of human cholesterol metabolism by sex steroids: Methods for joint interpretation of tracer and non-steadt state experiments. 8th International Atherosclerosis Symposium, Rome, Italy, 1988.

Russek, L.N., and R.D. Phair. Effects of reduced extracellular calcium on calcium metabolism in vascular smooth muscle. In Regulation and Contraction of Smooth Muscle, Alan R. Liss, p. 481, 1987.

Phair, R.D. and S.A. Strickberger. Intracellular calcium contents and fluxes: Increased in atherosclerotic rabbit aorta. Cell Calcium Metabolism '87, Seventh International Washington Spring Symposium, 79, 1987.

Bamberger, M.J., M.D. Lane, and R.D. Phair. Very low density lipoptorein (VLDL) assembly: differential transport of apoproteins through the secretory pathway. Federation Proceedings, 1987.

Phair, R.D., W.R. Hazzard, and D. Applebaum-Bowden. A mechanistic model of plasma lipoprotein dynamics in response to estrogen. In P.J. Nestel, ed., 7th International Atherosclerosis Symposium, Melbourne, Australia, p. 191-192, 1985.

Phair, R.D. and C.M. Hai. Long-term calcium efflux kinetics from rabbit aorta. Federation Proceedings, 1983.

Hai, C.M. and R.D. Phair. Kinetic identification of a mitochondrial calcium compartment in rabbit aorta. Federation Proceedings, 1983.

Phair, R.D., Dempsher, D.P., and C.M. Hai. Mechanistic and tracer kinetic models of calcium handling in arterial smooth muscle. Federation Proceedings 41:1630, 1982.

Back to the BioInformatics Services Homepage or Back to the cybertextbook Table of Contents or Back to Dr. Phair's Curriculum Vitae.