Grants & Publications


We are supported in part by The Open Medicine Foundation. OMF 


Kashi A, Davis R, and Phair RD. The IDO Metabolic Trap Hypothesis for the Etiology of ME/CFS. Diagnostics. Volume 29, issue 3, 26 July 2019. Diagnostics

Phair RD. Mechanistic Modeling confronts the complexity of molecular cell biology. Molecular Biology of the Cell. Volume 25, no 22, 3494-3496, 5 November 2014. Molecular Biology of the Cell

Nakahashi H, Kwon K, Resch W, Vian L, Dose M, Stavreva D, Hakim O, Pruett N, Nelson S, Yamane A, Qian J, Dubois W, Welsh S, Phair RD, Pugh B, Lobanenkov V, Hager GL, Casellas R. A genome-wide map of CTCF multivalency redefines the CTCF code. Cell Reports. Volume 3, Issue 5, 1678-1689, 23 May 2013. PubMed 

Ramos-Roman MA, Lapidot SA, Phair RD, Parks EJ. Insulin activation of plasma nonesterified fatty acid uptake in metabolic syndrome. Arterioscler Thromb Vasc Biol. 2012 Aug;32(8):1799-808. PubMed 

Phair RD. Why and how to expand the role of systems biology in pharmaceutical research and development.  Advances in Experimental Medicine and Biology, 2012;736:533-42  PubMed 

Lippincott-Schwartz, J, Phair RD. Lipids and Cholesterol as Regulators of Traffic in the Endomembrane System.  Annual Review of Biophysics, Feb 24, 2010  PubMed 

Melnick M, Phair RD, Lapidot SA, Jaskill T. Salivary gland branching morphogenesis: a quantitative systems analysis of the Eda/Edar/NFkB paradigm.  BioMed Central Developmental Biology, June 6, 2009  BioMed Central

Patterson GH, Hirschberg K, Polishchuk RS, Gerlich D, Phair RD, Lippincott-Schwartz J. Transport through the Golgi apparatus by rapid partitioning within a two-phase membrane system. Cell 2008 Jun 13; 133(6): 1055-1067. PMID 18555781Phair R, Patterson G, Hirschberg K, Chasson A, Lippincott-Schwartz J. Protein Trafficking in the Golgi apparatus: Can modeling and experiment work together to dethrone a reigning theory? Frontiers in Application of Systems Modeling and Simulation Proceedings of the International Conference on Systems Biology, Long Beach, CA October 2007. 

Darzacq X, Shav-Tal Y, de Turris V, Brody Y, Shenoy S, Phair R, Singer, R. In vivo dynamics of RNA polymerase II transcription. Nature Structural and Molecular Biology 2007 Sep; 14: 796-806. Nature Publishing Group 

Kruhlak M, Crouch EE, Orlov M, Montaño C, Gorski SA, Nussenzweig A, Misteli T, Phair RD, Casellas R. The ATM repair pathway inhibits RNA Polymerase I transcription in response to chromosome breaks. Nature 2007 Jun 7; 447: 730-4. PMID: 17554310

Liu W, Duden R, Phair RD, Lippincott-Schwartz J. cArfGAP1 dynamics and its role in COPI coat assembly on Golgi membranes of living cells. J Cell Biol. 2005 Mar 28;168(7):1053-63. PMID: 15795316

Lin Y, Dueker SR, Follett JR, Fadel JG, Arjomand A, Schneider PD, Miller JW, Green R, Buchholz BA, Vogel JS, Phair RD, Clifford AJ. Quantitation of in vivo human folate metabolism. Am J Clin Nutr. 2004 Sep;80(3):680-91. PMID: 15321809

Phair RD, Scaffidi P, Elbi C, Vecerova J, Dey A, Ozato K, Brown DT, Hager G, Bustin M, Misteli T. Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins. Mol Cell Biol. 2004 Jul;24(14):6393-402. PMID: 15226439

Phair RD, Gorski SA, Misteli T. Measurement of dynamic protein binding to chromatin in vivo, using photobleaching microscopy. Methods Enzymol. 2004;375:393-414. PMID: 14870680

Altan-Bonnet N, Phair RD, Polishchuk RS, Weigert R, Lippincott-Schwartz J. A role for Arf1 in mitotic Golgi disassembly, chromosome segregation, and cytokinesis. Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13314-9. Epub 2003 Oct 29. PMID: 14585930

Dundr M, Hoffmann-Rohrer U, Hu Q, Grummt I, Rothblum LI, Phair RD, Misteli T. A kinetic framework for a mammalian RNA polymerase in vivo. Science. 2002 Nov 22;298(5598):1623-6. PMID: 12446911

Presley JF, Ward TH, Pfeifer AC, Siggia ED, Phair RD, Lippincott-Schwartz J. Dissection of COPI and Arf1 dynamics in vivo and role in Golgi membrane transport. Nature. 2002 May 9;417(6885):187-93. PMID: 12000962

Chasson, AK and Phair RD. ProcessDB: a Cellular Process Database Supporting Large-Scale Interative Kinetic Modeling in Cell Biology. Proceedings of the Second International Conference on Systems Biology, 2001.

Phair RD, Misteli T. Kinetic modelling approaches to in vivo imaging. Nat Rev Mol Cell Biol. 2001 Dec;2(12):898-907. Review. PMID: 11733769

Nichols BJ, Kenworthy AK, Polishchuk RS, Lodge R, Roberts TH, Hirschberg K, Phair RD, Lippincott-Schwartz J. Rapid cycling of lipid raft markers between the cell surface and Golgi complex. J Cell Biol. 2001 Apr 30;153(3):529-41. PMID: 11331304

Hirschberg K, Phair RD, Lippincott-Schwartz J. Kinetic analysis of intracellular trafficking in single living cells with vesicular stomatitis virus protein G-green fluorescent protein hybrids. Methods Enzymol. 2000;327:69-89. No abstract available. PMID: 11044975

Phair RD, Misteli T. High mobility of proteins in the mammalian cell nucleus. Nature. 2000 Apr 6;404(6778):604-9. PMID: 10766243


Zaal KJ, Smith CL, Polishchuk RS, Altan N, Cole NB, Ellenberg J, Hirschberg K, Presley JF, Roberts TH, Siggia E, Phair RD, Lippincott-Schwartz J. Golgi membranes are absorbed into and reemerge from the ER during mitosis. Cell. 1999 Dec 10;99(6):589-601. PMID: 10612395

Hirschberg K, Miller CM, Ellenberg J, Presley JF, Siggia ED, Phair RD, Lippincott-Schwartz J. Kinetic analysis of secretory protein traffic and characterization of golgi to plasma membrane transport intermediates in living cells. J Cell Biol. 1998 Dec 14;143(6):1485-503. PMID: 9852146

Shamburek RD, Pentchev PG, Zech LA, Blanchette-Mackie J, Carstea ED, VandenBroek JM, Cooper PS, Neufeld EB, Phair RD, Brewer HB Jr, Brady RO, Schwartz CC. 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. J Lipid Res. 1997 Dec;38(12):2422-35. PMID: 9458266

Phair RD. Development of kinetic models in the nonlinear world of molecular cell biology. Metabolism. 1997 Dec;46(12):1489-95. Review. PMID: 9439549

Fayazi AH, Lapidot SA, Huang BK, Tucker RW, Phair RD. Resolution of the basal plasma membrane calcium flux in vascular smooth muscle cells. Am J Physiol. 1996 Jun;270(6 Pt 2):H1972-8. PMID: 8764246

Lapidot SA, Huang BK, Fayazi A, Russek LN, Strickberger SA, Brooks AE, Phair RD. Mechanisms for Ca signaling in vascular smooth muscle: resolved from 45Ca uptake and efflux experiments. Cell Calcium. 1996 Feb;19(2):167-84. PMID: 8689674

Lapidot SA, Phair RD. Platelet-derived growth factor causes sustained depletion of both inositol trisphosphate-sensitive and caffeine-sensitive intracellular calcium stores in vascular smooth muscle cells. Arterioscler Thromb Vasc Biol. 1995 Jan;15(1):44-51. PMID: 7749815

Georgopoulos A, Phair RD. Abnormal clearance of postprandial Sf 100-400 plasma lipoproteins in insulin-dependent diabetes mellitus. J Lipid Res. 1991 Jul;32(7):1133-41. PMID: 1940637

Hai CM, Phair RD. Forskolin and caffeine induce Ca2+ release from intracellular stores in rabbit aorta. Am J Physiol. 1989 Sep;257(3 Pt 1):C413-8. PMID: 2782384

Phair RD. Cellular calcium and atherosclerosis: a brief review. Cell Calcium. 1988 Dec;9(5-6):275-84. Review. PMID: 3066492

Strickberger SA, Russek LN, Phair RD. Evidence for increased aortic plasma membrane calcium transport caused by experimental atherosclerosis in rabbits. Circ Res. 1988 Jan;62(1):75-80. PMID: 3335059

Hai CM, Phair RD. Kinetic identification of an intracellular calcium compartment sensitive to phosphate and dinitrophenol in intact isolated rabbit aorta. Circ Res. 1986 Jul;59(1):85-92. PMID: 2426005

Phair RD, Hai CM. Resolution of intracellular calcium metabolism in intact segments of rabbit aorta. Circ Res. 1986 Jul;59(1):74-84. PMID: 2426004

Phair RD, Pek SB, Lands WE. Arachidonic acid induced release of insulin and glucagon: role of endogenous prostaglandins in pancreatic hormone secretion. Diabete Metab. 1984 May;10(2):71-7. PMID: 6430728

Dempsher DP, Gann DS, Phair RD. A mechanistic model of ACTH-stimulated cortisol secretion. Am J Physiol. 1984 Apr;246(4 Pt 2):R587-96. PMID: 6326602

Phair RD, Sparks HV. Adenosine content of skeletal muscle during active hyperemia and ischemic contraction. Am J Physiol. 1979 Jul;237(1):H1-9. PMID: 464063

Belloni FL, Phair RD, Sparks HV. The role of adenosine in prolonged vasodilation following flow-restricted exercise of canine skeletal muscle. Circ Res. 1979 Jun;44(6):759-66. PMID: 428070 

Berman M, Hall M 3rd, Levy RI, Eisenberg S, Bilheimer DW, Phair RD, Goebel RH. Metabolsim of apoB and apoC lipoproteins in man: kinetic studies in normal and hyperlipoproteininemic subjects. J Lipid Res. 1978 Jan;19(1):38-56. PMID: 202659

Phair RD, Hammond MG, Bowden JA, Fried M, Fisher WR, Berman M. Preliminary model for human lipoprotein metabolism in hyperlipoproteinemia. Fed Proc. 1975 Dec;34(13):2263-70. PMID: 172373

Eckman WW, Phair RD, Fenstermacher JD, Patlak CS, Kennedy C, Sokoloff L. Permeability limitation in estimation of local brain blood flow with [14C]antipyrine. Am J Physiol. 1975 Jul;229(1):215-21. PMID: 1096644