James Ferrell

Publications

• The Cdk1-APC/C cell cycle oscillator circuit functions as a time-delayed, ultrasensitive switch. Yang Q, Ferrell JE. Nat Cell Biol. 2013; 15 (5): 519-25
• Bistability, bifurcations, and Waddington's epigenetic landscape. Ferrell JE, Curr Biol. 2012; 22 (11): R458-66
• Spatial positive feedback at the onset of mitosis. Santos SD, Wollman R, Meyer T, Ferrell JE. Cell. 2012; 149 (7): 1500-13
• A mechanism for the evolution of phosphorylation sites. Pearlman SM, Serber Z, Ferrell JE. Cell. 2011; 147 (4): 934-46
• Modeling the cell cycle: why do certain circuits oscillate? Ferrell JE, Tsai TY, Yang Q. Cell. 2011; 144 (6): 874-85
• Ultrasensitivity in the Regulation of Cdc25C by Cdk1. Trunnell NB, Poon AC, Kim SY, Ferrell JE. Mol Cell. 2011; 41 (3): 263-74
• Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. Hendrickson DG, Hogan DJ, McCullough HL, Myers JW, Herschlag D, Ferrell JE, Brown PO. PLoS Biol. 2009; 7 (11): e1000238
• Tuning the activation threshold of a kinase network by nested feedback loops. Justman QA, Serber Z, Ferrell JE, El-Samad H, Shokat KM. Science. 2009; 324 (5926): 509-12
• Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Tsai TY, Choi YS, Ma W, Pomerening JR, Tang C, Ferrell JE. Science. 2008; 321 (5885): 126-9
• Substrate competition as a source of ultrasensitivity in the inactivation of Wee1. Kim SY, Ferrell JE. Cell. 2007; 128 (6): 1133-45
• Tuning bulk electrostatics to regulate protein function. Serber Z, Ferrell JE. Cell. 2007; 128 (3): 441-4
• Interlinked fast and slow positive feedback loops drive reliable cell decisions. Brandman O, Ferrell JE, Li R, Meyer T. Science. 2005; 310 (5747): 496-8
• STIM is a Ca2+ sensor essential for Ca2+-store-depletion-triggered Ca2+ influx. Liou J, Kim ML, Heo WD, Jones JT, Myers JW, Ferrell JE, Meyer T. Curr Biol. 2005; 15 (13): 1235-41
• Systems-level dissection of the cell-cycle oscillator: bypassing positive feedback produces damped oscillations. Pomerening JR, Kim SY, Ferrell JE. Cell. 2005; 122 (4): 565-78
• A positive-feedback-based bistable 'memory module' that governs a cell fate decision. Xiong W, Ferrell JE. Nature. 2003; 426 (6965): 460-5
• Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2. Pomerening JR, Sontag ED, Ferrell JE. Nat Cell Biol. 2003; 5 (4): 346-51
• The protein kinase p90 rsk as an essential mediator of cytostatic factor activity. Bhatt RR, Ferrell JE. Science. 1999; 286 (5443): 1362-5
• Requirement for MAPK activation for normal mitotic progression in Xenopus egg extracts. Guadagno TM, Ferrell JE. Science. 1998; 282 (5392): 1312-5
• The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Ferrell JE, Machleder EM. Science. 1998; 280 (5365): 895-8
• Ultrasensitivity in the mitogen-activated protein kinase cascade. Huang CY, Ferrell JE. Proc Natl Acad Sci U S A. 1996; 93 (19): 10078-83
• Bistability in one equation or fewer. Anderson GA, Liu X, Ferrell JE. Methods Mol Biol. 2012: 880 53-67
• Simple rules for complex processes: new lessons from the budding yeast cell cycle. Ferrell JE, Mol Cell. 2011; 43 (4): 497-500
• Systems biologists seek fuller integration of systems biology approaches in new cancer research programs. Wolkenhauer O, Auffray C, Baltrusch S, Blüthgen N, Byrne H, Cascante M, Ciliberto A, Dale T, Drasdo D, Fell D, Ferrell JE, Gallahan D, Gatenby R, Günther U, Harms BD, Herzel H, Junghanss C, Kunz M, van Leeuwen I, Lenormand P, Levi F, Linnebacher M, Lowengrub J, Maini PK, Malik A, Rateitschak K, Sansom O, Schäfer R, Schürrle K, Sers C, Schnell S, Shibata D, Tyson J, Vera J, White M, Zhivotovsky B, Jaster R. Cancer Res. 2010; 70 (1): 12-3
• The roles of cyclin A2, B1, and B2 in early and late mitotic events. Gong D, Ferrell JE. Mol Biol Cell. 2010; 21 (18): 3149-61
• Q&A: Cooperativity. Ferrell JE, J Biol. 2009; 8 (6): 53
• Q&A: systems biology. Ferrell JE, J Biol. 2009; 8 (1): 2
• Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, Goldbeter A, Hace N, Henney A, Hood L, Iyengar R, Jackson V, Kallioniemi O, Klingmüller U, Kolar P, Kolch W, Kyriakopoulou C, Laplace F, Lehrach H, Marcus F, Matrisian L, Nolan G, Pelkmans L, Potti A, Sander C, Seljak M, Singer D, Sorger P, Stunnenberg H, Superti-Furga G, Uhlen M, Vidal M, Weinstein J, Wigle D, Williams M, Wolkenhauer O, Zhivotovsky B, Zinovyev A, Zupan B. Mol Oncol. 2009; 3 (1): 9-17
• Signaling motifs and Weber's law. Ferrell JE, Mol Cell. 2009; 36 (5): 724-7
• Simple, realistic models of complex biological processes: positive feedback and bistability in a cell fate switch and a cell cycle oscillator. Ferrell JE, Pomerening JR, Kim SY, Trunnell NB, Xiong W, Huang CY, Machleder EM. FEBS Lett. 2009; 583 (24): 3999-4005
• A role for GPRx, a novel GPR3/6/12-related G-protein coupled receptor, in the maintenance of meiotic arrest in Xenopus laevis oocytes Rios-Cardona D, Ricardo-Gonzalez RR, Chawla A, Ferrell JE Jr.. Dev Biol. 2008: 317 380-388
• Feedback regulation of opposing enzymes generates robust, all-or-none bistable responses. Ferrell JE, Curr Biol. 2008; 18 (6): R244-5
• Rapid cycling and precocious termination of G1 phase in cells expressing CDK1AF. Pomerening JR, Ubersax JA, Ferrell JE. Mol Biol Cell. 2008; 19 (8): 3426-41
• Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. Hendrickson DG, Hogan DJ, Herschlag D, Ferrell JE, Brown PO. PLoS One. 2008; 3 (5): e2126
• Systems biology: On the cell cycle and its switches. Santos SD, Ferrell JE. Nature. 2008; 454 (7202): 288-9
• A clear view of the cell cycle [book review] Ferrell JE Jr., Curr Biol. 2007: 17 R231-R232
• Cyclin A2 regulates nuclear-envelope breakdown and the nuclear accumulation of cyclin B1. Gong D, Pomerening JR, Myers JW, Gustavsson C, Jones JT, Hahn AT, Meyer T, Ferrell JE. Curr Biol. 2007; 17 (1): 85-91
• Emi2 at the crossroads: where CSF meets MPF. Hansen DV, Pomerening JR, Summers MK, Miller JJ, Ferrell JE, Jackson PK. Cell Cycle. 2007; 6 (6): 732-8
• Journal club. Ferrell JE, Nature. 2007; 450 (7166): 5
• Mechanisms of specificity in protein phosphorylation. Ubersax JA, Ferrell JE. Nat Rev Mol Cell Biol. 2007; 8 (7): 530-41
• Systems biology. A clock with a flip switch. Poon AC, Ferrell JE. Science. 2007; 318 (5851): 757-8
• A noisy 'Start' to the cell cycle. Ubersax JA, Ferrell JE. Mol Syst Biol. 2006: 2 2006.0014
• B-Raf and C-Raf are required for Ras-stimulated p42 MAP kinase activation in Xenopus egg extracts. Yue J, Xiong W, Ferrell JE. Oncogene. 2006; 25 (23): 3307-15
• Investigating macromolecules inside cultured and injected cells by in-cell NMR spectroscopy. Serber Z, Selenko P, Hänsel R, Reckel S, Löhr F, Ferrell JE, Wagner G, Dötsch V. Nat Protoc. 2006; 1 (6): 2701-9
• Mechanistic studies of the mitotic activation of Mos. Yue J, Ferrell JE. Mol Cell Biol. 2006; 26 (14): 5300-9
• Minimizing off-target effects by using diced siRNAs for RNA interference. Myers JW, Chi JT, Gong D, Schaner ME, Brown PO, Ferrell JE. J RNAi Gene Silencing. 2006; 2 (2): 181-94
• Allelic variants of the canine heavy neurofilament (NFH) subunit and extensive phosphorylation in dogs with motor neuron disease. Green SL, Westendorf JM, Jaffe H, Pant HC, Cork LC, Ostrander EA, Vignaux F, Ferrell JE. J Comp Pathol. 2005; 132 (1): 33-50
• Dicer in RNAi: its roles in vivo and utility in vitro Myers JW, Ferrell JE Jr.. In: RNA Interference. From Basic Science to Drug Development. Edited by Appasani K, Cambridge University Press, Cambridge UK. 2005: 29-54
• Identification and comparative analysis of multiple mammalian Speedy/Ringo proteins. Cheng A, Xiong W, Ferrell JE, Solomon MJ. Cell Cycle. 2005; 4 (1): 155-65
• Multisite M-phase phosphorylation of Xenopus Wee1A. Kim SY, Song EJ, Lee KJ, Ferrell JE. Mol Cell Biol. 2005; 25 (23): 10580-90
• Silencing gene expression with Dicer-generated siRNA pools. Myers JW, Ferrell JE. Methods Mol Biol. 2005: 309 93-196
• Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Angeli D, Ferrell JE, Sontag ED. Proc Natl Acad Sci U S A. 2004; 101 (7): 1822-7
• Mos mediates the mitotic activation of p42 MAPK in Xenopus egg extracts. Yue J, Ferrell JE. Curr Biol. 2004; 14 (17): 1581-6
• Picking a winner: new mechanistic insights into the design of effective siRNAs. Gong D, Ferrell JE. Trends Biotechnol. 2004; 22 (9): 451-4
• Probing the precision of the mitotic clock with a live-cell fluorescent biosensor. Jones JT, Myers JW, Ferrell JE, Meyer T. Nat Biotechnol. 2004; 22 (3): 306-12
• Enforced proximity in the function of a famous scaffold. Ferrell JE, Cimprich KA. Mol Cell. 2003; 11 (2): 289-91
• Recombinant Dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencing. Myers JW, Jones JT, Meyer T, Ferrell JE. Nat Biotechnol. 2003; 21 (3): 324-8
• Selective regulation of neurite extension and synapse formation by the beta but not the alpha isoform of CaMKII. Fink CC, Bayer KU, Myers JW, Ferrell JE, Schulman H, Meyer T. Neuron. 2003; 39 (2): 283-97
• The JNK cascade as a biochemical switch in mammalian cells: ultrasensitive and all-or-none responses. Bagowski CP, Besser J, Frey CR, Ferrell JE. Curr Biol. 2003; 13 (4): 315-20
• Activation of p42 mitogen-activated protein kinase (MAPK), but not c-Jun NH(2)-terminal kinase, induces phosphorylation and stabilization of MAPK phosphatase XCL100 in Xenopus oocytes. Sohaskey ML, Ferrell JE. Mol Biol Cell. 2002; 13 (2): 454-68
• Overview of the Alliance for Cellular Signaling Gilman AG, 79 other authors including JEF. Nature. 2002: 242 703-706
• Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Ferrell JE, Curr Opin Cell Biol. 2002; 14 (2): 140-8
• Bistability in cell signaling: How to make continuous processes discontinuous, and reversible processes irreversible. Ferrell JE, Xiong W. Chaos. 2001; 11 (1): 227-236
• Bistability in the JNK cascade. Bagowski CP, Ferrell JE. Curr Biol. 2001; 11 (15): 1176-82
• Cell cycle Ferrell JE Jr., In: McGraw-Hill Encyclopedia of Science and Technology, ninth edition. 2001
• Multisite phosphorylation and the countdown to S phase. Deshaies RJ, Ferrell JE. Cell. 2001; 107 (7): 819-22
• Regulatory cascades: function and properties Ferrell JE Jr., Encyclopedia of Life Sciences, Macmillan Publishing Ltd.. 2001
• Six steps to destruction. Ferrell JE, Nature. 2001; 414 (6863): 498-9
• The classical progesterone receptor associates with p42 MAPK and is involved in phosphatidylinositol 3-kinase signaling in Xenopus oocytes. Bagowski CP, Myers JW, Ferrell JE. J Biol Chem. 2001; 276 (40): 37708-14
• c-Jun N-terminal kinase activation in Xenopus laevis eggs and embryos. A possible non-genomic role for the JNK signaling pathway. Bagowski CP, Xiong W, Ferrell JE. J Biol Chem. 2001; 276 (2): 1459-65
• Activation of Wee1 by p42 MAPK in vitro and in cycling xenopus egg extracts. Walter SA, Guadagno SN, Ferrell JE. Mol Biol Cell. 2000; 11 (3): 887-96
• Cloning and characterization of Xenopus Rsk2, the predominant p90 Rsk isozyme in oocytes and eggs. Bhatt RR, Ferrell JE. J Biol Chem. 2000; 275 (42): 32983-90
• Disease attributed to Mycobacterium chelonae in South African clawed frogs (Xenopus laevis). Green SL, Lifland BD, Bouley DM, Brown BA, Wallace RJ, Ferrell JE. Comp Med. 2000; 50 (6): 675-9
• Inhibition of progesterone-induced Xenopus oocyte maturation by Nm23 Kim SY, Ferrell JE Jr., Chae SK, Lee KJ. Cell Growth Diff. 2000: 11 485-490
• What do scaffold proteins really do? Ferrell JE, Sci STKE. 2000; 2000 (52): pe1
• Building a cellular switch: more lessons from a good egg. Ferrell JE, Bioessays. 1999; 21 (10): 866-70
• Distinct, constitutively active MAPK phosphatases function in Xenopus oocytes: implications for p42 MAPK regulation In vivo. Sohaskey ML, Ferrell JE. Mol Biol Cell. 1999; 10 (11): 3729-43
• Identification and management of an outbreak of Flavobacterium meningosepticum infection in a colony of South African clawed frogs (Xenopus laevis). Green SL, Bouley DM, Tolwani RJ, Waggie KS, Lifland BD, Otto GM, Ferrell JE. J Am Vet Med Assoc. 1999; 214 (12): 1833-8, 1792-3
• M phase phosphorylation of cytoplasmic dynein intermediate chain and p150(Glued). Huang CY, Chang CP, Huang CL, Ferrell JE. J Biol Chem. 1999; 274 (20): 14262-9
• Xenopus oocyte maturation: new lessons from a good egg. Ferrell JE, Bioessays. 1999; 21 (10): 833-42
• Assessing activities of blotted protein kinases Ferrell JE Jr, Martin GS. In: Protein Phosphorylation, Ed. by Hunter T, Sefton BM, Academic Press, San Diego. [This is a re-publication of Ferrell and Martin, Methods Enzymol., 200:430-435.]. 1998: 177-82
• How regulated protein translocation can produce switch-like responses. Ferrell JE, Trends Biochem Sci. 1998; 23 (12): 461-5
• A role for mitogen-activated protein kinase in the spindle assembly checkpoint in XTC cells. Wang XM, Zhai Y, Ferrell JE. J Cell Biol. 1997; 137 (2): 433-43
• Cell cycle Ferrell JE Jr., McGraw-Hill Encyclopedia of Science and Technology, 8th edition. 1997: 3 378-380
• Induction of a G2-phase arrest in Xenopus egg extracts by activation of p42 mitogen-activated protein kinase. Walter SA, Guadagno TM, Ferrell JE. Mol Biol Cell. 1997; 8 (11): 2157-69
• Mechanistic studies of the dual phosphorylation of mitogen-activated protein kinase. Ferrell JE, Bhatt RR. J Biol Chem. 1997; 272 (30): 19008-16
• Dependence of Mos-induced Cdc2 activation on MAP kinase function in a cell-free system. Huang CY, Ferrell JE. EMBO J. 1996; 15 (9): 2169-73
• MAP kinases in mitogenesis and development. Ferrell JE, Curr Top Dev Biol. 1996: 33 1-60
• Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs. Ferrell JE, Trends Biochem Sci. 1996; 21 (12): 460-6
• Evidence that inactive p42 mitogen-activated protein kinase and inactive Rsk exist as a heterodimer in vivo. Hsiao KM, Chou SY, Shih SJ, Ferrell JE. Proc Natl Acad Sci U S A. 1994; 91 (12): 5480-4
• Inhibition of c-Jun DNA binding by mitogen-activated protein kinase. Chou SY, Baichwal V, Ferrell JE. Mol Biol Cell. 1992; 3 (10): 1117-30
• Assessing activities of blotted protein kinases. Ferrell JE, Martin GS. Methods Enzymol. 1991: 200 430-5
• Cell cycle tyrosine phosphorylation of p34cdc2 and a microtubule-associated protein kinase homolog in Xenopus oocytes and eggs. Ferrell JE, Wu M, Gerhart JC, Martin GS. Mol Cell Biol. 1991; 11 (4): 1965-71
• Identification of a 42-kilodalton phosphotyrosyl protein as a serine(threonine) protein kinase by renaturation. Ferrell JE, Martin GS. Mol Cell Biol. 1990; 10 (6): 3020-6
• Intracellular localization of pp60c-src in human platelets. Ferrell JE, Noble JA, Martin GS, Jacques YV, Bainton DF. Oncogene. 1990; 5 (7): 1033-6
• Thrombin stimulates the activities of multiple previously unidentified protein kinases in platelets. Ferrell JE, Martin GS. J Biol Chem. 1989; 264 (34): 20723-9
• Tyrosine-specific protein phosphorylation is regulated by glycoprotein IIb-IIIa in platelets. Ferrell JE, Martin GS. Proc Natl Acad Sci U S A. 1989; 86 (7): 2234-8
• Membrane bilayer balance and platelet shape: morphological and biochemical responses to amphipathic compounds. Ferrell JE, Mitchell KT, Huestis WH. Biochim Biophys Acta. 1988; 939 (2): 223-37
• Platelet tyrosine-specific protein phosphorylation is regulated by thrombin. Ferrell JE, Martin GS. Mol Cell Biol. 1988; 8 (9): 3603-10
• Separation of phosphoinositides and other phospholipids by two-dimensional thin-layer chromatography. Mitchell KT, Ferrell JE, Huestis WH. Anal Biochem. 1986; 158 (2): 447-53
• Sulfhydryl reducing agents and shape regulation in human erythrocytes. Truong HT, Ferrell JE, Huestis WH. Blood. 1986; 67 (1): 214-21
• Computer-assisted mechanistic structure-activity studies: application to diverse classes of chemical carcinogens. Loew GH, Poulsen M, Kirkjian E, Ferrell J, Sudhindra BS, Rebagliati M. Environ Health Perspect. 1985: 61 69-96
• Lipid transfer between phosphatidylcholine vesicles and human erythrocytes: exponential decrease in rate with increasing acyl chain length Ferrell JE Jr., Lee KJ, Huestis WH. Biochemistry. 1985: 24 2857-2864
• Membrane bilayer balance and erythrocyte shape: a quantitative assessment. Ferrell JE, Lee KJ, Huestis WH. Biochemistry. 1985; 24 (12): 2849-57
• Phosphoinositide metabolism and the morphology of human erythrocytes. Ferrell JE, Huestis WH. J Cell Biol. 1984; 98 (6): 1992-8
• Analysis of chloride flux. Appendix to Newton AC, Cook SL, Huestis WH, Transfer of band 3, the erythrocyte anion transporter, between phospholipid vesicles and cells Ferrell JE Jr., Newton AC, Huestis WH. Biochemistry. 1983: 22 6116-6117
• Mechanistic structure-activity studies using quantum chemical methods: application to polycyclic aromatic hydrocarbons Loew GH, Ferrell JE Jr., Poulsen M. Structure-Activity Correlation as a Predictive Tool in Toxicology. Edited by L. Goldberg. Hemisphere, Washington.. 1983: 111-138
• Calcium does not mediate the shape change that follows ATP depletion in human erythrocytes. Ferrell JE, Huestis WH. Biochim Biophys Acta. 1982; 687 (2): 321-8
• Calmodulin-dependent spectrin kinase activity in human erythrocytes. Huestis WH, Nelson MJ, Ferrell JE. Prog Clin Biol Res. 1981: 56 137-55
• Mechanistic studies of addition of nucleophiles to arene oxides and diol epoxides: candidate ultimate carcinogens Loew GH, Pudzianowski AT, Czerwinski A, Ferrell JE Jr.. Int J Quantum Chem Quant Biol Symp. 1980: 7 223-244
• Quantum chemical studies of methylbenz[a]anthracenes: metabolism and correlations with carcinogenicity Loew GH, Poulsen M, Ferrell JE Jr., Chaet D. Chem-Biol Interactions. 1980: 31 319-340
• Adrenergic stimulation of membrane protein phosphorylation in human erythrocytes. Nelson MJ, Ferrell JE, Huestis WH. Biochim Biophys Acta. 1979; 558 (1): 136-40
• Mechanistic studies of arene oxide and diol epoxide rearrangement and hydrolysis reactions Ferrell JE Jr, Loew GH. J Am Chem Soc. 1979: 101 1379-1388
• Quantum chemical studies of polycyclic aromatic hydrocarbons and their metabolites: correlations to carcinogenicity Loew GH, Sudhindra BS, Ferrell JE Jr.. Chem-Biol Interactions. 1979: 26 75-89
• Structure/activity studies of flavonoids as inhibitors of cyclic AMP phosphodiesterase and relationship to quantum chemical indices. Ferrell JE, Chang Sing PD, Loew G, King R, Mansour JM, Mansour TE. Mol Pharmacol. 1979; 16 (2): 556-68