James Ferrell
Publications
- The Cdk1-APC/C cell cycle oscillator circuit functions as a time-delayed, ultrasensitive switch. Nat Cell Biol. 2013; (5): 519-25
- Bistability, bifurcations, and Waddington's epigenetic landscape. Curr Biol. 2012; (11): R458-66
- Spatial positive feedback at the onset of mitosis. Cell. 2012; (7): 1500-13
- A mechanism for the evolution of phosphorylation sites. Cell. 2011; (4): 934-46
- Modeling the cell cycle: why do certain circuits oscillate? Cell. 2011; (6): 874-85
- Ultrasensitivity in the Regulation of Cdc25C by Cdk1. Mol Cell. 2011; (3): 263-74
- Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol. 2009; (11): e1000238
- Tuning the activation threshold of a kinase network by nested feedback loops. Science. 2009; (5926): 509-12
- Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science. 2008; (5885): 126-9
- Substrate competition as a source of ultrasensitivity in the inactivation of Wee1. Cell. 2007; (6): 1133-45
- Tuning bulk electrostatics to regulate protein function. Cell. 2007; (3): 441-4
- Interlinked fast and slow positive feedback loops drive reliable cell decisions. Science. 2005; (5747): 496-8
- STIM is a Ca2+ sensor essential for Ca2+-store-depletion-triggered Ca2+ influx. Curr Biol. 2005; (13): 1235-41
- Systems-level dissection of the cell-cycle oscillator: bypassing positive feedback produces damped oscillations. Cell. 2005; (4): 565-78
- A positive-feedback-based bistable 'memory module' that governs a cell fate decision. Nature. 2003; (6965): 460-5
- Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2. Nat Cell Biol. 2003; (4): 346-51
- The protein kinase p90 rsk as an essential mediator of cytostatic factor activity. Science. 1999; (5443): 1362-5
- Requirement for MAPK activation for normal mitotic progression in Xenopus egg extracts. Science. 1998; (5392): 1312-5
- The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science. 1998; (5365): 895-8
- Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc Natl Acad Sci U S A. 1996; (19): 10078-83
- Bistability in one equation or fewer. Methods Mol Biol. 2012: 53-67
- Simple rules for complex processes: new lessons from the budding yeast cell cycle. Mol Cell. 2011; (4): 497-500
- Systems biologists seek fuller integration of systems biology approaches in new cancer research programs. Cancer Res. 2010; (1): 12-3
- The roles of cyclin A2, B1, and B2 in early and late mitotic events. Mol Biol Cell. 2010; (18): 3149-61
- Q&A: Cooperativity. J Biol. 2009; (6): 53
- Q&A: systems biology. J Biol. 2009; (1): 2
- Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Mol Oncol. 2009; (1): 9-17
- Signaling motifs and Weber's law. Mol Cell. 2009; (5): 724-7
- Simple, realistic models of complex biological processes: positive feedback and bistability in a cell fate switch and a cell cycle oscillator. FEBS Lett. 2009; (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 Dev Biol. 2008: 380-388
- Feedback regulation of opposing enzymes generates robust, all-or-none bistable responses. Curr Biol. 2008; (6): R244-5
- Rapid cycling and precocious termination of G1 phase in cells expressing CDK1AF. Mol Biol Cell. 2008; (8): 3426-41
- Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PLoS One. 2008; (5): e2126
- Systems biology: On the cell cycle and its switches. Nature. 2008; (7202): 288-9
- A clear view of the cell cycle [book review] Curr Biol. 2007: R231-R232
- Cyclin A2 regulates nuclear-envelope breakdown and the nuclear accumulation of cyclin B1. Curr Biol. 2007; (1): 85-91
- Emi2 at the crossroads: where CSF meets MPF. Cell Cycle. 2007; (6): 732-8
- Journal club. Nature. 2007; (7166): 5
- Mechanisms of specificity in protein phosphorylation. Nat Rev Mol Cell Biol. 2007; (7): 530-41
- Systems biology. A clock with a flip switch. Science. 2007; (5851): 757-8
- A noisy 'Start' to the cell cycle. Mol Syst Biol. 2006: 2006.0014
- B-Raf and C-Raf are required for Ras-stimulated p42 MAP kinase activation in Xenopus egg extracts. Oncogene. 2006; (23): 3307-15
- Investigating macromolecules inside cultured and injected cells by in-cell NMR spectroscopy. Nat Protoc. 2006; (6): 2701-9
- Mechanistic studies of the mitotic activation of Mos. Mol Cell Biol. 2006; (14): 5300-9
- Minimizing off-target effects by using diced siRNAs for RNA interference. J RNAi Gene Silencing. 2006; (2): 181-94
- Allelic variants of the canine heavy neurofilament (NFH) subunit and extensive phosphorylation in dogs with motor neuron disease. J Comp Pathol. 2005; (1): 33-50
- Dicer in RNAi: its roles in vivo and utility in vitro 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. Cell Cycle. 2005; (1): 155-65
- Multisite M-phase phosphorylation of Xenopus Wee1A. Mol Cell Biol. 2005; (23): 10580-90
- Silencing gene expression with Dicer-generated siRNA pools. Methods Mol Biol. 2005: 93-196
- Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Proc Natl Acad Sci U S A. 2004; (7): 1822-7
- Mos mediates the mitotic activation of p42 MAPK in Xenopus egg extracts. Curr Biol. 2004; (17): 1581-6
- Picking a winner: new mechanistic insights into the design of effective siRNAs. Trends Biotechnol. 2004; (9): 451-4
- Probing the precision of the mitotic clock with a live-cell fluorescent biosensor. Nat Biotechnol. 2004; (3): 306-12
- Enforced proximity in the function of a famous scaffold. Mol Cell. 2003; (2): 289-91
- Recombinant Dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencing. Nat Biotechnol. 2003; (3): 324-8
- Selective regulation of neurite extension and synapse formation by the beta but not the alpha isoform of CaMKII. Neuron. 2003; (2): 283-97
- The JNK cascade as a biochemical switch in mammalian cells: ultrasensitive and all-or-none responses. Curr Biol. 2003; (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. Mol Biol Cell. 2002; (2): 454-68
- Overview of the Alliance for Cellular Signaling Nature. 2002: 703-706
- Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr Opin Cell Biol. 2002; (2): 140-8
- Bistability in cell signaling: How to make continuous processes discontinuous, and reversible processes irreversible. Chaos. 2001; (1): 227-236
- Bistability in the JNK cascade. Curr Biol. 2001; (15): 1176-82
- Cell cycle In: McGraw-Hill Encyclopedia of Science and Technology, ninth edition. 2001
- Multisite phosphorylation and the countdown to S phase. Cell. 2001; (7): 819-22
- Regulatory cascades: function and properties Encyclopedia of Life Sciences, Macmillan Publishing Ltd.. 2001
- Six steps to destruction. Nature. 2001; (6863): 498-9
- The classical progesterone receptor associates with p42 MAPK and is involved in phosphatidylinositol 3-kinase signaling in Xenopus oocytes. J Biol Chem. 2001; (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. J Biol Chem. 2001; (2): 1459-65
- Activation of Wee1 by p42 MAPK in vitro and in cycling xenopus egg extracts. Mol Biol Cell. 2000; (3): 887-96
- Cloning and characterization of Xenopus Rsk2, the predominant p90 Rsk isozyme in oocytes and eggs. J Biol Chem. 2000; (42): 32983-90
- Disease attributed to Mycobacterium chelonae in South African clawed frogs (Xenopus laevis). Comp Med. 2000; (6): 675-9
- Inhibition of progesterone-induced Xenopus oocyte maturation by Nm23 Cell Growth Diff. 2000: 485-490
- What do scaffold proteins really do? Sci STKE. 2000; (52): pe1
- Building a cellular switch: more lessons from a good egg. Bioessays. 1999; (10): 866-70
- Distinct, constitutively active MAPK phosphatases function in Xenopus oocytes: implications for p42 MAPK regulation In vivo. Mol Biol Cell. 1999; (11): 3729-43
- Identification and management of an outbreak of Flavobacterium meningosepticum infection in a colony of South African clawed frogs (Xenopus laevis). J Am Vet Med Assoc. 1999; (12): 1833-8, 1792-3
- M phase phosphorylation of cytoplasmic dynein intermediate chain and p150(Glued). J Biol Chem. 1999; (20): 14262-9
- Xenopus oocyte maturation: new lessons from a good egg. Bioessays. 1999; (10): 833-42
- Assessing activities of blotted protein kinases 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. Trends Biochem Sci. 1998; (12): 461-5
- A role for mitogen-activated protein kinase in the spindle assembly checkpoint in XTC cells. J Cell Biol. 1997; (2): 433-43
- Cell cycle McGraw-Hill Encyclopedia of Science and Technology, 8th edition. 1997: 378-380
- Induction of a G2-phase arrest in Xenopus egg extracts by activation of p42 mitogen-activated protein kinase. Mol Biol Cell. 1997; (11): 2157-69
- Mechanistic studies of the dual phosphorylation of mitogen-activated protein kinase. J Biol Chem. 1997; (30): 19008-16
- Dependence of Mos-induced Cdc2 activation on MAP kinase function in a cell-free system. EMBO J. 1996; (9): 2169-73
- MAP kinases in mitogenesis and development. Curr Top Dev Biol. 1996: 1-60
- Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs. Trends Biochem Sci. 1996; (12): 460-6
- Evidence that inactive p42 mitogen-activated protein kinase and inactive Rsk exist as a heterodimer in vivo. Proc Natl Acad Sci U S A. 1994; (12): 5480-4
- Inhibition of c-Jun DNA binding by mitogen-activated protein kinase. Mol Biol Cell. 1992; (10): 1117-30
- Assessing activities of blotted protein kinases. Methods Enzymol. 1991: 430-5
- Cell cycle tyrosine phosphorylation of p34cdc2 and a microtubule-associated protein kinase homolog in Xenopus oocytes and eggs. Mol Cell Biol. 1991; (4): 1965-71
- Identification of a 42-kilodalton phosphotyrosyl protein as a serine(threonine) protein kinase by renaturation. Mol Cell Biol. 1990; (6): 3020-6
- Intracellular localization of pp60c-src in human platelets. Oncogene. 1990; (7): 1033-6
- Thrombin stimulates the activities of multiple previously unidentified protein kinases in platelets. J Biol Chem. 1989; (34): 20723-9
- Tyrosine-specific protein phosphorylation is regulated by glycoprotein IIb-IIIa in platelets. Proc Natl Acad Sci U S A. 1989; (7): 2234-8
- Membrane bilayer balance and platelet shape: morphological and biochemical responses to amphipathic compounds. Biochim Biophys Acta. 1988; (2): 223-37
- Platelet tyrosine-specific protein phosphorylation is regulated by thrombin. Mol Cell Biol. 1988; (9): 3603-10
- Separation of phosphoinositides and other phospholipids by two-dimensional thin-layer chromatography. Anal Biochem. 1986; (2): 447-53
- Sulfhydryl reducing agents and shape regulation in human erythrocytes. Blood. 1986; (1): 214-21
- Computer-assisted mechanistic structure-activity studies: application to diverse classes of chemical carcinogens. Environ Health Perspect. 1985: 69-96
- Lipid transfer between phosphatidylcholine vesicles and human erythrocytes: exponential decrease in rate with increasing acyl chain length Biochemistry. 1985: 2857-2864
- Membrane bilayer balance and erythrocyte shape: a quantitative assessment. Biochemistry. 1985; (12): 2849-57
- Phosphoinositide metabolism and the morphology of human erythrocytes. J Cell Biol. 1984; (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 Biochemistry. 1983: 6116-6117
- Mechanistic structure-activity studies using quantum chemical methods: application to polycyclic aromatic hydrocarbons 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. Biochim Biophys Acta. 1982; (2): 321-8
- Calmodulin-dependent spectrin kinase activity in human erythrocytes. Prog Clin Biol Res. 1981: 137-55
- Mechanistic studies of addition of nucleophiles to arene oxides and diol epoxides: candidate ultimate carcinogens Int J Quantum Chem Quant Biol Symp. 1980: 223-244
- Quantum chemical studies of methylbenz[a]anthracenes: metabolism and correlations with carcinogenicity Chem-Biol Interactions. 1980: 319-340
- Adrenergic stimulation of membrane protein phosphorylation in human erythrocytes. Biochim Biophys Acta. 1979; (1): 136-40
- Mechanistic studies of arene oxide and diol epoxide rearrangement and hydrolysis reactions J Am Chem Soc. 1979: 1379-1388
- Quantum chemical studies of polycyclic aromatic hydrocarbons and their metabolites: correlations to carcinogenicity Chem-Biol Interactions. 1979: 75-89
- Structure/activity studies of flavonoids as inhibitors of cyclic AMP phosphodiesterase and relationship to quantum chemical indices. Mol Pharmacol. 1979; (2): 556-68
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