Research Topics
Species | JAMES FERRELLSummaryAffiliation: Stanford University Country: USA Publications
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Publications
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 oocytesMichael L Sohaskey
Department of Molecular Pharmacology and Program in Cancer Biology, Stanford University School of Medicine, Stanford, California 94305 5174, USA
Mol Biol Cell 13:454-68. 2002..Our results provide mechanistic insight into the regulation of a dual-specificity MAPK phosphatase during meiotic maturation and the adaptation to cellular stress...- Robust, tunable biological oscillations from interlinked positive and negative feedback loopsTony Yu Chen Tsai
Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305 5174, USA
Science 321:126-9. 2008..Positive-plus-negative oscillators also appear to be more robust and easier to evolve, rationalizing why they are found in contexts where an adjustable frequency is unimportant... 
Modeling the cell cycle: why do certain circuits oscillate?James E Ferrell
Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305 5174, USA
Cell 144:874-85. 2011..Finally, we review the procedures of linear stability analysis, which allow one to determine whether a given ODE model and a particular set of kinetic parameters will produce oscillations...
Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistabilityJames E Ferrell
Department of Molecular Pharmacology, CCSR, 269 Campus Drive, Stanford University School of Medicine, Stanford, CA 94305 5174, USA
Curr Opin Cell Biol 14:140-8. 2002..Here we review the basic properties of bistable circuits, the requirements for construction of a satisfactory bistable switch, and the recent progress towards constructing and analysing bistable signaling systems...- Signaling motifs and Weber's lawJames E Ferrell
Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford CA 94305 5174, USA
Mol Cell 36:724-7. 2009..New experimental and theoretical studies reported by Uri Alon, Marc Kirschner, and colleagues in this issue of Molecular Cell suggest that Weber's law of sensory perception may apply to a number of cell signaling processes... - Simple, realistic models of complex biological processes: positive feedback and bistability in a cell fate switch and a cell cycle oscillatorJames E Ferrell
Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305 5174, USA
FEBS Lett 583:3999-4005. 2009..We believe that this type of reductionistic systems biology holds great promise for understanding complicated biochemical processes in simpler terms... - Systems biology. A clock with a flip switchAndy C Poon
Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA
Science 318:757-8. 2007 - Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2Joseph R Pomerening
Department of Molecular Pharmacology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA
Nat Cell Biol 5:346-51. 2003..We also show that Cdc2 activation exhibits hysteresis, a property of bistable systems with particular relevance to biochemical oscillators. These findings help establish the basic systems-level logic of the mitotic oscillator... - Substrate competition as a source of ultrasensitivity in the inactivation of Wee1Sun Young Kim
Department of Chemical and Systems Biology, Stanford University School of Medicine, Center for Clinical Sciences Research, Stanford, CA 94305 5174, USA
Cell 128:1133-45. 2007..Based on these findings, we were able to reconstitute a highly ultrasensitive Wee1 response with purified components. Competition provides a simple way of generating the equivalent of a highly cooperative allosteric response... - Rapid cycling and precocious termination of G1 phase in cells expressing CDK1AFJoseph R Pomerening
Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305 5174, USA
Mol Biol Cell 19:3426-41. 2008..We propose that the HeLa cell cycle is built upon an unreliable negative feedback oscillator and that the normal high reliability, slow pace and switch-like character of the cycle is imposed by a bistable CDK1/Wee1/Myt1/Cdc25 system... - A positive-feedback-based bistable 'memory module' that governs a cell fate decisionWen Xiong
Department of Molecular Pharmacology, Stanford University School of Medicine, Stanford, California 94305-5174, USA
Nature 426:460-5. 2003.... - Mechanisms of specificity in protein phosphorylationJeffrey A Ubersax
Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305 5174, USA
Nat Rev Mol Cell Biol 8:530-41. 2007..The responsibility for the recognition of substrates by protein kinases appears to be distributed among a large number of independent, imperfect specificity mechanisms... - Tuning bulk electrostatics to regulate protein functionZach Serber
Department of Chemical and Systems Biology, Stanford University School of Medicine, MC 5174, Stanford, CA 94305, USA
Cell 128:441-4. 2007..This provides a beautiful example of how phosphorylation can produce decisive changes in protein function through bulk electrostatics, without the necessity of intricate conformational changes... - Cyclin A2 regulates nuclear-envelope breakdown and the nuclear accumulation of cyclin B1Delquin Gong
Department of Chemical and Systems Biology, CCSR, MC 5174, Stanford University School of Medicine, Stanford, California 94305, USA
Curr Biol 17:85-91. 2007..Nevertheless cyclin B1 translocates to the nucleus just prior to NEB in a cyclin A2-dependent fashion and is capable of supporting NEB if rendered constitutively nuclear... - Mechanistic studies of the mitotic activation of MosJianbo Yue
Stanford University School of Medicine, Department of Molecular Pharmacology, CCSR Room 3155, Stanford, CA 94305 5174, USA
Mol Cell Biol 26:5300-9. 2006..Our work suggests that Ser 105 dephosphorylation represents a novel mechanism for reorienting helix alphaC... - Multisite M-phase phosphorylation of Xenopus Wee1ASun Young Kim
Department of Molecular Pharmacology, Stanford University School of Medicine, Stanford, CA 94305 5174, USA
Mol Cell Biol 25:10580-90. 2005..These results also show that multisite phosphorylation cooperatively inactivates Wee1A and cooperatively promotes Wee1A proteolysis... - Interlinked fast and slow positive feedback loops drive reliable cell decisionsOnn Brandman
Department of Molecular Pharmacology, Stanford University School of Medicine, Stanford, CA, 94305, USA
Science 310:496-8. 2005..Mathematical simulations revealed that linking fast and slow positive feedback loops creates a "dual-time" switch that is both rapidly inducible and resistant to noise in the upstream signaling system... - Systems-level dissection of the cell-cycle oscillator: bypassing positive feedback produces damped oscillationsJoseph R Pomerening
Department of Molecular Pharmacology, Stanford University School of Medicine, Stanford, California 94305, USA
Cell 122:565-78. 2005..This work also underscores the fundamental similarity of cell-cycle oscillations in embryos to repetitive action potentials in pacemaker neurons, with both systems relying on a combination of negative and positive-feedback loops... - Recombinant Dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencingJason W Myers
Department of Molecular Pharmacology, 269 Campus Drive, Stanford University School of Medicine, Stanford, CA 94305 5174, USA
Nat Biotechnol 21:324-8. 2003..Dicer-generated siRNAs (d-siRNAs) are effective in silencing transiently transfected reporter genes and endogenous genes, making in vitro dicing a useful, practical alternative for the production of siRNAs... - Mos mediates the mitotic activation of p42 MAPK in Xenopus egg extractsJianbo Yue
Department of Molecular Pharmacology, Stanford University, Stanford, CA 94305 5174, USA
Curr Biol 14:1581-6. 2004..Taken together, these data demonstrate that Mos is responsible for the mitotic activation of the p42 MAPK pathway in Xenopus egg extracts... - The JNK cascade as a biochemical switch in mammalian cells: ultrasensitive and all-or-none responsesChristoph P Bagowski
Department of Molecular Pharmacology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA
Curr Biol 13:315-20. 2003..These studies show that the JNK cascade commonly exhibits switch-like responses to a variety of stimuli... - Silencing gene expression with Dicer-generated siRNA poolsJason W Myers
Department of Molecular Pharmacology, Stanford University Medical School, CA, USA
Methods Mol Biol 309:93-196. 2005 - Selective regulation of neurite extension and synapse formation by the beta but not the alpha isoform of CaMKIICharles C Fink
Department of Molecular Pharmacology, Stanford University Medical School, Stanford, CA 94305, USA
Neuron 39:283-97. 2003..These results show that the two main neuronal CaMKII isoforms have markedly different roles in neuronal plasticity, with CaMKIIalpha regulating synaptic strength and CaMKIIbeta controlling the dendritic morphology and number of synapses... - A role for GPRx, a novel GPR3/6/12-related G-protein coupled receptor, in the maintenance of meiotic arrest in Xenopus laevis oocytesDiana Ríos-Cardona
Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305 5174, USA
Dev Biol 317:380-8. 2008..Morpholino injections did not cause spontaneous maturation of oocytes, but did accelerate progesterone-induced maturation. Thus, GPRx contributes to the maintenance of G2-arrest in immature X. laevis oocytes... - Picking a winner: new mechanistic insights into the design of effective siRNAsDelquin Gong
Department of Biological Sciences, Stanford University, Stanford, CA 94305-5020, USA
Trends Biotechnol 22:451-4. 2004..These strategies represent important steps towards the rational design of effective siRNAs... - Investigating macromolecules inside cultured and injected cells by in-cell NMR spectroscopyZach Serber
Department of Chemical and Systems Biology, Stanford University Medical School, 269 Campus Drive, Stanford, 94305 California, USA
Nat Protoc 1:2701-9. 2006..coli can be produced within 13-14 h. Preparing Xenopus oocyte samples for in-cell NMR experiments takes 6-14 h depending on the oocyte preparation scheme and the injection method used... - Enforced proximity in the function of a famous scaffoldJames E Ferrell
Department of Molecular Pharmacology, Stanford University School of Medicine, Stanford, CA 94305, USA
Mol Cell 11:289-91. 2003..Recent studies by Park, Zarrinipar, and Lim with reengineered Ste5 scaffold proteins underscore the fundamental importance of proximity in enzyme regulation and of keeping a proper distance for maintaining signaling specificity... - STIM is a Ca2+ sensor essential for Ca2+-store-depletion-triggered Ca2+ influxJen Liou
Department of Molecular Pharmacology, Stanford University Medical School, California 94305, USA
Curr Biol 15:1235-41. 2005..Our study suggests that STIM proteins function as Ca(2+) store sensors in the signaling pathway connecting Ca(2+) store depletion to Ca(2+) influx... - Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundanceDavid G Hendrickson
Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
PLoS ONE 3:e2126. 2008..Microarray analysis of Ago2 immunopurified samples provides a simple, direct method for experimentally identifying the targets of miRNAs and for elucidating roles of miRNAs in cellular regulation... - Probing the precision of the mitotic clock with a live-cell fluorescent biosensorJoshua T Jones
Department of Molecular Pharmacology, W200 Clark, 318 Campus Drive, Stanford University Medical School, Stanford, California 94305, USA
Nat Biotechnol 22:306-12. 2004..Inactivation of the spindle checkpoint by targeting the regulator Mad2 with RNAi consistently shortened mitosis, providing direct evidence that the internal mitotic timing mechanism is much faster in cells that lack the checkpoint... - Systems biology: On the cell cycle and its switchesSilvia D M Santos
Nature 454:288-9. 2008 - Feedback regulation of opposing enzymes generates robust, all-or-none bistable responsesJames E Ferrell
Curr Biol 18:R244-5. 2008 - Emi2 at the crossroads: where CSF meets MPFDavid V Hansen
Department of Tumor Biology and Angiogenesis, Genentech, Inc, South San Francisco, California 94080, USA
Cell Cycle 6:732-8. 2007..Finally, we propose that inactivation of Emi2 by Cdc2 permits mitotic progression during early embryonic cleavage cycles... - Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systemsDavid Angeli
Dipartimento di Sistemi e Informatica, University of Florence, 50139 Florence, Italy
Proc Natl Acad Sci U S A 101:1822-7. 2004.... - Identification and comparative analysis of multiple mammalian Speedy/Ringo proteinsAiyang Cheng
Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA
Cell Cycle 4:155-65. 2005..The existence of this growing family of CDK activators suggests that Speedy/Ringo proteins may play as complex a role in cell cycle control as the diverse family of cyclins... - A noisy 'Start' to the cell cycleJeffrey A Ubersax
Mol Syst Biol 2:2006.0014. 2006
Research Grants
- Bistability and Biological OscillationsJAMES FERRELL; Fiscal Year: 2007....
- SIGNALING CASCADES AND LOOPS IN XENOPUS OOCYTESJAMES FERRELL; Fiscal Year: 2007..abstract_text> ..
- Regulators of Cdc2/Cdk1JAMES FERRELL; Fiscal Year: 2007..In HeLa cells, some unidentified regulator or regulators determines the timing of cyclin B1-Cdk1 activation and nuclear translocation. We plan to carry out a systematic RNAi screen to identify these regulators. ..
- Regulators of Cdc2/Cdk1JAMES FERRELL; Fiscal Year: 2006..In HeLa cells, some unidentified regulator or regulators determines the timing of cyclin B1-Cdk1 activation and nuclear translocation. We plan to carry out a systematic RNAi screen to identify these regulators. ..
- Bistability and the Mitotic TriggerJAMES FERRELL; Fiscal Year: 2009..An understanding of the process also promises to shed light on cancer and cancer chemotherapy. ..
- Bistability and Biological OscillationsJAMES FERRELL; Fiscal Year: 2009..abstract_text> ..
- Regulators of Cdc2/Cdk1JAMES FERRELL; Fiscal Year: 2009..In HeLa cells, some unidentified regulator or regulators determines the timing of cyclin B1-Cdk1 activation and nuclear translocation. We plan to carry out a systematic RNAi screen to identify these regulators. ..
- Bistability and the Mitotic TriggerJames E Ferrell; Fiscal Year: 2010..An understanding of the process also promises to shed light on cancer and cancer chemotherapy. ..
- Regulators of Cdc2/Cdk1James E Ferrell; Fiscal Year: 2010....
- THE ROLE OF MAP KINASE IN THE CELL CYCLEJAMES FERRELL; Fiscal Year: 2005..Our overarching aim is to better understand the cell biology and biochemistry of oocyte maturation and early embryogenesis. ..
- THE ROLE OF MAP KINASE IN THE CELL CYCLEJAMES FERRELL; Fiscal Year: 1993..What biological processes are mediated by MAP kinase activation? 5.What proteins are phosphorylated by MAP kinase in vivo? Our central goal is to understand how MAP kinase contributes to the cell's decision to divide...
- MAP KINASE AND THE CELL CYCLEJAMES FERRELL; Fiscal Year: 2001..How does the MAPK cascade bring about Cdc2 activation? 4. How does activation of the MAPK cascade bring about G2 arrest in cycling extracts and embryos, and what is the significance of this arrest? ..
- SIGNALING CASCADES AND LOOPS IN XENOPUS OOCYTESJAMES FERRELL; Fiscal Year: 2003..4. To determine whether regulated nuclear translocation contributes to the ultrasensitive response of p42 MAPK to upstream activators. ..
- Bistability and the Mitotic TriggerJames E Ferrell; Fiscal Year: 2011..An understanding of the process also promises to shed light on cancer and cancer chemotherapy. ..