JAMES FERRELL

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc 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
    Michael 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
  2. pmc Robust, tunable biological oscillations from interlinked positive and negative feedback loops
    Tony Yu Chen Tsai
    Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305 5174, USA
    Science 321:126-9. 2008
  3. doi request reprint 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
  4. ncbi request reprint Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability
    James 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
  5. doi request reprint Signaling motifs and Weber's law
    James E Ferrell
    Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford CA 94305 5174, USA
    Mol Cell 36:724-7. 2009
  6. doi request reprint Simple, realistic models of complex biological processes: positive feedback and bistability in a cell fate switch and a cell cycle oscillator
    James E Ferrell
    Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305 5174, USA
    FEBS Lett 583:3999-4005. 2009
  7. ncbi request reprint Systems biology. A clock with a flip switch
    Andy C Poon
    Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305 5174, USA
    Science 318:757-8. 2007
  8. ncbi request reprint Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2
    Joseph R Pomerening
    Department of Molecular Pharmacology, Stanford University School of Medicine, Stanford, CA 94305 5174, USA
    Nat Cell Biol 5:346-51. 2003
  9. ncbi request reprint Substrate competition as a source of ultrasensitivity in the inactivation of Wee1
    Sun 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
  10. pmc Rapid cycling and precocious termination of G1 phase in cells expressing CDK1AF
    Joseph 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

Research Grants

  1. Bistability and Biological Oscillations
    JAMES FERRELL; Fiscal Year: 2007
  2. SIGNALING CASCADES AND LOOPS IN XENOPUS OOCYTES
    JAMES FERRELL; Fiscal Year: 2007
  3. Regulators of Cdc2/Cdk1
    JAMES FERRELL; Fiscal Year: 2007
  4. Regulators of Cdc2/Cdk1
    JAMES FERRELL; Fiscal Year: 2006
  5. Bistability and the Mitotic Trigger
    JAMES FERRELL; Fiscal Year: 2009
  6. Bistability and Biological Oscillations
    JAMES FERRELL; Fiscal Year: 2009
  7. Regulators of Cdc2/Cdk1
    JAMES FERRELL; Fiscal Year: 2009
  8. Bistability and the Mitotic Trigger
    James E Ferrell; Fiscal Year: 2010
  9. Regulators of Cdc2/Cdk1
    James E Ferrell; Fiscal Year: 2010
  10. THE ROLE OF MAP KINASE IN THE CELL CYCLE
    JAMES FERRELL; Fiscal Year: 2005

Collaborators

Detail Information

Publications36

  1. pmc 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
    Michael 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...
  2. pmc Robust, tunable biological oscillations from interlinked positive and negative feedback loops
    Tony 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...
  3. doi request reprint 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...
  4. ncbi request reprint Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability
    James 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...
  5. doi request reprint Signaling motifs and Weber's law
    James 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...
  6. doi request reprint Simple, realistic models of complex biological processes: positive feedback and bistability in a cell fate switch and a cell cycle oscillator
    James 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...
  7. ncbi request reprint Systems biology. A clock with a flip switch
    Andy C Poon
    Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305 5174, USA
    Science 318:757-8. 2007
  8. ncbi request reprint Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2
    Joseph 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...
  9. ncbi request reprint Substrate competition as a source of ultrasensitivity in the inactivation of Wee1
    Sun 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...
  10. pmc Rapid cycling and precocious termination of G1 phase in cells expressing CDK1AF
    Joseph 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...
  11. ncbi request reprint A positive-feedback-based bistable 'memory module' that governs a cell fate decision
    Wen Xiong
    Department of Molecular Pharmacology, Stanford University School of Medicine, Stanford, California 94305 5174, USA
    Nature 426:460-5. 2003
    ....
  12. ncbi request reprint Mechanisms of specificity in protein phosphorylation
    Jeffrey 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...
  13. ncbi request reprint Tuning bulk electrostatics to regulate protein function
    Zach 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...
  14. pmc Cyclin A2 regulates nuclear-envelope breakdown and the nuclear accumulation of cyclin B1
    Delquin 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...
  15. pmc Mechanistic studies of the mitotic activation of Mos
    Jianbo 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...
  16. pmc Multisite M-phase phosphorylation of Xenopus Wee1A
    Sun 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...
  17. pmc Interlinked fast and slow positive feedback loops drive reliable cell decisions
    Onn 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...
  18. ncbi request reprint Systems-level dissection of the cell-cycle oscillator: bypassing positive feedback produces damped oscillations
    Joseph 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...
  19. ncbi request reprint Recombinant Dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencing
    Jason 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...
  20. ncbi request reprint Mos mediates the mitotic activation of p42 MAPK in Xenopus egg extracts
    Jianbo 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...
  21. ncbi request reprint The JNK cascade as a biochemical switch in mammalian cells: ultrasensitive and all-or-none responses
    Christoph 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...
  22. ncbi request reprint Silencing gene expression with Dicer-generated siRNA pools
    Jason W Myers
    Department of Molecular Pharmacology, Stanford University Medical School, CA, USA
    Methods Mol Biol 309:93-196. 2005
  23. ncbi request reprint Selective regulation of neurite extension and synapse formation by the beta but not the alpha isoform of CaMKII
    Charles 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...
  24. pmc A role for GPRx, a novel GPR3/6/12-related G-protein coupled receptor, in the maintenance of meiotic arrest in Xenopus laevis oocytes
    Diana 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...
  25. ncbi request reprint Picking a winner: new mechanistic insights into the design of effective siRNAs
    Delquin 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...
  26. ncbi request reprint Investigating macromolecules inside cultured and injected cells by in-cell NMR spectroscopy
    Zach 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...
  27. ncbi request reprint Enforced proximity in the function of a famous scaffold
    James 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...
  28. pmc STIM is a Ca2+ sensor essential for Ca2+-store-depletion-triggered Ca2+ influx
    Jen 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...
  29. pmc Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance
    David 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...
  30. ncbi request reprint Probing the precision of the mitotic clock with a live-cell fluorescent biosensor
    Joshua 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...
  31. pmc Systems biology: On the cell cycle and its switches
    Silvia D M Santos
    Nature 454:288-9. 2008
  32. pmc Feedback regulation of opposing enzymes generates robust, all-or-none bistable responses
    James E Ferrell
    Curr Biol 18:R244-5. 2008
  33. ncbi request reprint Emi2 at the crossroads: where CSF meets MPF
    David 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...
  34. pmc Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems
    David Angeli
    Dipartimento di Sistemi e Informatica, University of Florence, 50139 Florence, Italy
    Proc Natl Acad Sci U S A 101:1822-7. 2004
    ....
  35. ncbi request reprint Identification and comparative analysis of multiple mammalian Speedy/Ringo proteins
    Aiyang 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...
  36. pmc A noisy 'Start' to the cell cycle
    Jeffrey A Ubersax
    Mol Syst Biol 2:2006.0014. 2006

Research Grants37

  1. Bistability and Biological Oscillations
    JAMES FERRELL; Fiscal Year: 2007
    ....
  2. SIGNALING CASCADES AND LOOPS IN XENOPUS OOCYTES
    JAMES FERRELL; Fiscal Year: 2007
    ..abstract_text> ..
  3. Regulators of Cdc2/Cdk1
    JAMES 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. ..
  4. Regulators of Cdc2/Cdk1
    JAMES 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. ..
  5. Bistability and the Mitotic Trigger
    JAMES FERRELL; Fiscal Year: 2009
    ..An understanding of the process also promises to shed light on cancer and cancer chemotherapy. ..
  6. Bistability and Biological Oscillations
    JAMES FERRELL; Fiscal Year: 2009
    ..abstract_text> ..
  7. Regulators of Cdc2/Cdk1
    JAMES 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. ..
  8. Bistability and the Mitotic Trigger
    James E Ferrell; Fiscal Year: 2010
    ..An understanding of the process also promises to shed light on cancer and cancer chemotherapy. ..
  9. Regulators of Cdc2/Cdk1
    James E Ferrell; Fiscal Year: 2010
    ....
  10. THE ROLE OF MAP KINASE IN THE CELL CYCLE
    JAMES FERRELL; Fiscal Year: 2005
    ..Our overarching aim is to better understand the cell biology and biochemistry of oocyte maturation and early embryogenesis. ..
  11. THE ROLE OF MAP KINASE IN THE CELL CYCLE
    JAMES 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...
  12. MAP KINASE AND THE CELL CYCLE
    JAMES 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? ..
  13. SIGNALING CASCADES AND LOOPS IN XENOPUS OOCYTES
    JAMES FERRELL; Fiscal Year: 2003
    ..4. To determine whether regulated nuclear translocation contributes to the ultrasensitive response of p42 MAPK to upstream activators. ..
  14. Bistability and the Mitotic Trigger
    James E Ferrell; Fiscal Year: 2011
    ..An understanding of the process also promises to shed light on cancer and cancer chemotherapy. ..