James E. Ferrell - Publications

Publications (70)

XB-PERS-1994

Publications By James E. Ferrell

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Robust trigger wave speed in Xenopus cytoplasmic extracts., Huang JH, Chen Y, Huang WYC, Tabatabaee S, Ferrell JE., Nat Commun. July 10, 2024; 15 (1): 5782.
Viscosity-dependent control of protein synthesis and degradation., Chen Y, Huang JH, Phong C, Ferrell JE., Nat Commun. March 8, 2024; 15 (1): 2149.
Measuring Molecular Diffusion in Self-Organizing Xenopus Extracts by Fluorescence Correlation Spectroscopy., Huang WYC, Ferrell JE, Cheng X., Methods Mol Biol. January 1, 2024; 2740 107-115.
Protein homeostasis from diffusion-dependent control of protein synthesis and degradation., Chen Y, Huang JH, Phong C, Ferrell JE., bioRxiv. April 28, 2023;
Cytoplasmic organization promotes protein diffusion in Xenopus extracts., Huang WYC, Cheng X, Ferrell JE., Nat Commun. September 23, 2022; 13 (1): 5599.
Xenopus laevis Egg Extract Preparation and Live Imaging Methods for Visualizing Dynamic Cytoplasmic Organization., Cheng X, Ferrell JE., J Vis Exp. June 6, 2021; (172):
Bistable, Biphasic Regulation of PP2A-B55 Accounts for the Dynamics of Mitotic Substrate Phosphorylation., Kamenz J, Gelens L, Ferrell JE., Curr Biol. February 22, 2021; 31 (4): 794-808.e6.
Real-Time Monitoring of APC /C-Mediated Substrate Degradation Using Xenopus laevis Egg Extracts., Kamenz J, Qiao R, Yang Q, Ferrell JE., Methods Mol Biol. January 1, 2021; 2329 29-38.
The nucleus serves as the pacemaker for the cell cycle., Afanzar O, Buss GK, Stearns T, Ferrell JE., Elife. December 7, 2020; 9
Spontaneous emergence of cell-like organization in Xenopus egg extracts., Cheng X, Ferrell JE., Science. November 1, 2019; 366 (6465): 631-637.
Apoptosis propagates through the cytoplasm as trigger waves., Cheng X, Ferrell JE., Science. August 10, 2018; 361 (6402): 607-612.
Robustly Cycling Xenopus laevis Cell-Free Extracts in Teflon Chambers., Chang JB, Ferrell JE., Cold Spring Harb Protoc. August 1, 2018; 2018 (8):
Desynchronizing Embryonic Cell Division Waves Reveals the Robustness of Xenopus laevis Development., Anderson GA, Gelens L, Baker JC, Ferrell JE., Cell Rep. October 3, 2017; 21 (1): 37-46.
The Prozone Effect Accounts for the Paradoxical Function of the Cdk-Binding Protein Suc1/Cks., Ha SH, Kim SY, Ferrell JE., Cell Rep. February 16, 2016; 14 (6): 1408-1421.
How Does the Xenopus laevis Embryonic Cell Cycle Avoid Spatial Chaos?, Gelens L, Huang KC, Ferrell JE., Cell Rep. August 4, 2015; 12 (5): 892-900.
Spatial trigger waves: positive feedback gets you a long way., Gelens L, Anderson GA, Ferrell JE., Mol Biol Cell. November 5, 2014; 25 (22): 3486-93.
Changes in oscillatory dynamics in the cell cycle of early Xenopus laevis embryos., Tsai TY, Theriot JA, Ferrell JE., PLoS Biol. February 1, 2014; 12 (2): e1001788.
Mitotic trigger waves and the spatial coordination of the Xenopus cell cycle., Chang JB, Ferrell JE., Nature. August 29, 2013; 500 (7464): 603-7.
The Cdk1-APC/C cell cycle oscillator circuit functions as a time-delayed, ultrasensitive switch., Yang Q, Ferrell JE., Nat Cell Biol. May 1, 2013; 15 (5): 519-25.
Bistability in one equation or fewer., Anderson GA, Liu X, Ferrell JE., Methods Mol Biol. January 1, 2012; 880 53-67.
Modeling the cell cycle: why do certain circuits oscillate?, Ferrell JE, Tsai TY, Yang Q., Cell. March 18, 2011; 144 (6): 874-85.
Ultrasensitivity in the Regulation of Cdc25C by Cdk1., Trunnell NB, Poon AC, Kim SY, Ferrell JE., Mol Cell. February 4, 2011; 41 (3): 263-74.
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. December 17, 2009; 583 (24): 3999-4005.
Signaling motifs and Weber's law., Ferrell JE., Mol Cell. December 11, 2009; 36 (5): 724-7.
Tuning the activation threshold of a kinase network by nested feedback loops., Justman QA, Serber Z, Ferrell JE, El-Samad H, Shokat KM., Science. April 24, 2009; 324 (5926): 509-12.
Rapid cycling and precocious termination of G1 phase in cells expressing CDK1AF., Pomerening JR, Ubersax JA, Ferrell JE., Mol Biol Cell. August 1, 2008; 19 (8): 3426-41.
Robust, tunable biological oscillations from interlinked positive and negative feedback loops., Tsai TY, Choi YS, Ma W, Pomerening JR, Tang C, Ferrell JE., Science. July 4, 2008; 321 (5885): 126-9.
A role for GPRx, a novel GPR3/6/12-related G-protein coupled receptor, in the maintenance of meiotic arrest in Xenopus laevis oocytes., Ríos-Cardona D, Ricardo-González RR, Chawla A, Ferrell JE., Dev Biol. May 1, 2008; 317 (1): 380-8.
Feedback regulation of opposing enzymes generates robust, all-or-none bistable responses., Ferrell JE., Curr Biol. March 25, 2008; 18 (6): R244-5.
Substrate competition as a source of ultrasensitivity in the inactivation of Wee1., Kim SY, Ferrell JE., Cell. March 23, 2007; 128 (6): 1133-45.
Emi2 at the crossroads: where CSF meets MPF., Hansen DV, Pomerening JR, Summers MK, Miller JJ, Ferrell JE, Jackson PK., Cell Cycle. March 15, 2007; 6 (6): 732-8.
Mechanistic studies of the mitotic activation of Mos., Yue J, Ferrell JE., Mol Cell Biol. July 1, 2006; 26 (14): 5300-9.
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. June 1, 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. January 1, 2006; 1 (6): 2701-9.
Multisite M-phase phosphorylation of Xenopus Wee1A., Kim SY, Song EJ, Lee KJ, Ferrell JE., Mol Cell Biol. December 1, 2005; 25 (23): 10580-90.
Interlinked fast and slow positive feedback loops drive reliable cell decisions., Brandman O, Ferrell JE, Li R, Meyer T., Science. October 21, 2005; 310 (5747): 496-8.
Systems-level dissection of the cell-cycle oscillator: bypassing positive feedback produces damped oscillations., Pomerening JR, Kim SY, Ferrell JE., Cell. August 26, 2005; 122 (4): 565-78.
Identification and comparative analysis of multiple mammalian Speedy/Ringo proteins., Cheng A, Xiong W, Ferrell JE, Solomon MJ., Cell Cycle. January 1, 2005; 4 (1): 155-65.
Mos mediates the mitotic activation of p42 MAPK in Xenopus egg extracts., Yue J, Ferrell JE., Curr Biol. September 7, 2004; 14 (17): 1581-6.
A positive-feedback-based bistable 'memory module' that governs a cell fate decision., Xiong W, Ferrell JE., Nature. November 27, 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. April 1, 2003; 5 (4): 346-51.
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. February 18, 2003; 13 (4): 315-20.
Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability., Ferrell JE., Curr Opin Cell Biol. April 1, 2002; 14 (2): 140-8.
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. February 1, 2002; 13 (2): 454-68.
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. October 5, 2001; 276 (40): 37708-14.
Bistability in the JNK cascade., Bagowski CP, Ferrell JE., Curr Biol. August 7, 2001; 11 (15): 1176-82.
Bistability in cell signaling: How to make continuous processes discontinuous, and reversible processes irreversible., Ferrell JE, Xiong W., Chaos. March 1, 2001; 11 (1): 227-236.
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. January 12, 2001; 276 (2): 1459-65.
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. December 1, 2000; 50 (6): 675-9.
Cloning and characterization of Xenopus Rsk2, the predominant p90 Rsk isozyme in oocytes and eggs., Bhatt RR, Ferrell JE., J Biol Chem. October 20, 2000; 275 (42): 32983-90.

Robust trigger wave speed in Xenopus cytoplasmic extracts., Huang JH, Chen Y, Huang WYC, Tabatabaee S, Ferrell JE., Nat Commun. July 10, 2024; 15 (1): 5782.

Viscosity-dependent control of protein synthesis and degradation., Chen Y, Huang JH, Phong C, Ferrell JE., Nat Commun. March 8, 2024; 15 (1): 2149.

Measuring Molecular Diffusion in Self-Organizing Xenopus Extracts by Fluorescence Correlation Spectroscopy., Huang WYC, Ferrell JE, Cheng X., Methods Mol Biol. January 1, 2024; 2740 107-115.

Protein homeostasis from diffusion-dependent control of protein synthesis and degradation., Chen Y, Huang JH, Phong C, Ferrell JE., bioRxiv. April 28, 2023;

Cytoplasmic organization promotes protein diffusion in Xenopus extracts., Huang WYC, Cheng X, Ferrell JE., Nat Commun. September 23, 2022; 13 (1): 5599.

Xenopus laevis Egg Extract Preparation and Live Imaging Methods for Visualizing Dynamic Cytoplasmic Organization., Cheng X, Ferrell JE., J Vis Exp. June 6, 2021; (172):

Bistable, Biphasic Regulation of PP2A-B55 Accounts for the Dynamics of Mitotic Substrate Phosphorylation., Kamenz J, Gelens L, Ferrell JE., Curr Biol. February 22, 2021; 31 (4): 794-808.e6.

Real-Time Monitoring of APC /C-Mediated Substrate Degradation Using Xenopus laevis Egg Extracts., Kamenz J, Qiao R, Yang Q, Ferrell JE., Methods Mol Biol. January 1, 2021; 2329 29-38.

The nucleus serves as the pacemaker for the cell cycle., Afanzar O, Buss GK, Stearns T, Ferrell JE., Elife. December 7, 2020; 9

Spontaneous emergence of cell-like organization in Xenopus egg extracts., Cheng X, Ferrell JE., Science. November 1, 2019; 366 (6465): 631-637.

Apoptosis propagates through the cytoplasm as trigger waves., Cheng X, Ferrell JE., Science. August 10, 2018; 361 (6402): 607-612.

Robustly Cycling Xenopus laevis Cell-Free Extracts in Teflon Chambers., Chang JB, Ferrell JE., Cold Spring Harb Protoc. August 1, 2018; 2018 (8):

Desynchronizing Embryonic Cell Division Waves Reveals the Robustness of Xenopus laevis Development., Anderson GA, Gelens L, Baker JC, Ferrell JE., Cell Rep. October 3, 2017; 21 (1): 37-46.

The Prozone Effect Accounts for the Paradoxical Function of the Cdk-Binding Protein Suc1/Cks., Ha SH, Kim SY, Ferrell JE., Cell Rep. February 16, 2016; 14 (6): 1408-1421.

How Does the Xenopus laevis Embryonic Cell Cycle Avoid Spatial Chaos?, Gelens L, Huang KC, Ferrell JE., Cell Rep. August 4, 2015; 12 (5): 892-900.

Spatial trigger waves: positive feedback gets you a long way., Gelens L, Anderson GA, Ferrell JE., Mol Biol Cell. November 5, 2014; 25 (22): 3486-93.

Changes in oscillatory dynamics in the cell cycle of early Xenopus laevis embryos., Tsai TY, Theriot JA, Ferrell JE., PLoS Biol. February 1, 2014; 12 (2): e1001788.

Mitotic trigger waves and the spatial coordination of the Xenopus cell cycle., Chang JB, Ferrell JE., Nature. August 29, 2013; 500 (7464): 603-7.

The Cdk1-APC/C cell cycle oscillator circuit functions as a time-delayed, ultrasensitive switch., Yang Q, Ferrell JE., Nat Cell Biol. May 1, 2013; 15 (5): 519-25.

Bistability in one equation or fewer., Anderson GA, Liu X, Ferrell JE., Methods Mol Biol. January 1, 2012; 880 53-67.

Modeling the cell cycle: why do certain circuits oscillate?, Ferrell JE, Tsai TY, Yang Q., Cell. March 18, 2011; 144 (6): 874-85.

Ultrasensitivity in the Regulation of Cdc25C by Cdk1., Trunnell NB, Poon AC, Kim SY, Ferrell JE., Mol Cell. February 4, 2011; 41 (3): 263-74.

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. December 17, 2009; 583 (24): 3999-4005.

Signaling motifs and Weber's law., Ferrell JE., Mol Cell. December 11, 2009; 36 (5): 724-7.

Tuning the activation threshold of a kinase network by nested feedback loops., Justman QA, Serber Z, Ferrell JE, El-Samad H, Shokat KM., Science. April 24, 2009; 324 (5926): 509-12.

Rapid cycling and precocious termination of G1 phase in cells expressing CDK1AF., Pomerening JR, Ubersax JA, Ferrell JE., Mol Biol Cell. August 1, 2008; 19 (8): 3426-41.

Robust, tunable biological oscillations from interlinked positive and negative feedback loops., Tsai TY, Choi YS, Ma W, Pomerening JR, Tang C, Ferrell JE., Science. July 4, 2008; 321 (5885): 126-9.

A role for GPRx, a novel GPR3/6/12-related G-protein coupled receptor, in the maintenance of meiotic arrest in Xenopus laevis oocytes., Ríos-Cardona D, Ricardo-González RR, Chawla A, Ferrell JE., Dev Biol. May 1, 2008; 317 (1): 380-8.

Feedback regulation of opposing enzymes generates robust, all-or-none bistable responses., Ferrell JE., Curr Biol. March 25, 2008; 18 (6): R244-5.

Substrate competition as a source of ultrasensitivity in the inactivation of Wee1., Kim SY, Ferrell JE., Cell. March 23, 2007; 128 (6): 1133-45.

Emi2 at the crossroads: where CSF meets MPF., Hansen DV, Pomerening JR, Summers MK, Miller JJ, Ferrell JE, Jackson PK., Cell Cycle. March 15, 2007; 6 (6): 732-8.

Mechanistic studies of the mitotic activation of Mos., Yue J, Ferrell JE., Mol Cell Biol. July 1, 2006; 26 (14): 5300-9.

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. June 1, 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. January 1, 2006; 1 (6): 2701-9.

Multisite M-phase phosphorylation of Xenopus Wee1A., Kim SY, Song EJ, Lee KJ, Ferrell JE., Mol Cell Biol. December 1, 2005; 25 (23): 10580-90.

Interlinked fast and slow positive feedback loops drive reliable cell decisions., Brandman O, Ferrell JE, Li R, Meyer T., Science. October 21, 2005; 310 (5747): 496-8.

Systems-level dissection of the cell-cycle oscillator: bypassing positive feedback produces damped oscillations., Pomerening JR, Kim SY, Ferrell JE., Cell. August 26, 2005; 122 (4): 565-78.

Identification and comparative analysis of multiple mammalian Speedy/Ringo proteins., Cheng A, Xiong W, Ferrell JE, Solomon MJ., Cell Cycle. January 1, 2005; 4 (1): 155-65.

Mos mediates the mitotic activation of p42 MAPK in Xenopus egg extracts., Yue J, Ferrell JE., Curr Biol. September 7, 2004; 14 (17): 1581-6.

A positive-feedback-based bistable 'memory module' that governs a cell fate decision., Xiong W, Ferrell JE., Nature. November 27, 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. April 1, 2003; 5 (4): 346-51.

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. February 18, 2003; 13 (4): 315-20.

Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability., Ferrell JE., Curr Opin Cell Biol. April 1, 2002; 14 (2): 140-8.

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. February 1, 2002; 13 (2): 454-68.

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. October 5, 2001; 276 (40): 37708-14.

Bistability in the JNK cascade., Bagowski CP, Ferrell JE., Curr Biol. August 7, 2001; 11 (15): 1176-82.

Bistability in cell signaling: How to make continuous processes discontinuous, and reversible processes irreversible., Ferrell JE, Xiong W., Chaos. March 1, 2001; 11 (1): 227-236.

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. January 12, 2001; 276 (2): 1459-65.

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. December 1, 2000; 50 (6): 675-9.

Cloning and characterization of Xenopus Rsk2, the predominant p90 Rsk isozyme in oocytes and eggs., Bhatt RR, Ferrell JE., J Biol Chem. October 20, 2000; 275 (42): 32983-90.

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