PUBLICATIONS:
2024
154: Huang JH, Chen Y, Huang WYC, Tabatabaee S, Ferrell JE Jr. Robust trigger wave speed in Xenopus cytoplasmic extracts. Nat Commun. 2024 Jul 10;15(1):5782.
153: Liu S, Ezran C, Wang MFZ, Li Z, Awayan K; Tabula Microcebus Consortium; Long JZ, De Vlaminck I, Wang S, Epelbaum J, Kuo CS, Terrien J, Krasnow MA, Ferrell JE Jr. An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome. Nat Commun. 2024 Mar 11;15(1):2188.
152: Chen Y, Huang JH, Phong C, Ferrell JE Jr. Viscosity-dependent control of protein synthesis and degradation. Nat Commun. 2024 Mar 8;15(1):2149.
151: Huang WYC, Boxer SG, Ferrell JE Jr. Membrane localization accelerates association under conditions relevant to cellular signaling. Proc Natl Acad Sci U S A. 2024 Mar 5;121(10):e2319491121.
150: Huang WYC, Ferrell JE Jr, Cheng X. Measuring Molecular Diffusion in Self-Organizing Xenopus Extracts by Fluorescence Correlation Spectroscopy. Methods Mol Biol. 2024;2740:107-115.
2023
149: Fan Y, Chai C, Li P, Zou X, Ferrell JE Jr, Wang B. Ultrafast distant wound response is essential for whole-body regeneration. Cell. 2023 Aug 17;186(17):3606-3618.e16..
2022
148: Ming J, Lin Z, Zhao J, Wan X; Tabula Microcebus Consortium; Yang C, Wu AR. FIRM: Flexible integration of single-cell RNA-sequencing data for large-scale multi-tissue cell atlas datasets. Brief Bioinform. 2022 Sep 20;23(5):bbac167. [as a member of the Tabula Microcebus Consortium].
147: Zhao J, Wang G, Ming J, Lin Z, Wang Y; Tabula Microcebus Consortium; Wu AR, Yang C. Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets. Nat Comput Sci. 2022 May;2(5):317-330. [as a member of the Tabula Microcebus Consortium].
146: Huang WYC, Cheng X, Ferrell JE Jr. Cytoplasmic organization promotes protein diffusion in Xenopus extracts. Nat Commun. 2022 Sep 23;13(1):5599.
145: The Tabula Microcebus Consortium, Ezran C, Liu S, et al. Mouse lemur transcriptomic atlas elucidates primate genes, physiology, disease, and evolution. bioRxiv [Preprint]. 2022 Dec 2022.08.06.503035.
2021
144: The Tabula Microcebus Consortium, Ezran C, Liu S, et al. Tabula Microcebus: A transcriptomic cell atlas of mouse lemur, an emerging primate model organism. bioRxiv [Preprint]. 2021.12.12.469460.
143: Song IK, Kim MS, Ferrell JE Jr, Shin DH, Lee KJ. Stepwise Oxidations Play Key Roles in the Structural and Functional Regulations of DJ-1. Biochem J. 2021 Sep 13:BCJ20210245.
142: Chen Y, Ferrell JE Jr. C. elegans colony formation as a condensation phenomenon. Nat Commun. 2021 Aug 16;12(1):4947.
141: Cheng X, Ferrell JE Jr. Xenopus laevis Egg Extract Preparation and Live Imaging Methods for Visualizing Dynamic Cytoplasmic Organization. J Vis Exp. 2021 Jun 6;(172).
140: Kamenz J, Qiao R, Yang Q, Ferrell JE Jr. Real-Time Monitoring of APC/C-Mediated Substrate Degradation Using Xenopus laevis Egg Extracts. Methods Mol Biol. 2021;2329:29-38.
139: Kamenz J, Gelens L, Ferrell JE Jr. Bistable, Biphasic Regulation of PP2A-B55 Accounts for the Dynamics of Mitotic Substrate Phosphorylation. Curr Biol. 2021 Feb 22;31(4):794-808.e6.
2020
138: Afanzar O, Buss GK, Stearns T, Ferrell JE Jr. The nucleus serves as the pacemaker for the cell cycle. Elife. 2020 Dec 7;9:e59989.
137: Lockhead S, Moskaleva A, Kamenz J, Chen Y, Kang M, Reddy AR, Santos SDM, Ferrell JE Jr. The apparent requirement for protein synthesis during G2 phase is due to checkpoint activation. Cell Rep. 2020 Jul 14;32(2):107901.
2019
136: Cheng X, Ferrell JE Jr. Cheng X, Ferrell JE Jr. Spontaneous emergence of cell-like organization in Xenopus egg extracts. Science. 2019 No 1;366(6465):631-637.
Noted in: Lee JJ. Cytoplasm of ruptured frog eggs organizes into cell-like structures that retain the ability to divide. Phys.Org 2019. https://phys.org/news/2019-11-cytoplasm-ruptured-frog-eggs-cell-like.html.
Noted in: Makowski E. Image of the day: scrambled frog eggs. The Scientist 2019. https://www.the-scientist.com/image-of-the-day/image-of-the-day--scrambled-frog-eggs--66681.
Noted in: Mitchison TJ, Field CM. Toward synthetic cells. Science 2019. https://science-sciencemag-org.laneproxy.stanford.edu/content/366/6465/569.
Noted in: Parry W. Unscrambled eggs: self-organization restores cells' order. Quanta Magazine 2020. https://www.quantamagazine.org/unscrambled-eggs-self-organization-restores-cells-order-20200102/.
134: Chung HK, Zou X, Bajar BT, Brand VR, Huo Y, Alcudia JF, Ferrell JE Jr, Lin MZ. A compact synthetic pathway rewires cancer signaling to therapeutic effector release. Science. 2019 May 3;364(6439). pii: eaat6982.
133: Roake CM, Chen L, Chakravarthy AL, Ferrell JE Jr, Raffa GD, Artandi SE. Disruption of Telomerase RNA Maturation Kinetics Precipitates Disease. Mol Cell. 2019 Mar 28. pii: S1097-2765(19)30144-3.
2018
132: Cheng X, Ferrell JE Jr. Apoptosis propagates through the cytoplasm as trigger waves. Science. 2018 Aug 10;361(6402):607-12.
Noted in: Biegler P. For unwanted cells, death comes in waves. Cosmos. 2018. https://cosmosmagazine.com/biology/for-unwanted-cells-death-comes-in-waves.
Noted in: Dormeil L. Here's how Stanford scientists measured the speed of death. Digital Trends. 2018. https://www.digitaltrends.com/cool-tech/stanford-university-measures-speed-of-death/.
Noted in: Hignett K. Death comes as an unrelenting tide of destruction. Newsweek. 2018. https://www.newsweek.com/death-comes-unrelenting-tide-destruction-study-shows-1067775.
Noted in: LePage M. We have measured the speed of death and it's 2 millimetres an hour. New Scientist. 2018. https://www.newscientist.com/article/2176397-we-have-measured-the-speed-of-death-and-its-2-millimetres-an-hour/.
Noted in: Saey TH. Here's how fast cell death can strike. Science News. 2018. https://www.sciencenews.org/article/speed-cell-death-apoptosis.
Noted in: Thirty micrometres a minute: scientists discover the speed of death. The Guardian (US Edition). 2018. https://www.theguardian.com/science/shortcuts/2018/aug/12/thirty-micrometre-minutes-scientists-discover-speed-of-death
131: Chang JB, Ferrell JE Jr. Robustly cycling Xenopus laevis cell-free extracts in
Teflon chambers. Cold Spring Harb Protoc. 2018 Aug 1;2018(8):pdb.prot097212.
2017
130: Anderson GA, Gelens L, Baker JC, Ferrell JE Jr. Desynchronizing embryonic cell division waves reveals the robustness of Xenopus laevis development. Cell Rep. 2017, Oct 3;21(1):37-46.
129: Lee JJ, Yang SY, Park J, Ferrell JE Jr, Shin DH, Lee KJ. Calcium ion induced structural changes promote dimerization of secratagogin, which is required for its insulin secretory function. Sci Rep. 2017 Published online Aug 1;7:6976.
128: Kamenz J, Ferrell JE Jr. The temporal ordering of cell-cycle phosphorylation. Mol Cell. 2017 Feb 2;65(3):371-373.
2016
127: Ha SH, Ferrell JE Jr. Thresholds and ultrasensitivity from negative cooperativity. Science. 2016 May 20;352(6288):990-3.
Recommended by the Faculty of 1000.
Noted in: VanHook AM. Papers of note. Sci. Signal. 2016 May 24;9(429):ec125. doi: 10.1126/scisignal.aag1804.
Noted in: Principles of Systems Biology-No. 6. Cell Syst. 2016 Jun 22;2(6):356-9. doi:10.1016/j.cels.2016.06.004. PubMed PMID: 27336964.
126: Ferrell JE Jr. Perfect and near-perfect adaptation in cell signaling. Cell Systems 2016 Feb 24;2:62-7. doi: 10.106/jcels.2016.02.006.
125: Ha SH, Kim SY, Ferrell JE Jr. The prozone effect accounts for the paradoxical
function of the Cdk-binding protein Suc1/Cks. Cell Rep. 2016 Feb 16;14(6):1408-21. doi: 10.1016/j.celrep.2016.01.033. Epub 2016 Feb 4.
2015
124: Gelens L, Huang KC, Ferrell JE Jr. How does the Xenopus laevis embryonic cell
cycle avoid spatial chaos? Cell Rep. 2015 Aug 4;12(5):892-900.
2014
123: Ferrell JE Jr, Ha SH. Ultrasensitivity part III: cascades, bistable switches,
and oscillators. Trends Biochem Sci. 2014 Dec;39(12):612-8. doi:
10.1016/j.tibs.2014.10.002. Epub 2014 Nov 10. Review.
122: Ferrell JE Jr, Ha SH. Ultrasensitivity part II: multisite phosphorylation,
stoichiometric inhibitors, and positive feedback. Trends Biochem Sci. 2014
Nov;39(11):556-69. Review.
121: Gelens L, Anderson GA, Ferrell JE Jr. Spatial trigger waves: positive feedback gets you a long way. Mol Biol Cell. 2014 Nov 5;25(22):3486-93.
120: Ferrell JE Jr, Ha SH. Ultrasensitivity part I: Michaelian responses and zero-order ultrasensitivity. Trends Biochem Sci. 2014 Oct;39(10):496-503.
119: Tsai TY, Theriot JA, Ferrell JE Jr. Changes in oscillatory dynamics in the cell cycle of early Xenopus laevis embryos. PLoS Biol. 2014 Feb 11;12(2):e1001788.
2013
118: Ferrell JE Jr. Feedback loops and reciprocal regulation: recurring motifs in the systems biology of the cell cycle. Curr Opin Cell Biol. 2013 Dec;25(6):676-86. Review.
117: Chang JB, Ferrell JE Jr. Mitotic trigger waves and the spatial coordination of the Xenopus cell cycle. Nature. 2013 Aug 29;500(7464):603-7.
Noted in: Ishihara K, Nguyen PA, Wühr M, Groen AC, Field CM, Mitchison TJ. Organization of early frog embryos by chemical waves emanating from centrosomes. Philos Trans R Soc Lond B Biol Sci. 2014 Sep 5;369(1650). pii: 20130454.
Noted in: Berndt JD, Gough NR. 2013: Signaling breakthroughs of the year. Sci Signal. 2014 Jan 7;7(307):eg1. doi: 10.1126/scisignal.2005013.
116: Yang Q, Ferrell JE Jr. The Cdk1-APC/C cell cycle oscillator circuit functions as a time-delayed, ultrasensitive switch. Nat Cell Biol. 2013 May;15(5):519-25.
2012
115: Anderson GA, Liu X, Ferrell JE Jr. Bistability in one equation or fewer. Methods Mol Biol. 2012;880:53-67. Review.
114: Santos SD, Wollman R, Meyer T, Ferrell JE Jr. Spatial positive feedback at the onset of mitosis. Cell. 2012 Jun 22;149(7):1500-13. doi:10.1016/j.cell.2012.05.028.
Recommended by the Faculty of 1000. http://f1000.com/prime/717959375
113: Ferrell JE Jr. Bistability, bifurcations, and Waddington's epigenetic landscape. Curr Biol. 2012 Jun 5;22(11):R458-66. Review.
112: Ferrell JE Jr. Dora B. Goldstein 1922-2011. Addiction. 2012 May;107(5):1013-4.
2011
111: Pearlman SM, Serber Z, Ferrell JE Jr. A mechanism for the evolution of phosphorylation sites. Cell. 2011 Nov 11;147(4):934-46.
Recommended by the Faculty of 1000. http://f1000.com/prime/13489061
110: Ferrell JE Jr. Simple rules for complex processes: new lessons from the budding yeast cell cycle. Mol Cell. 2011 Aug 19;43(4):497-500.
109: Ferrell JE Jr, Tsai TY, Yang Q. Modeling the cell cycle: why do certain circuits oscillate? Cell. 2011 Mar 18;144(6):874-85.
108: Trunnell NB, Poon AC, Kim SY, Ferrell JE Jr. Ultrasensitivity in the regulation of Cdc25C by Cdk1. Mol Cell. 2011 Feb 4;41(3):263-74.
Commentary: Goulev Y, Charvin G. Ultrasensitivity and positive feedback to promote sharp mitotic entry. Mol Cell. 2011 Feb 4;41(3):243-4.
2010
107: Gong D, Ferrell JE Jr. The roles of cyclin A2, B1, and B2 in early and late mitotic events. Mol Biol Cell. 2010 Sep 15;21(18):3149-61.
2009
106: Wolkenhauer O, Auffray C, Baltrusch S, Blüthgen N, Byrne H, Cascante M, Ciliberto A, Dale T, Drasdo D, Fell D, Ferrell JE Jr, 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. Systems biologists seek fuller integration of systems biology approaches in new cancer research programs. Cancer Res. 2010 Jan 1;70(1):12-3.
105: Ferrell JE Jr. Signaling motifs and Weber's law. Mol Cell. 2009 Dec 11;36(5):724-7.
104: Hendrickson DG, Hogan DJ, McCullough HL, Myers JW, Herschlag D, Ferrell JE, Brown PO. Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol. 2009 Nov;7(11):e1000238.
103: Ferrell JE Jr, Pomerening JR, Kim SY, Trunnell NB, Xiong W, Huang CY, Machleder EM. Simple, realistic models of complex biological processes: positive feedback and bistability in a cell fate switch and a cell cycle oscillator. FEBS Lett. 2009 Dec 17;583(24):3999-4005. Review.
102: Ferrell JE Jr. Q&A: Cooperativity. J Biol. 2009;8(6):53.
101: Justman QA, Serber Z, Ferrell JE Jr, El-Samad H, Shokat KM. Tuning the activation threshold of a kinase network by nested feedback loops. Science. 2009 Apr 24;324(5926):509-12.
Commentary: Skotheim JM. Cell signaling. To divide or not to divide. Science. 2009 Apr 24;324(5926):476-7.
100: Ferrell JE Jr. Q&A: systems biology. J Biol. 2009;8(1):2.
99: 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. Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Mol Oncol. 2009 Feb;3(1):9-17.
2008
98: Santos SD, Ferrell JE. Systems biology: On the cell cycle and its switches. Nature. 2008 Jul 17;454(7202):288-9.
97: Tsai TY, Choi YS, Ma W, Pomerening JR, Tang C, Ferrell JE Jr. Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science. 2008 Jul 4;321(5885):126-9.
96: Pomerening JR, Ubersax JA, Ferrell JE Jr. Rapid cycling and precocious termination of G1 phase in cells expressing CDK1AF. Mol Biol Cell. 2008 Aug;19(8):3426-41.
95: Hendrickson DG, Hogan DJ, Herschlag D, Ferrell JE, Brown PO. Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PLoS One. 2008 May 7;3(5):e2126. Erratum in: PLoS ONE. 2008;3(11).doi.org/10.1371/annotation/c8902b4c-30fc-42e7-b506-fc756a3cdd4e.
94: Ríos-Cardona D, Ricardo-González RR, Chawla A, Ferrell JE Jr. 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 May 1;317(1):380-8.
93: Ferrell JE Jr. Feedback regulation of opposing enzymes generates robust, all-or-none bistable responses. Curr Biol. 2008 Mar 25;18(6):R244-5.
2007
92: Poon AC, Ferrell JE Jr. Systems biology. A clock with a flip switch. Science. 2007 Nov 2;318(5851):757-8.
91: Ubersax JA, Ferrell JE Jr. Mechanisms of specificity in protein phosphorylation. Nat Rev Mol Cell Biol. 2007 Jul;8(7):530-41. Review. Erratum in: Nat Rev Mol Cell Biol. 2007 Aug;8(8):665.
90: Serber Z, Selenko P, Hänsel R, Reckel S, Löhr F, Ferrell JE Jr, Wagner G, Dötsch V. Investigating macromolecules inside cultured and injected cells by in-cell NMR spectroscopy. Nat Protoc. 2006;1(6):2701-9.
89: Kim SY, Ferrell JE Jr. Substrate competition as a source of ultrasensitivity in the inactivation of Wee1. Cell. 2007 Mar 23;128(6):1133-45.
88: Hansen DV, Pomerening JR, Summers MK, Miller JJ, Ferrell JE Jr, Jackson PK. Emi2 at the crossroads: where CSF meets MPF. Cell Cycle. 2007 Mar 15;6(6):732-8. Epub 2007 Mar 14.
87: Serber Z, Ferrell JE Jr. Tuning bulk electrostatics to regulate protein function. Cell. 2007 Feb 9;128(3):441-4.
86: Gong D, Pomerening JR, Myers JW, Gustavsson C, Jones JT, Hahn AT, Meyer T, Ferrell JE Jr. Cyclin A2 regulates nuclear-envelope breakdown and the nuclear accumulation of cyclin B1. Curr Biol. 2007 Jan 9;17(1):85-91.
85. Ferrell JE Jr. A clear view of the cell cycle. Curr Biol. 2007 Apr;17(7):R231-R232. Book review.
84. Ferrell JE. Journal club. Nature. 2007 Oct 31;450(7166):5-5.
2006
83: Yue J, Ferrell JE Jr. Mechanistic studies of the mitotic activation of Mos. Mol Cell Biol. 2006 Jul;26(14):5300-9.
82: Ubersax JA, Ferrell JE Jr. A noisy 'Start' to the cell cycle. Mol Syst Biol. 2006;2:2006.0014. Epub 2006 Mar 21.
81: Yue J, Xiong W, Ferrell JE. B-Raf and C-Raf are required for Ras-stimulated p42 MAP kinase activation in Xenopus egg extracts. Oncogene. 2006 Jun 1;25(23):3307-15.
80: Myers JW, Chi JT, Gong D, Schaner ME, Brown PO, Ferrell JE. Minimizing off-target effects by using diced siRNAs for RNA interference. J RNAi Gene Silencing. 2006 Jul 17;2(2):181-94.
2005
79: Kim SY, Song EJ, Lee KJ, Ferrell JE Jr. Multisite M-phase phosphorylation of Xenopus Wee1A. Mol Cell Biol. 2005 Dec;25(23):10580-90.
78: Brandman O, Ferrell JE Jr, Li R, Meyer T. Interlinked fast and slow positive feedback loops drive reliable cell decisions. Science. 2005 Oct 21;310(5747):496-8.
Recommended by the Faculty of 1000. http://f1000.com/prime/1029026
Commentary: Bornholdt S. Systems biology. Less is more in modeling large genetic networks. Science. 2005 Oct 21;310(5747):449-51.
Commentary: Adler EM, Gough NR, Ray LB. 2005: signaling breakthroughs of the year. Sci STKE. 2006 Jan 3;2006(316):eg1.
77: Pomerening JR, Kim SY, Ferrell JE Jr. Systems-level dissection of the cell-cycle oscillator: bypassing positive feedback produces damped oscillations. Cell. 2005 Aug 26;122(4):565-78.
Commentary: Cross FR, Siggia ED. Shake it, don't break it: positive feedback and the evolution of oscillator design. Dev Cell. 2005 Sep;9(3):309-10.
Commentary: Adler EM, Gough NR, Ray LB. 2005: signaling breakthroughs of the year. Sci STKE. 2006 Jan 3;2006(316):eg1.
76: Liou J, Kim ML, Heo WD, Jones JT, Myers JW, Ferrell JE Jr, Meyer T. STIM is a Ca2+ sensor essential for Ca2+-store-depletion-triggered Ca2+ influx. Curr Biol. 2005 Jul 12;15(13):1235-41.
Commentary: Adler EM, Gough NR, Ray LB. 2005: signaling breakthroughs of the year. Sci STKE. 2006 Jan 3;2006(316):eg1.
75: Myers JW, Ferrell JE. Silencing gene expression with Dicer-generated siRNA pools. Methods Mol Biol. 2005;309:93-196.
74: Myers JW, Ferrell JE Jr. Dicer in RNAi: its roles in vivo and utility in vitro. In RNA Interference: From Basic Science to Drug Development. 2005. Edited by K. Appasani, Cambridge University Press, Cambridge UK, pp. 29-54.
73: Green SL, Westendorf JM, Jaffe H, Pant HC, Cork LC, Ostrander EA, Vignaux F, Ferrell JE Jr. Allelic variants of the canine heavy neurofilament (NFH) subunit and extensive phosphorylation in dogs with motor neuron disease. J Comp Pathol. 2005 Jan;132(1):33-50.
72: Cheng A, Xiong W, Ferrell JE Jr, Solomon MJ. Identification and comparative analysis of multiple mammalian Speedy/Ringo proteins. Cell Cycle. 2005 Jan;4(1):155-65.
2004
71: Yue J, Ferrell JE Jr. Mos mediates the mitotic activation of p42 MAPK in Xenopus egg extracts. Curr Biol. 2004 Sep 7;14(17):1581-6.
70: Gong D, Ferrell JE Jr. Picking a winner: new mechanistic insights into the design of effective siRNAs. Trends Biotechnol. 2004 Sep;22(9):451-4.
69: Jones JT, Myers JW, Ferrell JE, Meyer T. Probing the precision of the mitotic clock with a live-cell fluorescent biosensor. Nat Biotechnol. 2004 Mar;22(3):306-12.
68: Angeli D, Ferrell JE Jr, Sontag ED. Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):1822-7.
2003
67: Xiong W, Ferrell JE Jr. A positive-feedback-based bistable 'memory module' that governs a cell fate decision. Nature. 2003 Nov 27;426(6965):460-5. Corrigendum in: Nature. 2007 Aug 30;448(7157):1076.
Commentary: Sible JC. Cell biology: thanks for the memory. Nature. 2003 Nov 27;426(6965):392-3. PubMed PMID: 14647363.
Commentary: LeBrasseur N. Eggs never forget. J Cell Biol. 2003 Dec 15;163(6):1187.
Commentary: Maturing from memory. Sci STKE. 2003 Dec 2;2003(211):tw462.
66: Fink CC, Bayer KU, Myers JW, Ferrell JE Jr, Schulman H, Meyer T. Selective regulation of neurite extension and synapse formation by the beta but not the alpha isoform of CaMKII. Neuron. 2003 Jul 17;39(2):283-97.
65: Pomerening JR, Sontag ED, Ferrell JE Jr. Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2. Nat Cell Biol. 2003 Apr;5(4):346-51.
64: Ferrell JE Jr, Cimprich KA. Enforced proximity in the function of a famous scaffold. Mol Cell. 2003 Feb;11(2):289-91. Review.
63: Bagowski CP, Besser J, Frey CR, Ferrell JE Jr. The JNK cascade as a biochemical switch in mammalian cells: ultrasensitive and all-or-none responses. Curr Biol. 2003 Feb 18;13(4):315-20.
62: Myers JW, Jones JT, Meyer T, Ferrell JE Jr. Recombinant Dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencing. Nat Biotechnol. 2003 Mar;21(3):324-8. Epub 2003 Feb 18.
2002
61: Gilman AG, Simon MI, Bourne HR, Harris BA, Long R, Ross EM, Stull JT, Taussig R, Bourne HR, Arkin AP, Cobb MH, Cyster JG, Devreotes PN, Ferrell JE, Fruman D, Gold M, Weiss A, Stull JT, Berridge MJ, Cantley LC, Catterall WA, Coughlin SR, Olson EN, Smith TF, Brugge JS, Botstein D, Dixon JE, Hunter T, Lefkowitz RJ, Pawson AJ, Sternberg PW, Varmus H, Subramaniam S, Sinkovits RS, Li J, Mock D, Ning Y, Saunders B, Sternweis PC, Hilgemann D, Scheuermann RH, DeCamp D, Hsueh R, Lin KM, Ni Y, Seaman WE, Simpson PC, O'Connell TD, Roach T, Simon MI, Choi S, Eversole-Cire P, Fraser I, Mumby MC, Zhao Y, Brekken D, Shu H, Meyer T, Chandy G, Heo WD, Liou J, O'Rourke N, Verghese M, Mumby SM, Han H, Brown HA, Forrester JS, Ivanova P, Milne SB, Casey PJ, Harden TK, Arkin AP, Doyle J, Gray ML, Meyer T, Michnick S, Schmidt MA, Toner M, Tsien RY, Natarajan M, Ranganathan R, Sambrano GR; Participating investigators and scientists of the Alliance for Cellular Signaling. Overview of the Alliance for Cellular Signaling. Nature. 2002 Dec 12;420(6916):703-6.
60: Ferrell JE Jr. Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr Opin Cell Biol. 2002 Apr;14(2):140-8. Review.
59: Sohaskey ML, Ferrell JE Jr. 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 Feb;13(2):454-68.
2001
58: Deshaies RJ, Ferrell JE Jr. Multisite phosphorylation and the countdown to S phase. Cell. 2001 Dec 28;107(7):819-22. Review.
57: Ferrell JE, Xiong W. Bistability in cell signaling: How to make continuous processes discontinuous, and reversible processes irreversible. Chaos. 2001 Mar;11(1):227-236.
56: Ferrell JE Jr. Six steps to destruction. Nature. 2001 Nov 29;414(6863):498-9.
55: Bagowski CP, Ferrell JE Jr. Bistability in the JNK cascade. Curr Biol. 2001 Aug 7;11(15):1176-82.
54: Bagowski CP, Myers JW, Ferrell JE Jr. The classical progesterone receptor associates with p42 MAPK and is involved in phosphatidylinositol 3-kinase signaling in Xenopus oocytes. J Biol Chem. 2001 Oct 5;276(40):37708-14.
53: Bagowski CP, Xiong W, Ferrell JE Jr. 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 Jan 12;276(2):1459-65.
52: Ferrell JE Jr. Cell cycle. In: McGraw-Hill Encyclopedia of Science and Technology. 2001. Ninth edition.
51: Ferrell JE Jr. Regulatory cascades: function and properties. In: Encyclopedia of Life Sciences. 2001. Macmillan Publishing Ltd.
2000
50: Ferrell JE Jr. What do scaffold proteins really do? Sci STKE. 2000 Oct 3;2000(52):pe1. Review.
49: Green SL, Lifland BD, Bouley DM, Brown BA, Wallace RJ Jr, Ferrell JE Jr. Disease attributed to Mycobacterium chelonae in South African clawed frogs (Xenopus laevis). Comp Med. 2000 Dec;50(6):675-9.
48: Kim SY, Ferrell JE Jr, Chae SK, Lee KJ. Inhibition of progesterone-induced Xenopus oocyte maturation by Nm23. Cell Growth Differ. 2000 Sep;11(9):485-90.
47: Bhatt RR, Ferrell JE Jr. Cloning and characterization of Xenopus Rsk2, the predominant p90 Rsk isozyme in oocytes and eggs. J Biol Chem. 2000 Oct 20;275(42):32983-90.
46: Walter SA, Guadagno SN, Ferrell JE Jr. Activation of Wee1 by p42 MAPK in vitro and in cycling xenopus egg extracts. Mol Biol Cell. 2000 Mar;11(3):887-96.
1999
45: Sohaskey ML, Ferrell JE Jr. Distinct, constitutively active MAPK phosphatases function in Xenopus oocytes: implications for p42 MAPK regulation In vivo. Mol Biol Cell. 1999 Nov;10(11):3729-43.
44: Bhatt RR, Ferrell JE Jr. The protein kinase p90 rsk as an essential mediator of cytostatic factor activity. Science. 1999 Nov 12;286(5443):1362-5.
43: Ferrell JE Jr. Building a cellular switch: more lessons from a good egg. Bioessays. 1999 Oct;21(10):866-70. Review.
42: Ferrell JE Jr. Xenopus oocyte maturation: new lessons from a good egg. Bioessays. 1999 Oct;21(10):833-42. Review.
41: Green SL, Bouley DM, Tolwani RJ, Waggie KS, Lifland BD, Otto GM, Ferrell JE Jr. 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 Jun 15;214(12):1833-8, 1792-3.
40: Huang CY, Chang CP, Huang CL, Ferrell JE Jr. M phase phosphorylation of cytoplasmic dynein intermediate chain and p150(Glued). J Biol Chem. 1999 May 14;274(20):14262-9.
1998
39: Ferrell JE Jr. How regulated protein translocation can produce switch-like responses. Trends Biochem Sci. 1998 Dec;23(12):461-5. Review.
38: Guadagno TM, Ferrell JE Jr. Requirement for MAPK activation for normal mitotic progression in Xenopus egg extracts. Science. 1998 Nov 13;282(5392):1312-5.
37: Ferrell JE Jr, Machleder EM. The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science. 1998 May 8;280(5365):895-8.
36: Ferrell JE Jr, Martin GS. Assessing activities of blotted protein kinases. In: Protein Phosphorylation. 1998. Ed. by Hunter T, Sefton BM, Academic Press, San Diego, pp. 177-82. [This is a re-publication of Ref. 23]
1997
35: Walter SA, Guadagno TM, Ferrell JE Jr. Induction of a G2-phase arrest in Xenopus egg extracts by activation of p42 mitogen-activated protein kinase. Mol Biol Cell. 1997 Nov;8(11):2157-69.
34: Ferrell JE Jr. How responses get more switch-like as you move down a protein kinase cascade. Trends Biochem Sci. 1997 Aug;22(8):288-9.
33: Ferrell JE Jr, Bhatt RR. Mechanistic studies of the dual phosphorylation of mitogen-activated protein kinase. J Biol Chem. 1997 Jul 25;272(30):19008-16.
32: Wang XM, Zhai Y, Ferrell JE Jr. A role for mitogen-activated protein kinase in the spindle assembly checkpoint in XTC cells. J Cell Biol. 1997 Apr 21;137(2):433-43.
31: Ferrell JE Jr. Cell cycle. In: McGraw-Hill Encyclopedia of Science and Technology, Eighth edition. 1997 3:378-80.
1996
30: Ferrell JE Jr. Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs. Trends Biochem Sci. 1996 Dec;21(12):460-6. Review.
29: Huang CY, Ferrell JE Jr. Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc Natl Acad Sci U S A. 1996 Sep 17;93(19):10078-83.
28: Huang CY, Ferrell JE Jr. Dependence of Mos-induced Cdc2 activation on MAP kinase function in a cell-free system. EMBO J. 1996 May 1;15(9):2169-73.
27: Ferrell JE Jr. MAP kinases in mitogenesis and development. Curr Top Dev Biol. 1996;33:1-60. Review.
1994
26: Hsiao KM, Chou SY, Shih SJ, Ferrell JE Jr. 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 Jun 7;91(12):5480-4.
1992
25: Chou SY, Baichwal V, Ferrell JE Jr. Inhibition of c-Jun DNA binding by mitogen-activated protein kinase. Mol Biol Cell. 1992 Oct;3(10):1117-30.
1991
24: Ferrell JE Jr, Wu M, Gerhart JC, Martin GS. Cell cycle tyrosine phosphorylation of p34cdc2 and a microtubule-associated protein kinase homolog in Xenopus oocytes and eggs. Mol Cell Biol. 1991 Apr;11(4):1965-71.
23: Ferrell JE Jr, Martin GS. Assessing activities of blotted protein kinases. Methods Enzymol. 1991;200:430-5.
1990
22: Ferrell JE Jr, Noble JA, Martin GS, Jacques YV, Bainton DF. Intracellular localization of pp60c-src in human platelets. Oncogene. 1990 Jul;5(7):1033-6.
21: Ferrell JE Jr, Martin GS. Identification of a 42-kilodalton phosphotyrosyl protein as a serine(threonine) protein kinase by renaturation. Mol Cell Biol. 1990 Jun;10(6):3020-6.
1989
20: Ferrell JE Jr, Martin GS. Thrombin stimulates the activities of multiple previously unidentified protein kinases in platelets. J Biol Chem. 1989 Dec 5;264(34):20723-9.
19: Ferrell JE Jr, Martin GS. Tyrosine-specific protein phosphorylation is regulated by glycoprotein IIb-IIIa in platelets. Proc Natl Acad Sci U S A. 1989 Apr;86(7):2234-8.
1988
18: Ferrell JE Jr, Martin GS. Platelet tyrosine-specific protein phosphorylation is regulated by thrombin. Mol Cell Biol. 1988 Sep;8(9):3603-10.
17: Ferrell JE Jr, Mitchell KT, Huestis WH. Membrane bilayer balance and platelet shape: morphological and biochemical responses to amphipathic compounds. Biochim Biophys Acta. 1988 Apr 7;939(2):223-37.
1986
16: Mitchell KT, Ferrell JE Jr, Huestis WH. Separation of phosphoinositides and other phospholipids by two-dimensional thin-layer chromatography. Anal Biochem. 1986 Nov 1;158(2):447-53.
15: Truong HT, Ferrell JE Jr, Huestis WH. Sulfhydryl reducing agents and shape regulation in human erythrocytes. Blood. 1986 Jan;67(1):214-21.
1985
14: Ferrell JE Jr, Lee KJ, Huestis WH. Lipid transfer between phosphatidylcholine vesicles and human erythrocytes: exponential decrease in rate with increasing acyl chain length. Biochemistry. 1985 Jun 4;24(12):2857-64.
13: Ferrell JE Jr, Lee KJ, Huestis WH. Membrane bilayer balance and erythrocyte shape: a quantitative assessment. Biochemistry. 1985 Jun 4;24(12):2849-57.
1984
12: Ferrell JE Jr, Huestis WH. Phosphoinositide metabolism and the morphology of human erythrocytes. J Cell Biol. 1984 Jun;98(6):1992-8.
11: Loew GH, Poulsen M, Kirkjian E, Ferrell J, Sudhindra BS, Rebagliati M. Computer-assisted mechanistic structure-activity studies: application to diverse classes of chemical carcinogens. Environ Health Perspect. 1985 Sep;61:69-96. Review.
1983
10: Ferrell JE Jr, Newton AC, Huestis WH. Analysis of chloride flux. Biochem. 1983 Dec 20;22(26):6116-7. Appendix to Newton AC, Cook SL, Huestis WH. Transfer of band 3, the erythrocyte anion transporter, between phospholipid vesicles and cells. Biochemistry. 1983 Dec 20;22(26):6110-7.
9: Loew GH, Ferrell JE Jr, Poulsen M. Mechanistic structure-activity studies using quantum chemical methods: application to polycyclic aromatic hydrocarbons. In: Structure-Activity Correlation as a Predictive Tool in Toxicology. 1983. Edited by L. Golberg. Hemisphere, Washington DC, 111-38.
1982
8: Ferrell JE Jr, Huestis WH. Calcium does not mediate the shape change that follows ATP depletion in human erythrocytes. Biochim Biophys Acta. 1982 May 7;687(2):321-8.
1981
7: Huestis WH, Nelson MJ, Ferrell JE Jr. Calmodulin-dependent spectrin kinase activity in human erythrocytes. Prog Clin Biol Res. 1981;56:137-55.
1980
6: Loew G, Poulsen M, Ferrell J, Chaet D. Quantum chemical studies of methylbenz[a]anthracenes: metabolism and correlations with carcinogenicity. Chem Biol Interact. 1980 Sep;31(3):319-40.
5: Loew GH, Pudzianowski AT, Czerwinski A, Ferrell JE Jr. Mechanistic studies of addition of nucleophiles to arene oxides and diol epoxides: candidate ultimate carcinogens. Int J Quantum Chem Quant Biol Symp. 1980 7:223-244.
1979
4: Nelson MJ, Ferrell JE Jr, Huestis WH. Adrenergic stimulation of membrane protein phosphorylation in human erythrocytes. Biochim Biophys Acta. 1979 Nov 16;558(1):136-40.
3: Ferrell JE Jr, Chang Sing PD, Loew G, King R, Mansour JM, Mansour TE. Structure/activity studies of flavonoids as inhibitors of cyclic AMP phosphodiesterase and relationship to quantum chemical indices. Mol Pharmacol. 1979 Sep;16(2):556-68.
2: Loew GH, Sudhindra BS, Ferrell JE Jr. Quantum chemical studies of polycyclic aromatic hydrocarbons and their metabolites: correlations to carcinogenicity. Chem Biol Interact. 1979 Jun;26(1):75-89.
1: Ferrell JE Jr, Loew GH. Mechanistic studies of arene oxide and diol epoxide rearrangement and hydrolysis reactions. J Am Chem Soc. 1979 Mar 1;101(6):1379-88. doi: 10.1021/ja00500a005.
